Miracle-dz/UniFAR-FTUs huggingface dataset:
Machine Learning Approach to Predicting COVID-19 Disease Severity Based on Clinical Blood Test Data: Statistical Analysis and Model Development

Background Accurate prediction of the disease severity of patients with COVID-19 would greatly improve care delivery and resource allocation and thereby reduce mortality risks, especially in less developed countries. Many patient-related factors, such as pre-existing comorbidities, affect disease severity and can be used to aid this prediction. Objective Because rapid automated profiling of peripheral blood samples is widely available, we aimed to investigate how data from the peripheral blood of patients with COVID-19 can be used to predict clinical outcomes. Methods We investigated clinical data sets of patients with COVID-19 with known outcomes by combining statistical comparison and correlation methods with machine learning algorithms; the latter included decision tree, random forest, variants of gradient boosting machine, support vector machine, k-nearest neighbor, and deep learning methods. Results Our work revealed that several clinical parameters that are measurable in blood samples are factors that can discriminate between healthy people and COVID-19–positive patients, and we showed the value of these parameters in predicting later severity of COVID-19 symptoms. We developed a number of analytical methods that showed accuracy and precision scores >90% for disease severity prediction. Conclusions We developed methodologies to analyze routine patient clinical data that enable more accurate prediction of COVID-19 patient outcomes. With this approach, data from standard hospital laboratory analyses of patient blood could be used to identify patients with COVID-19 who are at high risk of mortality, thus enabling optimization of hospital facilities for COVID-19 treatment.
You are welcome here: A practical guide to diversity, equity, and inclusion for undergraduates embarking on an ecological research experience

Abstract As we build a more diverse, equitable, and inclusive culture in the ecological research community, we must work to support new ecologists by empowering them with the knowledge, tools, validation, and sense of belonging in ecology to succeed. Undergraduate research experiences (UREs) are critical for a student's professional and interpersonal skill development and key for recruiting and retaining students from diverse groups to ecology. However, few resources exist that speak directly to an undergraduate researcher on the diversity, equity, and inclusion (DEI) dimensions of embarking on a first research experience. Here, we write primarily for undergraduate readers, though a broader audience of readers, especially URE mentors, will also find this useful. We explain many of the ways a URE benefits undergraduate researchers and describe how URE students from different positionalities can contribute to an inclusive research culture. We address three common sources of anxiety for URE students through a DEI lens: imposter syndrome, communicating with mentors, and safety in fieldwork. We discuss the benefits as well as the unique vulnerabilities and risks associated with fieldwork, including the potential for harassment and assault. Imposter syndrome and toxic field experiences are known to drive students, including students from underrepresented minority groups, out of STEM. Our goal is to encourage all students, including those from underrepresented groups, to apply for UREs, build awareness of their contributions to inclusion in ecology research, and provide strategies for overcoming known barriers.
A Fast Alternative to Soft Lithography for the Fabrication of Organ‐on‐a‐Chip Elastomeric‐Based Devices and Microactuators

Organ‐on‐a‐chip technology promises to revolutionize how pre‐clinical human trials are conducted. Engineering an in vitro environment that mimics the functionality and architecture of human physiology is essential toward building better platforms for drug development and personalized medicine. However, the complex nature of these devices requires specialized, time consuming, and expensive fabrication methodologies. Alternatives that reduce design‐to‐prototype time are needed, in order to fulfill the potential of these devices. Here, a streamlined approach is proposed for the fabrication of organ‐on‐a‐chip devices with incorporated microactuators, by using an adaptation of xurography. This method can generate multilayered, membrane‐integrated biochips in a matter of hours, using low‐cost benchtop equipment. These devices are capable of withstanding considerable pressure without delamination. Furthermore, this method is suitable for the integration of flexible membranes, required for organ‐on‐a‐chip applications, such as mechanical actuation or the establishment of biological barrier function. The devices are compatible with cell culture applications and present no cytotoxic effects or observable alterations on cellular homeostasis. This fabrication method can rapidly generate organ‐on‐a‐chip prototypes for a fraction of cost and time, in comparison to conventional soft lithography, constituting an interesting alternative to the current fabrication methods.
Reporting on one's behavior: a survey experiment on the nonvalidity of self-reported COVID-19 hygiene-relevant routine behaviors

Abstract Surveys based on self-reported hygiene-relevant routine behaviors have played a crucial role in policy responses to the COVID-19 pandemic. In this article, using anchoring to test validity in a randomized controlled survey experiment during the COVID-19 pandemic, we demonstrate that asking people to self-report on the frequency of routine behaviors are prone to significant measurement error and systematic bias. Specifically, we find that participants across age, gender, and political allegiance report higher (lower) frequencies of COVID-19-relevant behaviors when provided with a higher (lower) anchor. The results confirm that such self-reports should not be regarded as behavioral data and should primarily be used to inform policy decisions if better alternatives are not available. To this end, we discuss the use of anchoring as a validity test relative to self-reported behaviors as well as viable alternatives to self-reports when seeking to behaviorally inform policy decisions.
miR-375 Promotes Pancreatic Differentiation In Vitro by Affecting Different Target Genes at Different Stages

Human embryonic stem cells (hESCs) possess the ability to differentiate into insulin-producing cells (IPCs), which can be used to treat type I diabetes. miR-375 is an essential transcriptional regulator in the development and maturation of the pancreas. In this study, we optimized a protocol to differentiate hESCs into IPCs and successfully obtained IPCs. Then, we performed overexpression and inhibition experiments of miR-375 on cells at different stages of differentiation and performed RNA-seq. The results showed that the expression of miR-375 fluctuated during hESC differentiation and was affected by miR-375 mimics and inhibitors. miR-375 influences global gene expression and the target genes of miR-375. The overexpression of miR-375 can cause changes in multiple signaling pathways during pancreatic development. miR-375 is a major participant in the differentiation of pancreatic β-cells through different target genes at different stages. This study provides new ideas for further investigation of how microRNAs affect cell fate and gene transcription.
Synthesis, spectral investigation and development of tetrahedral copper(II) complexes as artificial metallonucleases and antimalarial agents

Seven new copper(II) complexes of type [Cu(A)(L)]⋅H2O (A = sparfloxacin, ciprofloxacin, levofloxacin, gatifloxacin, pefloxacin, ofloxacin, norfloxacin; L = 5-[(3-chlorophenyl)diazenyl]-4-hydroxy-1,3-thiazole-2(3H)-thione) were synthesized and characterized using elemental and thermogravimetric analyses, and electronic, electron paramagnetic resonance (EPR), Fourier transform infrared and liquid chromatography–mass spectroscopies. Tetrahedral geometry around copper is assigned in all complexes using EPR and electronic spectral analyses. All complexes were investigated for their interaction with herring sperm DNA utilizing absorption titration (Kb = 1.27–3.13 × 105 M−1) and hydrodynamic volume measurement studies. The studies suggest the classical intercalative mode of DNA binding. The cleavage reaction on pUC19 DNA was monitored by agarose gel electrophoresis. The results indicate that the Cu(II) complexes can more effectively promote the cleavage of plasmid DNA. The superoxide dismutase mimic activity of the complexes was evaluated by nitroblue tetrazolium assay, and the complexes catalysed the dismutation of superoxide at pH = 7.8 with IC50 values in the range 0.597–0.900 μM. The complexes were screened for their in vitro antibacterial activity against five pathogenic bacteria. All the complexes are good cytotoxic agents and show LC50 values ranging from 5.559 to 11.912 µg ml−1. All newly synthesized Cu(II) complexes were also evaluated for their in vitro antimalarial activity against Plasmodium falciparum strain (IC50 = 0.62–2.0 µg ml−1). Copyright © 2015 John Wiley & Sons, Ltd.
Characterization of the complete chloroplast genome of Pterocarya macroptera var. delavayi (Juglandaceae)

Abstract In this study, the complete chloroplast genome sequence of Pterocarya macroptera var. delavayi was reported and characterized. The chloroplast genome is 160,168 bp in length, and consists the typical quadripartite structure, a pair of inverted repeats (IRs, 26,007 bp) separated by a large single-copy region (89,701 bp) and a small single-copy region (18,453 bp). A total of 136 unique genes were predicted, including 88 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The GC content of the chloroplast genome is 36.2%. Phylogenetic analysis confirmed the close relationship between Pterocarya and Juglans.
Empirical method for rapid quantification of intrinsic fluorescence signals of key metabolic probes from optical spectra measured on tissue-mimicking turbid medium

Abstract. Significance: Optical fluorescence spectroscopy technique has been explored extensively to quantify both glucose uptake and mitochondrial metabolism with proper fluorescent probes in small tumor models in vivo. However, it remains a great challenge to rapidly quantify the intrinsic metabolic fluorophores from the optically measured fluorescence spectra that contain significant distortions due to tissue absorption and scattering. Aim: To enable rapid spectral data processing and quantify the in vivo metabolic parameters in real-time, we present an empirical ratio-metric method for rapid fluorescence spectra attenuation correction with high accuracy. Approach: A first-order approximation of intrinsic fluorescence spectra can be obtained by dividing the fluorescence spectra by diffuse reflectance spectra with some variable powers. We further developed this approximation for rapid extraction of intrinsic key metabolic probes (2-NBDG for glucose uptake and TMRE for mitochondrial function) by dividing the distorted fluorescence spectra by diffuse reflectance intensities recorded at excitation and emission peak with a pair of system-dependent powers. Tissue-mimicking phantom studies were conducted to evaluate the method. Results: The tissue-mimicking phantom studies demonstrated that our empirical method could quantify the key intrinsic metabolic probes in near real-time with an average percent error of ∼5 % . Conclusions: An empirical method was demonstrated for rapid quantification of key metabolic probes from fluorescence spectra measured on a tissue-mimicking turbid medium. The proposed method will potentially facilitate real-time monitoring of key metabolic parameters of tumor models in vivo using optical spectroscopy, which will significantly advance translational cancer research.
Ossification of the Posterior Longitudinal Ligament in the Cervical, Thoracic, and Lumbar Spine

Ossification of the posterior longitudinal ligament (OPLL) is a relatively rare disorder characterized by elongation of the posterior longitudinal ligament followed by the progressive development of ectopic osseous tissue along the ligament. OPLL is most commonly reported in the cervical spine, with fewer reported cases of thoracic or lumbar OPLL. The incidence of OPLL is high in east Asian populations with a much lower incidence in the United States. In this case report and review, we present the case of a 44-year-old female who was admitted to the hospital with a one-year history of progressive bilateral lower extremity weakness. Her lower extremity weakness had worsened over months and precipitated a gait disturbance that left her wheelchair-bound at the time of presentation. Additional presenting symptoms included lower back pain, stool incontinence, neck pain, and upper extremity paresthesias. Computed tomography of the spine revealed multiple areas of osteophyte formation and OPLL in the cervical spine from C2-5, thoracic spine from T6-10, and in the lumbar and sacral spine from L1-S1. There were notable areas of accompanying neural foraminal stenosis and central canal stenosis with visible spinal cord compression present in various locations. The patient did not undergo surgical intervention given the significant risk of multilevel surgery, and her symptoms were managed with medication. OPLL, particularly when not considered in lower-risk populations, can be a significant cause for progressive debilitating neurological abnormality. We report a rare case of OPLL occurring throughout the cervical, thoracic, lumbar, and sacral spine.
The longer you can look back , the farther you can look forward

We study corporate bond default rates using an extensive new data set spanning the 1866–2008 period. We find that the corporate bond market has repeatedly suffered clustered default events much worse than those experienced during the Great Depression. For example, during the railroad crisis of 1873–1875, total defaults amounted to 36 percent of the par value of the entire corporate bond market. We examine whether corporate default rates are best forecast by structural, reduced-form, or macroeconomic credit models and find that variables suggested by structural models outperform the others. Default events are only weakly correlated with business downturns. We find that over the long term, credit spreads are roughly twice as large as default losses, resulting in an average credit risk premium of about 80 basis points. We also find that credit spreads do not adjust in response to realized default rates. Kay Giesecke Stanford University giesecke@stanford.edu Francis A. Longstaff UCLA Anderson Graduate School of Management 110 Westwood Plaza, Box 951481 Los Angeles, CA 90095-1481 and NBER francis.longstaff@anderson.ucla. edu Stephen Schaefer London Business School Regents Park London, NW14SA United Kingdom sschaefer@london.edu Ilya Strebulaev Stanford University istrebulaev@stanford.edu The longer you can look back, the farther you can look forward. Winston S. Churchill
Manipulating Interactions between T4 Phage Long Tail Fibers and Escherichia coli Receptors

Understanding the host specificity of phages will lead to the development of phage therapy. The interaction between outer membrane protein C (OmpC), one of the Escherichia coli receptors, and the gp37 protein composing the digital tip (DT) region of the long tail fibers of bacteriophage T4 largely determines its host specificity. ABSTRACT Bacteriophages are the most abundant and diverse biological entities on Earth. Phages exhibit strict host specificity that is largely conferred by adsorption. However, the mechanism underlying this phage host specificity remains poorly understood. In this study, we examined the interaction between outer membrane protein C (OmpC), one of the Escherichia coli receptors, and the long tail fibers of bacteriophage T4. T4 phage uses OmpC of the K-12 strain, but not of the O157 strain, for adsorption, even though OmpCs from the two E. coli strains share 94% homology. We identified amino acids P177 and F182 in loop 4 of the K-12 OmpC as essential for T4 phage adsorption in the copresence of loops 1 and 5. Analyses of phage mutants capable of adsorbing to OmpC mutants demonstrated that amino acids at positions 937 and 942 of the gp37 protein, which is present in the distal tip (DT) region of the T4 long tail fibers, play an important role in adsorption. Furthermore, we created a T4 phage mutant library with artificial modifications in the DT region and isolated and characterized multiple phage mutants capable of adsorbing to OmpC of the O157 strain or lipopolysaccharide of the K-12 strain. These results shed light on the mechanism underlying the phage host specificity mediated by gp37 and OmpC and may be useful in the development of phage therapy via artificial modifications of the DT region of T4 phage. IMPORTANCE Understanding the host specificity of phages will lead to the development of phage therapy. The interaction between outer membrane protein C (OmpC), one of the Escherichia coli receptors, and the gp37 protein present in the distal tip (DT) region of the long tail fibers of T4 bacteriophages largely determines their host specificity. Here, we elucidated the amino acid residues important for the interaction between gp37 and OmpC. This result suggests that the shapes of both proteins at the binding interface play important roles in their interactions, which are likely mediated by multiple residues of both binding partners. Additionally, we successfully isolated multiple phage mutants capable of adsorbing to a variety of E. coli receptors using a mutant T4 phage library with artificial modifications in the DT region, providing a foundation for the alteration of the host specificity.
Effect of Staining Solutions on Color Stability, Gloss and Surface Roughness of Removable Partial Dental Prosthetic Polymers.

PURPOSE To assess the effect of commonly used solutions on color stability, gloss, and surface roughness of removable partial dental prostheses polymers. MATERIALS AND METHODS Discs (n = 112) were made of a poly(etheretherketone) (PEEK) polymer, a polyamide, an acetal resin and a heat-cured poly(methylmethacrylate) PMMA acrylic resin polished according to manufacturers' instructions. Seven specimens of each material were immersed in coffee, red wine, coca cola and distilled water for 30 days at 37ο C. Changes of color (ΔΕ*) and color coordinates L*α*b* after immersion were calculated with a colorimeter. Changes in the values of gloss and surface roughness parameters (Sa, Sz, Str, Sdr, Sci, Svi) were also measured. Two-way ANOVA and pairwise comparisons were used to evaluate the effect of material and staining solution on parameter value alterations (α = 0.05). RESULTS The two-way ANOVA revealed that the interaction between material and staining solution significantly affected color changes after immersion [F(9,96) = 44.67, p<0.001]. PEEK presented the lowest color change (ΔΕ* = 3.83 ±2) while polyamide had the highest color change overall (ΔΕ* = 14.59 ±8.65) (p<0.001). Coffee caused the highest color (ΔΕ* = 13.08 ±6.98) and gloss changes (ΔG = -6.36 ±19.2 GU) among different solutions (p<0.001). PEEK showed the highest alteration of gloss (ΔG = -11.31 ±15.49 GU), with significant difference with the other three materials (p<0.001). Insignificant interaction of material and immersing solution was found for surface roughness parameters (p>0.05). CONCLUSIONS Among the materials tested, PEEK seemed to be the most stable material when subjected to common, everyday staining solutions. Therefore PEEK could be a viable solution for an RPDP framework fabrication, expanding the material list of prosthetic options. Further research and clinical trials are required to confirm the above statement. This article is protected by copyright. All rights reserved.
Mesencephalic astrocyte-derived neurotrophic factor is secreted from interferon-γ–activated tumor cells through ER calcium depletion

The most successful immunotherapeutic agents are blocking antibodies to either programmed cell death-1 (PD-1), an inhibitory receptor expressed on T lymphocytes, or to its ligand, programmed cell death-ligand 1 (PD-L1). Nevertheless, many patients do not respond, and additional approaches, specifically blocking other inhibitory receptors on T cells, are being explored. Importantly, the source of the ligands for these receptors are often the tumor cells. Indeed, cancer cells express high levels of PD-L1 upon stimulation with interferon-γ (IFN-γ), a major cytokine in the tumor microenvironment. The increase in PD-L1 expression serves as a negative feedback towards the immune system, and allows the tumor to evade the attack of immune cells. A potential novel immunoregulator is mesencephalic astrocyte-derived neurotrophic factor (MANF), an endoplasmic reticulum (ER)-resident protein that is secreted from pancreatic beta cells upon cytokines activation, and can induce an alternatively activated macrophage phenotype (M2), and thus may support tumor growth. While MANF was shown to be secreted from pancreatic beta cells, its IFN-γ-induced secretion from tumor cells has never been assessed. Here we found that IFN-γ induced MANF secretion from diverse tumor cell-lines—melanoma cells, colon carcinoma cells and hepatoma cells. Mechanistically, there was no increase in MANF RNA or intracellular protein levels upon IFN-γ stimulation. However, IFN-γ induced ER calcium depletion, which was necessary for MANF secretion, as Dantrolene, an inhibitor of ER calcium release, prevented its secretion. Thus, MANF is secreted from IFN-γ-stimulated tumor cells, and further studies are required to assess its potential as a drug target for cancer immunotherapy.
Metal–Organic Frameworks Enhance Biomimetic Cascade Catalysis for Biosensing

Multiple enzymes‐induced biological cascade catalysis guides efficient and selective substrate transformations in vivo. The biomimetic cascade systems, as ingenious strategies for signal transduction and amplification, have a wide range of applications in biosensing. However, the fragile nature of enzymes greatly limits their wide applications. In this regard, metal–organic frameworks (MOFs) with porous structures, unique nano/microenvironments, and good biocompatibility have been skillfully used as carriers to immobilize enzymes for shielding them against hash surroundings and improving the catalytic efficiency. For another, nanomaterials with enzyme‐like properties and brilliant stabilities (nanozymes), have been widely applied to ameliorate the low stability of the enzymes. Inheriting the abovementioned merits of MOFs, the performances of MOFs‐immboilized nanozymes could be significantly enhanced. Furthermore, in addition to carriers, some MOFs can also serve as nanozymes, expanding their applications in cascade systems. Herein, recent advances in the fabrication of efficient MOFs‐involving enzymes/nanozymes cascade systems and biosensing applications are highlighted. Integrating diversified signal output modes, including colorimetry, electrochemistry, fluorescence, chemiluminescence, and surface‐enhanced Raman scattering, sensitive detection of various targets (including biological molecules, environmental pollutants, enzyme activities, and so on) are realized. Finally, challenges and opportunities about further constructions and applications of MOFs‐involving cascade reaction systems are briefly put forward.