• Journal of the Korea Institute of Information and Communication Engineering
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• v.23 no.11
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• pp.1357-1363
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• 2019

In this paper, we compares the performance of the gredient descent optimizers of the Faster Region-based Convolutional Neural Network (R-CNN) model for the chromosome object detection in digital images composed of human metaphase chromosomes. In faster R-CNN, the gradient descent optimizer is used to minimize the objective function of the region proposal network (RPN) module and the classification score and bounding box regression blocks. The gradient descent optimizer. Through performance comparisons among these four gradient descent optimizers in our experiments, we found that the Adamax optimizer could achieve the mean average precision (mAP) of about 52% when considering faster R-CNN with a base network, VGG16. In case of faster R-CNN with a base network, ResNet50, the Adadelta optimizer could achieve the mAP of about 58%.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.61-86
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• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.9
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• pp.3907-3909
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• 2014

Background: Cytogenetic abnormalities have important implications in diagnosis and prognosis of acute leukemia and are now considered an important part of the diagnostic workup at presentation. Karyotype, if known at the time of diagnosis, guides physicians to plan appropriate management strategies for their patients. Aim and Objectives: To determine the cytogenetic profile of acute lymphoblastic leukemia (ALL) in Pakistani children in order to have insights regarding behavior of the disease. Materials and Methods: A retrospective analysis of all the cases of ALL (<15years old) diagnosed at Aga Khan University from January 2006 to June 2011 was performed. Cytogenetic analysis was made for all cases using the trypsin-Giemsa banding technique. Karyotypes were interpreted using the International System for Human Cytogenetic Nomenclature (ISCN) criteria. Results: A total of 153 patients were diagnosed as ALL during the study period, of which 127 samples successfully yielded metaphase chromosomes. The male to female ratio was 1.8:1. A normal karyotype was present in 51.2% (n=65) of the cases whereas 48.8% (n=62) had an abnormal karyotype. Most of the abnormal cases showed hyperdiploidy(13.4%) followed by t(9;22)(q34;q11.2) (7.08%). Conclusions: This study revealed a relative lack of good prognostic cytogenetic aberrations in Pakistani children with ALL.

• Asian-Australasian Journal of Animal Sciences
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• v.9 no.4
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• pp.449-454
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• 1996

Cytogenetic effects of malathion and parathion, the organophosphorus pesticides were studied on goat lymphocytes in culture. The mitotic indices (% of blast cells + cells at metaphase) of goat lymphocytes showed corresponding decrease with the increase in dose of pesticides. Malathion had significant effect only at $150{\mu}g/ml$ or higher dosages while, parathion caused antimitotic effects even at the lowest dose ($5{\mu}g/ml$) tested. The clastogenic effects of malathion were significant ($p{\leq}0.05$) at $100{\mu}g/ml$. In higher doses, the effects were highly significant ($p{\leq}0.01$). The frequency of metaphase plates with chromosomal abnormalities were highest (22.0%) at $200{\mu}g/ml$. The incidences of chromosomal abnormalities were significant ($p{\leq}0.05$) in parathion treated series even at $5{\mu}g/ml$ dose level. At $10{\mu}g/ml$ or higher dose levels the difference between treatment groups and controls were more pronounced ($p{\leq}0.01$). Various types of chromosomal abnormalities were encountered in goat lymphocytes treated by malathion and parathion. However, the incidence of gaps, breaks, acentric fragments, dicentric chromosomes were higher than other types of structural and numerical abnormalities.

• Korean Journal of Animal Reproduction
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• v.20 no.4
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• pp.395-412
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• 1997

Mammalian eggs are ovulated arrested at meiotic metaphase II until fertilization. Generally in mammals, fertilization results in a series of intracellular calcium oscillations that are mediated by inositol triphosphate (IP$^3$) or cyclic adenosine diphosphoribose (cADPr). The high levels of maturation promotion factor (MPF) within the cell decrease, pronuclei form, the cytoskeleton is reorganized and proteins are post-translationally modified. If all is normal, the newly formed embryo initiates the developmental program specific to that species. Artificial methods of producing these effects in pig oocytes are discussed. One potential mechanism mediated via a signal transduction pathway is present in pig oocytes. Stimulation of this pathway leads to the early events following fertilization, and electrical stimulation leads to apparently normal de v velopment to day 12. Further studies are needed to determine which mechanism(s) the sperm uses to initiate development.

• Journal of Life Science
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• v.11 no.4
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• pp.354-361
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• 2001

Chromosomal characteristics of New Zealane White rabbit was studied at meiosis and mitosis. The meiotic chromosomal preparations were mad with the modified air-drying method and karyotype analysis was performed with the G-banding technique, using isolated mitotic metapase chromosomes of the New Zealand White rabbit. Chromosomes, sex vesicles and centromeres could be classified in the zygotene and the pachytene of the meiosis I. The hair-like processes projecting laterally from the axes of bivalent chromosomes at the mid-to-late pachytene were observed and made the appearance of the lampbrush chromosome structure. Chromosomes could be classified onthe basis of the numbers and locations of chiasma in the diakinesis. Twenty-one autosomal bivalents and a single unequal terminally associated X-Y bivalent were observe during the late prophase and the metaphase of the meiosis I. Most of the bivalent types observed in the New Zealand White rabbit spermatrocytes were 1CH, 1TAl, and 2TA bivalents. The mean chiasma frequency(CF) of the male New Zealand White rabbit was 30.2 and it was found that the CF value tended to decrease through diakinesis and the metaphase I. The karyotype of the New Zealand White rabbit was a male chromosome number of 44(2n=44) comprising 8 pairs of metacentric, 9 pairs of submetacentric, 4 pairs o acrocentric autosomes, metacentric X chromosome and acrocentric Y chromosome.

• Korean Journal of Medicinal Crop Science
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• v.14 no.6
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• pp.354-359
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• 2006

Chromosome analysis using mitosis, meiosis and bicolor FISH were carried out in Bupleurum latissimum Nakai, which is one of the endemic plants in Ulleung island of korea. The somatic methaphase chromosomes number of this plant was 2n = 2x = 16 and the chromosome complements consisted of six pairs of metacentrics and two pairs of submetacentrics. The size of chromosomes ranged 2.40${\sim}$4.20 ${\mu}$m and NOR (nucleolus organizer region) chromosome did not observed using conventional staining. In meiosis chromosomes, metaphase-I and anaphase-I were observed. Metaphase-I anaphase-I showed 8 bivalents and chromosomes migration to make two daughter cells. Using bicolor FISH, one pair of 5S and 45S rDNA signals were detected on the centromeric region of chromosome 3 and the end of short of chromosome 2,respectively. We also observed the NOR using 45S rDNA probe.

• Korean Journal of Medicinal Crop Science
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• v.12 no.6
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• pp.515-518
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• 2004

Anemarrhena asphodeloides, a medicinal plant, has chromosome number of 2n=2x=22. To characterize the somatic metaphase chromosomes, physical mapping of 45S and 5S rDNAs using McFISH (multi-color fluorescence in situ hybridization) was applied. Two pairs of 45S rDNA loci were detected on the terminal regions of the short arm of chromosomes 1 and 3. A pair of 5S rDNA signal was observed on the short arm of chromosome 3. 5S rDNA site seemed to be the same locus as one of the 45S rDNA site. McFISH was very useful tool for the localization and identification of rDNAs on the metaphase chromosomes in A. asphodeloides.

• Reproductive and Developmental Biology
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• v.32 no.2
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• pp.111-115
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• 2008

The aim of this study was to examine more effective cryoprotectant for the cryopreservation of mouse preantral follicles. Enzymetically isolated preantral follicles from 12-day-old mice were cryopreserved by a slow freezing protocol with 1.5 M propanediol (PROH), dimethyl sulphoxide (DMSO) or glycerol (GLY) and then grown and matured in vitro for 11 days after thawing. The survival of preantral follicles immediately after freezing and thawing was not different among the PROH (68.2%), DMSO (72.4%) and GLY (72.1%). After grown and matured in vitro, the rates of survival and metaphase II oocytes were 54.9% and 36.6% for PROH which was significantly higher rates (p<0.05) compared with the rates obtained from DMSO (16.9% and 9.0%) and GLY (16.3% and 7.5%). The diameter of metaphase II oocytes from pre antral follicles frozen in PROH ($67.4{\pm}1.8\;{\mu}m$) was significantly (p<0.05) smaller than that of the fresh preantral follicles ($69.1{\pm}2.3\;{\mu}m$). The results from the present study revealed that PROH is more suitable cryoprotectant for the cryopreservation of mouse preantral follicles.

• Journal of Veterinary Clinics
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• v.7 no.2
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• pp.517-519
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• 1990

In vitro maturation and fertilization of oocytes collected from slaughtered bovine ovaries were investigated. Immature bovine extrafollicular oocytes were cultured for 24 hrs. in TCM 199 supplemented with fetal calf serum in a humidified CO$_2$ incubator. Fertilization in vitro was performed using frozen-awed bull semen which was treated by Ca Ionophore A23187. Fourty percentage of oocytes cultured had matured to the metaphase II ; There were-no effects of the concentration of fetal calf serum and of the addition of HEPES on the maturation rate. The mean proportions of in vitro fertilized eggs and of cleaved eggs were 23.1％ and 14.4％, respectively.