Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression profile of 30,000 genes in rat hippocampus using SAGE

Using the serial analysis of gene expression (SAGE) method, we generated a gene expression profile of the rat hippocampus. A total of 76,790 SAGE tags was analyzed, allowing identification of 28,748 different tag species, each representing a unique mRNA transcript. The tags were divided into different abundancy classes, ranging from tags that were detected over 500 times to tags encountered only once in the 76,790 tags analyzed. The mRNA species detected more than 50 times represented 0.3% of the total number of unique tags while accounting for 22% of the total hippocampal mRNA mass. The majority of tags were encountered 5 times or less. The genes expressed at the highest levels were of mitochondrial origin, consistent with a high requirement for energy in neuronal tissue. At a lower level of expression, several neuron‐specific transcripts were encountered, encoding various neurotransmitter receptors, transporters, and enzymes involved in neurotransmitter synthesis and turnover, ion channels and pumps, and synaptic components. Comparison of relative expression levels demonstrated that glutamate receptors are the most frequent neurotransmitter receptors expressed in the hippocampus, consistent with the important role of glutamatergic neurotransmission in the hippocampus, while GABA receptors were present at approximately 10‐fold lower levels. Several kinases were present including CaMKII, which was expressed at high levels, consistent with its being the most abundant protein in the spines of hippocampal pyramidal cells. This is the first extensive inventory of gene expression in the hippocampus and serves as a reference for future studies aimed at elucidating hippocampal transcriptional responses under various conditions. Hippocampus 2001;11:430–444. © 2001 Wiley‐Liss, Inc.
Characterization of Atherosclerosis by Histochemical and Immunohistochemical Methods in African Grey Parrots (Psittacus erithacus) and Amazon Parrots (Amazona spp.)

Abstract The aim of the study was to characterize atherosclerotic changes in African grey parrots (Psittacus erithacus) and Amazon parrots (Amazona spp.) by histochemical and immunohistochemical methods. Samples of the aorta ascendens and trunci brachiocephalici from 62 African grey parrots and 35 Amazon parrots were stained by hematoxylin and eosin and Elastica van Gieson for grading of atherosclerosis in these birds. Four different stages were differentiated. The incidence of atherosclerosis in the examined parrots was 91.9% in African grey parrots and 91.4% in Amazon parrots. To evaluate the pathogenesis in birds, immunohistochemical methods were performed to demonstrate lymphocytes, macrophages, smooth muscle cells, and chondroitin sulfate. According to the missing lymphocytes and macrophages and the absence of invasion and proliferation of smooth muscle cells in each atherosclerotic stage, “response-to-injury hypothesis” seems inapplicable in parrots. Additionally, we found alterations of vitally important organs (heart, lungs) significantly correlated with atherosclerosis of the aorta ascendens.
Brain Nitric Oxides Synthase in Major Pelvic Ganglia of Aged (LETO) and Diabetic (OLETF) Rats

This study was conducted to evaluate the effects of aging and diabetes mellitus (DM) on brain nitric oxide synthase (bNOS) expression in major pelvic ganglia (MPG) of rats. Otsuka Long Evans Tokushima Fatty rats (12, 30, and 70 weeks old), which are genetic models with non-insulin-dependent DM (NIDDM), and age-matched nondiabetic Long Evans Tokushima Otsuka controls were used. The MPG of all rats in this study were subjected to cryo-sectioning and staining with bNOS polyclonal AB and rhodamine-conjugated rabbit IgG. Fluorescence intensities of the stained neurons were assessed in randomly selected fields per each specimen. Animals of both groups revealed significant decline in the staining intensity of their neurons with aging and the progress of DM, but diabetic rats showed more decline than controls. In conclusion, both aging and NIDDM could decrease bNOS expression in rat MPG. However, NIDDM has a more evident effect than aging on that expression. The decrease in bNOS may cause a disturbance in functions of the target pelvic structures of these ganglia under both conditions.
Influence of pre-mirna compositional properties on RISC complex recruitment and target selection

The mirna targets detection is a key goal of computational biology. This class of non-coding RNA have acquired appreciable importance in understanding molecular mechanism of diseases. In this paper we have investigated the relations between compositional fetures of microrna precursors and the target recognition of corresponding mature micrornas. In particular we want to determine the role of methylation on precursors. An increasing set of experimental evidences corroborate the hypothesis that microRNA methylation can be associated with pathological condition. Altered microRNA methylation seems to be associated with different cancers. In order to predict the set of microrna prone to methylation we have analysed the human precursors available in the MicroRNA registry release 16.0. Our analysis principally has been centered on compositional asymmetries correlated with the CG content. Unequal distribution of dinucleotide has been investigate at genomic level (CpG island) of region potentially coding mirna. The role of inhomogeneous distribution of CG in pre-mirna is not yet deeply analysed. It possible that the different frequency of these nucleotides can play a role both in mirna maturation process and/or DNA methylation. Our analysis has identified two extremal group of human pre-mirna: one that have high content of CG dinucleotides and the second lack of CG. The role compositional characteristics of mirnas. In particular premirna lacking CG dinucleotides seems to be involved in regulation of critical processes such gene transcription. Among these precursor we investigated the potential targets of hsa-let7a-1. on oxidative stress.
First-principles calculation of bulk photovoltaic effect in CH$_3$NH$_3$PbI$_3$ and CH$_3$NH$_3$PbI$_{3-x}$Cl$_{x}$

Hybrid halide perovskites exhibit nearly 20% power conversion efficiency, but the origin of their high efficiency is still unknown. Here, we compute the shift current, a dominant mechanism of bulk photovoltaic (PV) effect for ferroelectric photovoltaics, in CH$_3$NH$_3$PbI$_3$ and CH$_3$NH$_3$PbI$_{3-x}$Cl$_{x}$ from first principles. We find that these materials give approximately three times larger shift current PV response to near-IR and visible light than the prototypical ferroelectric photovoltaic BiFeO$_3$. The molecular orientations of CH$_3$NH$_3^{+}$ can strongly affect the corresponding PbI$_3$ inorganic frame so as to alter the magnitude of the shift current response. Specifically, configurations with dipole moments aligned in parallel distort the inorganic PbI$_3$ frame more significantly than configurations with near net zero dipole, yielding a larger shift current response. Furthermore, we explore the effect of Cl substitution on shift current, and find that Cl substitution at the equatorial site induces a larger response than does substitution at the apical site.
An Optimal Control of Bone Marrow in Cancer Chemotherapy by Artificial Neural Networks

Although neural network models for cancer chemotherapy have been analyzed since the early seventies, less research has been done in actually formulating them as optimal control problems. In this paper an artificial neural networks-based method for optimal control of bone marrow in cell-cycle-specific chemotherapy is proposed. In this method, we use artificial neural networks for approximating the optimal control problem which maximizes both bone marrow mass and drug`s dose at the same time. The corresponding model be transfer to Hamiltonian function and using Pontryagin principle we create the boundary conditions. After defining boundary conditions, we use the approximating property of artificial networks and put the boundary conditions in error functions to satisfy the limitations.
Human-robot collaboration in a Mobile Visual Sensor Network

This paper proposes and implements a framework for human-robot collaboration in a Mobile Visual Sensor Network (MVSN). A collaborative architecture for the proposed human-integrated MVSN was developed to allow the human operator and robots to collaborate to perform surveillance tasks. We successfully implemented the MVSN so the user can control the deployment of the mobile sensors through his head movement. We also explored using computer vision techniques and navigation techniques on the robot nodes to conduct active human target detection. The robot nodes, therefore, are able to detect human faces while exploring the unknown environment, and then relay the face images to the operator for target recognition. In this way, humans and robots can complement each other to accomplish surveillance tasks. Our experimental results validated the proposed framework.
A stem cell medium containing neural stimulating factor induces a pancreatic cancer stem-like cell-enriched population

Cancer stem cells (CSCs) have been studied for their self-renewal capacity and pluripotency, as well as their resistance to anticancer therapy and their ability to metastasize to distant organs. CSCs are difficult to study because their population is quite low in tumor specimens. To overcome this problem, we established a culture method to induce a pancreatic cancer stem-like cell (P-CSLC)-enriched population from human pancreatic cancer cell lines. Human pancreatic cancer cell lines established at our department were cultured in CSC-inducing media containing epidermal growth factor (EGF), basic fibroblast growth factor (bFGF), leukemia inhibitory factor (LIF), neural cell survivor factor-1 (NSF-1), and N-acetylcysteine. Sphere cells were obtained and then transferred to a laminin-coated dish and cultured for approximately two months. The surface markers, gene expression, aldehyde dehydrogenase (ALDH) activity, cell cycle, and tumorigenicity of these induced cells were examined for their stem cell-like characteristics. The population of these induced cells expanded within a few months. The ratio of CD24high, CD44high, epithelial specific antigen (ESA) high, and CD44variant (CD44v) high cells in the induced cells was greatly enriched. The induced cells stayed in the G0/G1 phase and demonstrated mesenchymal and stemness properties. The induced cells had high tumorigenic potential. Thus, we established a culture method to induce a P-CSLCenriched population from human pancreatic cancer cell lines. The CSLC population was enriched approximately 100-fold with this method. Our culture method may contribute to the precise analysis of CSCs and thus support the establishment of CSC-targeting therapy.
Technology-assisted writing opportunities for a man emerged from a minimally conscious state and affected by extensive motor disabilities

Objective: To assess a computer-aided technology for assisting writing in a man who emerged from a minimally conscious state and presented with extensive motor disabilities. Method: The technology served to present letters, in groups, at the centre of a computer screen and display (write) the letters selected by the man (i.e. through a simplified pointing response) on the upper half of that screen. Results: The results showed that the technology enabled the man to produce clear (readily readable) writing. This writing compared positively with the results obtained using a communication board containing the letters (i.e. a system already available to the man). Conclusion: Computer-aided technology may provide basic writing (communication) opportunities to persons emerged from a minimally conscious state and affected by extensive motor disabilities and lack of speech.
Convolutive Source Separation and Signal Modeling with ML

In independent component analysis (ICA) an instantaneous mix of sources can be recovered using maximum Likelihood (ML). In Convolutive blind source separation (BSS) the mixture arises as a combination of di erently convolved source signals due to time delays and a reverberating acoustic environment. Instead of modeling a particular time instant now a time window of the mixed signals has to be modeled. This allows to combine ICA with traditional ML signal modeling techniques. Here we use an auto-regressive (AR) model of the sources leading to a generalization of contextual ICA [18] to the convolutive case. This may improve source separation avoiding the typical whitening of the sources, and may allow us to incorporation simultaneous enhancing of the signal based on the AR models.
Microsatellite markers for Nuphar japonica (Nymphaeaceae), an aquatic plant in the agricultural ecosystem of Japan1

Premise of the study: Nuphar species (Nymphaeaceae) are representative aquatic plants in irrigation ponds in Japanese agricultural ecosystems. We developed 15 polymorphic microsatellite markers for N. japonica and confirmed their utility for its close relatives N. oguraensis var. akiensis and N. ×saijoensis, which originated from natural hybridization between N. japonica and N. oguraensis. Methods and Results: Genetic variation was characterized in 15 polymorphic loci in three populations of N. japonica. The average number of alleles per locus was 3.47 (range = 2–9; n = 32), and the average expected heterozygosity per locus was 0.84 (range = 0.5–1.0); 11 loci were amplified in N. oguraensis var. akiensis and 15 in N. ×saijoensis. Conclusions: The polymorphic microsatellite markers developed in this study will be useful for investigating the levels of genetic diversity within remnant populations of Nuphar taxa and could provide a valuable tool for conservation genetics of these taxa.
Measurement modelling and mapping of arsenic bioaccessibility in Northampton, United Kingdom

The human ingestion bioaccessibility of As was measured on 50 representative samples of soils selected from a 281-soil-sample geochemical survey of Northampton. The major and trace element content, pH and near infrared (NIR) spectra of the 281 soils were determined. A multiple linear regression (MLR) model using total As, major element composition and pH identified total As, pH and P to be the significant predictor variables for bioaccessible As (R2 = 0.72, median standard error of prediction = 1.5 mg kg−1 bioaccessible As). When spectral components (SC) derived from chemometric analysis of the NIR spectra were also included in the MLR, total As, pH, Mg and two NIR spectral components were found to be significant predictor variables (R2 = 0.84, median standard error of prediction = 1.2 mg kg−1 bioaccessible As). Correlation analysis of the SC with major element data suggested that the two NIR SC in the second model were related to different forms of Fe oxides in the soil. When plotted over a geological map of Northampton interpolated predictions of bioaccessible As showed clear geological control. The median total As concentration of the soils in Northampton was 30.2 mg kg−1 and the median bioaccessible As was 3.0 mg kg−1.
Resistance pattern of Helicobacter pylori strains to clarithromycin, metronidazole, and amoxicillin in Isfahan, Iran

Background: Helicobacter pylori (H. pylori) resistance to antibiotics has become a global problem and is an important factor in determining the outcome of treatment of infected patients. The purpose of this study was to determine the H. pylori resistance to clarithromycin, metronidazole, and amoxicillin in gastrointestinal disorders patients. Materials and Methods: In this study, a total of 260 gastric antrum biopsy specimens were collected from patients with gastrointestinal disorders who referred to Endoscopy Section of the Isfahan Hospitals. The E-test and Modified Disk Diffusion Method (MDDM) were used to verify the prevalence of antibiotic resistance in 78 H. pylori isolates to the clarithromycin, metronidazole, and amoxicillin. Results: H. pylori resistance to clarithromycin, metronidazole, and amoxicillin were 15.3, 55.1, and 6.4%, respectively. In this study, we had one multidrug resistance (MDR) isolates from patient with gastritis and peptic ulcer disease. Conclusion: Information on antibiotic susceptibility profile plays an important role in empiric antibiotic treatment and management of refractive cases. According to the results obtained in this study, H. pylori resistance to clarithromycin and metronidazole was relatively high. MDR strains are emerging and will have an effect on the combination therapy.
Midlife and late-life body mass index and late-life dementia: results from a prospective population-based cohort.

BACKGROUND Obesity has been consistently associated with dementia. The role of certain risk factors of dementia may change during life, and the importance of having a life-course perspective has been acknowledged. OBJECTIVE The aim of this study was to investigate the association of midlife and late-life body mass index (BMI) with late-life dementia/Alzheimer's disease (AD) and whether the association was independent of other obesity-related co-morbidities. METHODS The association between midlife BMI (mean age 50.2, SD 6.0) and late-life BMI (mean age 71.2, SD 4.0) and incident dementia later in life (mean age 75.7, SD 5.0) were investigated among 1,304 participants of the longitudinal population-based Cardiovascular risk factors, Aging and Dementia (CAIDE) study, conducted in Eastern Finland. The duration of follow-up was 26 years. The diagnosis of dementia was based on DSM-IV criteria and the probable and possible AD on the NINCDS-ADRDA criteria. RESULTS Higher midlife BMI was associated with higher risk of incident dementia (adjusted HR, 95% CI 1.07, 1.00-1.14). However, decrease in BMI from midlife to late-life was associated with higher risk of dementia (1.14, 1.03-1.25 for one-unit decrease) and AD (1.20, 1.09-1.33). High late-life BMI was associated with lower risk of AD (0.89, 0.81-0.98) but the association with dementia was less evident (0.94, 0.86-1.03). CONCLUSION Higher midlife BMI is related to higher risk of dementia and AD, independently of obesity-related risk factors and co-morbidities. Steeper decrease of BMI and low late-life BMI are associated with higher risk of dementia and AD. These findings highlight the importance of life-course perspective when assessing the association between BMI and cognition.
Extracting the author of web pages

In this paper, we define the problem of identifying the author of a Web page as a sub-problem of identifying the information sender configuration of a Web page. We propose a method that extracts the author name candidates from a Web page based on linguistic features, and rank the candidates based on local features such as distance from the main content. The evaluation shows that we can achieve more than 75% precision when evaluated with candidates ranked within top five.
Induced Pluripotent Stem Cells in Huntington’s Disease Research: Progress and Opportunity

Induced pluripotent stem cells (iPSCs) derived from controls and patients can act as a starting point for in vitro differentiation into human brain cells for discovery of novel targets and treatments for human disease without the same ethical limitations posed by embryonic stem cells. Numerous groups have successfully produced and characterized Huntington’s disease (HD) iPSCs with different CAG repeat lengths, including cells from patients with one or two HD alleles. HD iPSCs and the neural cell types derived from them recapitulate some disease phenotypes found in both human patients and animal models. Although these discoveries are encouraging, the use of iPSCs for cutting edge and reproducible research has been limited due to some of the inherent problems with cell lines and the technological differences in the way laboratories use them. The goal of this review is to summarize the current state of the HD iPSC field, and to highlight some of the issues that need to be addressed to maximize their potential as research tools.
On modeling the packet error statistics in bursty channels

Wireless channels usually face bursty errors, i.e., errors are prone to occur in clusters. These bit errors can be modeled using the Gilbert-Elliott model. When data packets are transferred over channels with bursty errors, packet error statistics are more important than bit error statistics to analyze the communication performance. This has been modeled as a discrete time Markov chain (DTMC) in previous work. However, whether this Markov chain is time-homogeneous has never been addressed. In this paper, we prove that the packet errors can be modeled only as a Markov chain without constant transition probabilities. Thus finding a constant transition matrix and then discussing performance is not accurate. Instead, a gap model is adopted and the packet error/error-free length distributions are thus analyzed.
ΔNp63 Controls a TLR3-Mediated Mechanism That Abundantly Provides Thymic Stromal Lymphopoietin in Atopic Dermatitis

In the skin lesions of atopic dermatitis (AD), keratinocytes release large quantities of thymic stromal lymphopoietin (TSLP), causing unfavorable inflammation along with skin damage. Nevertheless, how TSLP influences keratinocytes themselves is still unknown. In this study, we showed that ΔNp63, a p53-homologue, predominantly expressed in keratinocytes regulated the receptor complex of TSLP, which determines susceptibility to self-derived TSLP. Expression of TSLP receptors in skin tissues and keratinocytes was assessed by immunohistochemistry and quantitative RT-PCR, and in vitro studies were also performed to examine the functional relevance of ΔNp63 in the expression of TSLP receptors and the constituting autocrine and/or paracrine pathway of TSLP under the condition of stimuli to innate receptors sensing cell damage. The results showed that normal keratinocytes in the upper epidermis preferentially expressed TSLP receptors and conversely lacked ΔNp63, which has an inhibitory effect on the expression of TSLP receptors. Interestingly, the epidermis of AD lesions was found to abundantly contain keratinocytes with low or undetectable levels of ΔNp63 (ΔNp63lo/-). Moreover, in the absence of ΔNp63, keratinocytes readily presented TSLP and other cytokines by stimuli through Toll-like receptor 3 (TLR3). Together with the evidence that extrinsic TSLP itself augments TSLP production by keratinocytes without ΔNp63, the results indicate that ΔNp63lo/- keratinocytes generate TSLP through a putative autocrine and/or paracrine pathway upon TLR3 stimulation within AD lesions, since moieties of damaged cells and pathogens stimulate TLR3.
Adaptive Color Image Segmentation Using Fuzzy Min-Max Clustering

-This paper proposes a novel system for color image segmentation called “Adaptive color image segmentation using fuzzy min-max clustering (ACISFMC)”. The present work is an application of Simpson’s fuzzy min-max neural network (FMMN) clustering algorithm. ACISFMC uses a multilayer perceptron (MLP) like network which perform color image segmentation using multilevel thresholding. Threshold values used for finding clusters and their labels are found automatically using FMMN clustering technique. FMMN clustering technique uses a hyperbox fuzzy set concept. In the proposed work, Fuzzy entropy is used as a tool to decide number of clusters. ACISFMC uses saturation and intensity planes of HSV (hue, saturation, intensity) color space for segmentation. Here, neural network is used to find the number of objects automatically from an image. One of the good feature of this method is that, it does not require a priori knowledge to segment a color image. The algorithm is found to be robust and relatively computationally inexpensive for large variety of color images. One application of the proposed method is demonstrated here. Experimental evaluation demonstrates the performance of ACISFMC is robust for noisy images also.