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Optical coherence tomography (OCT) is a cross-sectional imaging method utilizing a low coherence interferometry. The lateral resolution of the OCT is limited by the numerical aperture (NA) of the imaging lens. Using a high NA lens improves the lateral resolution but reduces the depth of focus (DOF). In this study, we propose a method to improve the lateral resolution of OCT images by end-to-end training of a deep 1-D deconvolution network without use of high-resolution images.To improve the lateral resolution of the OCT, we trained the 1-D deconvolution network using lateral profiles of OCT images and the beam spot size. We used our image-guided laparoscopic surgical tool (IGLaST) to acquire OCT images of nonbiological and biological samples ex vivo. The OCT images were then blurred by applying Gaussian functions with various full width half maximums ranging from 40 to 160 µm. The network was trained using the blurred OCT images as input and the non-blurred original OCT images as output. We quantitatively evaluated the developed network in terms of similarity and signal-to-ratio (SNR), using in-vivo images of mesenteric tissue from a porcine model that was not used for training. In addition, we performed knife-edge tests and qualitative evaluation of the network to show the lateral resolution improvement of ex-vivo and in-vivo OCT images.The proposed method showed an improvement of image quality on both blurred images and non-blurred images. When the proposed deconvolution network was applied, the similarity to the non-blurred image was improved by 1.29 times, and the SNR was improved by 1.76 dB compared to the artificially blurred images, which was superior to the conventional deconvolution method. The knife-edge tests at distances at 200 to 1000 µm from the imaging probe showed an approximately 1.2 times improvement in lateral resolution. In addition, through qualitative evaluation, it was found that the image quality of both ex-vivo and in-vivo tissue images was improved with clear structure and less noise.This study showed the ability of the 1-D deconvolution network to improve the image quality of OCT images with variable lateral resolution. We were able to train the network with a small amount of data by constraining the network in 1-D. The quantitative evaluation showed better results than conventional deconvolution methods for various amount of blurring. Qualitative evaluation showed analogous results with quantitative results. This simple yet powerful image restoration method provides improved lateral resolution and suppresses background noise, making it applicable to a variety of OCT imaging applications.

We demonstrated a blood flow v isualization m ethod f or t he image-guided laparoscopic surgical tool (IGLaST). Using the inter A-line OCT decorrelations from a moving probe, blood flows in a phantom were successfully isolated from the background.

We have developed a compact optical endoscopic probe for in vivo fluorescence optical imaging device. We obtained fluorescence image for the colon tissue of a mouse using a compacted optical endoscopic probe with a designed endoscopic optical lens. In order to demonstrate endoscopic fluorescence imaging for the colon cancer, we have manufactured a compacted optical endoscopic probe to pass through the biopsy channel of electric flexible endoscope. The compacted optical endoscopic probe with maximum outside diameter of 2.8mm consists of fiber-optic illumination part and imaging part. The imaging part consists of a fiber-optic imaging bundle linked to an endoscopic optical lens and focus assembly. We considered a compact structure, sensitivity, and FOV for the design of the endoscopic optical lens. We have suggested an endoscopic optical lens with an FOV of 90 ° and DOF of 3 – 80mm. The optical system consists of glass-based aspheric lenses. The total track is less than 2.5 mm, and the diameter is limited to less than 1.5 mm to obtain a compact system. We have presented the compacted optical endoscopic probe for cancer imaging of a mouse. The proposed endoscopic optical lens showed sufficient sensitivity and a wide field of view for obtaining fluorescence imaging. We demonstrated endoscopic ex vivo fluorescence imaging for the colon cancer of a mouse using the compacted optical endoscopic probe.

We have designed a fiber probe based optical diagnose system for detection of interspecies transmissibility. We have showed the optical performance to measure the optical signal of the target sample by using the manufactured fiber probe. We have confirmed the capability of our system to be utilized to biomedical diagnose applications.

Not only static characteristics but also dynamic characteristics of the red blood cell (RBC) contains useful information for the blood diagnosis. Quantitative phase imaging (QPI) can capture sample images with subnanometer scale depth resolution and millisecond scale temporal resolution. Various researches have been used QPI for the RBC diagnosis, and recently many researches has been developed to decrease the process time of RBC information extraction using QPI by the parallel computing algorithm, however previous studies are interested in the static parameters such as morphology of the cells or simple dynamic parameters such as root mean square (RMS) of the membrane fluctuations. Previously, we presented a practical blood test method using the time series correlation analysis of RBC membrane flickering with QPI. However, this method has shown that there is a limit to the clinical application because of the long computation time. In this study, we present an accelerated time series correlation analysis of RBC membrane flickering using the parallel computing algorithm. This method showed consistent fractal scaling exponent results of the surrounding medium and the normal RBC with our previous research.

Analog mean-delay (AMD) method is a new powerful alternative method in determining the lifetime of a fluorescence molecule for high-speed confocal fluorescence lifetime imaging microscopy (FLIM). Even though the photon economy and the lifetime precision of the AMD method are proven to be as good as the state-of-the-art time-correlated single photon counting (TC-SPC) method, there have been some speculations and concerns about the accuracy of this method. In the AMD method, the temporal waveform of an emitted fluorescence signal is directly recorded with a slow digitizer whose bandwidth is much lower than the temporal resolution of lifetime to be measured. We found that the drifts and the fluctuations of the absolute zero position in a measured temporal waveform are the major problems in the AMD method. As a referencing technique, we already proposed dual-channel waveform measurement scheme that may suppress these errors. In this study, we have demonstrated real-time confocal AMD-FLIM system with dual-channel waveform measurement technique.

Obesity is one of the biggest problem in modern society. Smartphone could be a good tool to handle this problem. In this paper, we propose a new smartphone app to recommend diet, to offer a physical practice by motion games. Our Android smartphone application encourages friends to join group fitness programs. It interfaces with social network services and smart-TV.

The etching characteristics of the magnetic films (PtMn, CoFe) and hard mask materials (W, Ta) forming a magnetic tunnel junction (MTJ) stack in a CH3OH inductively coupled plasma (ICP) system were investigated. We examined the etch rates of the metal films as a function of substrate temperature, and assessed the microstructures of the etched surfaces using high resolution transmission electron microscopy (HR-TEM). We also analyzed the surface states using X-ray photoelectron spectroscopy (XPS) and TEM electron energy loss spectroscopy (TEM-EELS). The PtMn and CoFe etch rates increased as the temperature increased, whereas the etch rates of W and Ta decreased slightly. Therefore the etch selectivity increased linearly with increasing substrate temperature. The CH3OH plasma formed nonvolatile etching byproducts with the magnetic films and hard mask metals. In the case of PtMn and CoFe, the surface composition of the etching byproducts changed with increasing temperature; the relative concentration of pure metal compared with metal oxide or carbide increased as the substrate temperature rose. The etch rate was determined by the sputtering yield of the materials formed on the etched surface; accordingly the etch rates of those magnetic films would increase due to the higher sputtering yield of pure metal.

In this paper we describe the integrated development environment for embedded software education. Our environment uses a cheap and widely available portable game console, Nintendo DS-lite. We have integrated open source development tools, and have implemented download shell, remote debugger. The results are all open source, and were used for university class for real embedded software education.

UNLABELLED The mainstay of treatment of Osgood-Schlatter apophysitis is nonoperative. Surgical treatment has been described for patients who have failed nonoperative management of Osgood-Schlatter disease. The purpose of this study is to evaluate the functional outcome of ossicle excision and tibial tubercleplasty for unresolved Osgood-Schlatter disease that has failed nonoperative treatment. METHODS A retrospective review was performed on 16 knees in 15 patients who underwent ossicle excision and tibial tubercleplasty for unresolved Osgood-Schlatter disease. Functional outcome was assessed using the International Knee Documentation Committee, the Lysholm Knee Scale, and Tegner Activity Score. RESULTS Twelve patients (75%) returned to preoperative activities and sports, 2 patients (12.5%) partially returned, and 1 patient (6%) did not return. The mean postoperative Lysholm knee score was 76.5. Patients' individual scores ranged from 40 to 100. The mean International Knee Documentation Committee knee score was 75, ranging from 40 to 100. The mean Tegner activity level was 6.8 (range, 3-10). CONCLUSIONS It is our recommendation that when patients fail extensive nonoperative management, surgery to remove the symptomatic ossicle should be offered after skeletal maturity. When this is the case, the addition of tubercleplasty should be performed.

The supracondylar fracture of the distal humerus is the most common pediatric fracture in the elbow. This systematic review summarizes the existing data about the effect of medial and lateral (medial/lateral) entry pins versus only lateral entry pin fixation on the risk of iatrogenic nerve injury and deformity or loss of reduction. A literature search identified clinical trials and observational studies presenting the probability of nerve injury and/or deformity or loss of reduction associated with closed reduction and either medial/lateral entry or lateral entry pinning of supracondylar fractures in pediatric patients. Data from 2054 children were identified from 35 studies; 2 randomized trials, 6 cohort studies, and 25 case series. For operative fixation with medial/lateral entry pins, the probability of ulnar nerve injury is 5.04 times higher than with lateral entry pins. When all documented operative nerve injuries are included, the probability of iatrogenic nerve injury is 1.84 times higher with medial/lateral entry pins than with isolated lateral pins. Medial/lateral pin entry provides a more stable configuration, and the probability of deformity or loss of reduction is 0.58 times lower than with isolated lateral pin entry. When the prospective studies alone were analyzed, there were no significant difference in the probability of iatrogenic nerve injury or deformity and displacement, although the confidence intervals were wide. This systematic review indicates that medial/lateral entry pinning, of pediatric supracondylar fractures, remains the most stable configuration and that care needs to be taken regardless of technique to avoid iatrogenic nerve injury and loss of reduction.

DAB is a traditional digital radio broadcasting technology. To enhance the performance and quality of DAB system, DAB+ is standardized with outer coding and superior audio codec (HE-AACv2). Recently, as audio codec technology develops, state of the art audio codec, USAC has been standardized. This paper designs the DAB+ system with USAC to enhance the audio quality and efficiency. USAC can improve the audio quality and efficiency of the digital radio system better than HE-AACv2. This paper describes the design and implementation of digital audio broadcasting system with USAC audio codec based on DAB+ system.

This study looks for the first time at outcomes of arthroscopic hip surgeries in dancers. The subjects were thirty dancers, mean age 20.1 years (range: 14.1 to 38 years), each of whom had undergone arthroscopic debridement of a hip labral tear at least five months prior to follow-up (range: 5 to 51 months), and completed two questionnaires, the modified Harris Hip Score (HHS) and a Dance Questionnaire (DQ) devised specifically for this occasion. The questionnaire responses demonstrate a significant average increase (p < 0.001) in HH scores, from a preoperative mean of 52.7 to 91.5 postoperatively, which indicates marked improvement in pain reduction and restoration of function. DQ responses verify significant pain reduction (preoperative 7.49 to postoperative 2.47), and show that 15 patients had returned at follow-up to full functionality. Close examination of the cases of the other 15 subjects suggests that most of them would also have been dancing at full capacity but for factors extraneous to the surgery or related to the extreme demands of the discipline. It is concluded that, while labral tears are particularly debilitating in this population, most dancers with this injury can anticipate an acceptable outcome of surgical intervention, with decreased pain, increased function, and return to dance.

Images (e.g., figures) are important experimental results that are typically reported in bioscience full-text articles. Biologists need to access images to validate research facts and to formulate or to test novel research hypotheses. On the other hand, biologists live in an age of information explosion. As thousands of biomedical articles are published every day, systems that help biologists efficiently access images in literature would greatly facilitate biomedical research. We hypothesize that much of image content reported in a full-text article can be summarized by the sentences in the abstract of the article. In our study, more than one hundred biologists had tested this hypothesis and more than 40 biologists had evaluated a novel user-interface BioEx that allows biologists to access images directly from abstract sentences. Our results show that 87.8% biologists were in favor of BioEx over two other baseline user-interfaces. We further developed systems that explored hierarchical clustering algorithms to automatically identify abstract sentences that summarize the images. One of the systems achieves a precision of 100% that corresponds to a recall of 4.6%. Contact: hongyu@uwm.edu or hy52@columbia.edu

Cache memory is used in almost all computer systems today to bridge the ever increasing speed gap between the processor and main memory. However, its use in multitasking computer systems introduces additional preemption delay due to the reloading of memory blocks that are replaced during preemption. This cache-related preemption delay poses a serious problem in realtime computing systems where predictability is of utmost importance. We propose an enhanced technique for analyzing and thus bounding the cache-related preemption delay in fixed-priority preemptive scheduling focusing on instruction caching. The proposed technique improves upon previous techniques in two important ways. First, the technique takes into account the relationship between a preempted task and the set of tasks that execute during the preemption when calculating the cache-related preemption delay. Second, the technique considers the phasing of tasks to eliminate many infeasible task interactions. These two features are expressed as constraints of a linear programming problem whose solution gives a guaranteed upper bound on the cache-related preemption delay. This paper also compares the proposed technique with previous techniques using randomly generated task sets. The results show that the improvement on the worst-case response time prediction by the proposed technique over previous techniques ranges between 5 percent and 18 percent depending on the cache refill time when the task set utilization is 0.6. The results also show that as the cache refill time increases, the improvement increases, which indicates that accurate prediction of cache-related preemption delay by the proposed technique becomes increasingly important if the current trend of widening speed gap between the processor and main memory continues.

In multi-tasking real-time systems, inter-task cache interference due to preemptions degrades schedulability as well as performance. To address this problem, we propose a novel scheduling scheme, called limited preemptive scheduling (LPS), that limits preemptions to execution points with small cache-related preemption costs. Limiting preemptions decreases the cache-related preemption costs of tasks but increases blocking delay of higher priority tasks. The proposed scheme makes an optimal trade-off between these two factors to maximize the schedulability of a given task set while minimizing cache-related preemption delay of tasks. Experimental results show that the LPS scheme improves the maximum schedulable utilization by up to 40\% compared with the traditional fully preemptive scheduling (FPS) scheme. The results also show that up to 20\% of processor time is saved by the LPS scheme due to reduction in the cache-related preemption costs. Finally, the results show that both the improvement of schedulability and the saving of processor time by the LPS scheme increase as the speed gap between the processor and main memory widens.

Cache memories have been extensively used to bridge the speed gap between high speed processors and relatively slow main memory. However, they are not widely used in real-time systems due to their unpredictable performance. This paper proposes an instruction prefetching scheme called threaded prefetching as an alternative to instruction caching in real-time systems. In the proposed threaded prefetching, an instruction block pointer called a thread is assigned to each instruction memory block and is made to point to the next block on the worst case execution path that is determined by a compile-time analysis. Also, the thread is not updated throughout the entire program execution to guarantee predictability. This paper also compares the worst case performances of various previous instruction prefetching schemes with that of the proposed threaded prefetching. By analyzing several benchmark programs, we show that the worst case performance of the proposed scheme is significantly better than those of previous instruction prefetching schemes. The results also show that when the block size is large enough the worst case performance of the proposed threaded prefetching scheme is almost as good as that of an instruction cache with 100 % hit ratio.

Predictable performance is crucial for real-time computing systems. We propose a buffered threaded prefetch scheme as a predictable and high performance instruction memory hierarchy. We also give extensions to the timing schema[3] to analyze the timing effects of the proposed scheme. In the extended timing schema, we associate with each program construct what we call a WCTA (Worst Case Timing Abstraction), which contains detailed timing information of the program construct. By defining a concatenation operation on WCTAs, our revised timing schema accurately accounts for the timing effects of the buffered threaded prefetching not only within but also across program constructs. This paper shows, through analysis using a timing tool based on the extended timing schema, the buffered prefetch scheme significantly improves the worst case execution times of tasks.

Many embedded systems generate and store multimedia data streams continuously before eventually processing the stored stream at a later time. When the stream is stored in variable bandwidth, additional CPU processing is inevitably involved in locating the exact frame positions corresponding to specific times. In this paper, a new file system with time-based indexing scheme is proposed. This time-based indexing scheme periodically stores the relations between the time and data locations. With this index information, applications can pinpoint the exact frame location corresponding to a given time. To prove the usefulness and effectiveness, we implemented the proposed file system and the indexing scheme on a Linux-based DVR and then compared the performance with that of the ext2 file system.

Calcaneal fractures in children are rare injuries, and those with displaced intraarticular fracture patterns are found even less frequently. Recent data in the adult literature have suggested operative treatment of displaced intraarticular calcaneal fractures leads to a more favorable outcome. Most pediatric calcaneal fractures are due to low-energy trauma and are therefore minimally displaced and extraarticular. However, some children are exposed to high-energy trauma, leading to severe intraarticular injuries. Operatively treated calcaneal fractures in children have been poorly described in the literature. The purpose of this study was to analyze the outcomes of surgically treated displaced intraarticular calcaneal fractures in children.All children with closed displaced intraarticular calcaneal fractures treated with open reduction internal fixation at 1 institution were reviewed at an average of 67 months postoperatively. Preoperative and postoperative radiographs and preoperative computed tomographic scans were used to classify fractures. Functional outcome was assessed by the use of the subjective portions of the American Orthopaedic Foot and Ankle Society (AOFAS) hindfoot score.Fourteen fractures in 13 patients who met the inclusion criteria were treated with open reduction internal fixation. We found 7 tongue-type and 7 joint depression-type fractures based on the Essex-Lopresti classification. Based on the Sanders classification, we found 9 type II (2-part) fractures and 5 type III (3-part) fractures. The average preoperative and postoperative Bohler angles were 11.8 and 28.4 degrees (P0.0001), respectively. The average subjective AOFAS hindfoot score was 64 of a possible 68 points. Of 14 fractures, 13 were fixed with a buttressing plate laterally. One patient was fixed with a single 3.5-mm cortical screw and had the lowest AOFAS hindfoot score. Four minor complications in 3 patients were encountered.We found that most children with displaced intraarticular calcaneal fractures treated with open reduction and internal fixation at 1 institution had a good clinical outcome with few complications.

Physicians have many questions when caring for patients, and frequently need to seek answers for their questions. Information retrieval systems (e.g., PubMed) typically return a list of documents in response to a user’s query. Frequently the number of returned documents is large and makes physicians’ information seeking “practical only ‘after hours’ and not in the clinical settings”. Question answering techniques are based on automatically analyzing thousands of electronic documents to generate short-text answers in response to clinical questions that are posed by physicians. The authors address physicians’ information needs and described the design, implementation, and evaluation of the medical question answering system (MedQA). Although our long term goal is to enable MedQA to answer all types of medical questions, currently, we currently implement MedQA to integrate information retrieval, extraction, and summarization techniques to automatically generate paragraph-level text for definitional questions (i.e., “What is X?”). MedQA can be accessed at http://www.dbmi.columbia.edu/~yuh9001/research/MedQA.html.

A picture is worth a thousand words. Biomedical researchers tend to incorporate a significant number of images (i.e., figures or tables) in their publications to report experimental results, to present research models, and to display examples of biomedical objects. Unfortunately, this wealth of information remains virtually inaccessible without automatic systems to organize these images. We explored supervised machine-learning systems using Support Vector Machines to automatically classify images into six representative categories based on text, image, and the fusion of both. Our experiments show a significant improvement in the average F-score of the fusion classifier (73.66%) as compared with classifiers just based on image (50.74%) or text features (68.54%).

The published medical literature and online medical resources are important sources to help physicians make patient treatment decisions. Traditional sources used for information retrieval (e.g., PubMed) often return a list of documents in response to a user's query. Frequently the number of returned documents from large knowledge repositories is large and makes information seeking practical only ''after hours'' and not in the clinical setting. This study developed novel algorithms, and designed, implemented, and evaluated a medical definitional question answering system (MedQA). MedQA automatically analyzed a large number of electronic documents to generate short and coherent answers in response to definitional questions (i.e., questions with the format of ''What is X?''). Our preliminary cognitive evaluation shows that MedQA out-performed three other online information systems (Google, OneLook, and PubMed) in two important efficiency criteria; namely, time spent and number of actions taken for a physician to identify a definition. It is our contention that question answering systems that aggregate pertinent information scattered across different documents have the potential to address clinical information needs within a timeframe necessary to meet the demands of clinicians.

We propose an enhanced technique for analyzing, and thus bounding cache related preemption delay in fixed priority preemptive scheduling focusing on instruction caching. The proposed technique improves upon previous techniques in two important ways. First, the technique takes into account the relationship between a preempted task and the set of tasks that execute during the preemption when calculating the cache related preemption delay. Second, the technique considers phasing of tasks to eliminate many infeasible task interactions. These two features are expressed as constraints of a linear programming problem whose solution gives a guaranteed upper bound on the cache related preemption delay. The paper also compares the proposed technique with previous techniques. The results show that the proposed technique gives up to 60% tighter prediction of the worst case response time than the previous techniques.

This paper presents a case study of worst case timing analysis for a RISC processor. The target machine consists of the R3000 CPU and R3010 FPA (Floating Point Accelerator). This target machine is typical of a RISC system with pipelined execution units and cache memories. Our methodology is an extension of the existing timing schema. The extended timing schema provides means to reason about the execution time variation of a program construct by surrounding program constructs due to pipelined execution and cache memories of RISC processors. The main focus of this paper is on explaining the necessary steps for performing timing analysis of a given target machine within the extended timing schema framework. This paper also gives results from experiments using a timing tool for the target machine that is built based on the extended timing schema approach.

In multi-tasking real-time systems, inter-task cache interference due to preemptions degrades system performance and predictability, complicating system design and analysis. To address this problem, we propose a novel scheduling scheme, called LPS (Limited Preemptible Scheduling), that limits preemptions to predetermined points with small cache-related preemption costs. We also give an accompanying analysis method that determines the schedulability of a given task set under LPS. By limiting preemption points, the proposed LPS scheme reduces preemption costs and thus increases the system throughput. Experimental results show that LPS can increase schedulable utilization by more than 10 % and save processor time by up to 44 % as compared with a traditional fully preemptible scheduling scheme.

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Background Topic detection is a task that automatically identifies topics (e.g., "biochemistry" and "protein structure") in scientific articles based on information content. Topic detection will benefit many other natural language processing tasks including information retrieval, text summarization and question answering; and is a necessary step towards the building of an information system that provides an efficient way for biologists to seek information from an ocean of literature. Results We have explored the methods of Topic Spotting, a task of text categorization that applies the supervised machine-learning technique naïve Bayes to assign automatically a document into one or more predefined topics; and Topic Clustering, which apply unsupervised hierarchical clustering algorithms to aggregate documents into clusters such that each cluster represents a topic. We have applied our methods to detect topics of more than fifteen thousand of articles that represent over sixteen thousand entries in the Online Mendelian Inheritance in Man (OMIM) database. We have explored bag of words as the features. Additionally, we have explored semantic features; namely, the Medical Subject Headings (MeSH) that are assigned to the MEDLINE records, and the Unified Medical Language System (UMLS) semantic types that correspond to the MeSH terms, in addition to bag of words, to facilitate the tasks of topic detection. Our results indicate that incorporating the MeSH terms and the UMLS semantic types as additional features enhances the performance of topic detection and the naïve Bayes has the highest accuracy, 66.4%, for predicting the topic of an OMIM article as one of the total twenty-five topics. Conclusion Our results indicate that the supervised topic spotting methods outperformed the unsupervised topic clustering; on the other hand, the unsupervised topic clustering methods have the advantages of being robust and applicable in real world settings.

A variable sampling clock generator for two-dimensional image sampling is proposed that features very small point error in each scan line, fast frequency switching from one scan line to another, and phase coherency at sampling starting on each scan line. The sampling clock is generated by dividing a stable high-frequency master clock by integer values stored in a simplified master-clock divider ROM. The sample point error is kept below one half of the master-clock period on the whole image plane by the nearest-neighbor-sampling technique.