Abstract: The primary tool currently used to pre-process 10X chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 15 to 18 times faster than Cell Ranger on mouse and human samples. Our tool can also calculate chromatin interaction potential matrices and generate open chromatin signal and interaction traces for cell groups. We use scATAK tool to explore the chromatin regulatory landscape of a healthy adult human brain and unveil cell-type specific features, and show that it provides a convenient and computational efficient approach for pre-processing single-cell ATAC-seq data.
Abstract: Healthy and viable herbal supplement were prepared from wheat by a green route. This organic biomaterial was named Nutrition Bio-shield Superfood (NBS). The NBS supplement had various vitamins, macro and micro molecules, and ingredients. In this study, 20 small Balb/C labile specimens were used in a weighing 30 ± 5 range. The samples were randomly divided into different groups, then the groups were divided into 5 groups. According to the results of this study, the mean number of white blood cells and neutrophil percentage in the experimental group receiving healthy and live dietary supplement showed a significant increase at the 5% probability level in all three groups received 50, 100 and 150 mg/ kg body weight of the mouse compared to the control group. In general, the dietary supplement increases the level of immunity.
Abstract: X-ray Fluorescence Molecular Imaging (XFMI) holds great promise as a low-cost molecular imaging modality for biomedical applications with high chemical sensitivity. However, for in vivo biomedical applications, a key technical bottleneck is the relatively low chemical sensitivity of XFMI, especially at a reasonably low radiation dose. In laboratory x-ray source based XFMI, one of the main factors that limits the chemical sensitivity of XFMI is the scattered x-rays. We will present our latest findings on improving the chemical sensitivity of XFMI using excitation beam spectrum optimization. XFMI imaging experiments on two mouse-sized phantoms were conducted at three different excitation beam spectra. Our results show that the minimum detectable concentration (MDC) of iodine can be readily increased by five times via excitation spectrum optimization. Findings from this investigation could find use for in vivo pre-clinical small-animal XFMI in the future.
Abstract: Despite the appropriate characteristics of 177Lu and DOTATOC, to our best knowledge, the therapeutic benefit of 177Lu-DOTATOC complex in breast cancer has not been reported until now. In this study, biodistribution of 177Lu-DOTA-TOC in mouse tumor model for evaluation of possible utilization of this complex in breast cancer treatment was investigated.177Lu was prepared with the specific activity of 2.6-3 GBq.mg-1 and radionuclidic purity higher than 99%. The radiolabeled complex was prepared in the optimized conditions with the radiochemical purity higher than 99%. The final solution was injected to the BALB/c mice with adenocarcinoma breast cancer. The biodistribution results showed major accumulation in the kidneys as the major excretion route and the somatostatin receptor-positive tissues such as pancreas compared with the other tissues. Also, significant uptake was observed in tumor even in longer time after injection. According to the results obtained in this research study, somatostatin receptors expressed in breast cancers can be targeted with DOTATOC analogues especially with 177Lu-DOTATOC as an ideal therapeutic agent.
Abstract: This case study responds to the current trends in ICT. Mobile Touch iPads can provide very good assistance to disabled seniors. The intuitive tablet environment, the possibility of the formation environment and its portability, has a very positive effect on the use of particular communication. For comparison, using a conventional PC/notebook, word processor, keyboard and computer mouse compared to the iPad and selected applications. The results of this case study show that the use of mobile touch devices iPad for seniors with mental retardation is a great benefit. These devices do not require high demands on graphomotorics like a standard PC devices.
Abstract: Programming requires years of training. With natural language and end user development methods, programming could become available to everyone. It enables end users to program their own devices and extend the functionality of the existing system without any knowledge of programming languages. In this paper, we describe an Interactive Spreadsheet Processing Module (ISPM), a natural language interface to spreadsheets that allows users to address ranges within the spreadsheet based on inferred table schema. Using the ISPM, end users are able to search for values in the schema of the table and to address the data in spreadsheets implicitly. Furthermore, it enables them to select and sort the spreadsheet data by using natural language. ISPM uses a machine learning technique to automatically infer areas within a spreadsheet, including different kinds of headers and data ranges. Since ranges can be identified from natural language queries, the end users can query the data using natural language. During the evaluation 12 undergraduate students were asked to perform operations (sum, sort, group and select) using the system and also Excel without ISPM interface, and the time taken for task completion was compared across the two systems. Only for the selection task did users take less time in Excel (since they directly selected the cells using the mouse) than in ISPM, by using natural language for end user software engineering, to overcome the present bottleneck of professional developers.
Abstract: A suitable model membrane to study the pharmacological effect of pharmaceutical products is human stratum corneum because this layer of human skin is the outermost layer and it is an important barrier to be passed through. Other model membranes which were also used are for example skins from pig, mouse, reptile or fish. We are interested in fish skins in this project. The advantages of the fish skins are, that they can be obtained from the supermarket or fish shop. However, the fish skins should be freshly prepared and used directly without storage. In order to understand the effect of different model drugs e.g. lidocaine HCl, resveratrol, paracetamol, ibuprofen, acetyl salicylic acid on the properties of the model membrane from various types of fishes e.g. trout, salmon, cod, plaice permeation tests were performed and differential scanning calorimetry was applied.
Abstract: The purpose of the study is to develop a finite element model based on 3D bone structural images of Micro-CT and to analyze the stress distribution for the osteoporosis mouse femora. In this study, results of finite element analysis show that the early osteoporosis of mouse model decreased a bone density in trabecular region; however, the bone density in cortical region increased.
Abstract: Quantitative analyses of whisker movements provide a
means to study functional recovery and regeneration of mouse facial
nerve after an injury. However, accurate tracking of the mouse whisker
movement is challenging. Most methods for whisker tracking require
manual intervention, e.g. fixing the head of the mouse during a study.
Here we describe a semi-automated image processing method, which
is applied to high-speed video recordings of free-moving mice to track
the whisker movements. We first track the head movement of a mouse
by delineating the lower head contour frame-by-frame that allows for
detection of the location and orientation of the head. Then, a region of
interest is identified for each frame; the subsequent application of a
mask and the Hough transform detects the selected whiskers on each
side of the head. Our approach is used to examine the functional
recovery of damaged facial nerves in mice over a course of 21 days.
Abstract: The Smart Help for persons with disability (PWD) is a
part of the project SMARTDISABLE which aims to develop relevant
solution for PWD that target to provide an adequate workplace
environment for them. It would support PWD needs smartly through
smart help to allow them access to relevant information and
communicate with other effectively and flexibly, and smart editor
that assist them in their daily work. It will assist PWD in knowledge
processing and creation as well as being able to be productive at the
work place. The technical work of the project involves design of a
technological scenario for the Ambient Intelligence (AmI) - based
assistive technologies at the workplace consisting of an integrated
universal smart solution that suits many different impairment
conditions and will be designed to empower the Physically disabled
persons (PDP) with the capability to access and effectively utilize the
ICTs in order to execute knowledge rich working tasks with
minimum efforts and with sufficient comfort level. The proposed
technology solution for PWD will support voice recognition along
with normal keyboard and mouse to control the smart help and smart
editor with dynamic auto display interface that satisfies the
requirements for different PWD group. In addition, a smart help will
provide intelligent intervention based on the behavior of PWD to
guide them and warn them about possible misbehavior. PWD can
communicate with others using Voice over IP controlled by voice
recognition. Moreover, Auto Emergency Help Response would be
supported to assist PWD in case of emergency. This proposed
technology solution intended to make PWD very effective at the
work environment and flexible using voice to conduct their tasks at
the work environment. The proposed solution aims to provide
favorable outcomes that assist PWD at the work place, with the
opportunity to participate in PWD assistive technology innovation
market which is still small and rapidly growing as well as upgrading
their quality of life to become similar to the normal people at the
workplace. Finally, the proposed smart help solution is applicable in
all workplace setting, including offices, manufacturing, hospital, etc.
Abstract: This paper proposes a method to recognize the tip of a finger and space touch hand gesture using an infrared camera in a smart device environment. The proposed method estimates the tip of a finger with a curvature-based ellipse fitting algorithm, and verifies that the estimated object is indeed a finger with an ellipse fitting rectangular area. The feature extracted from the verified finger tip is used to implement the movement of a mouse and clicking gesture. The proposed algorithm was implemented with an actual smart device to test the proposed method. Empirical parameters were obtained from the keypad software and an image analysis tool for the performance optimization, and a comparative analysis with conventional research showed improved performance with the proposed method.
Abstract: Heterogeneous repolarization causes dispersion of the T-wave and has been linked to arrhythmogenesis. Such heterogeneities appear due to differential expression of ionic currents in different regions of the heart, both in healthy and diseased animals and humans. Mice are important animals for the study of heart diseases because of the ability to create transgenic animals. We used our previously reported model of mouse ventricular myocytes to develop 2D mouse ventricular tissue model consisting of 14,000 cells (apical or septal ventricular myocytes) and to study the stability of action potential propagation and Ca2+ dynamics. The 2D tissue model was implemented as a FORTRAN program code for highperformance multiprocessor computers that runs on 36 processors. Our tissue model is able to simulate heterogeneities not only in action potential repolarization, but also heterogeneities in intracellular Ca2+ transients. The multicellular model reproduced experimentally observed velocities of action potential propagation and demonstrated the importance of incorporation of realistic Ca2+ dynamics for action potential propagation. The simulations show that relatively sharp gradients of repolarization are predicted to exist in 2D mouse tissue models, and they are primarily determined by the cellular properties of ventricular myocytes. Abrupt local gradients of channel expression can cause alternans at longer pacing basic cycle lengths than gradual changes, and development of alternans depends on the site of stimulation.
Abstract: Mammalian genomes contain large number of
retroelements (SINEs, LINEs and LTRs) which could affect
expression of protein coding genes through associated transcription
factor binding sites (TFBS). Activity of the retroelement-associated
TFBS in many genes is confirmed experimentally but their global
functional impact remains unclear. Human SINEs (Alu repeats) and
mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich
gene rich genome segments consistent with the view that they
can contribute to regulation of gene expression. We have shown
earlier that Alu are involved in formation of cis-regulatory modules
(clusters of TFBS) in human promoters, and other authors reported
that Alu located near promoter CpG islands have an increased
frequency of CpG dinucleotides suggesting that these Alu are
undermethylated. Human Alu and mouse B1/B2 elements have an
internal bipartite promoter for RNA polymerase III containing
conserved sequence motif called B-box which can bind basal
transcription complex TFIIIC. It has been recently shown that TFIIIC
binding to B-box leads to formation of a boundary which limits
spread of repressive chromatin modifications in S. pombe. SINEassociated
B-boxes may have similar function but conservation of
TFIIIC binding sites in SINEs located near mammalian promoters
has not been studied earlier. Here we analysed abundance and
distribution of retroelements (SINEs, LINEs and LTRs) in annotated
sequences of the Database of mammalian transcription start sites
(DBTSS). Fractions of SINEs in human and mouse promoters are
slightly lower than in all genome but >40% of human and mouse
promoters contain Alu or B1/B2 elements within -1000 to +200 bp
interval relative to transcription start site (TSS). Most of these SINEs
is associated with distal segments of promoters (-1000 to -200 bp
relative to TSS) indicating that their insertion at distances >200 bp
upstream of TSS is tolerated during evolution. Distribution of SINEs
in promoters correlates negatively with the distribution of CpG
sequences. Using analysis of abundance of 12-mer motifs from the
B1 and Alu consensus sequences in genome and DBTSS it has been
confirmed that some subsegments of Alu and B1 elements are poorly
conserved which depends in part on the presence of CpG
dinucleotides. One of these CpG-containing subsegments in B1
elements overlaps with SINE-associated B-box and it shows better
conservation in DBTSS compared to genomic sequences. It has been
also studied conservation in DBTSS and genome of the B-box
containing segments of old (AluJ, AluS) and young (AluY) Alu
repeats and found that CpG sequence of the B-box of old Alu is
better conserved in DBTSS than in genome. This indicates that Bbox-
associated CpGs in promoters are better protected from
methylation and mutation than B-box-associated CpGs in genomic
SINEs. These results are consistent with the view that potential
TFIIIC binding motifs in SINEs associated with human and mouse
promoters may be functionally important. These motifs may protect
promoters from repressive histone modifications which spread from
adjacent sequences. This can potentially explain well known
clustering of SINEs in GC-rich gene rich genome compartments and
existence of unmethylated CpG islands.
Abstract: Mouse L929 fibroblastic cell line, which is widely
used in many experiment aspects, was tested for their differentiation
potency in osteogenic differentiation and adipogenic differentiation.
Human dermal fibroblasts, which their differentiation potency are
still be in confliction, also be taken in the experiment. The
differentiations were conducted by using the inducing medium
ingredients which is generally used to induce differentiation of stem
cells. By the inducing media used, L929 mouse fibroblasts
successfully underwent osteogenic differentiation and adipogenic
differentiation while human dermal fibroblasts underwent only
osteogenic differentiation but not for adipogenic differentiation.
Human dermal fibroblasts are hard to be differentiated in adipogenic
lineage and need specific proper condition for induction.
Abstract: This paper describes a 3D modeling system in
Augmented Reality environment, named 3DARModeler. It can be
considered a simple version of 3D Studio Max with necessary
functions for a modeling system such as creating objects, applying
texture, adding animation, estimating real light sources and casting
shadows. The 3DARModeler introduces convenient, and effective
human-computer interaction to build 3D models by combining both
the traditional input method (mouse/keyboard) and the tangible input
method (markers). It has the ability to align a new virtual object with
the existing parts of a model. The 3DARModeler targets nontechnical
users. As such, they do not need much knowledge of
computer graphics and modeling techniques. All they have to do is
select basic objects, customize their attributes, and put them together
to build a 3D model in a simple and intuitive way as if they were
doing in the real world. Using the hierarchical modeling technique,
the users are able to group several basic objects to manage them as a
unified, complex object. The system can also connect with other 3D
systems by importing and exporting VRML/3Ds Max files. A
module of speech recognition is included in the system to provide
flexible user interfaces.
Abstract: Tumor cells have an invasive and metastatic phenotype
that is the main cause of death for cancer patients. Tumor
establishment and penetration consists of a series of complex
processes involving multiple changes in gene expression. In this study,
intraperitoneal administration of a high concentration of ascorbic acid
inhibited tumor establishment and decreased tumor mass in BALB/C
mice implanted with S-180 sarcoma cancer cells. To identify proteins
involved in the ascorbic acid-mediated inhibition of tumor
progression, changes in the tumor proteome associated with ascorbic
acid treatment of BALB/C mice implanted with S-180 were
investigated using two-dimensional gel electrophoresis and mass
spectrometry. Twenty protein spots were identified whose expression
was different between control and ascorbic acid treatment groups.
Abstract: Anti-allergic effects of royal jelly were evaluated in a human-like mouse model of atopic dermatitis. NC/Nga mice were cutaneously applied with royal jelly for 6 weeks. Royal jelly-treated mice exhibited lower levels of serum total immunoglobulin E in comparison with controls. We found that the treatment decreased (11% to the control) expression of mRNA for aquaporin-3, which is involved in the modulation of epidermal hydration. Microarray analysis revealed more than 10-fold changes in the expression of several genes, such as transglutaminase 2, repetin, and keratins. In normal human epidermal keratinocytes, royal jelly extract suppressed interleukin-8 elevation induced by TNF-α and interferon-γ, suggesting direct anti-inflammatory activity in keratinocytes. Collectively, topical application of royal jelly may be useful for amelioration of lesions and inflammation in atopic dermatitis.
Abstract: An influence of intranasal combined injection of live
cold-adapted influenza vaccine with chitosan derivatives as adjuvants
on the subpopulation structure of mononuclear leukocytes of mouse
spleen which reflects the orientation of the immune response was
studied. It is found that the inclusion of chitosan preparations
promotes activation of cellular-level of immune response.
Abstract: SVM ( Support Vector Machine ) is a new method in the artificial neural network ( ANN ). In the steel making, how to use computer to predict the end point of BOF accuracy is a great problem. A lot of method and theory have been claimed, but most of the results is not satisfied. Now the hot topic in the BOF end point predicting is to use optical way the predict the end point in the BOF. And we found that there exist some regular in the characteristic curve of the flame from the mouse of pudding. And we can use SVM to predict end point of the BOF, just single spectrum intensity should be required as the input parameter. Moreover, its compatibility for the input space is better than the BP network.
Abstract: With the development of ubiquitous computing,
current user interaction approaches with keyboard, mouse and pen
are not sufficient. Due to the limitation of these devices the useable
command set is also limited. Direct use of hands as an input device is
an attractive method for providing natural Human Computer
Interaction which has evolved from text-based interfaces through 2D
graphical-based interfaces, multimedia-supported interfaces, to fully
fledged multi-participant Virtual Environment (VE) systems.
Imagine the human-computer interaction of the future: A 3Dapplication
where you can move and rotate objects simply by moving
and rotating your hand - all without touching any input device. In this
paper a review of vision based hand gesture recognition is presented.
The existing approaches are categorized into 3D model based
approaches and appearance based approaches, highlighting their
advantages and shortcomings and identifying the open issues.