Miracle-dz/UniFAR-FTUs huggingface dataset:
Anti-inflammatory genes in PBMCs post-spontaneous intracerebral hemorrhage

Abstract Background Neuroinflammation is important in the pathophysiology of spontaneous intracerebral hemorrhage (ICH) and peripheral inflammatory cells play a role in the clinical evolution and outcome. Methodology Blood samples from ICH patients (n = 20) were collected at admission for 5 consecutive days for peripheral blood mononuclear cells (PBMCs). Frozen PBMCs were used for real-time PCR using Taqman probes (NFKB1, SOD1, PPARG, IL10, NFE2L2, and REL) and normalized to GAPDH. Data on hospital length of stay and modified Rankin score (MRS) were collected with 90-day MRS ≤ 3 as favorable outcome. Statistical analysis of clinical characteristics to temporal gene expression from early to delayed timepoints was compared for MRS groups (favorable vs unfavorable) and hematoma volume. Principle findings and results IL10, SOD1, and REL expression were significantly higher at delayed timepoints in PBMCs of ICH patients with favorable outcome. PPARG and REL increased between timepoints in patients with favorable outcome. NFKB1 expression was not sustained, but significantly decreased from higher levels at early onset in patients with unfavorable outcome. IL10 expression showed a negative correlation in patients with high hematoma volume (>30 mL). Conclusions and significance Anti-inflammatory, pro-survival regulators were highly expressed at delayed time points in ICH patients with a favorable outcome, and IL10 expression showed a negative correlation to high hematoma volume.
Influence of palmitic acid and hexadecanol on the phase transition temperature and molecular packing of dipalmitoylphosphatidyl-choline monolayers at the air-water interface

Palmitic acid (PA) and 1-hexadecanol (HD) strongly affect the phase transition temperature and molecular packing of dipalmitoylphosphatidylcholine (DPPC) monolayers at the air–water interface. The phase behavior and morphology of mixed DPPC/PA as well as DPPC/HD monolayers were determined by pressure-area-isotherms and fluorescence microscopy. The molecular organization was probed by synchrotron grazing incidence x-ray diffraction using a liquid surface diffractometer. Addition of PA or HD to DPPC monolayers increases the temperature of the liquid-expanded to condensed phase transition. X-ray diffraction shows that DPPC forms mixed crystals both with PA and HD over a wide range of mixing ratios. At a surface pressure (π) of 40 mN/m, increasing the amount of the single chain surfactant leads to a reduction in tilt angle of the aliphatic chains from nearly 30° for pure DPPC to almost 0° in a 1:1 molar ratio of DPPC and PA or HD. At this composition we also find closest packing of the aliphatic chains. Furth.
Beneficial Influence of Agomelatine Treatment on Behavioral Impairments in AΒ-Induced Rat Model of Alzheimer’s Disease

Summary An increased risk of developing Alzheimer’s disease (AD) exists in patients with a history of depression. In the present study, we demonstrated that chronic agomelatine intraperitoneal treatment, at a dose of 40 mg/ kg for 21 days, starting one month after inducing AD by intracerebroventricular injection of amyloid-beta (Aβ) corrected anhedonia, decreased anxiety, and showed a potential to mitigate working memory errors during the last session in a radial arm maze. Altogether, our findings suggest that chronic agomelatine administration treatment could alleviate the burden of AD and may be considered a promising therapeutic approach to some adverse symptoms caused by the disease.
The potential antiepileptogenic effect of neuronal Cx36 gap junction channel blockage

Abstract Epilepsy is one of the most prevalent neurological disorders and can result in neuronal injury and degeneration. Consequently, research into new antiepileptic drugs capable of providing protection against neuronal injury and degeneration is extremely important. Neuronal Cx36 gap junction channels have been found to play an important role in epilepsy; thus, pharmacological interference using Cx36 gap junction channel blockers may be a promising strategy for disrupting the synchronization of neurons during seizure activity and protecting neurons. Based on these promising findings, several in vivo and in vitro studies are ongoing and the first encouraging results have been published. The results bring hope that neurons can be protected from injury and degeneration in patients with epilepsy, which is currently impossible.
The positive rate of IgM and IgG antibodies against SARS-CoV-2 is similar in severe and non-severe COVID-19 patients

Abstract Background: Coronavirus disease 2019 (COVID-19) has spread rapidly in China and globally. In order to control the spread of the epidemic, it is important to find an efficient diagnostic method. Objectives: The aim of this study was to assess the responses of antibodies during SARS-CoV-2 infection in relation to disease severity and to evaluate the association between the positive rate of antibody detection and nucleic acid test. Methods: Ninety patients with SARS-CoV-2 infection were recruited in this retrospective observational study. Demographic, clinical data, and SARS-CoV-2 IgM and IgG antibodies in serum specimens were detected at 4 and 6 weeks after diagnosis. Results: IgM and IgG antibody levels showed a decreased tendency, the titers at week 4 were higher than the titers at week 6: The positive rates of IgM at week 4 and 6 were 92.9% and 67.9%, respectively. The positive rates of IgG at week 4 and week 6 were 100%. No association was found between the positive rate of antibody detection at week 4 or 6 and that of nucleic acid test (P>0.05). No difference between the positive rate of antibodies against SARS-CoV-2 in severe and non-severe COVID-19 patients was observed. Conclusions: Antibody detection is an effective means in the diagnosis of COVID-19. The titer and positive rate of IgM are lower than those of IgG in the first six weeks after infection. Positive rate of antibodies was not different between severe and non-severe patients.
Nematic order on a deformable vesicle: theory and simulation

In membranes with nematic liquid-crystalline order, there is a geometric coupling between the nematic director and the shape: nonuniformity in the director induces curvature, and curvature provides an effective potential acting on the director. For a closed vesicle, there must be a total topological charge of +2, which normally occurs as four defects of charge +1/2 each. Previous research has suggested that these four defects will form a regular tetrahedron, leading to a tetrahedral shape of the vesicle, which may be useful in designing colloidal particles for photonic applications. Here, we use three approaches to investigate the behavior of a nematic vesicle: particle-based simulation, spherical harmonic expansion, and finite-element modeling. When liquid crystal has a purely 2D intrinsic interaction, we find that the perfect tetrahedral shape is stable over a wide range of parameters. However, when it has a 3D intrinsic and extrinsic interaction, the perfect tetrahedral shape is never stable; the vesicle is a distorted tetrahedron for small Frank constant and a highly elongated rectangle for larger Frank constant. These results show the difficulty in designing tetrahedral structures for photonic crystals.
Community Metabolic Interactions, Vitamin Production and Prebiotic Potential of Medicinal Herbs Used for Immunomodulation

Historically, the health benefits and immunomodulatory potential of medicinal herbs have been considered an intrinsic quality of the herb itself. We have hypothesized that the health benefits of medicinal herbs may be partially due to their prebiotic potential that alter gut microbiota leading to changes in short chain fatty acids and vitamin production or biotransformation of herb encoded molecules and secondary metabolites. Accumulating studies emphasize the relationship between the gut microbiota and host immune function. While largely unknown, these interactions are mediated by secreted microbial products that activate or repress a variety of immune cell types. Here we evaluated the effect of immunomodulatory, medicinal Ayurvedic herbs on gut microbiota in vitro using 16S rRNA sequencing to assess changes in community composition and functional potential. All immunomodulatory herbs displayed substantial prebiotic potential, targeting unique taxonomic groups. Application of genome reconstruction and analysis of biosynthetic capacity of herb selected communities suggests that many of the 11 herbs tested altered the community metabolism as the result of differential glycan harvest and sugar utilization and secreted products including multiple vitamins, butyrate, and propionate that may impact host physiology and immune function. Taken together, these results provide a useful framework for the further evaluation of these immunomodulatory herbs in vivo to maintain immune homeostasis or achieve desired regulation of immune components in the context of disease.
Variation and Change of Upwelling Dynamics Detected in the World’s Eastern Boundary Upwelling Systems

Global increases in temperature are altering land-sea temperature gradients. Bakun (1990) hypothesized that changes within these gradients will directly affect atmospheric pressure cells associated with the development of winds and will consequently impact upwelling patterns within ecologically important Eastern Boundary Upwelling Systems (EBUS). In this study we used daily time series of NOAA Optimally Interpolated sea surface temperature (SST) and ERA 5 reanalysis wind products to calculate a series novel of metrics related to upwelling dynamics. We then use these to objectively describe upwelling signals in terms of their frequency, intensity and duration throughout the four EBUS during summer months over the last 37 years (1982–2019). We found that a decrease (increase) in SST is associated with an increase (decrease) in the number of upwelling “events,” a decrease (increase) in the intensity of upwelling, and an increase (decrease) in the cumulative intensity of upwelling, with differences between EBUS and regions within EBUS. The Humboldt Current is the only EBUS that shows a consistent response from north to south with a general intensification of upwelling. However, we could not provide clear evidence for associated changes in the wind dynamics hypothesized to drive the upwelling dynamics.
Distinguishing HapMap Accessions Through Recursive Set Partitioning in Hierarchical Decision Trees

The HapMap (haplotype map) projects have produced valuable genetic resources in life science research communities, allowing researchers to investigate sequence variations and conduct genome-wide association study (GWAS) analyses. A typical HapMap project may require sequencing hundreds, even thousands, of individual lines or accessions within a species. Due to limitations in current sequencing technology, the genotype values for some accessions cannot be clearly called. Additionally, allelic heterozygosity can be very high in some lines, causing genetic and sometimes phenotypic segregation in their descendants. Genetic and phenotypic segregation degrades the original accession’s specificity and makes it difficult to distinguish one accession from another. Therefore, it is vitally important to determine and validate HapMap accessions before one conducts a GWAS analysis. However, to the best of our knowledge, there are no prior methodologies or tools that can readily distinguish or validate multiple accessions in a HapMap population. We devised a bioinformatics approach to distinguish multiple HapMap accessions using only a minimum number of genetic markers. First, we assign each candidate marker with a distinguishing score (DS), which measures its capability in distinguishing accessions. The DS score prioritizes those markers with higher percentages of homozygous genotypes (allele combinations), as they can be stably passed on to offspring. Next, we apply the “set-partitioning” concept to select optimal markers by recursively partitioning accession sets. Subsequently, we build a hierarchical decision tree in which a specific path represents the selected markers and the homogenous genotypes that can be used to distinguish one accession from others in the HapMap population. Based on these algorithms, we developed a web tool named MAD-HiDTree (Multiple Accession Distinguishment-Hierarchical Decision Tree), designed to analyze a user-input genotype matrix and construct a hierarchical decision tree. Using genetic marker data extracted from the Medicago truncatula HapMap population, we successfully constructed hierarchical decision trees by which the original 262 M. truncatula accessions could be efficiently distinguished. PCR experiments verified our proposed method, confirming that MAD-HiDTree can be used for the identification of a specific accession. MAD-HiDTree was developed in C/C++ in Linux. Both the source code and test data are publicly available at https://bioinfo.noble. org/MAD-HiDTree/.
The Cancer Rehabilitation Medicine Metrics Consortium: A Path to Enhanced, Multi-Site Outcome Assessment to Enhance Care and Demonstrate Value

Purpose A primary objective stated at the Cancer Rehabilitation Symposium at the National Institutes of Health was to improve outcome measurement. The purpose of this project was for the Cancer Rehabilitation Medicine Metrics Consortium (CRMMC) to develop an assessment tool to evaluate function in cancer patients via a data-driven and methodologically sound process. There is no agreed-upon measure of physical and cognitive function for cancer patients, making it difficult to demonstrate the value of rehabilitation interventions. Cancer patients are a particularly challenging population, with many tumor- and treatment-related variables impacting function. Methods Investigators from nine different cancer rehabilitation programs participated in a modified-Delphi process to delineate necessary aspects of an ideal patient assessment tool, including instrument type, domains evaluated, applicability across a range of patient traits, clinical feasibility, and item response characteristics. This involved numerous meetings, data review, and analysis of items involved in patient assessment. Results The CRMMC developed a 21-item patient-reported outcome measure based on item response theory. The process by which the short form was developed was documented and provides a framework for other clinicians to follow. Conclusion This document provides a framework for rehabilitation providers to follow when developing an assessment tool. This process is described in a stepwise fashion for reproducibility even in different, non-cancer populations.
Use of Functional Near Infrared Spectroscopy to Assess Syntactic Processing by Monolingual and Bilingual Adults and Children

This exploratory study assessed the use of functional Near Infrared Spectroscopy (fNIRS) to examine hemodynamic response patterns during sentence processing. Four groups of participants: monolingual English children, bilingual Chinese-English children, bilingual Chinese-English adults and monolingual English adults were given an agent selection syntactic processing task. Bilingual child participants were classified as simultaneous or sequential bilinguals to examine the impact of first language, age of second-language acquisition (AoL2A), and the length of second language experience on behavioral performance and cortical activation. Participants were asked to select the agent of four types of sentences: subject-verb-object (SVO), passive (PAS), subject-extracted relative clause (SR), and object-extracted relative clause (OR) adopted from the “Whatdunit” task by Montgomery et al. (2016). Semantic cues were removed by using inanimate nouns for agents and patients, which constrained participants to make decisions based on syntactic knowledge. Behavioral results showed greater accuracy for canonical SVO and SR sentence types than for noncanonical OR and PAS sentence types, which aligns with prior studies. Neuroimaging results revealed greater hemodynamic responses to relative clauses (i.e., SR and OR sentences) than to simple sentences (SVO and PAS), especially for Chinese-English bilinguals suggesting first-language transfer influencing sentence processing in English. The effects AoL2A and the length of second language experience showed no significant differences between simultaneous and sequential bilinguals or between bilingual adults and children for identifying the correct agent in each sentence. However, neuroimaging results demonstrated greater hemodynamic responses in right dorsolateral prefrontal cortex (DLPFC) and left inferior parietal lobule (IPL) in simultaneous bilinguals compared to sequential bilinguals and greater hemodynamic responses in left and right DLPFC and left IPL among bilingual adults. Different behavioral and neural hemodynamic response patterns afford new insights into the effects of syntactic knowledge on sentence processing.
SARS-CoV-2 Genomes From Oklahoma, United States

Genomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the current pandemic, it is essential that SARS-CoV-2 viruses are sequenced regularly to determine mutations and genomic modifications in different geographical locations. In this study, we sequenced SARS-CoV-2 from five clinical samples obtained in Oklahoma, United States during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and four during the peak in Oklahoma were sequenced. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K, and G204R in N gene were identified in the genomes sequenced in this study. Possible novel mutations were also detected in the S gene (G1167V), ORF1ab (A6269S and P3371S), ORF7b (T28I), and ORF8 (G96R). Phylogenetic analysis of the genomes showed similarity to other SARS-CoV-2 viruses reported from across the globe. Structural characterization indicates that the mutations in S gene possibly influences conformational flexibility and motion of the spike protein, and the mutations in N gene are associated with disordered linker region within the nucleocapsid protein.
Neuromorphic NEF-Based Inverse Kinematics and PID Control

Neuromorphic implementation of robotic control has been shown to outperform conventional control paradigms in terms of robustness to perturbations and adaptation to varying conditions. Two main ingredients of robotics are inverse kinematic and Proportional–Integral–Derivative (PID) control. Inverse kinematics is used to compute an appropriate state in a robot's configuration space, given a target position in task space. PID control applies responsive correction signals to a robot's actuators, allowing it to reach its target accurately. The Neural Engineering Framework (NEF) offers a theoretical framework for a neuromorphic encoding of mathematical constructs with spiking neurons for the implementation of functional large-scale neural networks. In this work, we developed NEF-based neuromorphic algorithms for inverse kinematics and PID control, which we used to manipulate 6 degrees of freedom robotic arm. We used online learning for inverse kinematics and signal integration and differentiation for PID, offering high performing and energy-efficient neuromorphic control. Algorithms were evaluated in simulation as well as on Intel's Loihi neuromorphic hardware.
Antibody Responses to Crude Gametocyte Extract Predict Plasmodium falciparum Gametocyte Carriage in Kenya

Background Malaria caused by Plasmodium falciparum remains a serious global public health challenge especially in Africa. Interventions that aim to reduce malaria transmission by targeting the gametocyte reservoir are key to malaria elimination and/or eradication. However, factors that are associated with gametocyte carriage have not been fully explored. Consequently, identifying predictors of the infectious reservoir is fundamental in the elimination campaign. Methods We cultured P. falciparum NF54 gametocytes (to stage V) and prepared crude gametocyte extract. Samples from a total of 687 participants (aged 6 months to 67 years) representing two cross-sectional study cohorts in Kilifi, Kenya were used to assess IgG antibody responses by ELISA. We also analyzed IgG antibody responses to the blood-stage antigen AMA1 as a marker of asexual parasite exposure. Gametocytemia and asexual parasitemia data quantified by microscopy and molecular detection (QT-NASBA) were used to determine the relationship with antibody responses, season, age, and transmission setting. Multivariable logistic regression models were used to study the association between antibody responses and gametocyte carriage. The predictive power of the models was tested using the receiver operating characteristic (ROC) curve. Results Multivariable logistic regression analysis showed that IgG antibody response to crude gametocyte extract predicted both microscopic (OR=1.81 95% CI: 1.06–3.07, p=0.028) and molecular (OR=1.91, 95% CI: 1.11–3.29, p=0.019) P. falciparum gametocyte carriage. Antibody responses to AMA1 were also associated with both microscopic (OR=1.61 95% CI: 1.08–2.42, p=0.020) and molecular (OR=3.73 95% CI: 2.03–6.74, p<0.001) gametocytemia. ROC analysis showed that molecular (AUC=0.897, 95% CI: 0.868–0.926) and microscopic (AUC=0.812, 95% CI: 0.758–0.865) multivariable models adjusted for gametocyte extract showed very high predictive power. Molecular (AUC=0.917, 95% CI: 0.891–0.943) and microscopic (AUC=0.806, 95% CI: 0.755–0.858) multivariable models adjusted for AMA1 were equally highly predictive. Conclusion In our study, it appears that IgG responses to crude gametocyte extract are not an independent predictor of gametocyte carriage after adjusting for AMA1 responses but may predict gametocyte carriage as a proxy marker of exposure to parasites. Serological responses to AMA1 or to gametocyte extract may facilitate identification of individuals within populations who contribute to malaria transmission and support implementation of transmission-blocking interventions.