Miracle-dz/UniFAR-FTUs huggingface dataset:
Upregulated SHP‐2 expression in the epileptogenic zone of temporal lobe epilepsy and various effects of SHP099 treatment on a pilocarpine model

Temporal lobe epilepsy (TLE) is defined as the sporadic occurrence of spontaneous recurrent seizures, and its pathogenesis is complex. SHP‐2 (Src homology 2‐containing protein tyrosine phosphatase 2) is a widely expressed cytosolic tyrosine phosphatase protein that participates in the regulation of inflammation, angiogenesis, gliosis, neurogenesis and apoptosis, suggesting a potential role of SHP‐2 in TLE. Therefore, we investigated the expression patterns of SHP‐2 in the epileptogenic brain tissue of intractable TLE patients and the various effects of treatment with the SHP‐2‐specific inhibitor SHP099 on a pilocarpine model. Western blotting and immunohistochemistry results confirmed that SHP‐2 expression was upregulated in the temporal neocortex of patients with TLE. Double‐labeling experiments revealed that SHP‐2 was highly expressed in neurons, astrocytes, microglia and vascular endothelial cells in the epileptic foci of TLE patients. In the pilocarpine‐induced C57BL/6 mouse model, SHP‐2 upregulation in the hippocampus began one day after status epilepticus, reached a peak at 21 days and then maintained a significantly high level until day 60. Similarly, we found a remarkable increase in SHP‐2 expression at 1, 7, 21 and 60 days post‐SE in the temporal neocortex. In addition, we also showed that SHP099 increased reactive gliosis, the release of IL‐1β, neuronal apoptosis and neuronal loss, while reduced neurogenesis and albumin leakage. Taken together, the increased expression of SHP‐2 in the epileptic zone may be involved in the process of TLE.
Age- and stress-associated C. elegans granulins impair lysosomal function and induce a compensatory HLH-30/TFEB transcriptional response

The progressive failure of protein homeostasis is a hallmark of aging and a common feature in neurodegenerative disease. As the enzymes executing the final stages of autophagy, lysosomal proteases are key contributors to the maintenance of protein homeostasis with age. We previously reported that expression of granulin peptides, the cleavage products of the neurodegenerative disease protein progranulin, enhance the accumulation and toxicity of TAR DNA binding protein 43 (TDP-43) in Caenorhabditis elegans (C. elegans). In this study we show that C. elegans granulins are produced in an age- and stress-dependent manner. Granulins localize to the endolysosomal compartment where they impair lysosomal protease expression and activity. Consequently, protein homeostasis is disrupted, promoting the nuclear translocation of the lysosomal transcription factor HLH-30/TFEB, and prompting cells to activate a compensatory transcriptional program. The three C. elegans granulin peptides exhibited distinct but overlapping functional effects in our assays, which may be due to amino acid composition that results in distinct electrostatic and hydrophobicity profiles. Our results support a model in which granulin production modulates a critical transition between the normal, physiological regulation of protease activity and the impairment of lysosomal function that can occur with age and disease.
The Influence of Sport Participation on African American Youth Binge Drinking

Abstract Background: The many negative consequences and high rates of use associated with youth binge drinking make further study into its causes and correlates vital. Sport participation is a relevant factor in predicting drinking behaviors among youth in need of further research. Objectives: The current study tests the influence of specific types of sport participation on the binge drinking behaviors of African American youth through binary logistic regression. Study of this particular sample is vital as race and sport participation have been shown to be critical variables associated with variations in drinking behaviors. Results: Results indicated that various types of sport participation were uniquely associated with drinking behaviors. Conclusion/Importance: Results are framed through social learning, social bond, and the power sport hypothesis in accordance with previous research.
The annexin A1/FPR2 signaling axis expands alveolar macrophages, limits viral replication, and attenuates pathogenesis in the murine influenza A virus infection model

Pattern recognition receptors (PRRs) are key elements in the innate immune response. Formyl peptide receptor (FPR) 2 is a PRR that, in addition to proinflammatory, pathogen‐derived compounds, also recognizes the anti‐inflammatory endogenous ligand annexin A1 (AnxA1). Because the contribution of this signaling axis in viral infections is undefined, we investigated AnxA1‐mediated FPR2 activation on influenza A virus (IAV) infection in the murine model. AnxA1‐treated mice displayed significantly attenuated pathology upon a subsequent IAV infection with significantly improved survival, impaired viral replication in the respiratory tract, and less severe lung damage. The AnxA1‐mediated protection against IAV infection was not caused by priming of the type I IFN response but was associated with an increase in the number of alveolar macrophages (AMs) and enhanced pulmonary expression of the AM‐regulating cytokine granulocyte‐M‐CSF (GM‐CSF). Both AnxA1‐mediated increase in AM levels and GM‐CSF production were abrogated when mouse (m)FPR2 signaling was antagonized but remained up‐regulated in mice genetically deleted for mFPR1, an mFPR2 isoform also serving as AnxA1 receptor. Our results indicate a novel protective function of the AnxA1‐FPR2 signaling axis in IAV pathology via GM‐CSF‐associated maintenance of AMs, expanding knowledge on the potential use of proresolving mediators in host defense against pathogens. —Schloer, S. , Hübel, N. , Masemann, D. , Pajonczyk, D. , Brunotte, L. , Ehrhardt, C. , Brandenburg, L. ‐O. , Ludwig, S. , Gerke, V. , Rescher, U. The annexin A1/FPR2 signaling axis expands alveolar macrophages, limits viral replication, and attenuates pathogenesis in the murine influenza A virus infection model. FASEB J. 33, 12188–12199 (2019). www.fasebj. org
Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers

With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.
Improving Stockline Detection of Radar Sensor Array Systems in Blast Furnaces Using a Novel Encoder–Decoder Architecture

The stockline, which describes the measured depth of the blast furnace (BF) burden surface with time, is significant to the operator executing an optimized charging operation. For the harsh BF environment, noise interferences and aberrant measurements are the main challenges of stockline detection. In this paper, a novel encoder–decoder architecture that consists of a convolution neural network (CNN) and a long short-term memory (LSTM) network is proposed, which suppresses the noise interferences, classifies the distorted signals, and regresses the stockline in a learning way. By leveraging the LSTM, we are able to model the longer historical measurements for robust stockline tracking. Compared to traditional hand-crafted denoising processing, the time and efforts could be greatly saved. Experiments are conducted on an actual eight-radar array system in a blast furnace, and the effectiveness of the proposed method is demonstrated on the real recorded data.
VOC biomarkers identification and predictive model construction for lung cancer based on exhaled breath analysis: research protocol for an exploratory study

Introduction Lung cancer is the most common cancer and the leading cause of cancer death in China, as well as in the world. Late diagnosis is the main obstacle to improving survival. Currently, early detection methods for lung cancer have many limitations, for example, low specificity, risk of radiation exposure and overdiagnosis. Exhaled breath analysis is one of the most promising non-invasive techniques for early detection of lung cancer. The aim of this study is to identify volatile organic compound (VOC) biomarkers in lung cancer and to construct a predictive model for lung cancer based on exhaled breath analysis. Methods and analysis The study will recruit 389 lung cancer patients in one cancer centre and 389 healthy subjects in two lung cancer screening centres. Bio-VOC breath sampler and Tedlar bag will be used to collect breath samples. Gas chromatography-mass spectrometry coupled with solid phase microextraction technique will be used to analyse VOCs in exhaled breath. VOC biomarkers with statistical significance and showing abilities to discriminate lung cancer patients from healthy subjects will be selected for the construction of predictive model for lung cancer. Ethics and dissemination The study was approved by the Ethics Committee of Sichuan Cancer Hospital on 6 April 2017 (No. SCCHEC-02-2017-011). The results of this study will be disseminated in presentations at academic conferences, publications in peer-reviewed journals and the news media. Trial registration number ChiCTR-DOD-17011134; Pre-results.
Using an Endogenous CRISPR-Cas System for Genome Editing in the Human Pathogen Clostridium difficile

Clostridium difficile represents today a real danger for human and animal health. It is the leading cause of diarrhea associated with health care in adults in industrialized countries. The incidence of these infections continues to increase, and this trend is accentuated by the general aging of the population. Many questions about the mechanisms contributing to C. difficile's success inside the host remain unanswered. The set of genetic tools available for this pathogen is limited, and new developments are badly needed. C. difficile has developed efficient defense systems that are directed against foreign DNA and that could contribute to its survival in phage-rich gut communities. We show how one such defense system, named CRISPR-Cas, can be hijacked for C. difficile genome editing. Our results also show a great potential for the use of the CRISPR-Cas system for the development of new therapeutic strategies against C. difficile infections. ABSTRACT The human enteropathogen Clostridium difficile constitutes a key public health issue in industrialized countries. Many aspects of C. difficile pathophysiology and adaptation inside the host remain poorly understood. We have recently reported that this bacterium possesses an active CRISPR-Cas system of subtype I-B for defense against phages and other mobile genetic elements that could contribute to its success during infection. In this paper, we demonstrate that redirecting this endogenous CRISPR-Cas system toward autoimmunity allows efficient genome editing in C. difficile. We provide a detailed description of this newly developed approach and show, as a proof of principle, its efficient application for deletion of a specific gene in reference strain 630Δerm and in epidemic C. difficile strain R20291. The new method expands the arsenal of the currently limiting set of gene engineering tools available for investigation of C. difficile and may serve as the basis for new strategies to control C. difficile infections. IMPORTANCE Clostridium difficile represents today a real danger for human and animal health. It is the leading cause of diarrhea associated with health care in adults in industrialized countries. The incidence of these infections continues to increase, and this trend is accentuated by the general aging of the population. Many questions about the mechanisms contributing to C. difficile's success inside the host remain unanswered. The set of genetic tools available for this pathogen is limited, and new developments are badly needed. C. difficile has developed efficient defense systems that are directed against foreign DNA and that could contribute to its survival in phage-rich gut communities. We show how one such defense system, named CRISPR-Cas, can be hijacked for C. difficile genome editing. Our results also show a great potential for the use of the CRISPR-Cas system for the development of new therapeutic strategies against C. difficile infections.
The Biochemistry and Evolution of the Dinoflagellate Nucleus

Dinoflagellates are known to possess a highly aberrant nucleus—the so-called dinokaryon—that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps most strikingly, (4) a deficit of histones—the canonical building blocks of all eukaryotic chromatin. Dinoflagellates belong to the Alveolata clade (dinoflagellates, apicomplexans, and ciliates) and, therefore, the biological oddities observed in dinoflagellate nuclei are derived character states. Understanding the sequence of changes that led to the dinokaryon has been difficult in the past with poor resolution of dinoflagellate phylogeny. Moreover, lack of knowledge of their molecular composition has constrained our understanding of the molecular properties of these derived nuclei. However, recent advances in the resolution of the phylogeny of dinoflagellates, particularly of the early branching taxa; the realization that divergent histone genes are present; and the discovery of dinoflagellate-specific nuclear proteins that were acquired early in dinoflagellate evolution have all thrown new light nature and evolution of the dinokaryon.
Obesity and Diabetes in the Winnebago Tribe of Nebraska: From Community Engagement to Action, 2014–2019

The Winnebago Tribe of Nebraska implemented interventions to promote the health of their people, focusing on community-selected and culturally adapted policies, systems, and environmental (PSE) improvements to reduce the prevalence of obesity and type 2 diabetes. The interventions were implemented as part of the Centers for Disease Control and Prevention’s (CDC’s) 2014–2019 Good Health and Wellness in Indian Country program. The Winnebago Tribe used CDC’s CHANGE community health assessment tool to prioritize and direct their interventions. They integrated findings from a community health assessment tool with observations from tribal working groups and implemented 6 new evidence-based PSE interventions. Their successful approaches — selected by the Winnebago community, culturally relevant, and driven by scientific assessment —demonstrate the value of flexibility in CDC grant programs.
Single-cell transcriptional logic of cell-fate specification and axon guidance in early-born retinal neurons

ABSTRACT Retinal ganglion cells (RGCs), cone photoreceptors (cones), horizontal cells and amacrine cells are the first classes of neurons produced in the retina. However, an important question is how this diversity of cell states is transcriptionally produced. Here, we profiled 6067 single retinal cells to provide a comprehensive transcriptomic atlas showing the diversity of the early developing mouse retina. RNA velocities unveiled the dynamics of cell cycle coordination of early retinogenesis and define the transcriptional sequences at work during the hierarchical production of early cell-fate specification. We show that RGC maturation follows six waves of gene expression, with older-generated RGCs transcribing increasing amounts of guidance cues for young peripheral RGC axons that express the matching receptors. Spatial transcriptionally deduced features in subpopulations of RGCs allowed us to define novel molecular markers that are spatially restricted. Finally, the isolation of such a spatially restricted population, ipsilateral RGCs, allowed us to identify their molecular identity at the time they execute axon guidance decisions. Together, these data represent a valuable resource shedding light on transcription factor sequences and guidance cue dynamics during mouse retinal development. Summary: Single-cell transcriptomics of early-born retinal neurons unveil cell cycle dynamics, differentiation waves for photoreceptors and RGCs, spatial position and new candidate genes for circuit formation with special emphasis on ipsilaterally projecting RGCs.
High-Throughput Immunological Analysis of Dictamni Cortex: Implication in the Quality Control of Herbal Medicine

Quality inconsistency of herbal medicine is an obstacle that limits the extensive use and study of traditional Chinese medicine. Differences in environmental conditions and processing methods of herbal medicine often result in varying clinical outcomes in patients. Standard chemical markers used for the quality control (QC) of herbal medicine are usually the most abundant and characteristic components, which may not be therapeutically relevant or cannot comprehensively reflect the biological quality of the herbs. In view of this, a novel QC method for better assessment of herbal medicine has been developed via bioactivities analysis. Immunological activities of Dictamni Cortex, a typical herbal medicine for the treatment of various inflammatory diseases, from different geographical locations in China, were evaluated. Upon in vitro treatment of their water and ethanol extracts, distinct patterns of inflammatory cytokines including tumor necrosis factor (TNF)-α, interleukin (IL)-10, IL-6, IL-12p70, IL-1β, and chemokine CXCL8 were released from the lipopolysaccharides- and/or phytohaemagglutinin-stimulated human peripheral blood mononuclear cells (PBMC). Thus, in addition to the commonly used morphological, chemical, or DNA markers, the novel high-throughput profiling of inflammatory cytokines and chemokines of PBMC upon treatment with herbal extracts could be an important reference to help for the quality control of herbal medicine in the future.
The Ketogenic Diet and Its Effect on Bone Mineral Density: A Retrospective Observational Cohort Study

Abstract Background During long-term follow-up of children treated with the ketogenic diet therapy (KDT) have an increased incidence of bone fractures. However, the exact contribution of KDT to a decreased bone mineral density (BMD) remains unclear. Objective This study aimed to evaluate (changes in) BMD in children treated with KDT and to evaluate whether intravenous bisphosphonate therapy may be effective. Design In this retrospective, observational cohort study, all children treated with KDT from 2010 until 2018 at the Radboudumc Amalia Children's hospital were included. Patients who were on KDT for more than 6 months and who had at least two dual-energy X-ray (DXA)-scans were eligible for inclusion for longitudinal analysis. Z-scores of DXA-scans were compared over the course of time. Results In 34 out of 68 patients, one or more lumbar DXA-scans were performed, with a mean lumbar Z-score of −1.32 ± 1.74. Of these 68 patients, 8.8% got a fracture during KDT, and also 8.8% got kidney stones. In 20 patients, more than one DXA-scan was performed. A statistically not significant decrease in BMD (0.22 Z-score/year) was found. However, there was an increase in BMD in the five patients treated with intravenous bisphosphonate therapy. This was statistically significant in comparison to the nonbisphosphonate treated group (p = 0.034). Conclusion Children on KDT have low normal BMD which may decrease further during KDT. For this reason monitoring of BMD is crucial, as is monitoring of kidney stones and hypercalciuria. Intravenous bisphosphonate therapy may have a positive effect, when other therapies have failed.
Cardiovascular Pleiotropic Effects of Natriuretic Peptides

Atrial natriuretic peptide (ANP) is a cardiac hormone belonging to the family of natriuretic peptides (NPs). ANP exerts diuretic, natriuretic, and vasodilatory effects that contribute to maintain water–salt balance and regulate blood pressure. Besides these systemic properties, ANP displays important pleiotropic effects in the heart and in the vascular system that are independent of blood pressure regulation. These functions occur through autocrine and paracrine mechanisms. Previous works examining the cardiac phenotype of loss-of-function mouse models of ANP signaling showed that both mice with gene deletion of ANP or its receptor natriuretic peptide receptor A (NPR-A) developed cardiac hypertrophy and dysfunction in response to pressure overload and chronic ischemic remodeling. Conversely, ANP administration has been shown to improve cardiac function in response to remodeling and reduces ischemia-reperfusion (I/R) injury. ANP also acts as a pro-angiogenetic, anti-inflammatory, and anti-atherosclerotic factor in the vascular system. Pleiotropic effects regarding brain natriuretic peptide (BNP) and C-type natriuretic peptide (CNP) were also reported. In this review, we discuss the current evidence underlying the pleiotropic effects of NPs, underlying their importance in cardiovascular homeostasis.
Accumulation of Amyloid Beta (Aβ) Peptide on Blood Vessel Walls in the Damaged Brain after Transient Middle Cerebral Artery Occlusion

It is well known that amyloid beta (Aβ) peptides are generated in blood vessels, released into the brain during thrombosis, and temporarily accumulate in this organ after injury. Here we demonstrate that 24 h after transient middle cerebral artery occlusion (tMCAO), one of the standard models of focal ischemic stroke, Aβ peptide accumulates in the brain, concentrating on the blood vessel walls. Because Aβ oligomers are known to induce significant damage to brain cells, they act as an additional damaging factor during ischemic stroke. Considering that they have been shown to form ion channels in cells, affecting osmotic balance, we used an Aβ peptide channel blocker, tromethamine (2-amino-2-(hydroxymethyl) propane-1,3-diol), to prevent this additional injury. Tromethamine injected 0.1 g/100 g body weight intraperitoneally at 5 min before tMCAO decreased water content in the damaged hemisphere, as measured by dry brain weight. Congo red staining, which binds only to Aβ oligomer plaques (amyloid), showed that there was no significant presence of plaques. Therefore, we suggest that Aβ peptide oligomers are responsible for some of the brain damage during stroke and that blockage of the ion channels that they form could be beneficial in treating this complex neurological syndrome.