Miracle-dz/UniFAR-FTUs huggingface dataset:
MicroRNA-330-3p Expression Indicates Good Prognosis and Suppresses Cell Proliferation by Targeting Bmi-1 in Osteosarcoma

Background/Aims: Growing evidence has shown that miR-330-3p is closely related to the biological behavior of cancer, including proliferation, metastasis, and prognosis. However, there have been no reports on miR-330-3p expression and function in osteosarcoma. Methods: Expression of miR-330-3p in osteosarcoma tissues and cell lines was examined by quantitative PCR. Effects of miR-330-3p on osteosarcoma cell proliferation were investigated in vitro with the Cell Counting Kit-8 colorimetric assay. Targets of miR-330-3p were identified by dual-luciferase reporter assay. Results: The results showed that expression of miR-330 decreased in osteosarcoma tissues and cell lines. Prognosis of patients with high miR-330-3p expression was much better than that of those with low expression (P=0.001), and multivariate analysis suggested that miR-330-3p is an independent prognostic factor for osteosarcoma. In addition, miR-330-3p overexpression significantly inhibited the growth of MG-63 and U2OS osteosarcoma cells. Dual-luciferase reporter assay demonstrated that Bmi-1 was a direct target gene of miR-330-3p, and in a recovery experiment, miR-330-3p suppressed osteosarcoma cell proliferation by directly targeting Bmi-1. Conclusion: Our results suggest that miR-330-3p acts as a tumor suppressor by regulating Bmi-1 expression in osteosarcoma. Thus, miR-330-3p may represent a novel therapeutic target for the treatment of osteosarcoma.
Strategic Interactions and Uncertainty in Decisions to Curb Greenhouse Gas Emissions

This paper examines the strategic interactions of two large regions making choices about greenhouse gas emissions in the face of rising global temperatures. Three central features are highlighted: uncertainty, the incentive for free riding, and asymmetric characteristics of decision makers. Optimal decisions are modelled in a fully dynamic, feedback Stackelberg pollution game. Global average temperature is modelled as a mean reverting stochastic process. A numerical solution of a coupled system of Hamilton-Jacobi-Bellman equations is implemented and the probability distribution of outcomes is illustrated with Monte Carlo simulation. When players are identical, the outcome of the game is much worse than the social planner’s outcome. An increase in temperature volatility reduces player utility, making cooperative action through a social planner more urgent. Asymmetric damages or asymmetric preferences for emissions reductions are shown to have important effffects on the strategic interactions of players.
PROCESSING PROTEINS IN SERUM BY DIGITAL MICROFLUIDICS

We present the first digital microfluidic (DMF)-driven method capable of processing proteins from heterogeneous fluids. In this study, proteins were extracted from serum and other heterogeneous mixtures from nanoliter-size droplets via precipitation. This method is an important step towards the construction of a fully automated system for clinical proteomics.
3 Analytical Evaluation of Herbal Drugs

Traditional herbal medicine and their preparations have been widely used for the thousands of years in developing and developed countries owing to its natural origin and lesser side effects or dissatisfaction with the results of synthetic drugs. However, one of the characteristics of oriental herbal medicine preparations is that all the herbal medicines, either presenting as single herbs or as collections of herbs in composite formulae, is extracted with boiling water during the decoction process. This may be the main reason why quality control of oriental herbal drugs is more difficult than that of western drug. As pointed in “General Guidelines for Methodologies on Research and Evaluation of Traditional Medicines (World Health Organization, 2000)”, “Despite its existence and continued use over many centuries, and its popularity and extensive use during the last decade, traditional medicine has not been officially recognized in most countries. Consequently, education, training and research in this area have not been accorded due attention and support. The quantity and quality of the safety and efficacy data on traditional medicine are far from sufficient to meet the criteria needed to support its use world-wide. The reasons for the lack of research data are due to not only to health care policies, but also to a lack of adequate or accepted research methodology for evaluating traditional medicine” (WHO, 2000, 2001).
Network Measures of Collaborative Support for Young Adults With Autism

OBJECTIVES: The treatment of autism requires complex, multimodal interventions, provided by parents and providers across settings. As young adults with autism spectrum disorder (ASD) transition into adulthood, new stakeholders are added to support planning for postsecondary employment. In this article, we investigate the use of dynamic social network measures that describe the resources of young adults throughout transition. METHODS: A longitudinal, dynamic social network survey (Social Dynamics of Intervention [SoDI]) was conceptualized, designed, and conducted as a feasibility test, measuring changes in collaboration among parents and school staff members who provided interventions for children with ASD in 2 urban public schools. Using the SoDI, we tracked the following over time: the team who provided interventions, their locations, the interventions they provided, the autism trainings they attended, and the density of the team’s problem-solving network for the child. RESULTS: Using the SoDI, we successfully identified stakeholders across settings who provided interventions for each child. Results indicated variation in the density of problem-solving and trust related to ASD intervention across teams as well as variation in intervention and autism knowledge networks during the school year. Adaptations of the SoDI for mapping pre- and posttransition resources and social connectivity across stakeholders for young adults with ASD are proposed in the Discussion section. CONCLUSIONS: Dynamic social network approaches can be used to capture changes in intervention, autism knowledge, and social connectivity, providing informative descriptive data about how vocational rehabilitation policies might increase employment supports during the transition process for young adults with ASD.
SATO: Surface Area Traversal Order for Shadow Ray Tracing

We present the surface area traversal order (SATO) metric to accelerate shadow ray traversal. Our formulation uses the surface area of each child node to compute the TO. In this metric, we give a traversal priority to the child node with the larger surface area to quickly find occluders. Our algorithm reduces the pre‐processing overhead significantly, and is much faster than other metrics. Overall, the SATO is useful for ray tracing large and complex dynamic scenes (e.g. a few million triangles) with shadows.
Using ECN Marks to Improve TCP Performance over Lossy Links

TCP was designed for wireline networks, where loss events are mostly caused by network congestion. The congestion control mechanism of current TCP uses loss events as the indicator of congestion, and reduces its congestion window size. However, when a lossy link is involved in a TCP connection, non-congestion random losses should also be considered. The congestion window size should not be decreased if a loss event is caused by link corruptions. To improve TCP performance over lossy links, in this paper, we rst present that zero congestion loss could be achieved by appropriately setting the ECN marking threshold in the RED buffer. Secondly, we propose a new TCP algorithm, called Differentiation Capable TCP (Diff-C-TCP). Diff-C-TCP makes an assumption that packet losses are caused by link corruptions, and uses ECN (Explicit Congestion Notication) to determine any loss that may occasionally happen due to network congestion. We have shown that Diff-C-TCP performs very well in the presence of a lossy link.
Estimating Conditional Intensity Function of a Neural Spike Train by Particle Markov Chain Monte Carlo and Smoothing

Understanding neural activities is fundamental and challenging in decoding how the brain processes information. An essential part of the problem is to define a meaningful and quantitative characterization of neural activities when they are represented by a sequence of action potentials or a neural spike train. The thesis approaches to use a point process to represent a neural spike train, and such representation provides a conditional intensity function (CIF) to describe neural activities. The estimation procedure for CIF, including particle Markov Chain Monte Carlo (PMCMC) and smoothing, is introduced and applied to a real data set. From the CIF and its derivative of a neural spike train, we can successfully observe adaption behavior. Simulation study verifies that the estimation procedure provides reliable estimate of CIF. This framework provides a definite quantification of neural activities and facilitates further investigation of understanding the brain from neurological perspective.
Thyroid Ultrasound Findings in Children from Three Japanese Prefectures: Aomori, Yamanashi and Nagasaki

Due to the likelihood of physical and mental health impacts following the unprecedented accident at the Fukushima Dai-ichi Nuclear Power Plant, the Fukushima prefectural government decided to conduct the Fukushima Health Management Survey to assist in the long-term health management of residents. This included thyroid ultrasound examination for all children in Fukushima. For appropriate evaluation of ultrasound screening of the thyroid, it is important to understand its reference data of thyroid findings in children in general. In order to analyze the frequencies of specific thyroid findings, we conducted ultrasound screening of the thyroid by the same procedures as used in Fukushima in 4,365 children, aged 3 to 18 years, from three Japanese prefectures. Overall, thyroid cysts were identified in 56.88% and thyroid nodules in 1.65% of the participants. Thyroid cysts and nodules with a maximum diameter of more than 5 mm were identified in 4.58% and 1.01%, respectively, and age-adjusted prevalences were 3.82% and 0.99%, respectively. Although the prevalence of cysts and nodules varied among the examination areas, no significant differences were observed among the three examination areas in the prevalence of cysts and nodules with a maximum diameter of more than 5 mm. Also, the prevalence of thyroid cysts and nodules, especially those with a maximum diameter of more than 5 mm, significantly increased with age, and showed a female predominance. We also identified ectopic thymus (1.95%), diffuse goiter (1.40%), ultimobranchial body (0.73%), lymph node swelling (0.21%) and thyroid agenesis (0.05%). This is the first ultrasound description of the age-adjusted prevalence of thyroid cysts and nodules, or of the prevalence of abnormalities other than cysts and nodules, such as ectopic thymus, in relation to age, in the general Japanese child population. We contend that this can provide relevant information for the Fukushima Health Management Survey and future population studies.
Rates and Predictors of Conversion to Open Surgery During Minimally Invasive Radical Cystectomy.

OBJECTIVE To assess the frequency of minimally invasive radical cystectomy (MIRC) conversion to open surgery, what factors influence conversion, whether or not the benefits of MIRC vs open radical cystectomy (ORC) persist after conversion, and compare ORC and MIRC outcomes. MATERIALS AND METHODS We performed a retrospective cohort study from the National Cancer Data Base (2010 to 2013) analyzing patients who underwent completed MIRC (n = 5750), converted MIRC (n = 245), and ORC (n = 12,053) without prior radiotherapy. Multivariable logistic and linear regression analyses were used to assess the association between covariates, open conversion as well as surgical approach, and secondary outcomes such as positive surgical margins (PSMs), use of lymphadenectomy, lymph node yield, hospital length of stay (LOS), and 30-day readmission. RESULTS Rates of conversion were independent of patient factors such as race, sex, use of neoadjuvant chemotherapy, and clinical stage. Conversion occurred in 245 of 5750 MIRCs (4.3%) and declined over time (5.8% in 2010 vs 3.2% in 2013, odds ratio [OR] 0.50, 95% confidence interval [CI] 0.34-0.75, p = 0.001). MIRC was associated with fewer positive margins, higher lymph node yield, shorter LOS, and fewer readmissions compared with ORC, however, patients requiring open conversion had longer median hospital stays (8 days vs 7 days, p = 0.013), lower median lymph node yields (14 vs 17, p = 0.007), more PSMs (17% vs 11%, p = 0.006), and more 30-day readmissions (14% vs 9%, p = 0.008) compared to nonconverted. Converted MIRC had similar hospital LOS and 30-day readmission rates compared to ORC. CONCLUSION Open conversion during MIRC is uncommon and has decreased in recent years despite the rising use of MIRC. MIRC had better short-term outcomes compared with ORC. These benefits were negated with open conversion; however, outcomes were similar compared to planned ORC.
Emotion recognition using parabolic phase space mapping for heart rate variability analysis

In this paper, extracted features from Parabolic Phase Space Mapping (PPSM) of RR time series and its extended version were used to distinguish four emotionstates (energetic, calm, happy, and anxious) induced by picture stimuli. In order to induce emotions, four groups of pictures with different emotional concepts were used as a visual stimulus while the lead II of ECG was recorded. Induced emotion was confiremed by self-assessment manikin test. The results show that extracted features were significantly different between energetic and calm, energetic and happy, energetic and anxious, calm and happy, calm and anxious, and happy and anxious (p<0.05).
A new method to study the change of miRNA–mRNA interactions due to environmental exposures

Motivation: Integrative approaches characterizing the interactions among different types of biological molecules have been demonstrated to be useful for revealing informative biological mechanisms. One such example is the interaction between microRNA (miRNA) and messenger RNA (mRNA), whose deregulation may be sensitive to environmental insult leading to altered phenotypes. The goal of this work is to develop an effective data integration method to characterize deregulation between miRNA and mRNA due to environmental toxicant exposures. We will use data from an animal experiment designed to investigate the effect of low‐dose environmental chemical exposure on normal mammary gland development in rats to motivate and evaluate the proposed method. Results: We propose a new network approach—integrative Joint Random Forest (iJRF), which characterizes the regulatory system between miRNAs and mRNAs using a network model. iJRF is designed to work under the high‐dimension low‐sample‐size regime, and can borrow information across different treatment conditions to achieve more accurate network inference. It also effectively takes into account prior information of miRNA‐mRNA regulatory relationships from existing databases. When iJRF is applied to the data from the environmental chemical exposure study, we detected a few important miRNAs that regulated a large number of mRNAs in the control group but not in the exposed groups, suggesting the disruption of miRNA activity due to chemical exposure. Effects of chemical exposure on two affected miRNAs were further validated using breast cancer human cell lines. Availability and implementation: R package iJRF is available at CRAN. Contacts: pei.wang@mssm.edu or susan.teitelbaum@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Comparative study of methods for atrial fibrillation cycle length estimation in fractionated electrograms

Complex fractionated atrial electrograms (CFAEs) are electrograms (EGMs) characterized by a high variability both in amplitude and waveforms, making the estimation of their cycle length (CL) a difficult task to perform. The CL is a widely employed parameter for the characterization of the electrical activity within the atria, thus serving to guide catheter ablation, one of the most effective cardiac procedures for the treatment of AF nowadays. The present study aims to compare the performance of three different methods estimating the CL from a set of 50 recordings with CFAEs previously annotated by two expert physicians. The first algorithm is based on an adaptive amplitude threshold, while the second method performs the detection of the highest activations and a later detection of peaks within intervals longer than 1.5 times the median cycle length of the EGM. Finally, we introduce a novel hybrid method which performs a main amplitude detection, which is facilitated by the equalization of high and low amplitude activations in CFAEs according to a fractionation parameter, and a subsequent search for lower activations within intervals longer than the median CL, decreasing the amplitude threshold proportionally to the intervals' length. Our method outperformed the other analyzed detectors, which confirms that the method proposed is a more accurate estimator of atrial CL for CFAEs.
Cytokine-induced memory-like natural killer cells exhibit enhanced responses against myeloid leukemia

Cytokine-induced differentiation of memory-like natural killer cells enhances antileukemia responses. Natural killers of leukemia Natural killer cells, part of the innate immune system, play a role in immune responses against exogenous pathogens as well as cancer. Recent studies have identified the existence of memory-like characteristics in some natural killer cells, and Romee et al. investigated these memory cells’ potential as a cancer therapy. The authors compared human natural killer memory cells to non-memory control cells, then demonstrated their effectiveness against myeloid leukemia models in vitro and in mice. They also performed a clinical trial in human patients with acute myeloid leukemia, where the natural killer memory-like cells again demonstrated antileukemia effects, some of which produced clinical remissions. Natural killer (NK) cells are an emerging cellular immunotherapy for patients with acute myeloid leukemia (AML); however, the best approach to maximize NK cell antileukemia potential is unclear. Cytokine-induced memory-like NK cells differentiate after a brief preactivation with interleukin-12 (IL-12), IL-15, and IL-18 and exhibit enhanced responses to cytokine or activating receptor restimulation for weeks to months after preactivation. We hypothesized that memory-like NK cells exhibit enhanced antileukemia functionality. We demonstrated that human memory-like NK cells have enhanced interferon-γ production and cytotoxicity against leukemia cell lines or primary human AML blasts in vitro. Using mass cytometry, we found that memory-like NK cell functional responses were triggered against primary AML blasts, regardless of killer cell immunoglobulin-like receptor (KIR) to KIR-ligand interactions. In addition, multidimensional analyses identified distinct phenotypes of control and memory-like NK cells from the same individuals. Human memory-like NK cells xenografted into mice substantially reduced AML burden in vivo and improved overall survival. In the context of a first-in-human phase 1 clinical trial, adoptively transferred memory-like NK cells proliferated and expanded in AML patients and demonstrated robust responses against leukemia targets. Clinical responses were observed in five of nine evaluable patients, including four complete remissions. Thus, harnessing cytokine-induced memory-like NK cell responses represents a promising translational immunotherapy approach for patients with AML.
Cinnamaldehyde loaded-microparticles obtained by complex coacervation: Influence of the process parameters on the morphology and the release of the core material

Encapsulation by complex coacervation includes several steps that have been developed in order to attain a better control over the whole process and to achieve an important delayed effect. This has been carried out for the encapsulation of cinnamaldehyde (CN) by the classical gelatin/acacia gum pair of coacervating polymers. This preparation was performed in different conditions (stirring speeds, cooling rate, emulsion and coacervate time, use of surfactant, and polymer concentration) in order to investigate their effect on the encapsulation efficiency and drug release kinetics. Optical microscopy studies showed spherical microcapsules. The yield of the encapsulation attains more than 88% of all prepared microcapsules. The mean Sauter diameter (d 32) of obtained microparticles was in the range from 124 to 200 µm. The microspheres were also characterized by the FTIR method; showing the presence of core and polymers in the microparticles. The release of cinnamaldehyde was performed in heterogeneous medium (Water / ethanol, v/v: 30/70) at 25±0.5°C using UV–Vis analysis. It was demonstrated that the drug release followed the Fickian diffusion mechanism. The data were best fitted to the Fick's law with high correlation coefficients (R²).
Flame retarded polyethylene/wood flour composites with high performances: Satisfying both sides with intumescent flame retardants and synergistic compatibilizers, respectively

WPC is inflammable that threatens the safety of life and property. To reduce the risk of conflagration, it is important to make WPC flame retardant. But the flame retarded WPC is usually highly loaded which deteriorates its mechanical properties. It is difficult to satisfy both sides. In this article, we make attempt to prepare the flame retarded polyethylene/wood flour (WF) composites with high mechanical properties by using an ammonium polyphosphate and phosphorus based intumescent flame retardants (IFR) system. To maintain the high performances of the flame retarded composites, the multi-monomer graft copolymers are synergistically used as the interfacial compatibilizers for the composites. Cone calorimeter testing, UL94 flame tests, limited oxygen index (LOI) and thermogravimetric analysis (TGA) are used to evaluate the flammability properties and thermal stability of the composites. Results show that WF enhances the flame retardancy of the composites with the help of suitable IFR system. The coordination of flame retardants with WF content is an effective measure to control the fire spreading and the risk of combustion. The incorporation of flame retardants transforms the role of WF from the inflammable material into the charring agent of IFR system. By using the IFR system, a highly flame retarded composite with V0 classification based on the vertical combustion testing was successfully prepared. With the help of the synergistic compatibilizers, it is possible to prepare an intumescable flame retarded rPE/WF composites with high performances. The incorporation of WF, and flame retardants can improve the thermal stability of the composites. POLYM. COMPOS. , 2016. © 2016 Society of Plastics Engineers