Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent advances in endotoxin tolerance

Endotoxin tolerance is defined as a reduced capacity of a cell to respond endotoxin (lipopolysaccharide, LPS) challenge after an initial encounter with endotoxin in advance. The body becomes tolerant to subsequent challenge with a lethal dose of endotoxin and cytokines release and cell/tissue damage induced by inflammatory reaction are significantly reduced in the state of endotoxin tolerance. The main characteristics of endotoxin tolerance are downregulation of inflammatory mediators such as tumor necrosis factor α (TNF‐α), interleukin‐1β (IL‐1β), and C‐X‐C motif chemokine 10 (CXCL10) and upregulation of anti‐inflammatory cytokines such as IL‐10 and transforming growth factor β (TGF‐β). Therefore, endotoxin tolerance is often regarded as the regulatory mechanism of the host against excessive inflammation. Endotoxin tolerance is a complex pathophysiological process and involved in multiple cellular signal pathways, receptor alterations, and biological molecules. However, the exact mechanism remains elusive up to date. To better understand the underlying cellular and molecular mechanisms of endotoxin tolerance, it is crucial to investigate the comprehensive cellular signal pathways, signaling proteins, cell surface molecules, proinflammatory and anti‐inflammatory cytokines, and other mediators. Endotoxin tolerance plays an important role in reducing the mortality of sepsis, endotoxin shock, and other endotoxin‐related diseases. Recent reports indicated that endotoxin tolerance is also related to other diseases such as cystic fibrosis, acute coronary syndrome, liver ischemia‐reperfusion injury, and cancer. The aim of this review is to discuss the recent advances in endotoxin tolerance mainly based on the cellular and molecular mechanisms by outline the current state of the knowledge of the involvement of the toll‐like receptor 4 (TLR4) signaling pathways, negative regulate factor, microRNAs, apoptosis, chromatin modification, and gene reprogramming of immune cells in endotoxin tolerance. We hope to provide a new idea and scientific basis for the rational treatment of endotoxin‐related diseases such as endotoxemia, sepsis, and endotoxin shock clinically.
POC-LUS guiding pleural puncture drainage to treat neonatal pulmonary atelectasis caused by congenital massive effusion

Abstract Point of care lung ultrasound (POC-LUS) has played important roles in diagnosing neonatal lung diseases and assisting in their treatment. A newborn infant with severe respiratory distress diagnosed as pulmonary atelectasis caused by congenital massive pleural effusion, whose consolidated lung recruitment after pleural puncture drainage under POC-LUS guidance. Lung ultrasound can be performed easily and timely at bed-side with free of radiation exposure, thus it should be used extensively in the neonatal department.
IntelligentCrowd: Mobile Crowdsensing via Multi-Agent Reinforcement Learning

The prosperity of smart mobile devices has made mobile crowdsensing (MCS) a promising paradigm for completing complex sensing and computation tasks. In the past, great efforts have been made on the design of incentive mechanisms and task allocation strategies from MCS platform's perspective to motivate mobile users’ participation. However, in practice, MCS participants face many uncertainties coming from their sensing environment as well as other participants’ strategies, and how do they interact with each other and make sensing decisions is not well understood. In this paper, we take MCS participants’ perspectives to derive an online sensing policy to maximize their payoffs via MCS participation. Specifically, we model the interactions of mobile users and sensing environments as a multi-agent Markov decision process. Each participant cannot observe others’ decisions, but needs to decide her effort level in sensing tasks only based on local information, e.g., her own record of sensed signals’ quality. To cope with the stochastic sensing environment, we develop an intelligent crowdsensing algorithm IntelligentCrowd by leveraging the power of multi-agent reinforcement learning (MARL). Our algorithm leads to the optimal sensing policy for each user to maximize the expected payoff against stochastic sensing environments, and can be implemented at the individual participant's level in a distributed fashion. Numerical simulations demonstrate that IntelligentCrowd significantly improves users’ payoffs in sequential MCS tasks under various sensing dynamics.
Efficacy of various intracanal medicaments against aerobic and facultative anaerobic microorganism found in human primary teeth with necrotic pulp: A randomized clinical trial

Aim: The aim of this in vivo study is to evaluate the antimicrobial efficacy of calcium hydroxide (Ca(OH)2), chlorhexidine (CHX), and metronidazole gel as intracanal medicaments against aerobic and facultative anaerobic microorganisms found in root canals of human primary teeth with necrotic pulp. Setting and Design: It is a double-blinded randomized clinical trial. Materials and Methods: Pulp canals of 45 single-rooted primary maxillary anterior teeth with pulp necrosis in 34 children were included in the study. They were divided into three groups of 15 samples each: Group I: Ca(OH)2; Group II: 1% CHX gel; and Group III: 1% metronidazole gel. Microbial count was obtained from each tooth at two different stages – (1) after instrumentation and (2) after placement of the medication. Statistical analysis using the SPSS 10.0 software program (SPSS Inc., Chicago, IL, USA) with Wilcoxon signed-rank test after grouping the samples was performed. Results: Ca(OH)2, 1% CHX gel, and 1% metronidazole gel were ineffective in completely eliminating aerobic and facultative anaerobic microorganism from root canal of human primary teeth with necrotic pulp. Conclusion: None of the commonly used intracanal medicaments, that is Ca(OH)2, 1% CHX gel, and 1% metronidazole gel, was effective in completely eliminating aerobic and facultative anaerobic microorganism from root canal of human primary teeth with necrotic pulp. Ineffectiveness of these medicaments against aerobic and facultative anaerobic microorganism has opened new door of research regarding the manner of bacterial growth in unfavorable environmental and nutritional conditions, the way root canal environment favors biofilm formation and the use of suitable intracanal medicaments against single and multispecies biofilms.
Long non‐coding RNA CRNDE promotes the proliferation, migration and invasion of hepatocellular carcinoma cells through miR‐217/MAPK1 axis

Hepatocellular carcinoma (HCC) is an invasive malignant tumour and the second major cause of cancer‐related deaths over the world. CRNDE and miR‐217 are non‐coding RNAs which play critical roles in cell growth, proliferation, migration. Mitogen‐activated protein kinase 1 (MAPK1) also participates in cancer cell process. Hence, this study aimed at investigating the effect of CRNDE on migration and invasion of HCC and figuring out the role of miR‐217 and MAPK1 in this process. The overexpression of CRNDE was demonstrated by a microarray‐based lncRNA profiling study. CRNDE expression in HCC was verified by qRT‐PCR. MTT assay and BrdU staining were applied to detect cell proliferation level. Transwell assay was utilized to examine cell migration and invasiveness abilities. Wound healing assay was performed for further exploration of cell migration capacity. MiR‐217 was predicted by bioinformatics. The dual luciferase reporter assay was performed to corroborate the targeting relationship between CRNDE, miR‐217 and MAPK1. MAPK1, the downstream target of miR‐217, was predicted using bioinformatics and was further confirmed by qRT‐PCR and Western blot. The interaction between CRNDE, miR‐217 and MAPK1 was studied by qRT‐PCR, Western blot, MTT, BrdU, transwell assay and wound healing assay. CRNDE was up‐regulated in HCC tissues and HCC cell lines. The high expression of CRNDE facilitated cell proliferation, migration and invasion, while the inhibited one affected on the contrary. MiR‐217, negatively correlated with CRNDE expression, was the target of CRNDE and was more lowly expressed in HCC. With the high expression of miR‐217, HCC cell proliferation, migration and invasion were suppressed. MAPK1, the possible target of miR‐217, was negatively correlated with miR‐217 but positively correlated with CRNDE and had the same effect in HCC formation process as CRNDE. Long non‐coding RNA CRNDE promotes the proliferation, migration and invasion of HCC cells through miR‐217/MAPK1 axis.
Non-line-of-sight Reconstruction Using Efficient Transient Rendering

Being able to see beyond the direct line of sight is an intriguing prospect and could benefit a wide variety of important applications. Recent work has demonstrated that time-resolved measurements of indirect diffuse light contain valuable information for reconstructing shape and reflectance properties of objects located around a corner. In this article, we introduce a novel reconstruction scheme that, by design, produces solutions that are consistent with state-of-the-art physically based rendering. Our method combines an efficient forward model (a custom renderer for time-resolved three-bounce indirect light transport) with an optimization framework to reconstruct object geometry in an analysis-by-synthesis sense. We evaluate our algorithm on a variety of synthetic and experimental input data, and show that it gracefully handles uncooperative scenes with high levels of noise or non-diffuse material reflectance.
Modification of a Putative Third Sodium Site in the Glycine Transporter GlyT2 Influences the Chloride Dependence of Substrate Transport

Neurotransmitter removal from glycine-mediated synapses relies on two sodium-driven high-affinity plasma membrane GlyTs that control neurotransmitter availability. Mostly glial GlyT1 is the main regulator of glycine synaptic levels, whereas neuronal GlyT2 promotes the recycling of synaptic glycine and supplies neurotransmitter for presynaptic vesicle refilling. The GlyTs differ in sodium:glycine symport stoichiometry, showing GlyT1 a 2:1 and GlyT2 a 3:1 sodium:glycine coupling. Sodium binds to the GlyTs at two conserved Na+ sites: Na1 and Na2. The location of GlyT2 Na3 site remains unknown, although Glu650 has been involved in the coordination. Here, we have used comparative MD simulations of a GlyT2 model constructed by homology to the crystalized DAT from Drosophila melanogaster by placing the Na3 ion at two different locations. By combination of in silico and experimental data obtained by biochemical and electrophysiological analysis of GlyTs mutants, we provide evidences suggesting the GlyT2 third sodium ion is held by Glu-250 and Glu-650, within a region with robust allosteric properties involved in cation-specific sensitivity. Substitution of Glu650 in GlyT2 by the corresponding methionine in GlyT1 reduced the charge-to-flux ratio to the level of GlyT1 without producing transport uncoupling. Chloride dependence of glycine transport was almost abolished in this GlyT2 mutant but simultaneous substitution of Glu250 and Glu650 by neutral amino acids rescued chloride sensitivity, suggesting that protonation/deprotonation of Glu250 substitutes chloride function. The differential behavior of equivalent GlyT1 mutations sustains a GlyT2-specific allosteric coupling between the putative Na3 site and the chloride site.
Landscape genetics identifies streams and drainage infrastructure as dispersal corridors for an endangered wetland bird

Abstract Anthropogenic alterations to landscape structure and composition can have significant impacts on biodiversity, potentially leading to species extinctions. Population‐level impacts of landscape change are mediated by animal behaviors, in particular dispersal behavior. Little is known about the dispersal habits of rails (Rallidae) due to their cryptic behavior and tendency to occupy densely vegetated habitats. The effects of landscape structure on the movement behavior of waterbirds in general are poorly studied due to their reputation for having high dispersal abilities. We used a landscape genetic approach to test hypotheses of landscape effects on dispersal behavior of the Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered subspecies endemic to the Hawaiian Islands. We created a suite of alternative resistance surfaces representing biologically plausible a priori hypotheses of how gallinules might navigate the landscape matrix and ranked these surfaces by their ability to explain observed patterns in genetic distance among 12 populations on the island of O`ahu. We modeled effective distance among wetland locations on all surfaces using both cumulative least‐cost‐path and resistance‐distance approaches and evaluated relative model performance using Mantel tests, a causal modeling approach, and the mixed‐model maximum‐likelihood population‐effects framework. Across all genetic markers, simulation methods, and model comparison metrics, surfaces that treated linear water features like streams, ditches, and canals as corridors for gallinule movement outperformed all other models. This is the first landscape genetic study on the movement behavior of any waterbird species to our knowledge. Our results indicate that lotic water features, including drainage infrastructure previously thought to be of minimal habitat value, contribute to habitat connectivity in this listed subspecies.
Limited-Stage Hodgkin Lymphoma: Minimizing Toxicity

Abstract Early-stage classic Hodgkin lymphoma has been highly curable using extended-field radiation therapy (RT) alone, combined-modality therapy consisting of chemotherapy and RT, and more recently chemotherapy alone. Radiation therapy either to an extended field (extended-field RT) or to various iterations of an involved field (involved-field RT) is potentially associated with late morbidity and mortality, particularly second primary cancers and cardiovascular complications. Treatment with chemotherapy alone, when possible, can achieve a high cure rate while avoiding these risks. This review describes the evolution of treatment for early-stage classic Hodgkin lymphoma.
PENGEMBANGAN BAHAN AJAR MATEMATIKA DENGAN MEMANFAATKAN GEOGEBRA UNTUK MENINGKATKAN PEMAHAMAN KONSEP

Penelitian ini bertujuan untuk dapat mengetahui karakteristik buku yang memadai bagi peningkatan pemahaman konsep terhadap matematika, khususnya pada pokok bahasan fungsi dengan memanfaatkan program Geogebra. Metode penelitian yang digunakan yaitu penelitian dan pengembangan, dimana penelitian ini dimaksudkan untuk mengembangkan dan menghasilkan produk tertentu, serta menguji keefektifan produk tersebut. Subyek dalam penelitian ini adalah siswa SMP Negeri 6 Kota Serang dengan uji skala terbatas dilakukan pada 5 siswa, sedangkan uji lapangan dilakukan terhadap 15 siswa. Kesimpulan yang diperoleh dalam penelitian ini siswa yang menggunakan bahan ajar dengan memanfaatkan program Geogebra mengalami peningkatan pemahaman konsep dibandingkan dengan siswa sebelum menggunakan bahan ajar. (Artikel ini sudah terbit di Jurnal Gauss: Jurnal Pendidikan Matematika, Prodi Pendidikan Matematika, Universitas Serang Raya, Vol. 01, No. 01 Mei 2018, hal. 26-36)
Contextual and temporal variability in large-scale functional network interactions underlying attention

ii LAY SUMMARY . iii PREFACE . iv TABLE OF CONTENTS . v LIST OF TABLES . xi LIST OF FIGURES . xii ACKNOWLEDGMENTS . xiv CHAPTER 1 INTRODUCTION . 1 Attention as a multifaceted process . 2 Non-invasive brain network mapping in humans . 5 Temporal and contextual variability in network organization . 5 Graph theory . 5 Key networks involved in attention . 6 The dorsal attention network . 6 The default network . 8 The salience networks . 9 The frontoparietal control network . 10 Overview of the current research questions . 12 The relationship between perceptual and conceptual attention networks . 12 The organization of the frontoparietal control network . 13 Network configurations during different forms of internal attention . 15 CHAPTER 2 EXPERIMENT 1: INTERACTIONS BETWEEN THE DEFAULT NETWORK AND DORSAL ATTENTION NETWORK VARY ACROSS DEFAULT SUBSYSTEMS, TIME, AND COGNITIVE STATE . 17
On the viability of unsupervised T-cell receptor sequence clustering for epitope preference

MOTIVATION The T-cell receptor (TCR) is responsible for recognizing epitopes presented on cell surfaces. Linking TCR sequences to their ability to target specific epitopes is currently an unsolved problem, yet one of great interest. Indeed, it is currently unknown how dissimilar TCR sequences can be before they no longer bind the same epitope. This question is confounded by the fact that there are many ways to define the similarity between two TCR sequences. Here we investigate both issues in the context of TCR sequence unsupervised clustering. RESULTS We provide an overview of the performance of various distance metrics on two large independent datasets with 412 and 2835 TCR sequences respectively. Our results confirm the presence of structural distinct TCR groups that target identical epitopes. In addition, we put forward several recommendations to perform unsupervised T-cell receptor sequence clustering. AVAILABILITY AND IMPLEMENTATION Source code implemented in Python 3 available at https://github.com/pmeysman/TCRclusteringPaper. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Predicting the Usefulness of Amazon Reviews Using Off-The-Shelf Argumentation Mining

Internet users generate content at unprecedented rates. Building intelligent systems capable of discriminating useful content within this ocean of information is thus becoming a urgent need. In this paper, we aim to predict the usefulness of Amazon reviews, and to do this we exploit features coming from an off-the-shelf argumentation mining system. We argue that the usefulness of a review, in fact, is strictly related to its argumentative content, whereas the use of an already trained system avoids the costly need of relabeling a novel dataset. Results obtained on a large publicly available corpus support this hypothesis.
Angiotensin (1–7) inhibits arecoline‐induced migration and collagen synthesis in human oral myofibroblasts via inhibiting NLRP3 inflammasome activation

Arecoline induces oral submucous fibrosis (OSF) via promoting the reactive oxygen species (ROS). Angiotensin (1–7) (Ang‐(1–7)) protects against fibrosis by counteracting angiotensin II (Ang‐II) via the Mas receptor. However, the effects of Ang‐(1–7) on OSF remain unknown. NOD‐like receptors (NLRs) family pyrin domain containing 3 (NLRP3) inflammasome is identified as the novel mechanism of fibrosis. Whereas the effects of arecoline on NLRP3 inflammasome remain unclear. We aimed to explore the effect of Ang‐(1–7) on NLRP3 inflammasome in human oral myofibroblasts. In vivo, activation of NLRP3 inflammasomes with an increase of Ang‐II type 1 receptor (AT1R) protein level and ROS production in human oral fibrosis tissues. Ang‐(1–7) improved arecoline‐induced rats OSF, reduced protein levels of NADPH oxidase 4 (NOX4) and the NLRP3 inflammasome. In vitro, arecoline increased ROS along with upregulation of the angiotensin‐converting enzyme (ACE)/Ang‐II/AT1R axis and NLRP3 inflammasome/interleukin‐1β axis in human oral myofibroblasts, which were reduced by NOX4 inhibitor VAS2870, ROS scavenger N‐acetylcysteine, and NOX4 small interfering RNA (siRNA). Furthermore, arecoline induced collagen synthesis or migration via the Smad or RhoA‐ROCK pathway respectively, which could be inhibited by NLRP3 siRNA or caspase‐1 blocker VX‐765. Ang‐(1–7) shifted the balance of RAS toward the ACE2/Ang‐(1–7)/Mas axis, inhibited arecoline‐induced ROS and NLRP3 inflammasome activation, leading to attenuation of migration or collagen synthesis. In summary, Ang‐(1–7) attenuates arecoline‐induced migration and collagen synthesis via inhibiting NLRP3 inflammasome in human oral myofibroblasts.
The Role of Hysteroscopy in Evaluating Postmenopausal Asymptomatic Women with Thickened Endometrium

Backgrounds and Aims: This study aims to compare hysteroscopic and histological findings in asymptomatic postmenopausal patients with thickened endometrium. Materials and Methods: A retrospective study involving case records of 295 asymptomatic postmenopausal women with a thickened endometrium >5 mm diagnosed at transvaginal ultrasound (TVS). Patients (women) underwent hysteroscopy with biopsy between 2009 and 2015, and they were followed up at National Cancer Institute of Bari and at University Hospital of Pisa. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of hysteroscopy were evaluated. Results: Inclusion criteria were TVS, hysteroscopy, and endometrial biopsy. When the hysteroscopic findings were normal, a sensitivity of 100%, specificity of 98.6%, PPV of 95.2%, and NPV of 100% were achieved. For polyps and myomas, we found 100%, 98.7%, 99.5%, and 100%, respectively. In case of endometrial hyperplasia, a sensitivity of 66.7%, a specificity of 100%, a PPV of 100%, and a NPV of 98.1% were achieved. For endometrial cancer hysteroscopy, sensitivity, specificity, PPV, and NPV were 100%, 99.6%, 75%, and 100%, respectively. Conclusions: Hysteroscopy allows an accurate diagnosis in benign endometrial pathology and suspect of malignant endometrial pathology in postmenopausal women with thickened endometrium.
Diversity and abundance of macro‐invertebrates on abandoned cattle kraals in a semi‐arid savanna

Abstract Abandoned cattle (Bos taurus) kraals are sources of habitat heterogeneity in dystrophic semi‐arid African savannas with a strong positive effect on soil nutrients and plant productivity. However, little is known regarding how macro‐invertebrate assemblages vary between abandoned kraals and the surrounding savanna matrix. We tested whether herbaceous biomass and basal and aerial covers and soil nutrients have an effect on aboveground and belowground macro‐invertebrate assemblages. Twelve abandoned kraals were contrasted with their paired control plots for soil characteristics, herbaceous productivity, and macro‐invertebrate assemblages in Save Valley Conservancy, Zimbabwe. Abandoned kraals had significantly higher concentrations of soil nitrogen (N), phosphorus (P), potassium (K), and calcium (Ca) as well as herbaceous biomass and basal and aerial covers than control plots. Both aboveground and belowground macro‐invertebrate species richness were higher on abandoned kraals. However, only belowground macro‐invertebrate diversity (Shannon H′ and Hill number 1) was significantly higher on abandoned kraals. Soil nutrients and herbaceous productivity had positive and significant correlations with the dominant taxa (Coleoptera, Hymenoptera, Hemiptera, Isoptera, and Myriapoda) on abandoned kraals. These results add to the growing body of evidence that abandoned kraals exert significant effects on savanna spatial heterogeneity years later, with implications on ecosystem processes and functioning.
A Clinical Study of Ninjin'yoeito With Regard to Frailty

Frailty in older people is strongly associated with poor nutrition, which is particularly important in the present-day superaging society. This study initially investigated a number of cases of frailty where there was a speedy recovery after administration of a dual deficiency of qi and blood preparation, ninjin'yoeito (NYT), formulated for frail patients who suffer from kiketuryokyo status. Based on these observations, a more extensive investigation involving a greater number of cases was completed. The findings of the effects of NYT on frailty are reported here.