Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism study of self-organized TiO2 nanotube arrays by anodization

Based on analysis of the current–time curve and observation of surface morphology including top, cross-section, bottom and substrate views by scanning electron microscopy (SEM), a new growth, dissolution–breakdown model, of self-organized titania nanotube arrays is presented. By this model, many phenomena raised during anodization are explained, such as the sharp decrease of current in initial period, current transient, occurring of ridges on tube walls, and formation of not pores but tubes etc. Furthermore, the reason for the occurrence of a porous structure, the balance between internal energy and surface energy, was proposed too. This study may also shed light on the formation of porous oxide films on other valve metals.
Zinc(II) Extraction from Hydrochloric Acid Solutions using Amberlite XAD-7 Impregnated with Cyphos IL 101 (Tetradecyl(Trihexyl)Phosphonium Chloride)

Abstract Cyphos IL 101 (tetradecyl(trihexyl)phosphonium chloride) was immobilized on Amberlite XAD-7. The extractant impregnated resin (EIR) was very efficient at removing Zn(II) from HCl solutions (optimum found between 2 and 4 M HCl). Metal ions were removed as anionic chlorocomplexes (ZnCl4 2−) by ion exchange mechanism. The sorption strongly depended on the Cyphos IL 101 concentration in the EIR. The maximum sorption capacity was close to 20 mg Zn(II) g−1 EIR (i.e. 0.40 mol Zn(II) mol−1 Cyphos IL 101). The uptake kinetics were controlled by intraparticle diffusion (De: 1.2 10−11 − 6 10−11 m2 min−1). Zn(II) can be easily desorbed using a number of eluents (including water and 0.1 M solution of HNO3, H2SO4, and Na2SO4), which maintained performance levels over 5 cycles.
Vitamin C, Thiamine, and Hydrocortisone in the Treatment of Sepsis: A Meta-Analysis and Trial Sequential Analysis of Randomized Controlled Trials

Background: There is a conflicting body of evidence regarding the benefit of vitamin C, thiamine, and hydrocortisone in combination as an adjunctive therapy for sepsis with or without septic shock. We aimed to assess the efficacy of this treatment among predefined populations. Methods: A literature review of major electronic databases was performed to include randomized controlled trials (RCTs) evaluating vitamin C, thiamine, and hydrocortisone in the treatment of patients with sepsis with or without septic shock in comparison to the control group. Results: Seven studies met our inclusion criteria, and 6 studies were included in the final analysis totaling 839 patients (mean age 64.2 ± 18; SOFA score 8.7 ± 3.3; 46.6% female). There was no significant difference between both groups in long term mortality (Risk Ratio (RR) 1.05; 95% CI 0.85-1.30; P = 0.64), ICU mortality (RR 1.03; 95% CI 0.73-1.44; P = 0.87), or incidence of acute kidney injury (RR 1.05; 95% CI 0.80-1.37; P = 0.75). Furthermore, there was no significant difference in hospital length of stay, ICU length of stay, and ICU free days on day 28 between the intervention and control groups. There was, however, a significant difference in the reduction of SOFA score on day 3 from baseline (MD −0.92; 95% CI −1.43 to −.41; P < 0.05). In a trial sequential analysis for mortality outcomes, our results are inconclusive for excluding lack of benefit of this therapy. Conclusion: Among patients with sepsis with or without septic shock, treatment with vitamin C, thiamine, and hydrocortisone was not associated with a significant reduction in mortality, incidence of AKI, hospital and ICU length of stay, or ICU free days on day 28. There was a significant reduction of SOFA score on day 3 post-randomization. Further studies with a larger number of patients are needed to provide further evidence on the efficacy or lack of efficacy of this treatment.
Isolation of Acetylated and Unmodified Protein N-Terminal Peptides by Strong Cation Exchange Chromatographic Separation of TrypN-Digested Peptides

We developed a simple and rapid method to enrich protein N-terminal peptides, in which the protease TrypN is first employed to generate protein N-terminal peptides without Lys or Arg and internal peptides with two positive charges at their N termini, and then, the N-terminal peptides with or without N-acetylation are separated from the internal peptides by strong cation exchange chromatography according to a retention model based on the charge/orientation of peptides. This approach was applied to 20 μg of human HEK293T cell lysate proteins to profile the N-terminal proteome. On average, 1550 acetylated and 200 unmodified protein N-terminal peptides were successfully identified in a single LC/MS/MS run with less than 3% contamination with internal peptides, even when we accepted only canonical protein N termini registered in the Swiss-Prot database. Because this method involves only two steps, protein digestion and chromatographic separation, without the need for tedious chemical reactions, it should be useful for comprehensive profiling of protein N termini, including proteoforms with neo-N termini.
The loopometer: a quantitative in vivo assay for DNA-looping proteins

Abstract Proteins that can bring together separate DNA sites, either on the same or on different DNA molecules, are critical for a variety of DNA-based processes. However, there are no general and technically simple assays to detect proteins capable of DNA looping in vivo nor to quantitate their in vivo looping efficiency. Here, we develop a quantitative in vivo assay for DNA-looping proteins in Escherichia coli that requires only basic DNA cloning techniques and a LacZ assay. The assay is based on loop assistance, where two binding sites for the candidate looping protein are inserted internally to a pair of operators for the E. coli LacI repressor. DNA looping between the sites shortens the effective distance between the lac operators, increasing LacI looping and strengthening its repression of a lacZ reporter gene. Analysis based on a general model for loop assistance enables quantitation of the strength of looping conferred by the protein and its binding sites. We use this ‘loopometer’ assay to measure DNA looping for a variety of bacterial and phage proteins.
Design and Characterization of a Screw Extrusion Hot-End for Fused Deposition Modeling

The filament is the most widespread feedstock material form used for fused deposition modeling printers. Filaments must be manufactured with tight dimensional tolerances, both to be processable in the hot-end and to obtain printed objects of high quality. The ability to successfully feed the filament into the printer is also related to the mechanical properties of the filament, which are often insufficient for pharmaceutically relevant excipients. In the scope of this work, an 8 mm single screw hot-end was designed and characterized, which allows direct printing of materials from their powder form and does not require an intermediate filament. The capability of the hot-end to increase the range of applicable excipients to fused deposition modeling was demonstrated by processing and printing several excipients that are not suitable for fused deposition modeling in their filament forms, such as ethylene vinyl acetate and poly(1-vinylpyrrolidone-co-vinyl acetate). The conveying characteristic of the screw was investigated experimentally with all materials and was in agreement with an established model from literature. The complete design information, such as the screw geometry and the hot-end dimensions, is provided in this work.
Genome-Wide Circular RNA Expression Patterns Reflect Resistance to Immunomodulatory Drugs in Multiple Myeloma Cells

Simple Summary Multiple myeloma (MM) constitutes the second most common hematological malignancy and is caused by aberrant plasma cell proliferation in the bone marrow. While recent improvements in the treatment of MM has been observed using immunomodulatory drugs (IMiDs), patients often relapse due to acquired drug resistance and no cure for the disease is currently available. In this report, we profile circular RNA (circRNA) expression patterns in cultured MM cells being sensitive to IMiDs and their resistant counterparts. CircRNAs constitute a large class of non-coding RNA molecules with emerging roles in cancer development and progression, but have not previously been explored in this context. We found that global circRNA expression patterns reflect IMiD sensitivity, but the most downregulated circRNA in IMiD resistant MM cells did not seem to be a direct driver of IMiD resistance. Future studies should investigate other circRNA candidates identified here in the context of IMiD resistance. Abstract Immunomodulatory drugs (IMiDs), such as lenalidomide and pomalidomide, may induce significant remissions in multiple myeloma (MM) patients, but relapses are frequently observed and the underlying molecular mechanisms for this are not completely understood. Circular RNAs (circRNAs) constitute an emerging class of non-coding RNAs with important roles in cancer. Here, we profiled genome-wide expression patterns of circRNAs in IMiD-sensitive MM cells and their resistant counterparts as well as in IMiD-resistant cells treated with specific epigenetic drugs alone or in combination. We found that genome-wide circRNA expression patterns reflect IMiD sensitivity and ciRS-7 (also known as CDR1as) was the most downregulated circRNA upon acquired resistance. The depletion of ciRS-7 correlated with increased methylation levels of the promoter CpG island of its host gene, LINC00632. Expression of LINC00632 and ciRS-7 was partly restored by treatment with a combination of an EZH2 inhibitor (EPZ-6438) and a DNA methyl transferase inhibitor (5-azacytidine), which also restores the IMiD sensitivity of the cells. However, knockdown of ciRS-7 did not affect IMiD sensitivity and we found that ciRS-7 also becomes epigenetically silenced after prolonged cell culture without drug-exposure. In conclusion, we found that genome-wide circRNA expression patterns reflect IMiD sensitivity in an in vitro model of acquired resistance.
Correlation of Influenza B Haemagglutination Inhibiton, Single-Radial Haemolysis and Pseudotype-Based Microneutralisation Assays for Immunogenicity Testing of Seasonal Vaccines

Influenza B is responsible for a significant proportion of the global morbidity, mortality and economic loss caused by influenza-related disease. Two antigenically distinct lineages co-circulate worldwide, often resulting in mismatches in vaccine coverage when vaccine predictions fail. There are currently operational issues with gold standard serological assays for influenza B, such as lack of sensitivity and requirement for specific antigen treatment. This study encompasses the gold standard assays with the more recent Pseudotype-based Microneutralisation assay in order to study comparative serological outcomes. Haemagglutination Inhibition, Single Radial Haemolysis and Pseudotype-based Microneutralisation correlated strongly for strains in the Yamagata lineage; however, it correlated with neither gold standard assays for the Victoria lineage.
Lid Flare Measurement with Lateral Midpupil Distances

ABSTRACT Purpose To assess the sensitivity and specificity of lateral midpupil lid distances for the detection of upper lid lateral flare. Methods Lateral lid flare was determined by unanimous agreement among six experienced oculoplastic surgeons in the grading of photographs obtained for patients with Graves orbitopathy (GO). Bézier lines were employed to extract the upper eyelid contours of the patients and a control group of age and sex matched subjects. Custom software was employed to determine 5 lateral midpupil eyelid distances. The sensitivity and specificity of each measurement in detecting lateral flare were estimated from receiver operating characteristic curves. The non-parametric Kruskal–Wallis one-way analysis of variance (ANOVA) with Dunn’s posthoc test was used to compare the median values of the contour parameters between groups. Results The degree of agreement between judges evaluated with the Fleiss’ Kappa test was relatively high (K = 0.69, z = 16.6, p < .0001). The raters classified 12 lids with lateral lid flare (LLF) and 7 without LLF in patients with GO. There was no agreement on the presence or absence of LLF in 11 lids. In all eyes, lateral midpupil lid distances diminished from the center of the eyelid towards the lateral canthus. Receiver operating characteristic analysis for the midpupil distances revealed that the fourth distance from the center demonstrated high sensitivity and specificity in detecting flare. At this location (2.5 mm medial to the lateral canthus) a midpupil distance equal to or greater than 60% of the margin reflex distance (MRD1) indicated the presence of flare. Conclusions – A single measurement of a lateral midpupil eyelid distance 2.5 mm medial to the lateral canthus is a sensitive and specific measurement for the diagnosis of the LLF.
Electrophoretic Extraction of Cells/Particles in a Counter Current Extractor

Abstract Electrophoretic separation is a leading method for resolving mixtures of charged macromolecules or cells. In the present work, a combination of free electrophoresis and multistage extraction called Electrophoretic Counter Current Extractor was explored. A simple mathematical model was developed to describe the mass and heat transfer during the electrophoretic separation. In order to validate the model and also to test the extractor, the extraction of fixed human Red Blood Cells and Latex particles of different sizes suspended in phosphate buffer, was performed at different electric field strengths. The experimental results were found to agree reasonably well with those predicted by the model.
Deep Convolutional and LSTM Networks on Multi-Channel Time Series Data for Gait Phase Recognition

With an ageing society comes the increased prevalence of gait disorders. The restriction of mobility leads to a considerable reduction in the quality of life, because associated falls increase morbidity and mortality. Consideration of gait analysis data often alters surgical recommendations. For that reason, the early and systematic diagnostic treatment of gait disorders can spare a lot of suffering. As modern gait analysis systems are, in most cases, still very costly, many patients are not privileged enough to have access to comparable therapies. Low-cost systems such as inertial measurement units (IMUs) still pose major challenges, but offer possibilities for automatic real-time motion analysis. In this paper, we present a new approach to reliably detect human gait phases, using IMUs and machine learning methods. This approach should form the foundation of a new medical device to be used for gait analysis. A model is presented combining deep 2D-convolutional and LSTM networks to perform a classification task; it predicts the current gait phase with an accuracy of over 92% on an unseen subject, differentiating between five different phases. In the course of the paper, different approaches to optimize the performance of the model are presented and evaluated.
Genomic characteristics and prognostic significance of co‐mutated ASXL1/SRSF2 acute myeloid leukemia

The ASXL1 and SRSF2 mutations in AML are frequently found in patients with preexisting myeloid malignancies and are individually associated with poor outcomes. In this multi‐institutional retrospective analysis, we assessed the genetic features and clinical outcomes of 43 patients with ASXL1mutSRSF2mut AML and compared outcomes to patients with either ASXL1 (n = 57) or SRSF2 (n = 70) mutations. Twenty‐six (60%) had secondary‐AML (s‐AML). Variant allele fractions suggested that SRSF2 mutations preceded ASXL1 mutational events. Median overall survival (OS) was 7.0 months (95% CI:3.8,15.3) and was significantly longer in patients with de novo vs s‐AML (15.3 vs 6.4 months, respectively; P = .04 on adjusted analysis). Compared to ASXL1mutSRSF2wt and ASXL1wtSRSF2mut, co‐mutated patients had a 1.4 and 1.6 times increase in the probability of death, respectively (P = .049), with a trend towards inferior OS (median OS = 7.0 vs 11.5 vs 10.9 months, respectively; P = .10). Multivariable analysis suggests this difference in OS is attributable to the high proportion of s‐AML patients in the co‐mutated cohort (60% vs 32% and 23%, respectively). Although this study is limited by the retrospective data collection and the relatively small sample size, these data suggest that ASXL1mutSRSF2mut AML is a distinct subgroup of AML frequently associated with s‐AML and differs from ASXL1mutSRSF2wt/ASXL1wtSRSF2mut with respect to etiology and leukemogenesis.
Gut-Brain-Microbiota Axis: Antibiotics and Functional Gastrointestinal Disorders

Gut microbiota composition and function are major areas of research for functional gastrointestinal disorders. There is a connection between gastrointestinal tract and central nervous system and this is mediated by neurotransmitters, inflammatory cytokines, the vagus nerve and the hypothalamic-pituitary-adrenal axis. Functional gastrointestinal disorders are prevalent diseases affecting more than one third of the population. The etiology of these disorders is not clarified. Visceral hyperalgesia is the main hypothesis for explaining clinical symptoms, however gut-brain axis disorder is a new terminology for functional disorders. In this review, microbiota-gut-brain axis connection pathways and related disorders are discussed. Antibiotics are widely used in developed countries and recent evidence indicates antibiotic-induced dysbiosis as an important factor for functional disorders. Antibiotics exert negative effects on gut microbiota composition and functions. Antibiotic-induced dysbiosis is a major factor for occurrence of post-infectious irritable bowel syndrome. Cognitive and mood disorders are also frequent in functional gastrointestinal disorders. Animal and human trials show strong evidence for the causal relationship between gut microbiota and brain functions. Therapeutic implications of these newly defined pathogenic pathways are also discussed.
The CDCP1 Signaling Hub: A Target for Cancer Detection and Therapeutic Intervention

CUB-domain containing protein 1 (CDCP1) is a type I transmembrane glycoprotein that is upregulated in malignancies of the breast, lung, colorectum, ovary, kidney, liver, pancreas, and hematopoietic system. Here, we discuss CDCP1 as an important hub for oncogenic signaling and its key roles in malignant transformation and summarize approaches focused on exploiting it for cancer diagnosis and therapy. Elevated levels of CDCP1 are associated with progressive disease and markedly poorer survival. Predominantly located on the cell surface, CDCP1 lies at the nexus of key tumorigenic and metastatic signaling cascades, including the SRC/PKCδ, PI3K/AKT, WNT, and RAS/ERK axes, the oxidative pentose phosphate pathway, and fatty acid oxidation, making important functional contributions to cancer cell survival and growth, metastasis, and treatment resistance. These findings have stimulated the development of agents that target CDCP1 for detection and treatment of a range of cancers, and results from preclinical models suggest that these approaches could be efficacious and have manageable toxicity profiles.
A case–control study examining the association of smad7 and TLR single nucleotide polymorphisms on the risk of colorectal cancer in ulcerative colitis

Ulcerative colitis (UC) is characterized by chronic mucosal inflammation and an increased risk of colorectal cancer. smad7, TLR2 and TLR4 modulate intestinal inflammation and their polymorphisms affect the risk of development of sporadic colorectal cancer. The aim of the current study was to examine the association between single nucleotide polymorphisms (SNPs) in smad7, TLR2 and TLR4 and the development of colorectal cancer in patients with UC.
From Transcriptomics to Treatment in Inherited Optic Neuropathies

Inherited optic neuropathies, including Leber Hereditary Optic Neuropathy (LHON) and Dominant Optic Atrophy (DOA), are monogenetic diseases with a final common pathway of mitochondrial dysfunction leading to retinal ganglion cell (RGC) death and ultimately loss of vision. They are, therefore, excellent models with which to investigate this ubiquitous disease process—implicated in both common polygenetic ocular diseases (e.g., Glaucoma) and late-onset central nervous system neurodegenerative diseases (e.g., Parkinson disease). In recent years, cellular and animal models of LHON and DOA have matured in parallel with techniques (such as RNA-seq) to determine and analyze the transcriptomes of affected cells. This confluence leaves us at a particularly exciting time with the potential for the identification of novel pathogenic players and therapeutic targets. Here, we present a discussion of the importance of inherited optic neuropathies and how transcriptomic techniques can be exploited in the development of novel mutation-independent, neuroprotective therapies.
The In Vitro Proinflammatory Properties of Water Accommodated Sediment Extracts from a Creosote‐Contaminated US Environmental Protection Agency Superfund Site

The southern branch of the Elizabeth River near Portsmouth, Virginia, USA, is one of the most creosote‐polluted subestuaries in North America and the former location of the Atlantic Wood US Environmental Protection Agency Superfund site. We previously demonstrated that adult Atlantic Wood killifish collected in situ had severe hepatic lesions, including hepatoblastoma and hepatocellular carcinoma, as well as suppressed circulating antibody responses compared to a historical reference site. Moreover, several innate immune functions were higher in Atlantic Wood fish, including elevated expression of hepatic cyclooxygenase‐2 (COX‐2), suggesting a proinflammatory environment. To further examine the potential of Atlantic Wood contaminants to modulate innate immune function(s), the present study used RAW264.7 mouse macrophages as an in vitro model to develop new approach methodologies for rapid screening. Lipopolysaccharide (LPS)–stimulated nitric oxide secretion by macrophages is a rapid, sensitive, and predictive in vitro system for screening potentially immunotoxic contaminants as single compounds or as complex mixtures. Compared to the reference site, filter‐sterilized Atlantic Wood sediment extracts (water accommodated fractions) induced nitric oxide and IL‐6 secretion as well as inducible nitric oxide synthase and COX‐2 proteins at levels comparable to or higher than those induced by LPS treatments alone. Extracts also increased phagocytic activity by macrophages. Using a limulus lysate assay, we show that bacterial endotoxin levels in Atlantic Wood extracts are higher than in reference extracts and that polymyxin‐B chelation ameliorates proinflammatory effects. These findings illuminate the reality of sediment constituents other than toxic compounds previously associated with developmental abnormalities and carcinogenesis in killifish from the Atlantic Wood site. Perhaps these data also suggest the presence of contaminant‐adapted consortia of sediment microbes at many heavily polluted sites worldwide compared to less contaminated sites. Environ Toxicol Chem 2021;40:1576–1585. © 2021 SETAC