Miracle-dz/UniFAR-FTUs huggingface dataset:
Forecasting and control of lactate bifurcation in Chinese hamster ovary cell culture processes

Biomanufacturing exhibits inherent variability that can lead to variation in performance attributes and batch failure. To help ensure process consistency and product quality the development of predictive models and integrated control strategies is a promising approach. In this study, a feedback controller was developed to limit excessive lactate production, a widespread metabolic phenomenon that is negatively associated with culture performance and product quality. The controller was developed by applying machine learning strategies to historical process development data, resulting in a forecast model that could identify whether a run would result in lactate consumption or accumulation. In addition, this exercise identified a correlation between increased amino acid consumption and low observed lactate production leading to the mechanistic hypothesis that there is a deficiency in the link between glycolysis and the tricarboxylic acid cycle. Using the correlative process parameters to build mechanistic insight and applying this to predictive models of lactate concentration, a dynamic model predictive controller (MPC) for lactate was designed. This MPC was implemented experimentally on a process known to exhibit high lactate accumulation and successfully drove the cell cultures towards a lactate consuming state. In addition, an increase in specific titer productivity was observed when compared with non‐MPC controlled reactors.
Bimodal Response to Shiga Toxin 2 Subtypes Results from Relatively Weak Binding to the Target Cell

There are two major antigenic forms of Shiga toxin (Stx), Stx1 and Stx2, which bind the same receptor and act on the same target but nonetheless differ in potency. Stx1a is more toxic to cultured cells, but Stx2 subtypes are more potent in animal models. To understand this phenomenon in cultured cells, we used a system that combines flow cytometry with a fluorescent reporter to monitor the Stx-induced inhibition of protein synthesis in single cells. ABSTRACT There are two major antigenic forms of Shiga toxin (Stx), Stx1 and Stx2, which bind the same receptor and act on the same target but nonetheless differ in potency. Stx1a is more toxic to cultured cells, but Stx2 subtypes are more potent in animal models. To understand this phenomenon in cultured cells, we used a system that combines flow cytometry with a fluorescent reporter to monitor the Stx-induced inhibition of protein synthesis in single cells. We observed that Vero cells intoxicated with Stx1a behave differently than those intoxicated with Stx2 subtypes: cells challenged with Stx1a exhibited a population-wide loss of protein synthesis, while cells exposed to Stx2a or Stx2c exhibited a dose-dependent bimodal response in which one subpopulation of cells was unaffected (i.e., no loss of protein synthesis). Cells challenged with a hybrid toxin containing the catalytic subunit of Stx1a and the cell-binding subunit of Stx2a also exhibited a bimodal response to intoxication, while cells challenged with a hybrid toxin containing the catalytic subunit of Stx2a and the cell-binding subunit of Stx1a exhibited a population-wide loss of protein synthesis. Other experiments further supported a primary role for the subtype of the B subunit in the outcome of host-Stx interactions. Our collective observations indicate that the bimodal response to Stx2 subtypes is due to relatively weak binding between Stx2 and the host cell that reduces the total functional pool of Stx2 in comparison to that of Stx1a. This explains, in part, the molecular basis for the differential cellular toxicity between Stx1a and Stx2 subtypes.
Tranexamic acid in cardiac surgery: a systematic review and meta-analysis (protocol)

Introduction Bleeding during cardiac surgery is associated with increased morbidity and mortality. Tranexamic acid is an antifibrinolytic with proven efficacy in major surgeries. Current clinical practice guidelines recommend intraoperative use in cardiac procedures. However, several complications have been reported with tranexamic acid including seizures. This review intends to summarise the evidence examining the efficacy and safety of tranexamic acid in patients undergoing cardiac surgery. Methods/design We will search MEDLINE, Embase, PubMED, ACPJC, CINAHL and the Cochrane trial registry for eligible randomised controlled trials, the search dates for all databases will be from inception until 1 January 2019, investigating the perioperative use of topical and/or intravenous tranexamic acid as a stand-alone antifibrinolytic agent compared with placebo in patients undergoing open cardiac surgery. We categorised outcomes as patient critical or patient important. Selected patient-critical outcomes are: mortality (intensive care unit, hospital and 30-day endpoints), reoperation within 24 hours, postoperative bleeding requiring transfusion of packed red blood cells, myocardial infarction, stroke, pulmonary embolism, bowel infarction, upper or lower limb deep vein thrombosis and seizures. Those outcomes, we perceived as clinical experts to be most patient valued and patients were not involved in outcomes selection process. We will not apply publication date, language, journal or methodological quality restrictions. Two reviewers will independently screen and identify eligible studies using predefined eligibility criteria and then review full reports of all potentially relevant citations. A third reviewer will resolve disagreements if consensus cannot be achieved. We will present the results as relative risk with 95% CIs for dichotomous outcomes and as mean difference or standardised mean difference for continuous outcomes with 95% CIs. We will assess the quality of evidence using the Grading of Recommendations, Assessment, Development and Evaluation approach. Ethics and dissemination Formal ethical approval is not required as primary data will not be collected. The results will be disseminated through a peer-reviewed publication Trial registration number CRD42018105904
Exocyst-mediated apical Wg secretion activates signaling in the Drosophila wing epithelium

Wnt proteins are secreted signaling factors that regulate cell fate specification and patterning decisions throughout the animal kingdom. In the Drosophila wing epithelium, Wingless (Wg, the homolog of Wnt1) is secreted from a narrow strip of cells at the dorsal-ventral boundary. However, the route of Wg secretion in polarized epithelial cells remains poorly understood and key proteins involved in this process are still unknown. Here, we performed an in vivo RNAi screen and identified members of the exocyst complex to be required for apical but not basolateral Wg secretion. Specifically blocking the apical Wg secretion leads to reduced downstream signaling. Using an in vivo ‘temporal-rescue’ assay, our results further indicate that apically secreted Wg activates target genes that require high signaling activity. In conclusion, our results demonstrate that the exocyst is required for an apical route of Wg secretion from polarized wing epithelial cells.
Cardiometabolic Risk and Cognitive Decline: The Role of Socioeconomic Status in Childhood and Adulthood

Socioeconomic conditions in childhood predict cognitive functioning in later life. It is unclear whether poor childhood socioeconomic status (SES) also predicts the acceleration of cognitive decline. One proposed pathway is via cardiometabolic risk, which has been linked to both childhood SES and earlier onset of cognitive impairment. Using data from the Health and Retirement Study, we examine the impact of childhood SES on cognitive trajectories over six years and test whether it operates through increased cardiometabolic risk and adult SES. We find that higher childhood SES leads to slower cognitive decline, partially due to lower levels of cardiometabolic risk. However, these pathways operate entirely through adult socioeconomic attainment. The results have important implications for future trends in cognitive population health within the context of growing social inequality and reduced social mobility.
Propensity score-integrated power prior approach for incorporating real-world evidence in single-arm clinical studies

ABSTRACT We are now at an amazing time for medical product development in drugs, biological products and medical devices. As a result of dramatic recent advances in biomedical science, information technology and engineering, ``big data’’ from health care in the real-world have become available. Although big data may not necessarily be attuned to provide the preponderance of evidence to a clinical study, high-quality real-world data can be transformed into scientific evidence for regulatory and healthcare decision-making using proven analytical methods and techniques, such as propensity score methodology and Bayesian inference. In this paper, we extend the Bayesian power prior approach for a single-arm study (the current study) to leverage external real-world data. We use propensity score methodology to pre-select a subset of real-world data containing patients that are similar to those in the current study in terms of covariates, and to stratify the selected patients together with those in the current study into more homogeneous strata. The power prior approach is then applied in each stratum to obtain stratum-specific posterior distributions, which are combined to complete the Bayesian inference for the parameters of interest. We evaluate the performance of the proposed method as compared to that of the ordinary power prior approach by simulation and illustrate its implementation using a hypothetical example, based on our regulatory review experience.
Evaluation of immune response to recombinant Bacillus anthracis LFD1-PA4 chimeric protein.

Background Anthrax is a particularly dangerous infectious disease that affects humans and livestock. Efficacious vaccines that can rapidly induce a long-term immune response are required to prevent anthrax infection in humans. Domains 4 and 1 of the protective antigen (PA) and lethal factor (LF), respectively, have very high antigenic properties. Aims In this experimental study, the pET28a-lfD1-pa4 expression vector was designed, constructed and transferred into E. coli BL21 (DE3) plysS. Methods For this purpose, pa4 gene was amplified by polymerase chain reaction (PCR) and cloned in a pGEM T-easy vector. The pGEM-pa4 and pGEM-lfD1 were digested by XbaI and HindIII enzymes. The ligation reaction was performed by ligase T4 enzyme and the gene cassette, lfD1-pa4, was subcloned in pET28a and transferred to E. coli BL21 (DE3) PlysS. Expression and puriﬁcation of chimeric proteins were conﬁrmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting techniques. The chimera LFD1-PA4 and mixed LFD1+PA4 proteins were injected four times into mice and antibody production was relativity evaluated by enzyme-linked immunosorbent assay (ELISA) test. Results The results showed that both chimeric and mixed proteins are immunogenic, but LFD1-PA4 has a higher potential to stimulate mice immune system. Conclusion LFD1-PA4 chimeric protein induced a higher immune response than LFD1+PA4 mixed protein and elicited antibody responses to LF and edema factor (EF), therefore, it holds promise to be a more effective trivalent vaccine candidate to use in anthrax prevention.
Hypoxia‐Inducible Factor‐2α Reprograms Liver Macrophages to Protect Against Acute Liver Injury Through the Production of Interleukin‐6

Acetaminophen (APAP) overdose represents the most frequent cause of acute liver failure, resulting in death or liver transplantation in more than one third of patients in the United States. The effectiveness of the only antidote, N‐acetylcysteine, declines rapidly after APAP ingestion, long before patients are admitted to the clinic with symptoms of severe liver injury. The direct hepatotoxicity of APAP triggers a cascade of innate immune responses that may exacerbate or limit the progression of tissue damage. A better understanding of this complex mechanism will help uncover targets for therapeutic interventions.
Encapsulation of glucose oxidase in Fe(III)/tannic acid nanocomposites for effective tumor ablation via Fenton reaction

Increasing the content of reactive oxygen species (ROS) with the assistance of nanoformulations in cancer cells via the Fenton reaction is considered an effective method to treat cancer. However, the efficiency of the Fenton reaction is affected by the level of H2O2, the selection of iron ions in different nanoformulations, etc. Herein, we use FeIII-tannic acid (FeIIITA) nanocomposites as the carrier to deliver glucose oxidase (GOD) which can solve the problem of insufficient endogenous H2O2 by catalytically converting the glucose. In comparison with traditional Fe2+/Fe3+, FeIIITA nanocomposites perform higher catalytic activity in converting H2O2 to high toxic hydroxyl radicals (·OH) due to the TA-mediated reduction of Fe3+. So, the integration of GOD and TA in the construction of nanocomposites significantly enhances the efficiency of the Fenton reaction. In vitro experiments show that ·OH produced by GOD-FeIIITA nanocomposites can not only achieve a good anticancer effect at a low concentration but also promote degradability of the nanocomposites. When it is only 1.08 μg · ml−1, the cell apoptosis rate has reached 76.91%. In vivo experiments further demonstrate that GOD-FeIIITA nanocomposites can significantly inhibit tumor growth. So this work lays a good foundation for Fenton reaction-based cancer treatment.
Homer1 mediates CaSR-dependent activation of mTOR complex 2 and initiates a novel pathway for AKT-dependent β-catenin stabilization in osteoblasts

The calcium-sensing receptor (CaSR) is critical for skeletal development, but its mechanism of action in osteoblasts is not well-characterized. In the central nervous system (CNS), Homer scaffolding proteins form signaling complexes with two CaSR-related members of the G protein–coupled receptor (GPCR) family C, metabotropic glutamate receptor 1 (mGluR1) and mGluR5. Here, we show that CaSR and Homer1 are co-expressed in mineralized mouse bone and also co-localize in primary human osteoblasts. Co-immunoprecipitation experiments confirmed that Homer1 associates with CaSR in primary human osteoblasts. The CaSR–Homer1 protein complex, whose formation was increased in response to extracellular Ca2+, was bound to mechanistic target of rapamycin (mTOR) complex 2 (mTORC2), a protein kinase that phosphorylates and activates AKT Ser/Thr kinase (AKT) at Ser473. siRNA-based gene-silencing assays with primary osteoblasts revealed that both CaSR and Homer1 are required for extracellular Ca2+-stimulated AKT phosphorylation and thereby inhibit apoptosis and promote AKT-dependent β-catenin stabilization and cellular differentiation. To confirm the role of the CaSR–Homer1 complex in AKT initiation, we show that in HEK-293 cells, co-transfection with both Homer1c and CaSR, but neither with Homer1c nor CaSR alone, establishes sensitivity of AKT–Ser473 phosphorylation to increases in extracellular Ca2+ concentrations. These findings indicate that Homer1 mediates CaSR-dependent AKT activation via mTORC2 and thereby stabilizes β-catenin in osteoblasts.
Abandoning inhalational anaesthesia

1Consultant, Department of Anaesthesia, Sussex University Hospitals NHS Trust, Brighton, East Sussex, UK 2Consultant, Department of Anaesthesia,WythenshaweHospital, Manchester University NHS Foundation Trust, Manchester, UK . Correspondence to: S.White Email: stuart.white6@nhs.net Accepted: 20August 2019
Intravenous Bone Marrow Mononuclear Cells for Acute Ischemic Stroke: Safety, Feasibility, and Effect Size from a Phase I Clinical Trial

Cellular therapy is a promising investigational modality to enhance poststroke recovery. We conducted a single‐arm, phase I clinical trial to determine the safety and feasibility of intravenous (IV) administration of autologous bone marrow mononuclear cells (MNCs) after acute ischemic stroke (AIS). Patients with moderate severity of AIS underwent bone marrow harvest followed by IV reinfusion of MNCs within 24–72 hours of onset. A target dose of 10 million cells per kilogram was chosen based on preclinical data. Patients were followed up daily during hospitalization and at 1, 3, 6, 12, and 24 months for incidence of adverse events using laboratory, clinical (12 months), and radiological (24 months) parameters. The trial was powered to detect severe adverse events (SAEs) with incidences of at least 10% and planned to enroll 30 patients. Primary outcomes were study‐related SAEs and the proportion of patients successfully completing study intervention. A propensity score‐based matched control group was used for the estimation of effect size (ES) for day‐90 modified Rankin score (mRS). There were no study‐related SAEs and, based on a futility analysis, enrolment was stopped after 25 patients. All patients successfully completed study intervention and most received the target dose. Secondary analysis estimated the ES to be a reduction of 1 point (95% confidence interval: 0.33–1.67) in median day‐90 mRS for treated patients as compared with the matched control group. Bone marrow harvest and infusion of MNCs is safe and feasible in patients with AIS. The estimated ES is helpful in designing future randomized controlled trials. Stem Cells 2019;37:1481–1491
Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.
Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids

The interplay between food production animals, humans and the environment with respect to the transmission of drug-resistant pathogens is widely debated and poorly understood. Pandemic uropathogenic Escherichia coli ST131-H30Rx, with conserved fluoroquinolone and cephalosporin resistance, are not frequently identified in animals. However, the phylogenetic precursor lineage ST131-H22 in animals and associated meat products is being reported with increasing frequency. Here we characterized two highly related ST131-H22 strains, one from a healthy pig and the other from a human infection (in 2007 and 2009, respectively). We used both long and short genome sequencing and compared them to ST131-H22 genome sequences available in public repositories. Even within the context of H22 strains, the two strains in question were highly related, separated by only 20 core SNPs. Furthermore, they were closely related to a faecal strain isolated in 2010 from a geographically distinct, healthy human in New South Wales, Australia. The porcine and hospital strains carried highly similar HI2-ST3 multidrug resistant plasmids with differences in the hospital strain arising due to IS-mediated insertions and rearrangements. Near identical ColV plasmids were also present in both strains, further supporting their shared evolutionary history. This work highlights the importance of adopting a One Health approach to genomic surveillance to gain insights into pathogen evolution and spread.
Pre-exercise hypohydration prevalence in soccer players: A quantitative systematic review.

ABSTRACT Pre-exercise hypohydration can impair soccer performance and has been extensively studied in different soccer populations. Therefore, the aim of this systematic review was to report hypohydration prevalence, measured by blood or urine samples, in different soccer populations based on sex (males and females), performance level (professional and recreational players) and context (training sessions and games). The Pubmed, Web of Science and SPORTDiscus databases were systematically searched until November 2018. Data were pooled to compare hypohydration prevalence between the different subgroups. Following the systematic search selection process, 24 studies were included. The results indicated that overall pre-exercise hypohydration prevalence was 63.3%, 37.4% and 58.8% for urine specific gravity (USG), urine osmolality (U Osm) and urine colour, respectively. Furthermore, no study implemented blood samples to examine hypohydration prevalence in soccer players. The subgroup analyses using USG data indicated that pre-exercise hypohydration prevalence was significantly higher amongst males (66.0%; p = 0.001), professional soccer players (66.2%; p = 0.020) and before a training session (79.6%; p < 0.001). Pre-exercise hypohydration prevalence was 46.8% among female soccer players, 55.6% in recreational soccer players and 41,3% before a game. The subgroup analyses using U Osm data indicated that hypohydration prevalence was significantly higher before a training session (52.6%; p = 0.023). Based on these results, it can be concluded that hypohydration prevalence in soccer players is of major concern. Future research should explore how pre-exercise hydration status can be improved in a sustainable way.
Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes in Pyrus

Negatively selected genes (NSGs) and positively selected genes (PSGs) are the two types of most nuclear protein-coding genes in organisms. However, the evolutionary rates and characteristics of different types of genes have been rarely understood. In the present study, we investigate the rates of synonymous substitution (Ks) and the rates of non-synonymous substitution (Ka) by comparing the orthologous genes of two sequenced Pyrus species, Pyrus bretschneideri and Pyrus communis. Subsequently, we compared the evolutionary rates, gene structures, and expression profiles during different fruit development between PSGs and NSGs. Compared with the NSGs, the PSGs have fewer exons, shorter gene length, lower synonymous substitution rates and have higher evolutionary rates. Remarkably, gene expression patterns between two Pyrus species fruit indicated functional divergence for most of the orthologous genes derived from a common ancestor, and subfunctionalization for some of them. Overall, the present study shows that PSGs differs from NSGs not only under environmental selective pressure (Ka/Ks), but also in their structural, functional, and evolutionary properties. Additionally, our resulting data provides important insights for the evolution and highlights the diversification of orthologous genes in two Pyrus species.