Reinterpretation of the protein identification process for proteomics data
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- Interdisciplinary Bio Central
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- 제1권3호
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- pp.9.1-9.6
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- 2009
Introduction: In the mass spectrometry-based proteomics, biological samples are analyzed to identify proteins by mass spectrometer and database search. Database search is the process to select the best matches to the experimental mass spectra among the amino acid sequence database and we identify the protein as the matched sequence. The match score is defined to find the matches from the database and declare the highest scored hit as the most probable protein. According to the score definition, search result varies. In this study, the difference among search results of different search engines or different databases was investigated, in order to suggest a better way to identify more proteins with higher reliability. Materials and Methods: The protein extract of human mesenchymal stem cell was separated by several bands by one-dimensional electrophorysis. One-dimensional gel was excised one by one, digested by trypsin and analyzed by a mass spectrometer, FT LTQ. The tandem mass (MS/MS) spectra of peptide ions were applied to the database search of X!Tandem, Mascot and Sequest search engines with IPI human database and SwissProt database. The search result was filtered by several threshold probability values of the Trans-Proteomic Pipeline (TPP) of the Institute for Systems Biology. The analysis of the output which was generated from TPP was performed. Results and Discussion: For each MS/MS spectrum, the peptide sequences which were identified from different conditions such as search engines, threshold probability, and sequence database were compared. The main difference of peptide identification at high threshold probability was caused by not the difference of sequence database but the difference of the score. As the threshold probability decreases, the missed peptides appeared. Conversely, in the extremely high threshold level, we missed many true assignments. Conclusion and Prospects: The different identification result of the search engines was mainly caused by the different scoring algorithms. Usually in proteomics high-scored peptides are selected and low-scored peptides are discarded. Many of them are true negatives. By integrating the search results from different parameter and different search engines, the protein identification process can be improved.
광섬유 브래그 격자(fiber Bragg grating: FBG)를 이용한 스트레인 센서는 출력 값으로 브래그 반사 파장의 변화를 제공하게 된다. 본 논문에서는 브래그 격자 스트레인 센서에서 출력되는 빛을 도파로 어레이 격자(arrayed waveguide grating: AWG)에 입력시켜서 파장의 변화를 측정하는 방법을 제안한다. FBG에 스트레인이 가해지게 되면 브래그 반사 파장이 이동하게 되어 AWG를 지나서 출력되는 채널별 광 파워가 변하게 되며, 이 값들의 조합으로 구해지는 centroid 값을 계산하면 브래그 반사 파장과 인가된 스트레인 값을 얻을 수 있다. 브래그 격자의 반사 스펙트럼의 대역폭이 centroid 값에 미치는 영향을 고려하여 3-dB 대역폭이 5.4 nm인 chirped FBG를 사용하였으며, 저항 측정방식의 기존 스트레인 센서와 비교하여 오차범위가 2% 이내인 결과를 확인 하였다. FBG 센서를 외팔보에 부착하여 진동에 따른 스트레인 값을 실시간으로 측정한 결과 진동 주파수 17.8 Hz, damping 시상수 0.96 초를 얻을 수 있었다.
본 논문에서는 빠른 정착시간을 갖는 전류셀(Current Cell) 매트릭스의 구조와 출력의 Gain error를 보정할 수 있는 Self calibration current bias 회로의 기능을 가진 고성능 10-bit D/A 변환기를 제안한다. 매트릭스 구조 회로의 복잡성으로 인한 지연시간의 증가 및 전력 소모를 최소화하기 위해 상위 6MSB(Most Significant Bit)전류원 매트릭스와 하위 4LSB(Least Significant Bit)전류원 매트릭스로 구성된 2단 매트릭스 구조로 설계되어 있다. 이러한 6+4 분할 구조를 사용함으로써 전류 원이 차지하는 면적과 Thermometer decoder 부분의 논리회로를 가장 최적화 시켜 회로의 복잡성과 Chip 사이즈를 줄일 수 있었고 낮은 Glitch 특성을 갖는 저 전력 D/A 변환기를 구현하였다. 또한 self Calibration이 가능한 Current Bias를 설계함으로서 이전 D/A 변환기들의 칩 외부에 구현하던 Termination 저항을 칩 내부에 구현하고 출력의 선형성 및 정확성을 배가시켰다. 본 연구에서는 3.3V의 공급전압을 가지는 0.35㎛ 2-poly 4-metal N-well CMOS 공정을 사용하였고, 모의 실험결과에서 선형성이 매우 우수한 출력을 확인하였다. 또한 소비전력은 45m W로 다른 10bit D/A 변환기에 비해 매우 낮음을 확인 할 수 있었다. 실제 제작된 칩은 Spectrum analyzer에 의한 측정결과에서 100㎒ 샘플링 클럭 주파수와 10㎒ 입력 신호 주파수에서 SFDR은 약 65㏈로 측정되었고, INL과 DNL은 각각 0.5 LSB 이하로 나타났다. 유효 칩 면적은 Power Guard ring을 포함하여 1350㎛ × 750 ㎛ 의 면적을 갖는다.
Fuzzy logic based Control Theory has gained much interest in the industrial world, thanks to its ability to formalize and solve in a very natural way many problems that are very difficult to quantify at an analytical level. This paper shows a solution for treating membership function inside hardware circuits. The proposed hardware structure optimizes the memoried size by using particular form of the vectorial representation. The process of memorizing fuzzy sets, i.e. their membership function, has always been one of the more problematic issues for the hardware implementation, due to the quite large memory space that is needed. To simplify such an implementation, it is commonly [1,2,8,9,10,11] used to limit the membership functions either to those having triangular or trapezoidal shape, or pre-definite shape. These kinds of functions are able to cover a large spectrum of applications with a limited usage of memory, since they can be memorized by specifying very few parameters ( ight, base, critical points, etc.). This however results in a loss of computational power due to computation on the medium points. A solution to this problem is obtained by discretizing the universe of discourse U, i.e. by fixing a finite number of points and memorizing the value of the membership functions on such points [3,10,14,15]. Such a solution provides a satisfying computational speed, a very high precision of definitions and gives the users the opportunity to choose membership functions of any shape. However, a significant memory waste can as well be registered. It is indeed possible that for each of the given fuzzy sets many elements of the universe of discourse have a membership value equal to zero. It has also been noticed that almost in all cases common points among fuzzy sets, i.e. points with non null membership values are very few. More specifically, in many applications, for each element u of U, there exists at most three fuzzy sets for which the membership value is ot null [3,5,6,7,12,13]. Our proposal is based on such hypotheses. Moreover, we use a technique that even though it does not restrict the shapes of membership functions, it reduces strongly the computational time for the membership values and optimizes the function memorization. In figure 1 it is represented a term set whose characteristics are common for fuzzy controllers and to which we will refer in the following. The above term set has a universe of discourse with 128 elements (so to have a good resolution), 8 fuzzy sets that describe the term set, 32 levels of discretization for the membership values. Clearly, the number of bits necessary for the given specifications are 5 for 32 truth levels, 3 for 8 membership functions and 7 for 128 levels of resolution. The memory depth is given by the dimension of the universe of the discourse (128 in our case) and it will be represented by the memory rows. The length of a world of memory is defined by: Length = nem (dm(m)+dm(fm) Where: fm is the maximum number of non null values in every element of the universe of the discourse, dm(m) is the dimension of the values of the membership function m, dm(fm) is the dimension of the word to represent the index of the highest membership function. In our case then Length=24. The memory dimension is therefore 128*24 bits. If we had chosen to memorize all values of the membership functions we would have needed to memorize on each memory row the membership value of each element. Fuzzy sets word dimension is 8*5 bits. Therefore, the dimension of the memory would have been 128*40 bits. Coherently with our hypothesis, in fig. 1 each element of universe of the discourse has a non null membership value on at most three fuzzy sets. Focusing on the elements 32,64,96 of the universe of discourse, they will be memorized as follows: The computation of the rule weights is done by comparing those bits that represent the index of the membership function, with the word of the program memor . The output bus of the Program Memory (μCOD), is given as input a comparator (Combinatory Net). If the index is equal to the bus value then one of the non null weight derives from the rule and it is produced as output, otherwise the output is zero (fig. 2). It is clear, that the memory dimension of the antecedent is in this way reduced since only non null values are memorized. Moreover, the time performance of the system is equivalent to the performance of a system using vectorial memorization of all weights. The dimensioning of the word is influenced by some parameters of the input variable. The most important parameter is the maximum number membership functions (nfm) having a non null value in each element of the universe of discourse. From our study in the field of fuzzy system, we see that typically nfm 3 and there are at most 16 membership function. At any rate, such a value can be increased up to the physical dimensional limit of the antecedent memory. A less important role n the optimization process of the word dimension is played by the number of membership functions defined for each linguistic term. The table below shows the request word dimension as a function of such parameters and compares our proposed method with the method of vectorial memorization[10]. Summing up, the characteristics of our method are: Users are not restricted to membership functions with specific shapes. The number of the fuzzy sets and the resolution of the vertical axis have a very small influence in increasing memory space. Weight computations are done by combinatorial network and therefore the time performance of the system is equivalent to the one of the vectorial method. The number of non null membership values on any element of the universe of discourse is limited. Such a constraint is usually non very restrictive since many controllers obtain a good precision with only three non null weights. The method here briefly described has been adopted by our group in the design of an optimized version of the coprocessor described in [10].
There are several ways to demonstrate white organic light emitting diodes (OLEDs) for displays and solid state lighting applications. Among these approaches are the stacked three primary or two complementary colors light-emitting layers, multiple-doped emissive layer, and excimer and exciplex emission [1-10]. We report on white phosphorescent excimer devices by using two light emitting materials based on platinum complexes. These devices showed a peak EQE of 15.7%, with an EQE of 14.5% (17 lm/W) at
쐐기필터를 통과한 방사선은 잦아진 일차선의 스펙트럼과 일치하지 않는다. 4~10 MV 엑스선의 15~60
본 논문에서는 DisplayPort용 전자기기 또는 클록 발생을 요구하는 다양한 회로에서 발생 할 수 있는 전자방해(EMI) 현상을 줄일 수 있는 위상 동기 루프와 확산 대역 클록 발생기를 구현 하였다. 이 시스템은 기본적으로 송신용 위상 동기 루프와 확산 대역 클록 발생기 구현을 위한 전하펌프2 와 기준주파수 분주기 등으로 구성된다. 본 논문에서는 2.7Gbps/1.62Gbps DisplayPort 응용 회로에 적합 하도록 10개의 다중 위상 신호를 출력 할 수 있는 270MHz/162MHz 듀얼 모드 위상 동기 루프를 설계 하였고 추가적으로 1.35GHz/810MHz의 위상 동기 루프를 설계하여 지터를 크게 감소시킬 수 있는 구조를 제안하였다. 270MHz/162MHz 위상 동기 루프와 5:1 시리얼라이저 2개, 그리고 1.35GHz 위상 동기 루프와 2:1 시리얼라이저를 연동함으로써 지터 성분을 크게 줄일 수 있다. 위상 동기 루프에서 사용 된 주파수 전환 다중위상 전압제어 발진기와 더불어 DisplayPort 규격에 맞는 주파수 전환이 가능 하도록 분주기를 공유하고 50% duty ratio를 보장할 수 있는 주파수 분주기 구조를 제안 하였다. 또한, 지터를 줄이기 위해서 출력전류 오차를 크게 줄일 수 있는 전하펌프 구조를 제안 하였다. 0.13 um CMOS 공정을 사용하여 설계 하였으며, 270MHz/162MHz PLL의 칩 면적은
본 논문에서는 Bare-die Chip 형태의 Drive amplifier를 Ajinomoto Build-up Film (ABF)와 FR-4로 구성된 PCB에 내장함으로써 28 GHz 대역 모듈에서 적용될 수 있는 내장형 능동소자 모듈을 구현하였다. 내장형 모듈에 사용된 유전체 ABF는 유전율 3.2, 유전손실 0.016의 특성을 가지고 있으며, Cavity가 형성되어 Drive amplifier가 내장되는 FR4는 유전율 3.5, 유전손실 0.02의 특성을 가진다. 제안된 내장형 Drive amplifier는 총 2가지 구조로 공정하였으며 측정을 통해 각각의 S-Parameter특성을 확인하였다. 공정을 진행한 2가지 구조는 Bare-die Chip의 패드가 위를 향하는 Face-up 내장 구조와 Bare-die Chip의 패드가 아래를 향하는 Face-down내장 구조이다. 구현한 내장형 모듈은 Taconic 사의 TLY-5A(유전율 2.17, 유전손실 0.0002)를 이용한 테스트 보드에 실장 하여 측정을 진행하였다. Face-down 구조로 내장한 모듈은 Face-up 구조에 비해 Bare-die chip의 RF signal패드에서부터 형성된 패턴까지의 배선 길이가 짧아 이득 성능이 좋을 것이라 예상하였지만, Bare-die chip에 위치한 Ground가 Through via를 통해 접지되는 만큼 Drive amplifier에 Ground가 확보되지 않아 발진이 발생한다는 것을 확인하였다. 반면 Bare-die chip의 G round가 부착되는 PCB의 패턴에 직접적으로 접지되는 Face-up 구조는 25 GHz에서부터 30 GHz까지 약 10 dB 이상의 안정적인 이득 특성을 냈으며 목표주파수 대역인 28 GHz에서의 이득은 12.32 dB이다. Face-up 구조로 내장한 모듈의 출력 특성은 신호 발생기와 신호분석기를 사용하여 측정하였다. 신호 발생기의 입력전력(Pin)을 -10 dBm에서 20 dBm까지 인가하여 측정하였을 때, 구현한 내장형 모듈의 이득압축점(P1dB)는 20.38 dB으로 특성을 확인할 수 있었다. 측정을 통해 본 논문에서 사용한 Drive amplifier와 같은 Bare-die chip을 PCB에 내장할 때 Ground 접지 방식에 따라 발진이 개선된다는 것을 검증하였으며, 이를 통해 Chip Face-up 구조로 Drive amplifier를 내장한 모듈은 밀리미터파 대역의 통신 모듈에 충분히 적용될 수 있을 것이라고 판단된다.
The wall shear stress in the vicinity of end-to end anastomoses under steady flow conditions was measured using a flush-mounted hot-film anemometer(FMHFA) probe. The experimental measurements were in good agreement with numerical results except in flow with low Reynolds numbers. The wall shear stress increased proximal to the anastomosis in flow from the Penrose tubing (simulating an artery) to the PTFE: graft. In flow from the PTFE graft to the Penrose tubing, low wall shear stress was observed distal to the anastomosis. Abnormal distributions of wall shear stress in the vicinity of the anastomosis, resulting from the compliance mismatch between the graft and the host artery, might be an important factor of ANFH formation and the graft failure. The present study suggests a correlation between regions of the low wall shear stress and the development of anastomotic neointimal fibrous hyperplasia(ANPH) in end-to-end anastomoses. 30523 T00401030523 ^x Air pressure decay(APD) rate and ultrafiltration rate(UFR) tests were performed on new and saline rinsed dialyzers as well as those roused in patients several times. C-DAK 4000 (Cordis Dow) and CF IS-11 (Baxter Travenol) reused dialyzers obtained from the dialysis clinic were used in the present study. The new dialyzers exhibited a relatively flat APD, whereas saline rinsed and reused dialyzers showed considerable amount of decay. C-DAH dialyzers had a larger APD(11.70
The wall shear stress in the vicinity of end-to end anastomoses under steady flow conditions was measured using a flush-mounted hot-film anemometer(FMHFA) probe. The experimental measurements were in good agreement with numerical results except in flow with low Reynolds numbers. The wall shear stress increased proximal to the anastomosis in flow from the Penrose tubing (simulating an artery) to the PTFE: graft. In flow from the PTFE graft to the Penrose tubing, low wall shear stress was observed distal to the anastomosis. Abnormal distributions of wall shear stress in the vicinity of the anastomosis, resulting from the compliance mismatch between the graft and the host artery, might be an important factor of ANFH formation and the graft failure. The present study suggests a correlation between regions of the low wall shear stress and the development of anastomotic neointimal fibrous hyperplasia(ANPH) in end-to-end anastomoses. 30523 T00401030523 ^x Air pressure decay(APD) rate and ultrafiltration rate(UFR) tests were performed on new and saline rinsed dialyzers as well as those roused in patients several times. C-DAK 4000 (Cordis Dow) and CF IS-11 (Baxter Travenol) reused dialyzers obtained from the dialysis clinic were used in the present study. The new dialyzers exhibited a relatively flat APD, whereas saline rinsed and reused dialyzers showed considerable amount of decay. C-DAH dialyzers had a larger APD(11.70