Compression Techniques for DNA Sequences: A Thematic Review

Rosario Gilmary,Akila Venkatesan,Govindasamy Vaiyapuri 한국정보과학회 2021 Journal of Computing Science and Engineering Vol.15 No.2

Deoxyribonucleic acid (DNA) is the basic entity that carries genetic instructions. This information is used in the evolution, progression, and improvement of all species. It is estimated that 10 CD-ROMs are required to store the genomic data of an individual being. With the increase in DNA sequencing equipment, an extensive heap of genomic data is created. The increase in DNA data in public databases is surpassing the rate of growth in storage space, thereby raising a significant concern related to data storage, transmission, retrieval, and search. To reduce the data storage and storage expense, lossless compression procedures were applied. Conventional compression methods are not proficient while compressing the biological data. Hence, several unique and contemporary lossless compression mechanisms were used to achieve improved compression ratio in biological sequences. Here, we scrutinize the diverse existing compression procedures that are appropriate for the compression of DNA sequences. The efficiency of algorithms is compared in terms of compression ratio, the ratio of the capacity of the compressed folder, and compression/decompression time. Main challenges and future research directions in DNA compression are also presented. Emphasis has been given to special references related to contemporary techniques.

On-the-fly Data Compression for Efficient TCP Transmission

( Min Wang ),( Junfeng Wang ),( Xuan Mou ),( Sunyoung Han ) 한국인터넷정보학회 2013 KSII Transactions on Internet and Information Syst Vol.7 No.3

Data compression at the transport layer could both reduce transmitted bytes over network links and increase the transmitted application data (TCP PDU) in one RTT at the same network conditions. Therefore, it is able to improve transmission efficiency on Internet, especially on the networks with limited bandwidth or long delay links. In this paper, we propose an on-the-fly TCP data compression scheme, i.e., the TCPComp, to enhance TCP performance. This scheme is primarily composed of the compression decision mechanism and the compression ratio estimation algorithm. When the application data arrives at the transport layer, the compression decision mechanism is applied to determine which data block could be compressed. The compression ratio estimation algorithm is employed to predict compression ratios of upcoming application data for determining the proper size of the next data block so as to maximize compression efficiency. Furthermore, the assessment criteria for TCP data compression scheme are systematically developed. Experimental results show that the scheme can effectively reduce transmitted TCP segments and bytes, leading to greater transmission efficiency compared with the standard TCP and other TCP compression schemes.

흉부 전산화단층촬영 영상을 이용한 소아의 적정한 흉부압박 깊이 측정

진수영,오성범,김용오 대한응급의학회 2016 대한응급의학회지 Vol.27 No.3

Purpose: The purpose of this study was to assess optimal chest compression depth for infants and children compared with adults, when the simulated compression depth was delivered according to the current guidelines. Methods: A total of 467 consecutive chest computed tomography scans (93 of infants, 110 of children, and 264 of adults) were reviewed. The anteroposterior (AP) diameter and compressible diameter (CD) for infants and children were measured at the inter-nipple level and at the middle of the lower half of the sternum for adults. Compression ratio (CR) to CD was calculated at simulated one-fourth, onethird, and one-half AP compressions in infants and children and simulated 5-cm, 6-cm compressions in adult. Results: In adults, the CRs to CD at simulated 5-cm, 6-cm compression depth were 41.7±0.16%, 50.0±7.3%, respectively. In children and infants, the CRs to CD at onethird chest compression were, respectively, 55.1±2.4%, 51.8±2.4% and 82.7±3.7%, 77.7±3.6% at one-half chest compression. The CRs to CD of 4-cm compression depth in infants and 5-cm compression depth in children were 74.4±10.9%, 62.5±8.7%, respectively. The CRs to CD for children and infants were significantly higher compared with adults (p<0.001). The CR to CD of 4-cm compression depth in children was similar to that of 6-cm compression depth in adults (50.0±6.9% vs 50.0±7.3%, p=0.985). Conclusion: The current pediatric guideline for compression depth was too deep compared with adults. We suggest that one third of the AP chest diameter or approximately 4- cm in children and less than 4-cm in infants is more appropriate.

Lossless Image Compression Using Differential Pulse Code Modulation and Its Application

Rime Raj Singh Tomar,Kapil Jain 보안공학연구지원센터 2016 International Journal of Signal Processing, Image Vol.9 No.1

Images include information about human body which is used for different purpose such as medical examination security and other plans Compression of images is used in some applications such as profiling information and transmission systems. Regard to importance of images information, lossless or loss compression is preferred. Lossless compressions are JPEG, JPEG-LS and JPEG2000 are few well-known methods for lossless compression. We will use differential pulse code modulation for image compression with Huffman encoder, which is one of the latest and provides good compression ratio, peak signal to noise ratio and minimum mean square error. In real time application which needs hardware implementation, low complex algorithm accelerate compression process. In this paper, we use differential pulse code modulation for image compression lossless and near-lossless compression method is introduced which is efficient due to its high compression ratio and simplicity. This method is consists of a new transformation method called Enhanced DPCM Transformation (EDT) which has a good energy compaction and a suitable Huffman encoding. After introducing this compression method it is applied on different images from Corel dataset for experimental results and analysis. Also we compare it with other existing methods with respect to parameter compression ratio, peak signal noise ratio and mean square error.

펼쳐진 상태의 구급차용 침대차에서 시행하는 한 손 가슴 압박의 효과 및 압박에 영향을 미치는 구조자의 특성 분석

서용송,강지훈,김양원,윤유상,박철호,지재구,이시원 대한응급의학회 2022 대한응급의학회지 Vol.33 No.1

Objective: When rescuers move from ambulance to resuscitation area, they press the chest with one-hand by the stretchers. The purpose of this study was to investigate the effect of one-hand chest compression on unfolded stretchers and analyze the characteristics of rescuers that affect compression. Methods: A manikin simulation study was planned. A total of 28 participants performed one-hand chest compression for one minute to a manikin on the unfolded stretchers. The depth of compression, the extent of recoil and compression frequency were measured, and the results were analyzed. Correlation analysis was done between participant characteristics and depth and frequency of compression. Linear regression analysis was done for variables with significant correlation. Results: Four participants were excluded due to wrist or shoulder pain. A total of 24 participants (13 male; 11 female) were enrolled. The mean depth of compression was 34.88±11.06 cm; the mean extent of recoil was 50.00±0 cm. The mean frequency of compression was 104.71±11.07 per minute. The extent of recoil and frequency of compression were satisfied with cardiopulmonary resuscitation (CPR) guidelines. The depth of compression was highly correlated with participants’ sex (r=-0.88), height (r=0.86), and weight (r=0.78). When adjusted for sex, the depth of compression increased as height and weight increased. Conclusion: Mechanical chest compression device should be used when CPR is required while moving a cardiac arrest patient by the stretchers. If CPR needs to be done manually, moving distance should be minimized. Finally, a new type of stretcher that fits the body shape of Koreans should be developed.

Stent Compression in Iliac Vein Compression Syndrome Associated with Acute Ilio-Femoral Deep Vein Thrombosis

조훈,김진우,홍유선,임상현,원제환 대한영상의학회 2015 Korean Journal of Radiology Vol.16 No.4

This study was conducted to evaluate stent compression in iliac vein compression syndrome (IVCS) and to identify its association with stent patency. Between May 2005 and June 2014, after stent placement for the treatment of IVCS with acute ilio-femoral deep vein thrombosis, follow-up CT venography was performed in 48 patients (35 women, 13 men; age range 23–87 years; median age 56 years). Using follow-up CT venography, the degree of the stent compression was calculated and used to divide patients into two groups. Possible factors associated with stent compression and patency were evaluated. The cumulative degree of stent compression and patency rate were analyzed. All of the stents used were laser-cut nitinol stents. The proportion of limbs showing significant stent compression was 33%. Fifty-six percent of limbs in the significant stent compression group developed stent occlusion. On the other hand, only 9% of limbs in the insignificant stent compression group developed stent occlusion. Significant stent compression was inversely correlated with stent patency (p < 0.001). The median patency period evaluated with Kaplan-Meier analysis was 20.0 months for patients with significant stent compression. Other factors including gender, age, and type of stent were not correlated with stent patency. Significant stent compression occurred most frequently (87.5%) at the upper end of the stent (ilio-caval junction). Significant compression of nitinol stents placed in IVCS highly affects stent patency. Therefore, in order to prevent stent compression in IVCS, nitinol stents with higher radial resistive force may be required.

Lossless Image Compression using Differential Pulse Code Modulation and Its purpose

Rime Raj Singh Tomar,Kapil Jain 보안공학연구지원센터 2015 International Journal of Signal Processing, Image Vol.8 No.9

Images include information about human body which is used for different purposes such as medical, security and other plans. Compression of images is used in some applications such as profiling data and transmission systems. Regard to importance of images information, lossless or lossy compression is preferred. Lossless compressions are JPEG, JPEG-LS and JPEG 2000 is few well-known methods for lossless compression. We will use differential pulse code modulation for image compression with Huffman encoder, which is one of the latest and provides good compression ratio, peak signal noise ratio and minimum mean square error. In real time application which needs hardware implementation, low complex algorithm accelerates compression process. In this dissertation, we use differential pulse code modulation for image compression lossless and near-lossless compression method is introduced which is efficient due to its high compression ratio and simplicity. This method is consists of a new transformation method called Enhanced DPCM Transformation (EDT) which has a good energy compaction and a suitable Huffman encoding. After introduce this compression method, it is apply on different images from Corel dataset for experimental results and analysis. As well we compare it with other existing methods with respect to parameter compression ratio, peak signal noise ratio and mean square error.

심폐소생술에서 심장맛사지의 경과시간에 따른 정확도 변화

유인술,곽동진 대한응급의학회 1998 대한응급의학회지 Vol.9 No.1

Background: Provision of early adequate chest compression remains a standard of care for optimal outcome in cardiopulmonary arrest. Inadequate chest compression during CPR may result in the insufficient blood flow to preserve critical organ function. Therefore, authors performed this study to characterize fatigue0induced deterioration in the adequacy of closed-chest compression performed over period 5 minutes and to determine whether CPR providers recognize the effects of fatigue on compression adequacy. Method: Prospectively we carried out the study with an electronic CPR teaching mannequin(ResusciAnnie with Skillmeter,Laerdal)placed on a patient stretcher. The mannequin was equipped with a real-time remote display that records the numbers of total and correct compressions. Compression are judged as correct by the mannequin if both depth and placement are appropriate in keeping with standard advanced cardiac life support guidelines. Our study subjects were 27 nurses and doctors, each with certification of BLS and experience of CPR in ED. Each subject performed a 5minute session of chest compressions. Also subjects were asked to verbally indicate the point during their 5 minute compression period at which they felt too fatigued to provide effective compressions. For statistical analysis, one-way repeated-measures ANOVA and regression test was used. Result: The number of total compressions attempted per minute did not decrease significantly(P=.565). But we found 81.0% of compressions performed during the first 1 minute to be correct. The percentages for minutes 2 through 5 were decreased significantly as follows: 73.0%, 68.0%, 65.0%, 57.0%(P=.0003). Regression analysis revealed a decrement in compression adequacy of 13.0% per minutes after the first 1 minute of compression. The time of indicated fatigue was 220±29 seconds(mean±SD) Conclusion: Although compression rate was maintained over time, chest compression quality declined significantly over the study period. Because CPR providers could not recognize their ability to provide compression, cardiac arrest team leaders should carefully monitor compression adequacy and change the CPR providers each 3 minutes during CPR to assure maximally effective care for patients receiving CPR.

압축력을 병용한 하악골 신장술

황영섭,허준,김욱규,박성진,황대석,김용덕,정인교,김규천,Hwang, Young-Seob,Heo, June,Kim, Uk-Kyu,Park, Seong-Jin,Hwang, Dae-Seok,Kim, Yong-Deok,Chung, In-Kyo,Kim, Kyu-Cheon 대한악안면성형재건외과학회 2006 Maxillofacial Plastic Reconstructive Surgery Vol.28 No.6

The purpose of this study was to investigate the biomechanical, histologic findings of distracted regenerate and TMJ response in modified distraction osteogenesis (DO) technique combined with compression force as biomechanical stimulation method which has been suggested in 2002, and developed thereafter by authors. This study was performed with two experiments. First experiment was designed to explore the optimal ratio of compression force versus distraction force for the new DO technique. Second experiment was planned to evaluate the reaction of TMJ tissue, especially condyle, disc after application of the DO technique with compression force. Total 52 New Zealand adult male-rabbits with 3.0kg body weight were used for the study. For the first study, 30 adult male-rabbits underwent osteotomy at one side of mandibular body and a external distraction device was applied on each rabbit with same manner. In the control group of 10 rabbits, final 8 mm of distraction with 1 mm rate per day was done with conventional DO technique after 5 latency days. For the experimental group of 20 rabbits, a compression force with 1 mm rate per day was added to the distracted mandible on 3-latency day after over-distraction (over-lengthening). As the amount of the rate of compression versus distraction, experimental subgroup I (10 rabbits) was set up as 2 mm compression versus 10 mm distraction (1/5) and experimental subgroup II (10 rabbits) was set up as 3 mm compression versus 11 mm distraction (about 1/3). All 30 rabbits were set up to obtain final 8 mm distraction and sacrificed on postoperative 55 day to analysis on biomechanical, and histologic findings of the bone regenerates. For second study, 22 adult male-rabbits were used to evaluate TMJ response after the DO method application with compression force. In the control group, 10 rabbits was used to be performed with conventional DO method, on the other hand, in a experimental group of 10 rabbits, 10 mm distraction with 2 mm compression (1/5 ratio) was done. The remaining 2 rabbits served as the normal control group. Histomorphologic examinations on both condyle, histological studies on condyle, disc were done at 1, 2, 3, 4, 7 weeks after distraction force application. The results were as follows: 1. On the bone density findings, the experimental group II (force ratio - 1/3) showed higher bone density than the other experimental group (force ratio - 1/5) and control group (control group - $0,2906\;g/cm^2$, experimental group I - $0.2961\;g/cm^2$, experimental group II - $0.3328\;g/cm^2$). 2. In the histologic findings, more rapid bone maturation like as wide lamellar bone site, more trabeculae formation was observed in two experimental groups compared to the conventional DO control group. 3. In morphologic findings of condyle, there were no differences of size and architecture in the condyle in the control and experimental groups. 4. In histologic findings of condyles, there were thicker fiberous and proliferative layers in experimental group than those of control group until 2 weeks after distraction with compression force. But, no differences were seen between two groups on 3, 4, 7 weeks after compression. 5. In histologic findings of disc, more collagen contents in extracellular matrix, more regular fiber bundles, and less elastin fibers were seen in experimental group than control group until 2 weeks after distraction with compression. But, no differences were seen between two groups on 3, 4, 7 weeks after distraction with compression. From this study, we could identify that the new distraction osteogenesis technique with compression stimulation might improve the quality of bone regeneration. The no remarkable differences on TMJ response between control and experimental groups were seen and TMJ tissues were recovered similarly to normal TMJ condition after 3 weeks.

수축력과 신장력을 병용한 골신장술에서의 다양한 힘의 비와 부여시기에 따른 신연골 반응

김욱규,신상훈,정인교,김철훈,허준,윤일,Kim, Uk-Kyu,Shin, Sang-Hun,Chung, In-Kyo,Kim, Cheol-Hun,Huo, Jun,Yun, Il 대한악안면성형재건외과학회 2005 Maxillofacial Plastic Reconstructive Surgery Vol.27 No.5

The purpose of this study was to identify the effectiveness of the modified distraction osteogenesis (DO) method with the concept of overdistraction and compression stimulation which have been previously suggested by the authors in 2002 and to explore the optimal distraction-compression ratio and appropriate latency period for the compression force application during consolidation. The experimental specimens were assessed with radiography, histologic findings, and dual energy x-ray absorptiometry (DEXA) after the conventional DO method and the modified DO technique had been applied on rat mandibles. Total 60 rats were used for the study. In experimental group of 54 adult rats, mandibular osteotomies between the first and second molar areas were performed and customized external distractors were applied. The surgeries on 6 rats of control group also were done with same osteotomy technique and DO device application. Final amount of distraction was set-up as 2 mm on both groups. But, in a experimental group of 54 rats, distraction osteogenesis with a compression force were performed with the different distraction-compression ratio and variant latency periods for compression. The three ratio-subgroups were made as distraction 4 mm group with compression 2 mm, distraction 3 mm group with compression 1 mm, and distraction 2.5 mm group with compression 0.5 mm. In addition, The three subgroups with 3, 7, 11 days latency period prior compression were allocated on each ratio-subgroups. Total 9 subgroups consisted of 6 rats on each subgroup. In control group of 6 rats, conventional distraction technique were routinely performed. The rats of control groups were sacrificed on postoperative 3, 6 weeks after 2 mm distraction. The rats in the experimental groups also were sacrificed on the same euthanasia days of control groups to compare the wound healing. Final available specimens were 55 rats except 5 due to osteomyelitis, device dislodgement. Distraction-compression combined group on 6 weeks generally had showed increased bone mineral density than the same period group of conventional distraction technique on the DEXA study. More matured lamellar bone state and extended trabecular pattern in the combined group than those of control group were also observed in the histologic findings on 6 weeks. In the distraction-compression combined groups, the bone density of 2.5 mm distraction subgroups with 0.5 mm compression showed the highest value on the DEXA study among various force ratio groups. In the distraction-compression combined groups, the bone density of 3 day latency period subgroups showed the highest value on the DEXA study among various latency period groups for the compression application. From this study, we could deduce that 1/5 force ratio for the compression versus distraction, 3 day latency period prior compression application would be the most effective condition if modified distraction osteogenesis technique might be applicable. The modified DO method with a compression force may improve the quality of bone regenerate and shorten total treatment period in comparison with conventional DO technique clinically.