Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulatory Effects of Combined Dietary Supplementation With Essential Oils and Organic Acids on Microbial Communities of Cobb Broilers

The emergence and spread of antibiotic resistance genes in pathogenic microorganisms have resulted in many countries restricting the use of antibiotics as growth promoters in animal feed. The combined use of essential oils and organic acids can help maintain intestinal health, improve animal growth performance, and alleviate the negative effects of banned antibiotics for certain economically important animals. Although the modes of action for the combined dietary supplementation of essential oils and organic acids such as thymol-citric acid (EOA1) and thymol-butyric acid (EOA2) remain unclear, it is speculated that their activities are achieved through beneficial modulation of gastrointestinal microbial communities and inhibition of pathogen growth. In this study, 16S rDNA amplicon sequencing was used to analyze the effects of treatment with EOA1 and EOA2 on the jejunal, cecal, and fecal microbial communities of Cobb broilers while also evaluating effects over different broiler ages. The intestinal microbial communities of broilers developed with increasing age, and Lactobacillus gradually came to dominate the intestinal communities of treated broilers. Further, the microbial communities of feces were more complex than those of the jejuna and ceca. We systematically elucidate that the longitudinal changes in the intestinal microbial communities of Cobb broiler chickens at different ages. Meanwhile, we found that the addition of EOA1 or EOA2 to the diet: (1) inhibited the proliferation of Ralstonia pickettii and Alcaligenaceae in the jejuna on day 28, (2) promoted the colonization and growth of beneficial bacteria such as Lactobacillus, Clostridia, and Bacteroidia at various growth stages, and (3) enriched the abundance of certain microbiota functions, including biological pathways related to metabolism (e.g., enzyme families). Taken together, the results of this study demonstrate that EOA1 and EOA2 dietary supplementation can affect various microbial metabolic pathways related to the metabolism and absorption of nutrients via regulation of the intestinal microbial community structures of Cobb broilers.
Revisiting the Development of Vaccines Against Pathogenic Leptospira: Innovative Approaches, Present Challenges, and Future Perspectives

Human vaccination against leptospirosis has been relatively unsuccessful in clinical applications despite an expressive amount of vaccine candidates has been tested over years of research. Pathogenic Leptospira encompass a great number of serovars, most of which do not cross-react, and there has been a lack of genetic tools for many years. These obstacles have hampered the understanding of the bacteria’s biology and, consequently, the identification of an effective antigen. Thus far, many approaches have been used in an attempt to find a cost-effective and broad-spectrum protective antigen(s) against the disease. In this extensive review, we discuss several strategies that have been used to develop an effective vaccine against leptospirosis, starting with Leptospira-inactivated bacterin, proteins identified in the genome sequences of pathogenic Leptospira, including reverse vaccinology, plasmid DNA, live vaccines, chimeric multi-epitope, and toll- and nod-like receptors agonists. This overview should be able to guide scientists working in the field to select potential antigens and to choose the appropriate formulation to administer the candidates.
Regional Pole Placement Design Based Stabilization for Cart Inverted Pendulum System

The inverted pendulum has been considered as a benchmark control problem due to its nonlinearity and stabilization around the unstable equilibrium point. To achieve stabilization, it is well known that all the closed loop system poles should lie in left half of s-plane. In present work, different approaches have taken to shift the system poles to left half of the plane. At first Linear Quadratic Regulator (LQR) is used, where the desired pole locations can be achieved by suitably selecting weight matrix of cost function. With this guaranteed cost control scheme, one does not have to bother about specifying closed-loop poles. Next, a two loop PID is designed based on pole matching conditions. Where the closed loop with unknown controller coefficient characteristic equation is compared with desired characteristics, to find out the controller gains. In both the methods, one has to deal with point wise pole placing, which can be tricky sometimes. With the recent development of LMIs tool, regional pole placement is well suited to achieve the goal. At last, a regional pole placement controller is synthesized, where desired specifications are transformed into LMI regions. In present case, a conical sector of left half plane is taken so that stabilisation with better transient performance can be achieved
Fossil Leaves of Meliosma (Sabiaceae) With Associated Pollen and a Eupodid Mite From the Eocene of Maoming Basin, South China

A first occurrence of the genus Meliosma (Sabiaceae) is reported from the upper Eocene of the Maoming Basin of South China. This fossil is one of the oldest reliable records of the genus within its modern center of diversity. Fossil leaves are assigned to a new species, Meliosma eosinica sp. nov. based on leaf morphology and epidermal characters. The leaf epidermal anatomy of fossil Meliosma is illustrated for the first time. We also provide the first SEM observation of pollen grains associated with Meliosma. This study also documents an occurrence of mites within the leaf domatia previously unknown from the fossil record. We presume that the studied mite belongs to the superfamily Eupodoidea (Arthropoda), and probably the family Eupodidae, which comprises very small soft-bodied cosmopolitan mites occupying a wide range of terrestrial habitats. Additionally, we analyze the damage types on the fossil leaves of Meliosma. They exhibit exclusively external foliage feeding damage caused by arthropods and traces of probable fungal infection. A review of currently known fossil occurrences of leaves, fruits, and wood of Meliosma provides evidence for the geological and geographical distribution of the genus.
Trajectories of Vital Signs and Risk of In-Hospital Cardiac Arrest

Background: Little is known about the trajectories of vital signs prior to in-hospital cardiac arrest (IHCA), which could explain the heterogeneous processes preceding this event. We aimed to identify clinically relevant subphenotypes at high risk of IHCA in the emergency department (ED). Methods: This retrospective cohort study used electronic clinical warehouse data from a tertiary medical center. We retrieved data from 733,398 ED visits over a 7-year period. We selected one ED visit per person and retrieved patient demographics, triage data, vital signs (systolic blood pressure [SBP], heart rate [HR], body temperature, respiratory rate, oxygen saturation), selected laboratory markers, and IHCA status. Group-based trajectory modeling was performed. Results: There were 37,697 adult ED patients with a total of 1,507,121 data points across all vital-sign categories. Three to four trajectory groups per vital-sign category were identified, and the following five trajectory groups were associated with a higher rate of IHCA: low and fluctuating SBP, high and fluctuating HR, persistent hypothermia, recurring tachypnea, and low and fluctuating oxygen saturation. The IHCA-prone trajectory group was associated with a higher triage level and a higher mortality rate, compared to other trajectory groups. Except for the persistent hypothermia group, the other four trajectory groups were more likely to have higher levels of C-reactive protein, lactic acid, cardiac troponin I, and D-dimer. Multivariable analysis revealed that hypothermia (adjusted odds ratio [aOR], 2.20; 95% confidence interval [95%CI], 1.35–3.57) and recurring tachypnea (aOR 2.44; 95%CI, 1.24–4.79) were independently associated with IHCA. Conclusions: We identified five novel vital-sign sub-phenotypes associated with a higher likelihood of IHCA, with distinct patterns in clinical course and laboratory markers. A better understanding of the pre-IHCA vital-sign trajectories may help with the early identification of deteriorating patients.
The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I

Complex I (CI) is the largest protein complex in the mitochondrial oxidative phosphorylation electron transport chain of the inner mitochondrial membrane and plays a key role in the transport of electrons from reduced substrates to molecular oxygen. CI is composed of 14 core subunits that are conserved across species and an increasing number of accessory subunits from bacteria to mammals. The fact that adding accessory subunits incurs costs of protein production and import suggests that these subunits play important physiological roles. Accordingly, knockout studies have demonstrated that accessory subunits are essential for CI assembly and function. Furthermore, clinical studies have shown that amino acid substitutions in accessory subunits lead to several debilitating and fatal CI deficiencies. Nevertheless, the specific roles of CI’s accessory subunits have remained mysterious. In this review, we explore the possible roles of each of mammalian CI’s 31 accessory subunits by integrating recent high-resolution CI structures with knockout, assembly, and clinical studies. Thus, we develop a framework of experimentally testable hypotheses for the function of the accessory subunits. We believe that this framework will provide inroads towards the complete understanding of mitochondrial CI physiology and help to develop strategies for the treatment of CI deficiencies.
Identification of Five Cytotoxicity-Related Genes Involved in the Progression of Triple-Negative Breast Cancer

Background: Breast cancer is one of the deadly tumors in women, and its incidence continues to increase. This study aimed to identify novel therapeutic molecules using RNA sequencing (RNA-seq) data of breast cancer from our hospital. Methods: 30 pairs of human breast cancer tissue and matched normal tissue were collected and RNA sequenced in our hospital. Differentially expressed genes (DEGs) were calculated with raw data by the R package “edgeR”, and functionally annotated using R package “clusterProfiler”. Tumor-infiltrating immune cells (TIICs) were estimated using a website tool TIMER 2.0. Effects of key genes on therapeutic efficacy were analyzed using RNA-seq data and drug sensitivity data from two databases: the Cancer Cell Line Encyclopedia (CCLE) and the Cancer Therapeutics Response Portal (CTRP). Results: There were 2,953 DEGs between cancerous and matched normal tissue, as well as 975 DEGs between primary breast cancer and metastatic breast cancer. These genes were primarily enriched in PI3K-Akt signaling pathway, calcium signaling pathway, cAMP signaling pathway, and cell cycle. Notably, CD8+ T cell, M0 macrophage, M1 macrophage, regulatory T cell and follicular helper T cell were significantly elevated in cancerous tissue as compared with matched normal tissue. Eventually, we found five genes (GALNTL5, MLIP, HMCN2, LRRN4CL, and DUOX2) were markedly corelated with CD8+ T cell infiltration and cytotoxicity, and associated with therapeutic response. Conclusion: We found five key genes associated with tumor progression, CD8+ T cell and therapeutic efficacy. The findings would provide potential molecular targets for the treatment of breast cancer.
Spatiotemporal Variations in Seed Set and Pollen Limitation in Populations of the Rare Generalist Species Polemonium caeruleum in Poland

A vast majority of angiosperms are pollinated by animals, and a decline in the number and diversity of insects often affects plant reproduction through pollen limitation. This phenomenon may be particularly severe in rare plant species, whose populations are shrinking. Here, we examined the variability in factors shaping reproductive success and pollen limitation in red-listed Polemonium caeruleum L. During a 5-year study in several populations of P. caeruleum (7–15, depending on year), we assessed the degree of pollen limitation based on differences in seed set between open-pollinated (control) and hand-pollinated flowers. We analysed the effects of flower visitors, population size, and meteorological data on plant reproductive success and pollen limitation. Our study showed that pollen limitation rarely affected P. caeruleum populations, and was present mainly in small populations. Pollen limitation index was negatively affected by the size of population, visitation frequency of all insects, and when considering the visitation frequency of individual groups, also by honeybee visits. Seed production in control treatment was positively influenced by the population size, average monthly precipitation in June and visits of hoverflies, while visits of honeybees, average monthly temperature in September, and average monthly precipitation in August influenced seed production negatively. As generalist plant P. caeruleum can be pollinated by diverse insect groups, however, in small populations their main visitors, the honeybees and bumblebees, may be less attracted, eventually leading to the disappearance of these populations. In pollination of P. caeruleum managed honeybees may play a dual role: while they are the most frequent and efficient flower visitors, their presence decreases seed set in open-pollinated flowers, which is most probably related to efficient pollen collection by these insects.
Prescription Medications and Co-Morbidities in Late Middle-Age are Associated with Greater Cognitive Declines: Results from WRAP

The present study investigated: 1) sex differences in polypharmacy, comorbidities, self-rated current health (SRH), and cognitive performance, 2) associations between comorbidities, polypharmacy, SRH, and objective measures of health, and 3) associations of these factors with longitudinal cognitive performance. Analyses included 1039 eligible Wisconsin Registry for Alzheimer’s Prevention (WRAP) participants who were cognitively unimpaired at baseline and had ≥2 visits with cognitive composites, self-reported health history, and concurrent medication records. Repeated measures correlation (rmcorr) examined the associations between medications, co-morbidities, SRH, and objective measures of health (including LIfestyle for BRAin Health Index (LIBRA), and depression). Linear mixed-effect models examined associations between medications, co-morbidities, and cognitive change over time using a preclinical Alzheimer’s cognitive composite (PACC3) and cognitive domain z-scores (executive function, working memory, immediate learning, and delayed recall). In secondary analyses, we also examined whether the number of medications interacted with co-morbidities and whether they modified age-related cognitive trajectories. The number of prescribed medications was associated with worse SRH and a higher number of self-reported co-morbidities. More prescribed medications were associated with a faster decline in executive function, and more comorbidities were associated with faster PACC3 decline. Those with a non-elevated number of co-morbidities and medications performed an average of 0.26 SD higher (better) in executive function and an average of 0.18 SD higher on PACC3 than those elevated on both. Associations between medications, co-morbidities, and executive function, and PACC3 suggest that persons with more co-morbidities and medications may be at increased risk of reaching clinical levels of impairment earlier than healthier, less medicated peers.
An Optimization-Based Method for the Explicit Production Data Analysis of Gas Wells

This work aims at the exploration of production data analysis (PDA) methods without iterations. It can overcome limitations of the advanced type curve analysis relying on the iterative calculation of material-balance pseudotime and current explicit methods reckoning on specific production schedule assumptions. The dynamic material balance equation (DMBE) is strictly proved by the integral variable substitution based on the gas flow equation under the boundary dominated flow (BDF) condition and the static material balance equation (SMBE) of a gas reservoir. We introduce the pseudopressure level function γ(p) and the recovery factor function R(p) to rewrite the DMBE in terms of observed variable Y and estimated variable Y e; then the PDA can be transformed into an optimization problem of minimizing the error between Y and Y e. An optimization-based method for the explicit production data analysis of gas wells (OBM-EPDA), therefore, is developed in the paper, capable of determining the BDF constant and gas reserves explicitly and accurately for variable rate and/or variable flowing pressure systems. Three stimulated cases demonstrate the applicability and validity of OBM-EPDA with small errors less than 1% for estimated values of both reserves and Y. Not second to previous studies, the field case analysis further proves its practicability. It is shown that the nonlinear relation of γ to R can be represented by a polynomial function merely dependent on the inherent properties of the gas production system even before sorting out the production data. The errors of observed variable Y provided by OBM-EPDA facilitate the data quality control, and the elimination of outliers not subject to the BDF condition improves the reliability of the analysis. For various gas systems producing whether at a constant rate, a constant bottomhole pressure (BHP), or under variable rate and variable BHP conditions, the proposed method gives insights into the well-controlled volume and production capacity of the gas well whether in a low-pressure or high-pressure gas reservoir, where the compressibilities of rock and bound water are considered.
Mapping Intellectual Structure for the Long Non-Coding RNA in Hepatocellular Carcinoma Development Research

Background: Emerging research suggests that long non-coding RNAs (lncRNAs) play an important role in a variety of developmental or physiological processes of hepatocellular carcinoma (HCC). Various differentially expressed lncRNAs have been identified in HCC. Thus, a deeper analysis of recent research concerning lncRNA and HCC development could provide scientists with a valuable reference for future studies. Methods: Related publications were retrieved from the Web of Science Core Collection database. CiteSpace version 5.6. R4 was employed to conduct bibliometric analysis. Several network maps were constructed to evaluate the collaborations between different countries, institutions, authors, journals, and keywords. Results: A total of 2,667 records were initially found from the year of 2010–2020. The annual related publications output had increased dramatically during these years. Although China was the most prolific country in terms of research publication, the United States played a leading role in collaborative network. The Nanjing Medical University was the most productive institute in the field of lncRNAs in HCC development. Gang Chen was the most prolific researcher, while Yang F was the most frequently co-cited author. Oncotarget, Cell, and Oncogene were the most highly co-cited journals. The most recent burst keywords were interaction, database, and pathway. Conclusion: This study provides a comprehensive overview for the field of lncRNAs in HCC development based on bibliometric and visualized methods. The results would provide a reference for scholars focusing on this field.
Deep Learning Algorithm Trained on Brain Magnetic Resonance Images and Clinical Data to Predict Motor Outcomes of Patients With Corona Radiata Infarct

The early and accurate prediction of the extent of long-term motor recovery is important for establishing specific rehabilitation strategies for stroke patients. Using clinical parameters and brain magnetic resonance images as inputs, we developed a deep learning algorithm to increase the prediction accuracy of long-term motor outcomes in patients with corona radiata (CR) infarct. Using brain magnetic resonance images and clinical data obtained soon after CR infarct, we developed an integrated algorithm to predict hand function and ambulatory outcomes of the patient 6 months after onset. To develop and evaluate the algorithm, we retrospectively recruited 221 patients with CR infarct. The area under the curve of the validation set of the integrated modified Brunnstrom classification prediction model was 0.891 with 95% confidence interval (0.814–0.967) and that of the integrated functional ambulatory category prediction model was 0.919, with 95% confidence interval (0.842–0.995). We demonstrated that an integrated algorithm trained using patients’ clinical data and brain magnetic resonance images obtained soon after CR infarct can promote the accurate prediction of long-term hand function and ambulatory outcomes. Future efforts will be devoted to finding more appropriate input variables to further increase the accuracy of deep learning models in clinical applications.
HTLV-1's Foxy Strategy for Survival and Transmission

Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of adult T-cell leukemia-lymphoma (ATL) and inflammatory diseases including HTLV-1-associated myelopathy (HAM). A remarkable feature of HTLV-1 is that this virus transmits primarily through cell-to-cell contact. HTLV-1 increases the number of infected cells in vivo to ensure its survival and transmission. Therefore, survival of HTLV-1-infected cells in vivo is very critical for transmission under the host immune surveillance. HTLV-1 possesses multiple strategies to evade host immune responses. Among viral genes, Tax and HTLV-1 bZIP factor (HBZ) play crucial roles in the proliferation of infected cells and the subsequent development of ATL. Although Tax strongly activates the NF-kB pathway, the immunogenicity of Tax is very high; it is a major target of cytotoxic T lymphocytes. Therefore, the virus minimizes Tax production, expressing it only intermittently in vivo. On the other hand, the immunogenicity of HBZ is low, and its expression is maintained in all ATL cases. HBZ transforms the immunophenotype of infected cells into regulatory T cell-like (CD4+ CD25+ CCR4+ TIGIT+ Foxp3+), and promotes the production of immunosuppressive cytokines. Furthermore, HBZ mRNA not only encodes the protein but also functions itself like long non-coding RNA. As a result, Tax and HBZ enable long-term escape from host immunity, persistent infection, and proliferation of infected cells. Here, we review the viral strategies to counteract to host immune surveillance system.
A Brief Introduction on the Development of Ti-Based Metallic Glasses

Ti-based metallic glasses (MGs) possess high specific strength, low elastic modulus, high elasticity, high wear and corrosion resistance, and excellent biocompatibility, which make them highly attractive as lightweight high-strength materials as well as biomaterials. However, the glass forming ability (GFA) of Ti-based MGs, particularly those bearing no toxic, noble, or heavy metals, that is, Be, Pd, or Cu alike, largely sets back their wide applications for the restricted critical glass forming size of these Ti-based MGs. In this review, the outlines in developing Ti-based MGs are delineated in order to provide an overall view on the efforts ever made to fabricate bulk size Ti-based MGs. The state of the art in the knowledge on the GFA of Ti-based MGs is briefly introduced, and possible directions for fabricating bulk size toxic and noble element free Ti-based MGs are discussed.