Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovering the Role of MicroRNAs in Microcystin-Induced Toxicity in Fish

MicroRNAs (miRNAs) form a class of endogenously expressed small, non-coding RNAs, that play key roles in the regulation of gene expression of a broad spectrum of biological processes. However, in the field of toxinology, a science of naturally occurring toxins, the relationship between toxicity and microRNA expression is poorly understood. Microcystins (MCs) are potent cyclic peptide hepatotoxins produced by cyanobacteria, which pose a seri‐ ous threat to aquatic organisms and may also affect human health through the consumption of contaminated waters or food. Although a number of cell physiologic pathways, potential targets for miRNA regulation, are implicated in the response to MCs in animals, no research so far investigated the role for miRNA genes in the mechanism of microcystin (MC)-induced toxicity in fish. The chapter aims to summarize recent achievements of our team in the field, focusing on expression profiling in vivo of liver microRNA levels of whitefish (Coregonus lav‐ aretus) following MC-LR exposure.
In vitro cytotoxicities of ionic liquids: Effect of cation rings, functional groups, and anions

In vitro cytotoxicities were measured for ionic liquids (ILs) containing various cations and anions using the MCF7 human breast cancer cell line. We measured the cytotoxicities of ionic liquids containing the cations pyridinium, pyrrolidinium, piperidinium, or imidazolium with various alkyl chain lengths, and the anions bromide, bis(trifluoromethanesulfone)imide (Tf2N), trifluoromethylsulfonate (TfO), or nonafluoromethylsulfonate (NfO). Three new hydrophobic, task‐specific ionic liquids (TSILs), namely, [MBCNPip]+[Tf2N]−, [MPS2Pip]+[Tf2N]−, and [MPS2Pyrro]+[Tf2N]− designed for metal‐ion extraction were also evaluated. IC50 values of the ionic liquids toward the MCF7 cells ranged from 8 μM to 44 mM. The toxicity depended significantly on the nature of the cations and anions, especially when the cations contained a long side chain. TSILs studied in this work were less toxic than the classical ILs. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Efficient search for the top-k probable nearest neighbors in uncertain databases

Uncertainty pervades many domains in our lives. Current real-life applications, e.g., location tracking using GPS devices or cell phones, multimedia feature extraction, and sensor data management, deal with different kinds of uncertainty. Finding the nearest neighbor objects to a given query point is an important query type in these applications.In this paper, we study the problem of finding objects with the highest marginal probability of being the nearest neighbors to a query object. We adopt a general uncertainty model allowing for data and query uncertainty. Under this model, we define new query semantics, and provide several efficient evaluation algorithms. We analyze the cost factors involved in query evaluation, and present novel techniques to address the trade-offs among these factors. We give multiple extensions to our techniques including handling dependencies among data objects, and answering threshold queries. We conduct an extensive experimental study to evaluate our techniques on both real and synthetic data.
Central CRF inhibits gastric emptying of a nutrient solid meal in rats: the role of CRF2 receptors.

Corticotropin-releasing factor (CRF)-related peptides exhibit different affinity for the receptor subtypes 1 and 2 cloned in the rat brain. We investigated, in conscious rats, the effects of intracisternal (i.c.) injection of CRF (rat/human) on the 5-h rate of gastric emptying of a solid nutrient meal (Purina chow and water ad libitum for 3 h) and the CRF receptor subtype involved. CRF, urotensin I (suckerfish), and sauvagine (frog) injected i.c. inhibited gastric emptying in a dose-dependent manner, with ED50 values of 0.31, 0.13, and 0.08 microgram/rat, respectively. Rat CRF-(6-33) (0.1-10 micrograms i.c.) had no effect. The nonselective CRF1 and CRF2 receptor antagonist, astressin, injected i.c. completely blocked the inhibitory effect of i.c. CRF, urotensin I, and sauvagine with antagonist-to-agonist ratios of 3:1, 10:1, and 16:1, respectively. The CRF1-selective receptor antagonist NBI-27914 injected i.c. at a ratio of 170:1 had no effect. These data show that central CRF and CRF-related peptides are potent inhibitors of gastric emptying of a solid meal with a rank order of potency characteristic of the CRF2 receptor subtype affinity (sauvagine > urotensin I > CRF). In addition, the reversal by astressin but not by the CRF1-selective receptor antagonist further supports the view that the CRF2 receptor subtype is primarily involved in central CRF-induced delayed gastric emptying.
NONLINEAR THEORY OF FLAME FRONT INSTABILITY

Abstract A nonlinear, nonstationary equation describing evolution of weakly curved premixed flames with arbitrary gas expansion, subject to the Landau-Dar-rieus instability, is derived. The new equation respects all the conservation laws to be satisfied across the flame front, correctly taking into account influence of vorticity, generated in the flame, on the flame front structure and flame velocity. Analytical solutions of the derived equation are found.
Evaluation of Effect of Median U-Turns on Multilane Primary Highway Capacity in Thailand through Traffic Micro-Simulation Models

This article aims to analyze the effect of median U-turns and estimate the capacity of primary highways in Thailand using a traffic micro-simulation model. Six-lane and four-lane primary highways were selected for the study. The base condition results determined that the maximum capacity of a six-lane primary highway was 2,130 passenger cars/hour/lane, while the four-lane primary highway capacity was recorded as 2,194 passenger cars/hour/lane. Both results were slightly higher than those of the HCM2010 approach. Under prevailing conditions, both sections exhibited lower capacities than the HCM results by approximately 33.7% and 19.8% for the six-lane and four-lane primary highways, respectively, causing the impact of the median U-turn and highway characteristics in Thailand to directly affect traffic and driving behavior. Using the micro-simulation results, an equation was also regressed for estimating the capacity resulting from the impact of the median U-turns and heavy vehicles. These results may be used as guidelines for the design and analysis of multilane highways in Thailand.
Relationship Between Mathematics and Science Achievement at the 8th Grade.

Mathematics and science achievements have been assessed in the Third International Mathematics and Science Study (TIMSS) and its repetition (TIMSS-R). Most existing reports are largely separated into the subject domains. This article is focused on an examination of the relationship between mathematics and science achievements based on student test scores. Moderate correlation coefficients have been found from the statistical analyses on the TIMSS and TIMSS-R measurement scales. These empirical findings may help mathematics and science educators assess the need for curriculum integration advocated by several professional organizations in the U.S. and other nations.
Fast, Simple and Accurate Handwritten Digit Classification by Training Shallow Neural Network Classifiers with the ‘Extreme Learning Machine’ Algorithm

Recent advances in training deep (multi-layer) architectures have inspired a renaissance in neural network use. For example, deep convolutional networks are becoming the default option for difficult tasks on large datasets, such as image and speech recognition. However, here we show that error rates below 1% on the MNIST handwritten digit benchmark can be replicated with shallow non-convolutional neural networks. This is achieved by training such networks using the ‘Extreme Learning Machine’ (ELM) approach, which also enables a very rapid training time (∼ 10 minutes). Adding distortions, as is common practise for MNIST, reduces error rates even further. Our methods are also shown to be capable of achieving less than 5.5% error rates on the NORB image database. To achieve these results, we introduce several enhancements to the standard ELM algorithm, which individually and in combination can significantly improve performance. The main innovation is to ensure each hidden-unit operates only on a randomly sized and positioned patch of each image. This form of random ‘receptive field’ sampling of the input ensures the input weight matrix is sparse, with about 90% of weights equal to zero. Furthermore, combining our methods with a small number of iterations of a single-batch backpropagation method can significantly reduce the number of hidden-units required to achieve a particular performance. Our close to state-of-the-art results for MNIST and NORB suggest that the ease of use and accuracy of the ELM algorithm for designing a single-hidden-layer neural network classifier should cause it to be given greater consideration either as a standalone method for simpler problems, or as the final classification stage in deep neural networks applied to more difficult problems.
Paraxial Coupling of Propagating Modes in Three-Dimensional Waveguides with Random Boundaries

We analyze long range wave propagation in three-dimensional random waveguides. The waves are trapped by top and bottom boundaries, but the medium is unbounded in the two remaining directions. We consider scalar waves, and motivated by applications in underwater acoustics, we take a pressure release boundary condition at the top surface and a rigid bottom boundary. The wave speed in the waveguide is known, but the top boundary has small random fluctuations that cause significant cumulative scattering of the waves over long distances of propagation. To quantify the scattering effects, we study the evolution of the random amplitudes of the waveguide modes. We obtain that in the long range limit they satisfy a system of paraxial equations driven by a Brownian field. We use this system to estimate three important mode-dependent scales: the scattering mean free path, the cross-range decoherence length, and the decoherence frequency. Understanding these scales is important in imaging and communication problems, .
An Introduction of Genetics in Otosclerosis

Objective To present an easy to read systematic review concerning the genetic etiology of otosclerosis to help health care providers in counseling otosclerosis patients more accurately. Data Sources PubMed, Embase, CINAHL, and the Cochrane Library. Review Methods Studies on the genetic etiology of otosclerosis were selected. Association studies and family-based studies were included for further review. After quality assessment (risk of bias), data were extracted from the included studies. When available, odds ratios were presented. In case of corresponding genetic anomalies between the studies, it was the aim to combine results. Results The number of available studies with low risk of bias is limited to 2 association studies and 1 family-based study. These high-quality studies show that otosclerosis in Japanese patients is not linked to the NOG gene and that a polymorphism in the Sp1 binding site located on the COL1A1 gene is associated with otosclerosis as well as OTSC1. Association and family-based studies with moderate risk of bias show a statistically significant association with the ACE gene, AGT gene, OTSC2, RELN gene, TGFB1 gene, 11q13.1, OTSC2, OTSC5, OTSC8, and OTSC10. These results may be spurious associations due to their bias and low statistical power. Conclusion The present systematic review shows that there is scattered evidence of limited quality and a lack of replication studies. It is not possible to point out 1 or more responsible genes, which play a key role within the genetic pathophysiologic mechanism of otosclerosis.
Acoustic Properties of Multi-Layer Wool Nonwoven Structures

ABSTRACT Wool insulating materials provide good acoustic insulation and are increasingly used for room insulation. These insulating materials are usually produced using nonwoven techniques. The structure and nonwovens parameters affect the acoustic properties of the product. During the investigation, acoustic properties of needle punched and stitch-bonded wool nonwovens were examined. Sound absorption coefficient and noise reduction coefficient for monolayer and multi-layer structures were determined. Relations between acoustic characteristics and nonwoven thickness, surface density, and air permeability were revealed. For the multi-layer structures, an increase of sound absorption with an increase in layer numbers was observed. The increase in sound absorption coefficient was correlated with the decrease in air permeability.
Analysis of Problem-Solving-Based Online Asynchronous Discussion Pattern

This research explores the process of asynchronous problem-solving-based discussion activities and aims to understand limitations likely to arise during learners’ problem-solving discussions. The research has combined lag-sequential analysis and quantitative content analysis, and expects to use such analyzing methods to further understand the sequential pattern of students’ problem-solving discussion behaviors and knowledge-construction levels. In order to avoid influence caused by teachers’ subjective guiding methods and ensure objective observations, we observed learners’ online problem-solving discussions without intervention or guidance from the teachers. From the sequential pattern derived, we have not only induced a pattern of students’ discussion behavior but also discovered that, compared to discussion activity based on a single topic appointed by the teacher, the problem-solving online discussion activity is more helpful for students’ knowledge construction. In addition, this research also revealed certain limitations toward the content and behavior of students’ discussion without teachers’ guidance. Based on the results, this paper proposes a strategy in which teachers can intervene and guide, which is expected to enhance the depth of students’ discussion and knowledge construction when a teacher is applying a problem-based learning activity. Keyword
Configuration comparison among kinematically optimized continuum manipulators for robotic surgeries through a single access port

SUMMARY Many recent developments of surgical robots focus on less invasive paradigms, such as laparoscopic SPA (Single Port Access) surgery, NOTES (Natural Orifice Translumenal Endoscopic Surgery), laryngoscopic MIS (Minimally Invasive Surgery), etc. A configuration similarity shared by these surgical robots is that two or more manipulators are inserted through one access port (a laparoscope, an endoscope, or a laryngoscope) for surgical interventions. However, upon designing such a surgical robot, the structure of the inserted manipulators has not been thoroughly explored based on evaluation of their performances. This paper presents a comparison for kinematic performances among three different continuum manipulators. They all could be applied in the aforementioned surgical robots. The structural parameters of these continuum manipulators are firstly optimized to assure a more fair and consistent comparison. This study is conducted in a dimensionless manner and provides scalable results for a wide spectrum of continuum manipulator designs as long as their segments have a constant curvature. The results could serve as a design reference for future developments of surgical robots which use one access port and continuum mechanisms.
A Panel of 3 Markers Including p16, ProExC, or HPV ISH is Optimal for Distinguishing Between Primary Endometrial and Endocervical Adenocarcinomas

Endometrial and endocervical adenocarcinomas may seem histologically identical and it can be difficult to determine primary site of origin based on morphology alone. As the distinction is significant and cannot always be made on the basis of clinical findings, various immunohistochemical panels have been proposed to aid in determining site of origin. Stains for vimentin, estrogen receptor (ER), progesterone receptor (PR), monoclonal carcinoembryonic antigen, p16 and ProExC, and HPV in situ hybridization (ISH), were performed on 283 tissue microarray (TMA) cores and 38 whole sections. The TMA consisted of 214 endometrial carcinomas, 33 endocervical adenocarcinomas, and 36 problematic cases. The endometrial and endocervical carcinomas represented usual endometrioid and mucinous types, and special variants (uterine serous carcinoma, uterine clear cell carcinoma, minimal deviation endocervical adenocarcinoma, cervical small cell carcinoma, adenoid basal cell carcinoma, mesonephric carcinoma). Univariate analysis showed that 6 markers (vimentin, ER, PR, p16, ProExC, and HPV ISH) performed well in distinguishing between endocervical and endometrial origin for the usual endometrioid and mucinous types. Multivariate analysis showed that vimentin, p16, and HPV ISH are the strongest predictors of site. Using a script written in R, the diagnostic accuracy of all possible combinations of markers was evaluated and it was shown that a 3 marker panel including vimentin, ER, or PR, and an HPV marker (p16, ProExC, or HPV ISH) is optimal for determining site of origin for usual endometrial and endocervical adenocarcinomas. However, these panels do not perform well with special variant carcinomas.
Parsing Noisy Sentences

This paper describes a method to parse and understand a "noisy" sentence that possibly includes errors caused by a speech recognition device. Our parser is connected to a speech recognition device which takes a continuously spoken sentence in Japanese and produces a sequence of phonemes. The output sequence of phonemes can quite possibly include errors: altered phonemes, extra phonemes and missing phonemes. The task is to parse the noisy phoneme sequence and understand the meaning of the original input sentence, given an augmented context-free grammar whose terminal symbols are phonemes. A very efficient parsing method is required, as the task's search space is much larger than that of parsing un-noisy sentences. We adopt the generalized LR parsing algorithm, and a certain scoring scheme to select the most likely sentence out of multiple sentence candidates. The use of a confusion matrix, which is created in advance by analyzing a large set of input/output pairs, is discussed to improve the scoring accuracy. The system has been integrated into CMU's knowledge-based machine translation system.
Assessment of total sialic acid and lipid-bound sialic acid in management of brain tumors

Background: Glycoconjugate molecules expressed at the plasma membrane of mammalian cells have been reported to be associated with tumor progression. The measurement of total sialic acid (TSA) and lipid-bound sialic acid (LBSA) in the cerebrospinal fluid (CSF) is suggested to be useful for the diagnosis of brain tumors. But there are very few reports available on the serum glycoconjugate levels in patients with brain tumors. Objective: The objective of this study is to check the feasibility of using serum glycoconjugates such as TSA and LBSA as tumor markers in brain tumor patients. Materials and Methods: Colorimetric estimation of TSA using diphenylamine was done on 100 patients with intracranial tumors; follow-up study was carried out in 24 cases. The LBSA fraction was isolated from the serum of 68 brain tumor patients and evaluated using phosphotungstic acid and resorcinol; follow-up study was done on 23 patients. The various types of brain tumors included in this study were glioma, meningioma, and acoustic neurinoma as well as some other types such as medulloblastoma, secondary tumors, and craniopharyngioma. Results: There was no significant difference between the TSA and LBSA concentrations seen in pretreatment or post-treatment cases and that seen in control subjects. Discussion: TSA and LBSA do not have the ability to discriminate between benign and malignant brain tumors. TSA and LBSA appear to be tumor markers of very limited value in patients with brain tumors.
Enhancement in leaf photosynthesis and upregulation of Rubisco in the C4 sorghum plant at elevated growth carbon dioxide and temperature occur at early stages of leaf ontogeny.

Rising atmospheric carbon dioxide (CO2) concentration and temperature will influence photosynthesis, growth and yield of agronomic crops. To investigate effects of elevated CO2 and high temperature on leaf gas exchanges, activities of Rubisco and phosphoenolpyruvate carboxylase (PEPC) and growth of grain sorghum (Sorghum bicolor L. Moench), plants were grown in controlled environments at day-time maximum/night-time minimum temperatures of 30/20°C or 36/26°C at ambient (350 µmol mol-1) or elevated (700 µmol mol-1) CO2. Gas-exchange rates, activities of Rubisco and PEPC and growth parameters (leaf, stem and total dry weights) were determined at different stages of leaf development. Between 6 and 25 days after leaf tip emergence, leaf carbon exchange rate (CER) of elevated CO2 plants was greater at 30/20°C and 36/26°C than that of ambient CO2 plants at the same temperatures. The positive response of CER to elevated CO2 was greater in young leaves than in old leaves. In young leaves, elevated CO2 enhanced Rubisco activity at 30/20°C and 36/26°C, whereas PEPC activity was not affected by elevated CO2 at 30/20°C but was marginally enhanced at 36/26°C. At 30/20°C, growth parameters were not affected by elevated CO2 until 50 days after sowing (DAS); at 36/26°C, they were progressively enhanced by elevated CO2 to as high as 49 to 62% by 50 DAS. Leaf CER and Rubisco activity were enhanced by elevated CO2 at early stages of leaf ontogeny for the C4 grain sorghum. Such enhancement should have a significant role in dry matter production under elevated CO2.
Defining the pathways of symbiotic Epichloë colonization in grass embryos with confocal microscopy

ABSTRACT Asexual cool-season grass endophytes of the genus Epichloë (Ascomycota: Clavicipitaceae) are strictly vertically disseminated. The hosts of these mutualistic fungi express no symptoms during the fungal lifecycle that takes place entirely within the plant, while their hosts receive beneficial outcomes. These fungi are distributed in two major locations within the mature seeds of their hosts; namely, within the embryo (including the scutellum, coleoptile, plumule, radicle, and coleorhiza tissues) and between the aleurone and pericarp layers, with the latter hyphae playing no role in transmission of the fungus to the next plant generation. Conflicting evidence remains in the literature on the timing of embryo colonization. In a detailed investigation, utilizing confocal microscopy to observe the distribution of Epichloë coenophiala strain AR601 in tall fescue (Lolium arundinaceum), we tracked endophyte hyphal colonization in the ovary (pre-fertilization) through to the fully mature seed stage. Confocal microscopy images revealed that at the early and mature developmental stages of the embryo sac, before host grass fertilization, there were large quantities of endophyte mycelium present, especially around the antipodal cells, indicating that this endophyte enters the embryo sac before the fertilization stage. After host fertilization, fungal hyphae could be seen in the true embryo and early nonstarchy endosperm. Understanding the mechanisms of transmission to the seed is important for commercial seed producers and end users.