An incremental approach to automated protein localisation

Tscherepanow M, Jensen N, Kummert F. An incremental approach to automated protein localisation. BMC Bioinformatics. 2008;9(1): 445.Background: The subcellular localisation of proteins in intact living cells is an important means for gaining information about protein functions. Even dynamic processes can be captured, which can barely be predicted based on amino acid sequences. Besides increasing our knowledge about intracellular processes, this information facilitates the development of innovative therapies and new diagnostic methods. In order to perform such a localisation, the proteins under analysis are usually fused with a fluorescent protein. So, they can be observed by means of a fluorescence microscope and analysed. In recent years, several automated methods have been proposed for performing such analyses. Here, two different types of approaches can be distinguished: techniques which enable the recognition of a fixed set of protein locations and methods that identify new ones. To our knowledge, a combination of both approaches – i.e. a technique, which enables supervised learning using a known set of protein locations and is able to identify and incorporate new protein locations afterwards – has not been presented yet. Furthermore, associated problems, e.g. the recognition of cells to be analysed, have usually been neglected. Results: We introduce a novel approach to automated protein localisation in living cells. In contrast to well-known techniques, the protein localisation technique presented in this article aims at combining the two types of approaches described above: After an automatic identification of unknown protein locations, a potential user is enabled to incorporate them into the pre-trained system. An incremental neural network allows the classification of a fixed set of protein location as well as the detection, clustering and incorporation of additional patterns that occur during an experiment. Here, the proposed technique achieves promising results with respect to both tasks. In addition, the protein localisation procedure has been adapted to an existing cell recognition approach. Therefore, it is especially well-suited for high-throughput investigations where user interactions have to be avoided. Conclusion: We have shown that several aspects required for developing an automatic protein localisation technique – namely the recognition of cells, the classification of protein distribution patterns into a set of learnt protein locations, and the detection and learning of new locations – can be combined successfully. So, the proposed method constitutes a crucial step to render image-based protein localisation techniques amenable to large-scale experiments

Automated Adaptation Strategies for Stream Learning

Automation of machine learning model development is increasingly becoming an established research area. While automated model selection and automated data pre-processing have been studied in depth, there is, however, a gap concerning automated model adaptation strategies when multiple strategies are available. Manually developing an adaptation strategy can be time consuming and costly. In this paper we address this issue by proposing the use of flexible adaptive mechanism deployment for automated development of adaptation strategies. Experimental results after using the proposed strategies with five adaptive algorithms on 36 datasets confirm their viability. These strategies achieve better or comparable performance to the custom adaptation strategies and the repeated deployment of any single adaptive mechanism

Chip-Scale Lidar

The superiority of lidar compared to radio-frequency and ultrasonic solutions in terms of depth and lateral resolution has been known for decades. In recent years, both application pull such as 3D vision for robotics, rapid prototyping, self-driving cars, and medical diagnostics, as well as technology developments such as integrated optics and tunable lasers have resulted in new activities. Pulsed, amplitude-modulated continuous-wave (AMCW), and frequency-modulated continuous-wave (FMCW) lidars can all be used for ranging. The latter option enables excellent depth resolution at the micron level. Achieving this level of performance is contingent on a precision light source with accurate frequency modulation. This thesis presents a fully integrated solution realizing an electro-optical phase-locked loop (EO-PLL) fabricated on separate complementary metal-oxide-semiconductor (CMOS) and silicon-photonic wafers interconnected with through-silicon vias (TSVs). The system performs 180,000 range measurements per second, with a root-mean square (RMS) depth precision of 8 µm at distances of ±5cm from the range baseline increasing to 4.2 mm RMS error at a range of 1.4 m, limited by the coherence length of the laser used in these experiments. Optical elements including input light couplers, waveguides, and photodiodes are realized on a 3 mm by 3 mm silicon-photonic chip. The 0.18 µm CMOS application-specific integrated circuit (ASIC) of the same area comprises the front-end trans-impedance amplifier, analog electro-optical PLL, and digital control circuitry consuming 1.7 mA from a 1.8-V supply and 14.1 mA from a 5-V supply. The latter includes 12.5 mA bias current for the distributed Bragg reflector (DBR) section of the tunable laser. Also presented in the thesis is a novel dual mode lidar that combines FMCW and chirped-AMCW operation to simultaneously achieve precision depth resolution and a longer operating range not limited by Laser coherence length

Effect of prioperative tight glucose control on the outcomes of care in patients with type 2 diabetes undergoing coronary artery bypass grafting

AMAÇ: Koroner Arter Bypass Greftli (KABG) Tip 2 diabetes mellituslu hastalarda perioperatifsıkı glikoz kontrolünün bakım sonuçlarından kan glikoz düzeyi, hiperglisemi, hipoglisemi, yoğunbakım ünitesi, hastane de kalma süresi ve maliyete etkisini incelemektir.YÖNTEM: Araştırma yarı deneysel girişimsel olarak Temuz 2009-Şubat 2010 tarihleri arasındaİran'da Madani Kalp Hastanesinde yapılmıştır. Araştırmada DEÜ Hemşirelik Yüksekokulu(B.30.2.BEÜ.0.Y3.02.05/593- 22.04.2009) ve İran'da Tabriz Üniversitesi Tıp Bilimleri KalpDamar Araştırma Merkezi Etik Kurulu'ndan (01.07.2009 -3.1021) onay ve hastaneyönetiminden izin alınmıştır. Araştırmanın amacı ve girişim açıklanarak hasta ve birinci dereceyakınlarından izin alınmıştır. Örnekleme, erişkin, Tip 2 DM'li, ilk kez açık ve kapalı teknikleKABG ameliyatı planlanan 50 deney, 50 kontrol grubu toplam 100 hasta alınmıştır. Deneygrubuna Subkutan ve Kolumnar İntravenöz İnsülin İnfüzyon Protokolü kontrol grubuna ise rutinprotokoller uygulanmıştır. Veriler, Hastaların Sosyo-Demografik, Klinik Özelliklerini BelirlemeFormu ve perioperatif dönem boyunca Kan Glikoz Düzeyi ve İnsülin (SC/İV) Tedavisini İzlemeÇizelgesi ile toplanmıştır. Veriler, bağımsız guruplarda t-testi, tekrarlı ölçümlerde tek yönlüANOVA-Bonferroni, pearson ki-kare, fisher's Exace testi ve Man-Whitney-U testikullanılmıştır.BULGULAR: Deney ve kontrol grubu hastalarının sırasıyla kan glikoz ortalamaları, preoperatifdönem 1. gün (183.34±38.72; 230.75±91.47 mg/dL; p=0.005), intraoperatif dönemde(135.72±16.74; 218.60±51.25 mg/dL; p<0.001), postoperatif yoğun bakım 1. gün (119.79±9.30mg/dL; 209.75±28.74 mg/dL; P<0.001); postoperatif yoğun bakım 2. gün (122.94±9.50 mg/dL;183.72±24.18 mg/dL; P<0.001); postoperatif 3. gün klinik izlemde (136.30±14.84 mg/dL;200.03±41.70 mg/dL; p<0.001) anlamlı düzeyde farklıdır ve deney grubunda glisemik kontroldaha iyi sağlanmıştır. Deney grubunda kontrol grubuna göre hastane maliyeti (421.61±60.53;612.65±173.59 dolar; p<0.001) daha düşük, yoğun bakım ünitesinde (45:38:34±12:48:22;63:36:22±28:24:30 saat; p=0.004) ve hastanede (141:58±36:26:19; 221:55±109.16 saat;p<0.001) daha kısa süre kaldığı saptanmıştır. Deney grubunda perioperatif hiperglisemi görülmeortalaması (1.66±1.02; 10.34±5.70; p<0.001) düşük, hipoglisemi görülme ortalaması (0.10±0.30;0.24±0.68; p=0.42) ise her iki grupta benzerdir.SONUÇ VE UYGULAMADA KULLANIMI: KABG'li Tip 2 DM tanısı olan deney grubuhastalarında Subkutan ve İntravenöz Kolmunar İnsülin İnfüzyon Protokolü ile yönetilen sıkıglikoz kontrolü (90-140mgdL), perioperatif dönem boyunca daha kısa sürede glisemik kontrolsağlanmıştır. Deney grubunda maliyet, postoperatif yoğun bakım ve hastanede kalma süresi vekomplikasyonlardan hiperglisemi görülme ortalaması azaltılmıştır. Bu sonuca dayalı KABGameliyatı planlanan Tip 2 DM tanısı olan hastalarda perioperatif dönem boyunca sıkı kanglisemik kontrolün uygulamada kullanılması önerilmektedir.PURPOSE: We hypothesized that tight glycemic control in the perioperative period would reduce blood glucose levels, reduce the ICU length of stay and the hospital stay and hospital cost, decreases incidence of hyperglycemia and hypoglycemia. METHOD: We performed an interventional, quasi experimental study involving one hundred patients with diabetes mellitus undergoing primary on cardiopulmonary and off cardiopulmonary CABG. 50 patients were in the experimental group and 50 patients were in the control group. These patients were admitted to the Madani Heart Hospital during July 2009 and February 2010. Approval of the study was obtained by the Dokuz Eylül Universty School of Nursing Ethics Committe (B.30.2.BEÜ.0.Y3.02.05/593- 22.04.2009), Cardiovascular Research Center Tabriz Universty of Medical Sciences Iran, Ethics Committe (01.07.2009 -3.1021). Written permission was obtained from the hospital director as well. An informed consent was obtained from each patient and their family members enrolled in the study. The Subcutaneous Insulin protocol and Columnar Insulin Dosing Chart was used in the experimental group and the conventional protocol was used in the control group. Data was obtained from the patients demographic and historical variables form, perioperative period Columnar Insulin Dosing Chart flow sheet and Subcutaneous Insulin order sheet The two study groups were compared on continuous variables via independent-sample tests, Mann-Whitney U, pearson ï£2 and Fisher's exact tests, repeated measures ANOVAs with Bonferroni correction in the computer.RESULTS: The patients of experimental and control group in the firtst day of preoperative (183.3438.72; 230.7591.47 mg/dL; p=0.005) intraoperative (135.7216.74; 218.6051.25 mg/dL; p0.001), ICU 1 day ( 119.79  9.30; 209.75  28.74 mg/dL; P 0 .001) ); ICU 2 day ( 122.94  9.50; 183.72  24.18 mg/dL; P  0.001); and postoperative period 3 day (136.30  14.84; 200.03  41.70 mg/dL; p0.001) glucose control was significantly better with tight glycemic control. Tight grup had lower hospital cost (421.6160.53; 612.65173.59dollar; p0.001) and a shorter ICU length of stay (45:38:3412:48:22; 63:36:2228:24:30 hour; p=0.004) and hospital length of stay (141:5836:26:19; 221:55109.16 hour; p0.001). And also decreased the incidence of hyperglycemia on the perioperative period (1.661.02;10.345.70; p0.001), but the perioperative period was be similarly in the incidence of hypoglycemia (0.100.30; 0.24 0.68; p=0.42).CONCLUSION AND IMLICATION IN PRACTICE: Perioperative tight glycemic control with Subcutaneous Insulin Orders (80-150 mgdL ) and Columnar Insulin Dosing Chart (90-140 mgdL) in diabetic coronary artery bypass graft patients decreases serum glucose levels, reduce the ICU length of stay and the hospital stay and hospital cost, decreases incidence of hyperglycemia. Tight glycemic control should become the standard of care for glycometabolic control in patients with diabetes undergoing coronary artery bypass grafting

Chip-Scale Lidar

The superiority of lidar compared to radio-frequency and ultrasonic solutions in terms of depth and lateral resolution has been known for decades. In recent years, both application pull such as 3D vision for robotics, rapid prototyping, self-driving cars, and medical diagnostics, as well as technology developments such as integrated optics and tunable lasers have resulted in new activities.Pulsed, amplitude-modulated continuous-wave (AMCW), and frequency-modulated continuous-wave (FMCW) lidars can all be used for ranging. The latter option enables excellent depth resolution at the micron level. Achieving this level of performance is contingent on a precision light source with accurate frequency modulation. This thesis presents a fully integrated solution realizing an electro-optical phase-locked loop (EO-PLL) fabricated on separate complementary metal-oxide-semiconductor (CMOS) and silicon-photonic wafers interconnected with through-silicon vias (TSVs).The system performs 180,000 range measurements per second, with a root-mean square (RMS) depth precision of 8 μm at distances of ±5cm from the range baseline increasing to 4.2 mm RMS error at a range of 1.4 m, limited by the coherence length of the laser used in these experiments. Optical elements including input light couplers, waveguides, and photodiodes are realized on a 3 mm by 3 mm silicon-photonic chip. The 0.18 μm CMOS application-specific integrated circuit (ASIC) of the same area comprises the front-end trans-impedance amplifier, analog electro-optical PLL, and digital control circuitry consuming 1.7 mA from a 1.8-V supply and 14.1 mA from a 5-V supply. The latter includes 12.5 mA bias current for the distributed Bragg reflector (DBR) section of the tunable laser. Also presented in the thesis is a novel dual mode lidar that combines FMCW and chirped-AMCW operation to simultaneously achieve precision depth resolution and a longer operating range not limited by Laser coherence length

ART-based Fusion of Multi-Modal Information for Mobile Robots

Berghöfer E, Schulze D, Tscherepanow M, Wachsmuth S. ART-based Fusion of Multi-Modal Information for Mobile Robots. In: Iliadis L, Jayne C, eds. Proceedings of the International Conference on Engineering Applications of Neural Networks (EANN). IFIP Advances in Information and Communication Technology. Vol 363. Berlin: Springer; 2011: 1-10.Robots operating in complex environments shared with humans are confronted with numerous problems. One important problem is the identification of obstacles and interaction partners. In order to reach this goal, it can be beneficial to use data from multiple available sources, which need to be processed appropriately. Furthermore, such environments are not static. Therefore, the robot needs to learn novel objects. In this paper, we propose a method for learning and identifying obstacles based on multi-modal information. As this approach is based on Adaptive Resonance Theory networks, it is inherently capable of incremental online learning