Quantitative Analyses for Early Tempo-spatial Patterning of Differentiated Human Induced Pluripotent Stem Cells on Micropatterns using Time-lapse Bright-field Microscopy Images

Three germ layer formation on micropatterns are extremely useful for quantitative analysis of hiPSC (human induced pluripotent stem cells) pluripotency. Spatial patterns of stem cells differentiated on the micropatterns will be formed from about 24 hours after differentiation induction and usually quantitated near 48 hours. To delineate the germ layer formation process, temporal changes in spatial patterning of germ layers should be analyzed by noninvasive microscopy. This study proposed a series of image processing methods combined with a U-net automatic segmentation to segment differentiated hiPSCs captured by bright-field microscopy. High segmentation accuracy (83.3%) for the test bright-field images compared with their concurrent Hoechst images (85%) was achieved. Tempo-spatial patterning and formation process of germ layers on the micropatterns can be visualized and quantified by segmenting time-lapse bright-field microscopy images using our method.

Quantitative Analysis of Differentiation Activity for Mouse Embryonic Stem Cells by Deep Learning for Cell Center Detection using Three-Dimensional Confocal Fluorescence Microscopy Images

Accurate single cell segmentation provides means to monitor the behavior of single cell within a population of cells. Time-lapse fluorescence images are used to reveal heterogeneous nature of single mouse embryonic stem cell (ESC) colony and monitor fluctuations of the cell states. Automatic quantification of speed and status shifts of the ESCs depends on accurate single cell segmentation that is used to calculate the 3D center of every cell and track this cell for the quantification. This study proposes a new 3D U-net to accurately detect center of each single cell in 3D confocal images. The dimension of input 3D images to the U-net is flexible so that multiple center detections from different image directions can be implemented simultaneously to improve the center detection accuracy. This study showed that our method can improve accuracy for cell center detection and thus the quantification for ESC speeds and status shifts.

Human induced pluripotent stem cell formation and morphology prediction during reprogramming with time-lapse bright-field microscopy images using deep learning methods

BACKGROUND AND OBJECTIVE

Human induced pluripotent stem cells (hiPSCs) represent an ideal source for patient specific cell-based regenerative medicine; however, efficiency of hiPSC formation from reprogramming cells is low. We use several deep-learning results from time-lapse brightfield microscopy images during culture, to early detect the cells potentially reprogramming into hiPSCs and predict the colony morphology of these cells for improving efficiency of culturing a new hiPSC line.

METHODS

Sets of time-lapse bright-field images are taken to track reprogramming process of CD34+ cells biologically identified as just beginning reprogramming. Prior the experiment, 9 classes of templates with distinct cell features clipped from microscopy images at various reprogramming stages are used to train a CNN model. The CNN is then used to classify a microscopy image as probability images of these classes. Probability images of some class are used to train a densely connected convolutional network for extracting regions of this class on a microscopy image. A U-net is trained to segment cells on the time-lapse images in early reprogramming stage during culture. The segmented cells are classified by the extracted regions to count various types of cells appearing in the early reprogramming stage for predicting the identified cells potentially forming hiPSCs. The probability images of hiPSC classes are also used to train a spatiotemporal RNN for predicting the future hiPSC colony morphology of the potential cells.

RESULTS

Experimental results show the prediction (before 7 days after of beginning of the reprogramming) achieved 0.8 accuracy, and 66% of the identified cells under different culture conditions, predicted as forming, finally formed hiPSCs. The predicted hiPSC images and extracted colonies on the images show the prediction for future 1.5 days achieved high accuracy of hiPSC colony areas and image similarity.

CONCLUSIONS

Our study proposes a method using several deep learning models to efficiently select the reprogramming cells possibly forming hiPSCs and to predict the shapes of growing hiPSC colonies. The proposed method is expected to improve the efficiency when establishing a new hiPSC line culture.

U-net structures for segmentation of single mouse embryonic stem cells using three-dimensional confocal microscopy images

Cell segmentation at a single cell resolution is required to provide insights for basic biology and application study. However, there are issues of low signal-to-noise ratio, weak fluorescence response, and insufficient resolution along the image stacking direction in 3D confocal images (volume). It has been difficult to segment out single cells from close or contacted cells in a cell volume using image processing methods or together with geometric processing methods. Recently, 3D deep learning methods have been used to avoid tedious parameter settings in the image and geometric processing, but still not easy to segment out close or contacted single cells. This paper proposes a 2D U-net to segment cell regions in high accuracy and computing performance. Better 3D cell images and single cell segmentation for close or contacted cells are achieved by combining a 3D U-net to detect the centers of single cells in the volume.

Prediction of Human Induced Pluripotent Stem Cell Formation Based on Deep Learning Analyses Using Time-lapse Brightfield Microscopy Images

We use deep learning methods to predict human induced pluripotent stem cell (hiPSC) formation using time-lapse brightfield microscopy images taken from a cell identified as the beginning of entered into the reprogramming process. A U-net is used to segment cells and a CNN is used to classify the segmented cells into eight types of cells during the reprogramming and hiPSC formation based on cellular morphology on the microscopy images. The numbers of respective types of cells in cell clusters before the hiPSC formation stage are used to predict if hiPSC regions can be well formed lately. Experimental results show good prediction by the criteria using the numbers of different cells in the clusters. Time-series images with respective types of classified cells can be used to visualize and quantitatively analyze the growth and transition among dispersed cells not in cell clusters, various types of cells in the clusters before the hiPSC formation stage and hiPSC cells.

Visualization and quantitative analyses for mouse embryonic stem cell tracking by manipulating hierarchical data structures using time-lapse confocal microscopy images

We present a cell tracking method for time-lapse confocal microscopy (3D) images that uses dynamic hierarchical data structures to assist cell and colony segmentation and tracking. During the segmentation, the cell and colony numbers and their geometric data are recorded for each 3D image set. In tracking, the colony correspondences between neighboring frames of time-lapse 3D images are first computed using the recorded colony centers. Then, cell correspondences in the correspondent colonies are computed using the recorded cell centers. The examples show the proposed cell tracking method can achieve high tracking accuracy for time-lapse 3D images of undifferentiated but self-renewing mouse embryonic stem (mES) cells where the number and mobility of ES cells in a cell colony may change suddenly by a colony merging or splitting, and cell proliferation or death. The geometric data in the hierarchical data structures also help the visualization and quantitation of the cell shapes and mobility.

High Resolution U-Net for Quantitatively Analyzing Early Spatial Patterning of Human Induced Pluripotent Stem Cells on Micropatterns

Human induced pluripotent stem cells (hiPSCs) can differentiate into three germ layer cells, i.e. ectoderm, mesoderm and endoderm, on micropatterned chips in highly synchronous and reproducible manners. The cells are confined within the chip, expanding two-dimensionally as almost in the form of monolayer, thus to be ideal for serving quantitative analysis of their pluripotency. We present a new U-Net (MP-UNet) structure for cell segmentation of early spatial patterning of hiPSCs on micropattern chips using Hoechst fluorescence images. In this structure, the encoding/decoding layers can be dynamically adjusted to extract sufficient image features and be flexible to image sizes. Dice and weight loss functions are designed to identify slight difference in low signal-to-noise ratio, high boundary-to-area ratio and compacted cell images. Several sizes of Hoechst images were tested to show MP-UNet can achieve high accuracy in cell regions and number counting for various sizes of micropattern chips, thus to be excellent quantitative tool for early spatial patterning of hiPSCs.

Prediction for Morphology and States of Stem Cell Colonies using a LSTM Network with Progressive Training Microscopy Images

We present a new LSTM (P-LSTM: Progressive LSTM) network, aiming to predict morphology and states of cell colonies from time-lapse microscopy images. Apparent short-term changes occur in some types of time-lapse cell images. Therefore, long-term-memory dependent LSTM networks may not predict accurately. The P-LSTM network incorporates the images newly generated from cell imaging progressively into LSTM training to emphasize the LSTM short-term memory and thus improve the prediction accuracy. The new images are input into a buffer to be selected for batch training. For real-time processing, parallel computation is introduced to implement concurrent training and prediction on partitioned images.Two types of stem cell images were used to show effectiveness of the P-LSTM network. One is for tracking of ES cell colonies. The actual and predicted ES cell images possess similar colony areas and the same transitions of colony states (moving, merging or morphology changing), although the predicted colony mergers may delay in several time-steps. The other is for prediction of iPS cell reprogramming from the CD34+ human cord blood cells. The actual and predicted iPS cell images possess high similarity evaluated by the PSNR and SSIM similarity evaluation metrics, indicating the reprogramming iPS cell colony features and morphology can be accurately predicted.

Human Induced Pluripotent Stem Cell Reprogramming Prediction in Microscopy Images using LSTM based RNN

We present a LSTM (Long Short-Term Memory) based RNN (recurrent neural network) method for predicting human induced Pluripotent Stem (hiPS) cells in the reprogramming process. The method uses a trained LSTM network by time-lapse microscopy images to predict growth and transition of reprogramming processes of CD34+ human cord blood cells into hiPS cells. The prediction can be visualized by output time-series probability images. The growth and transition are thus analyzed quantitatively by region areas of distinct cells emerged during the iPS formation processes. The experimental results show that our LSTM network is a potentially powerful tool to predict the cells at the distinct phases of the reprogramming to hiPS cells. This method should be extremely useful not only for basic biology of iPS cells but also detection of the reprogramming cells that will become genuine hiPS cells even at early stages of hiPS formation. Such predictive power should greatly reduce cost, labor and time required for establishment of the genuine hiPS cells, thereby accelerating the practical use of hiPS cells in regenerative medicine.

Neuropathic Pain Experiences of Spinal Cord Injury Patients

BACKGROUND

Neuropathic pain (NP) is a common, severe problem that affects spinal cord injury (SCI) patients. Only SCI patients truly understand the impact and extent of this type of pain.

PURPOSE

The aim of this study was to understand the NP experienced by SCI patients and the influence of this type of pain on their daily life.

METHOD

A qualitative design was used. An interview guide including a semistructured questionnaire and in-depth interviews was conducted with SCI patients with NP in a neurorehabilitation department at a medical center in northern Taiwan. The data were collected using a purposive sampling method. Content analysis was performed on the interview data, which were obtained from 13 SCI patients with NP.

RESULTS

Three themes and eight subthemes were identified that described the NP experience of the participants and the influence of NP on their daily life. The three themes included elusive pain (changing and individual pain sensations, erratically haunting threat, and phantom limb sensations), complicated feelings about pain (converting depression into an active attitude toward life, having feelings of anticipation and anxiety about future pain relief, and facing and experiencing pain), and renewed hope (bravely fighting pain and seeking pain relief methods).

CONCLUSIONS

This study revealed three important themes of NP experienced by SCI patients, including elusive pain, complicated feelings about pain, and renewed hope. Nurses should understand the nature of NP, provide a thorough pain assessment, and design a proper pain management plan to care effectively for patients with NP.

Volume Manipulation Based on 3D Reconstructed Surfaces for Joint Function Evaluation and Surgery Simulation

In joint surgery, evaluation of the relative positions and angles among joint structures (bones, ligaments, muscle, and cartilages, etc.) in range of motion, lifting and weight bearing of the joint is required. However, current volume visualization techniques provide only static 3D images of anatomic structures in volume data. We propose a method to manipulate (reposition, resize and bend) the joint structures in a volume, by which surgeons can visualize and evaluate the critical positions or angles of the joint structures, and thus plan surgery to correct the morphologic pathology of the joint structures. We also propose a system with a real-time cutting simulation function together with the proposed structure manipulation functions by which surgeons can rehearse and verify joint surgery.

Posterior communicating aneurysm with oculomotor nerve palsy: clinical outcome after aneurysm clipping

AIM

One of the clinical presentations of intracranial aneurysm is unilateral oculomotor nerve palsy (ONP). The most common location is the posterior communicating artery. Surgical clipping and/or endovascular coiling of the aneurysm are the treatments. The aim of this study was to identify the factors that influence the postoperative recovery of patients who have posterior communicating aneurysm with ONP.

MATERIAL AND METHODS

We included 13 patients diagnosed at our hospital from 1993 to 2008 with posterior communicating aneurysm with ONP. Ten patients underwent craniotomy to clip the aneurysm; 3 patients refused surgery.

RESULTS

Five (50%) patients presented with periorbital pain. Seven (70%) patients had complete ONP recovery with a median recovery time of 58 days. We found that the first recovered component of ONP after clipping was the parasympathetic fibers with a mean recovery time of 4.4 days. Nine patients had a good recovery outcome; one patient died from postoperative vasospasm. There was no significant linear trend in complete recovery rate across palsy symptom periods. However, the palsy symptom period was significant correlated with recovery time.

CONCLUSION

Early decompression of the posterior communicating aneurysm yielded satisfactory recovery and ONP can be reversible. In our patients, the first component of oculomotor function to recover was the parasympathetic fibers.

Dumbbell-shaped primitive neuroectodermal tumor mimicking trigeminal schwannoma: a case report and review of literature

Primitive neuroectodermal tumor (PNET) is presumably of neural crest origin, and cases of supratentorial PNET in adult are extremely rare. We reported a case of PNET presenting as a dumbbell-shaped tumor at the middle cranial fossa of skull base mimicking trigeminal schwannoma both clinically and radiologically. The patient underwent surgery on July 13, 2010, using a combination of subtemporal, pterional and retrosigmoid approaches, to achieve decompression and obtain a histological diagnosis. The patient worsened neurologically two weeks after surgery. Her consciousness level became comatose due to tumor bleeding with compression of the brain stem and her precarious physical condition prevented receiving further treatment with adjuvant radiation therapy and chemotherapy. The correct diagnosis of PNET is important because its management differs dramatically from that for trigeminal schwannoma.

Nuclear condensation and cell cycle arrest induced by telomerase siRNA in neuroblastoma cells

Neuroblastoma is a type of malignant extracranial tumor that occurs in children. Advanced neuroblastoma, and tumors with MYCN amplification in particular, have poor prognoses. Therefore, it is important to find an effective cure for this disease. Small interfering RNA (siRNA) disrupts gene function by specifically binding to target mRNA. In this study, we used siRNA against telomerase to treat neuroblastoma, to evaluate any anti-proliferative effect on these cells. We evaluated cell viability by WST-1 assay on neuroblastoma cells treated with or without telomerase siRNA. Nuclear condensation, an indicator for apoptotic cells, was determined by DAPI labeling following siRNA treatment. The effectiveness of telomerase siRNA on altering the neuroblastoma cell cycle was detected by flow cytometry. Our results indicated that telomerase siRNA reduces the viability of neuroblastoma cells and increases the percentage of cells in the cell cycle's sub-G1 phase. We found that telomerase siRNA increases the percentage of condensed DNA in neuroblastoma cells. In conclusion, using siRNA against telomerase could be further developed as a therapy for the treatment of neuroblastoma.

Involvement of Smac, p53, and caspase pathways in induction of apoptosis by gossypol in human retinoblastoma cells

PURPOSE

Retinoblastoma is a malignant tumor of the retina usually occurring in young children. To date, the conventional treatments for retinoblastoma have been enucleation, cryotherapy, external beam radiotherapy, or chemotherapy. Most of these treatments, however, have possible side effects, including blindness, infections, fever, gastrointestinal toxicity, and neurotoxicity. More effective treatments are therefore imperative. Gossypol has been reported as a potential inhibitor of cell proliferation in various types of cancers, such as prostate cancer, breast cancer, leukemia, and lung cancer. This study investigates the possible antiproliferative effect of gossypol on retinoblastoma.

METHODS

Human retinoblastoma cells were cultured with various concentrations of gossypol and checked for cell viability with a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Nuclear condensation caused by cell apoptosis was detected by staining retinoblastoma cells with 4',6-diamidino-2-phenylindole (DAPI), counting those with condensed nuclei, and determining the percentage of apoptotic cells. In addition, the stages of apoptosis and phases in cell cycles were examined with flow cytometry. The possible signal transduction pathways involved were examined with a protein array assay and western blot analysis.

RESULTS

After incubation, the cell survival rate was significantly lower after treatment with 5, 10, and 20 µM of gossypol. The maximum antisurvival effect of gossypol was observed at 20 µM, and the number of apoptotic cells was higher in the preparations cultured with 10 and 20 µM of gossypol. The results in flow cytometry indicated that at concentrations of 10 and 20 µM, gossypol increased the proportion of early- and late-apoptotic retinoblastoma cells and induced cell arrest of retinoblastoma cells at the same concentrations. This antiproliferative effect was later confirmed by upregulating the expression of death receptor 5 (DR5), caspase 8, caspase 9, caspase 3, cytochrome C, tumor protein 53 (p53), and second mitochondria-derived activator of caspases (Smac) in the signal transduction pathways.

CONCLUSIONS

We concluded that gossypol has an antiproliferative effect on retinoblastoma cells.

Combination of nerve blockade and intravenous alfentanil is better than single treatment in relieving postoperative pain

BACKGROUND/PURPOSE

Multimodal analgesia can improve perioperative analgesia but knowledge of combination protocols is still incomplete. This study was designed to evaluate whether the combination of sciatic nerve blockade (SNB) and intravenous alfentanil (IVA) is more effective than either single treatment in relieving postoperative pain in rats.

METHODS

In a plantar incision model, withdrawal thresholds were evaluated by von Frey test before incision as baselines and for 7 days after incision. The animals were randomly allocated into various groups to receive SNB with 1% or 2% lidocaine, IVA of 50 or 150 μg/kg, or combined treatments (SNB 1% + 50 μg/kg IVA or SNB 2% + 150 μg/kg IVA) before incision. The results were compared with those of sham procedures--i.e., injections of peri-sciatic or intravenous saline, or a combination of both.

RESULTS

Plantar incision caused postoperative allodynia for 3 days. SNB with 2% lidocaine reduced allodynia at 1 hour, 3 hours, day 1, and day 2, but not at postoperative 5 hours or days 3-7, whereas 150 μg/kg IVA produced short analgesia for only 3 hours after surgery. Neither low-dose SNB nor low-dose IVA had a significant effect. When high-dose SNB and high-dose IVA were combined, a strong antiallodynic effect was shown in an additive manner. No synergism was evidently displayed by the combination.

CONCLUSION

Our results indicated that in an incisional pain model, multimodal analgesia is superior to single or no pretreatment; however, the combination of multimodal analgesic treatments should be individually discerned depending on nociceptive types and analgesic mechanisms.

Resection of giant olfactory groove meningioma with extradural devascularization

A 55-year-old male patient presented with a giant olfactory groove meningioma supplied by both ophthalmic arteries. The tumor was debulked through a bifrontal craniotomy, but the surgery was discontinued because of extensive blood loss. During a second operation, the dura of the frontal base was dissected extradurally before the tumor was removed. The meningeal blood supply was occluded with bipolar coagulation of the epidural meningeal vessels around the crista galli. The highly vascular tumor then was totally removed with considerably less blood loss. The patient's postoperative course was uneventful. Because the ophthalmic artery cannot be embolized preoperatively, the direct extradural approach to the skull base to devascularize the blood supply around the olfactory groove may reduce blood loss and facilitate resection.

Accurate visual and haptic burring surgery simulation based on a volumetric model

Burring surgery is mainly implemented for fine or critical structures and widely used in orthopedic, oral and maxillofacial, ENT and neurosurgery departments to delicately cut or polish bones, joints or other tissues. This paper describes a volume manipulation method that extends a voxel with multiple values to represent accurate burred changes on tissue surfaces. Tissue surface reconstruction is implemented for the local burred surface to provide a real-time visual response. A burring force vector for a haptic response is calculated by detecting which parts of a bur contact tissue and summated from tissue removal loads on the contacted parts. A spine surgery example showed that rough surface features by gross cutting or smooth features by fine cutting can be clearly demonstrated and high haptic reality can be achieved by our simulations. The burring surgery simulator with the accurate visual and haptic responses can be an effective rehearsing and training tool.

An unusual primitive neuroectodermal tumor in the thoracic epidural space

Primitive neuroectodermal tumor (PNET) is a generic term used to describe a group of histologically indistinguishable neoplasms, including cerebellar medulloblastomas, which are located at various sites in the central nervous system. Primary epidural PNETs are rare and few patients have been reported. We report a 15-year-old girl who presented with gradual onset, over 1 month, of upper back pain and bilateral lower leg weakness. A thoracic spine MRI showed a dumbbell-shaped epidural mass at T2-4 with right paraspinal and posterior mediastinal extension. Surgical resection of the epidural tumor for decompression was performed. The pathologic examination revealed a PNET. Primary spinal PNETs typically have a poor prognosis and optimal therapy has not yet been defined. Surgical resection, with the combination of chemo-radiotherapy or radiotherapy, leads to better outcomes. However, primary epidural PNETs may be classified as a subtype of spinal PNETs because they are free from intrathecal invasion. For these patients, surgery alone and surgery combined with radiotherapy or chemo-radiotherapy remain controversial. Our patient received surgery alone and, 1y ear later, has experienced no local recurrence within the epidural space but the mediastinal part of the tumor has enlarged.

REAL-TIME THREE-DIMENSIONAL RECONSTRUCTION FOR VOLUME-BASED SURGERY SIMULATIONS

This paper describes a three-dimensional reconstruction method to provide real-time visual responses for volume (constituted by tomographic slices) based surgery simulations. The proposed system uses dynamical data structures to record tissue triangles obtained from 3D reconstruction computation. Each tissue triangle in the structures can be modified or every structure can be deleted or allocated independently. Moreover, triangle reconstruction is optimized by only deleting or adding vertices from manipulated voxels that are classified as erosion (in which the voxels are changed from tissue to null) or generation (the voxels are changed from null to tissue). Therefore, by manipulating these structures, 3D reconstruction can be locally implemented for only manipulated voxels to achieve the highest efficiency without reconstructing tissue surfaces in the whole volume as general methods do. Three surgery simulation examples demonstrate that the proposed method can provide time-critical visual responses even under other time-consuming computations such as volume manipulations and haptic interactions.

Fingerprint verification on medical image reporting system

The healthcare industry is recently going through extensive changes, through adoption of robust, interoperable healthcare information technology by means of electronic medical records (EMR). However, a major concern of EMR is adequate confidentiality of the individual records being managed electronically. Multiple access points over an open network like the Internet increases possible patient data interception. The obligation is on healthcare providers to procure information security solutions that do not hamper patient care while still providing the confidentiality of patient information. Medical images are also part of the EMR which need to be protected from unauthorized users. This study integrates the techniques of fingerprint verification, DICOM object, digital signature and digital envelope in order to ensure that access to the hospital Picture Archiving and Communication System (PACS) or radiology information system (RIS) is only by certified parties.

Evaluation of optimal cerebral perfusion pressure in severe traumatic brain injury

Traumatic brain injury (TBI) is a major cause of death and disability. In the 2000 guidelines, one of the suggestions for TBI treatment was to maintain cerebral perfusion pressure (CPP) < or = 70 mmHg. But in the 2003 guidelines, the suggestion was changed to < or = 60 mmHg. There have been some discrepancies of opinions about this recommendation in recent publications. In this study, we retrospectively reviewed 305 severe TBI (STBI) patients with Glasgow Coma Scales (GCS) < or = 8 between January 1, 2002 and March 31, 2003. The study group was stratified according to use or nonuse of intracranial pressure (ICP) monitoring, ICP levels, ages, and GCS levels in order to test the correlation between CCP and the prognosis. The patients < 50-year-old, with higher GCS level, with ICP monitoring, and with ICP levels < 20 mmHg had lower mortality rates and better prognosis (GOS) (p < 0.05 or 0.001). The patients in the GCS 3-5 subgroup had a significantly lower mortality and better prognosis if the CPP value was maintained higher than 70 mmHg (p < 0.05) The optimal CPP maintained < or = 60 mmHg did not fit in all STBI patients. Our study concludes that it is critical to maintain CPP substantially higher in lower GCS level patients.

Bone drilling haptic interaction for orthopedic surgical simulator

Drilling procedure is widely used in orthopedic surgery to position reduced fractured bones and prosthetic components. However, successful execution of bone drilling requires a high level of dexterity and experience, because the drilling resistance is large and sometimes vibrates violently to difficultly grasp the hand-piece or even break the slender drill. This paper introduces haptic functions that are added to a volume based surgical simulator to simulate the drilling process. These haptic functions compute drilling forces and torques based on reliable metal removing theorem. Therefore, accurate prediction for the drilling process can be obtained to provide effective surgery training and rehearsal. A simulation example of screw and plate surgery for positioning the hip trochanter fracture illustrates the practicality and versatility of the proposed method.

Glenoid and humerus bone analysis using CT transverse sections to automate gleno-humeral joint diagnoses and surgery managements

This paper describes an image analysis method that evaluates the glenoid and humerus bone morphology to automate the gleno-humeral (GH) joint diagnoses and surgical managements. This method uses radial B-spline curves to approximate ellipse-like shoulder structures including the humeral stem, tubercle and contact joint as well as the glenoid on every CT transverse section. Radius changes from structure centers to bone boundaries are recognized as convex, concave, separate and hole features that are then identified as pathological spurs, fractures and tumors. The centers and radii of these structures from the transverse sections are integrated to determine the properties of the humeral stem and contact joint with the glenoid, including the stem axis as well as the contact joint and glenoid centers, radii and attitudes. Based on the geometric evaluations of these structures and features, the GH joint surgery including tumor dissect and bone graft, open reduction using screws and plate or nails, and arthroplasty are automatically managed to achieve the normal GH joint functions including dissection of tumors, reduction of fractures or dislocations, and free GH joint motions. This prototype system can be used as a qualitative and quantitative tool for the GH joint diseases diagnoses and surgery managements. A series of examples and case studies illustrate the effectiveness of this automated method.

Development of a personal digital assistant-based wireless application in clinical practice

PURPOSE

Our study aims to develop a personal digital assistant (PDA)-based wireless application in medical information processing by using Bluetooth and IEEE 802.11b wireless standards and SyncML codes.

METHODS

In this study, an "integrated database access module" is used to provide a unified integrated access interface while consistency of wireless data transmission is achieved by using the standardized SyncML protocol. A prototype of the system has been developed, implemented, and tested for its mobility, usability, stability, and performance with questionnaire survey.

RESULTS

Response time for browsing/searching was usually less than 3s. The average time intervals needed for data transmissions were 68.6+/-8.5s for Bluetooth and 47.0+/-4.8s for 802.11b. The five-point Likert scale (from 1=least to 5=most) questionnaire survey of 30 medical professionals yielded a high degree of satisfaction with the system's mobility (4.18+/-0.89), usability (4.69+/-0.90), stability (3.81+/-0.94), and performance (3.97+/-0.88).

CONCLUSION

The results of our study suggested that PDA applications which exploit wireless communication are convenient and feasible in clinical practice.

Injury-induced Janus kinase/protein kinase C-dependent phosphorylation of growth-associated protein 43 and signal transducer and activator of transcription 3 for neurite growth in dorsal root ganglion

Elevation of corticosteroids and excessive glutamate release are the two major stress responses that occur sequentially during traumatic CNS injury. We have previously reported that sequential application of corticosterone and kainic acid (CORT + KA) mimicking the nerve injury condition results in synergistic enhancement of neurite outgrowth and expression of growth-associated protein 43 (GAP-43) in cultured dorsal root ganglion (DRG). GAP-43 is known to promote neurite extension when phosphorylated by protein kinase C (PKC). In addition, PKC can phosphorylate the signal transducer and activator of transcription 3 (STAT3) at Ser727, which is phosphorylated primarily by Janus kinase (JAK) at Tyr705. In this study, we further examine the role of PKC in this stress-induced growth-promoting effect. In the cultured DRG neurons, the JAK inhibitor AG-490 and the PKC inhibitor Ro-318220 reduced the CORT + KA-enhanced neurite growth effect when applied prior to CORT and KA treatment, respectively. Both AG-490 and Ro-318220 diminished the CORT + KA-enhanced GAP-43 expression, phosphorylation, and axonal localization. Furthermore, CORT + KA treatment synergistically phosphorylated STAT3 at Ser727 but not at Tyr705. Similar phenomena were observed in an animal model of acute spinal cord injury (SCI), in which phosphorylation of GAP-43 and phospho-Ser727-STAT3 was elevated in the injured DRG 4 hr after the impact injury. Further treatment with the therapeutic glucocorticoid methylprednisolone enhanced the phosphorylation of GAP-43 in both the DRG and the spinal cord of SCI rats. These results suggest that elevated glucocorticoids and overexcitation following CNS injury contribute to nerve regeneration via induction of JAK/PKC-mediated GAP-43 and STAT3 activities.

Cytologic diagnosis of a metastatic oligodendroglioma in a pleural effusion. A case report

BACKGROUND

Extraneural metastasis of oligodendroglioma is extremely rare and is diagnosed primarily by biopsy or autopsy and very occasionally by fine needle cytologic examination. We report a case of metastatic oligodendroglioma diagnosed by cytologic examination of a pleural effusion. Such a diagnosis has not been reported before.

CASE

A 64-year-old woman developed anemia and bilateral pleural effusion 7 years after an operation for an oligodendroglioma over the left frontal lobe. Cytologic examination of the pleural effusion showed aggregates of atypical polygonal cells containing round, hyperchromatic nuclei and scanty, granular cytoplasm in Liu's and Papanicolaou stain and cell blocks. Immunohistochemical staining of the tumor cells revealed a positive reaction for antibodies to glial fibrillary acidic protein, S-100 and Olig2. Pleural biopsy confirmed the cytologic diagnosis of pleural effusion. A pathologic fracture of the right humeral and femoral bones was noted 1 month later, and the specimen also showed infiltrating oligodendroglioma cells in bone tissue.

CONCLUSION

To the best of our knowledge, this is the first metastatic oligodendroglioma diagnosed by pleural cytology. Fine needle cytology can provide a reliable and rapid way to detect an extracranial metastatic oligodendroglioma in different organs.

Third calcium ion found in an inhibitor-bound phospholipase A2

The lipolytic enzyme phospholipase A2 plays a crucial role in lipid metabolism and catalyzes hydrolysis of the fatty-acid ester bond at the sn-2 position of phospholipids. Here, the crystal structure (1.7 A resolution) of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2 complexed with an organic molecule, p-methoxybenzoic acid (anisic acid), is reported. Residues 60-70 (the surface-loop residues) are ordered and adopt conformations which are different from those normally found in structures in which a second calcium ion is present. It is interesting to note that for the first time a third calcium ion has been identified. In addition, four Tris (2-amino-2-hydroxymethyl-1,3-propanediol) molecules were located. It is believed that one of the Tris molecules plays a role in clamping the third calcium ion and that another is involved in controlling the dynamics of the surface loop through hydrogen bonds.

Three-dimensional hip morphology analysis using CT transverse sections to automate diagnoses and surgery managements

This paper describes an image analysis method that evaluates bone morphology of hip structures including the femur stem, trochanter, neck and head, acetabulum, and pelvis to automate hip diagnoses and surgical managements. On every CT transverse section, radial B-spline curves are used to approximate the ellipse-like acetabulum and femur head and stem. The femur neck is approximated as trapezoid-like and the pelvis horizontally symmetrical structure. The centers of the ellipse-like structures from transverse sections are used to determine 3D axes of the femur stem, head, and acetabulum. The centerlines of the neck or the pelvis on the sections are used to determine the neck axis or pelvis centerplane. Boundary changes of these structures are recognized as concave, convex and hole features that are then identified as fractures, tumors, and spurs. Based on the geometric evaluations of these structures and features, hip surgeries including tumor dissect and bone graft, open reduction using plates, screws and nails, and arthroplasty are automatically managed to achieve the normal hip function including dissection of tumors and reduction of dislocations and angular deviations between the hip structures. This prototype system can be used as a qualitative and quantitative tool for the diagnosis of various hip diseases and for the planning of accurate surgical procedures. A series of examples and four case studies illustrate this automated method can be used to accurately diagnose hip diseases and manage hip surgeries, and train operators.

Volume Manipulations for Simulating Bone and Joint Surgery

Bone and joint surgery is widely used in orthopedic, oral, and maxillofacial, and dental and plasty departments to correct bone and joint pathology such as bone and joint tumors and fractures, and skeletal morphological deformities. This article presents a voxel structure to represent topologically and geometrically correct surfaces and algorithms to accurately compute intersections of tool swept surfaces with bones based on this voxel structure. This article then presents various volume manipulation algorithms to operate on virtual bones, bone grafts, and prostheses for bone and joint surgery simulations. A complicated knee arthroplasty illustrates the practicality and versatility of the proposed method.

Automatic spinal disease diagnoses assisted by 3D unaligned transverse CT slices

This paper describes a three-dimensional (3D) reconstruction method and an automatic diagnosis method for spinal diseases using unaligned transverse slices that have arbitrary angles and intervals but do not intersect to each other at regions of interest. The 3D reconstruction method extends the marching cube algorithm to generate triangulated isosurfaces for these unaligned slices. The automatic spinal disease diagnostic method analyses boundaries of discs and vertebral bodies on unaligned transverse slices to estimate the presence and extent of disc herniation and canal compression, and deformities in the spinal curve. The prototype system can be used as a qualitative and quantitative tool for the diagnosis of various spinal diseases using unaligned transverse slices.

Phospholipids chiral at phosphorus. Properties of small unilamellar vesicles of chiral thiophosphatidylcholine

The recent observation of the differences in the biophysical properties between 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and the Rp, Sp, and Rp + Sp isomers of 1,2-dipalmitoyl-sn-glycero-3-thiophosphocholine (DPPsC) in the multilamellar phase [Tsai, M.-D., Jiang, R.-T., & Bruzik, K. (1983) J. Am. Chem. Soc. 105, 2478-2480] prompted us to investigate the biophysical properties of the small unilamellar vesicles (SUV) of the above phospholipids. It was found that DPPC and DPPsC isomers showed approximately the same critical micelle concentrations and formed spherical SUV upon injection of their ethanolic solutions into an aqueous solution. However, the average sizes of the SUV of DPPsC isomers were significantly greater than that of DPPC prepared under the same conditions, as shown by their electron micrographs. The results of both 31P NMR line widths and the ratios of the entrapped solute to the total phospholipids further supported the following order in the average radius of the SUV: (Sp)-DPPsC greater than (Rp + Sp)-DPPsC greater than (Rp)-DPPsC greater than DPPC. Complete lysis of the SUV by melittin was demonstrated in all four cases. The DPPsC isomers showed gel-liquid-crystal transition temperatures of 43.8 +/- 0.1 degrees C, which are considerably higher than that of DPPC (37.9 degrees C) under the same conditions. In the SUV of an equimolar mixture of DPPC and (Rp + Sp)-DPPsC, DPPsC preferred to stay in the inner layer on the basis of 31P NMR studies by use of a shift reagent PrCl3.(ABSTRACT TRUNCATED AT 250 WORDS)

Solution structures of two FHA1-phosphothreonine peptide complexes provide insight into the structural basis of the ligand specificity of FHA1 from yeast Rad53

Rad53, a yeast checkpoint protein involved in regulating the repair of DNA damage, contains two forkhead-associated domains, FHA1 and FHA2. Previous combinatorial library screening has shown that FHA1 strongly selects peptides containing a pTXXD motif. Subsequent location of this motif within the sequence of Rad9, the target protein, coupled with spectroscopic analysis has led to identification of a tight binding sequence that is likely the binding site of FHA1: (188)SLEV(pT)EADATFVQ(200). We present solution structures of FHA1 in complex with this pT-peptide and with another Rad9-derived pT-peptide that has ca 30-fold lower affinity, (148)KKMTFQ(pT)PTDPLE(160). Both complexes showed intermolecular NOEs predominantly between three peptide residues (pT, +1, and +2 residues) and five FHA1 residues (S82, R83, S85, T106, and N107). Furthermore, the following interactions were implicated on the basis of chemical shift perturbations and structural analysis: the phosphate group of the pT residue with the side-chain amide group of N86 and the guanidino group of R70, and the carboxylate group of Asp (at the +3 position) with the guanidino group of R83. The generated structures revealed a similar binding mode adopted by these two peptides, suggesting that pT and the +3 residue Asp are the major contributors to binding affinity and specificity, while +1 and +2 residues could provide additional fine-tuning. It was also shown that FHA1 does not bind to the corresponding pS-peptides or a related pY-peptide. We suggest that differentiation between pT and pS-peptides by FHA1 can be attributed to hydrophobic interactions between the methyl group of the pT residue and the aliphatic protons of R83, S85, and T106 from FHA1.

Solution structure of the yeast Rad53 FHA2 complexed with a phosphothreonine peptide pTXXL: comparison with the structures of FHA2-pYXL and FHA1-pTXXD complexes

It was proposed previously that the FHA2 domain of the yeast protein kinase Rad53 has dual specificity toward pY and pT peptides. The consensus sequences of pY peptides for binding to FHA2, as well as the solution structures of free FHA2 and FHA2 complex with a pY peptide derived from Rad9, have been obtained previously. We now report the use of a pT library to screen for binding of pT peptides with the FHA2 domain. The results show that FHA2 binds favorably to pT peptides with Ile at the +3 position. We then searched the Rad9 sequences with a pTXXI/L motif, and tested the binding affinity of FHA2 toward ten pT peptides derived from Rad9. One of the peptides, (599)EVEL(pT)QELP(607), displayed the best binding affinity (K(d)=12.9 microM) and the greatest chemical shift changes. The structure of the FHA2 complex with this peptide was then determined by solution NMR and the structure of the complex between FHA2 and the pY peptide (826)EDI(pY)YLD(832) was further refined. Structural comparison of these two complexes indicates that the Leu residue at the +3 position in the pT peptide and that at the +2 position in the pY peptide occupy a very similar position relative to the binding site residues from FHA2. This can explain why FHA2 is able to bind both pT and pY peptides. This position change from +3 to +2 could be the consequence of the size difference between Thr and Tyr. Further insight into the structural basis of ligand specificity of FHA domains was obtained by comparing the structures of the FHA2-pTXXL complex obtained in this work and the FHA1-pTXXD complex reported in the accompanying paper.

Solution structure of a viral DNA polymerase X and evidence for a mutagenic function

The African swine fever virus DNA polymerase X (ASFV Pol X or Pol X), the smallest known nucleotide polymerase, has recently been reported to be an extremely low fidelity polymerase that may be involved in strategic mutagenesis of the viral genome. Here we report the solution structure of Pol X. The structure, unique within the realm of nucleotide polymerases, consists of only palm and fingers subdomains. Despite the absence of a thumb subdomain, which is important for DNA binding in other polymerases, we show that Pol X binds DNA with very high affinity. Further structural analyses suggest a novel mode of DNA binding that may contribute to low fidelity synthesis. We also demonstrate that the ASFV DNA ligase is a low fidelity ligase capable of sealing a nick that contains a G-G mismatch. This supports the hypothesis of a virus-encoded, mutagenic base excision repair pathway consisting of a tandem Pol X/ligase mutator.

Virtual reality orthopedic surgery simulator

This paper describes a highly interactive virtual reality orthopedic surgery simulator. The simulator allows surgeons to use various surgical instruments to operate on virtual rigid anatomic structures, such bones, prostheses and bone grafts, to simulate every procedure on the rigid structures for complex orthopedic surgeries, including arthroplasty, corrective or open osteotomy, open reduction of fractures and amputation. A comparative study of the simulator with paper simulation was performed and showed that interns and residents found the simulator to be a useful learning tool, and that visiting doctors could use it effectively for planning verification and rehearsal of operations.

DNA polymerase beta: pre-steady-state kinetic analyses of dATP alpha S stereoselectivity and alteration of the stereoselectivity by various metal ions and by site-directed mutagenesis

The first pre-steady-state kinetic analysis of the stereoselectivity of a DNA polymerase, Pol beta from rat brain, toward Rp and Sp isomers of dATPalphaS, and alteration of the stereoselectivity by various metal ions and by site-directed mutagenesis are reported. Diastereomers of dATPalphaS were synthesized by enzymatic methods to >98% purity. The rate of polymerization (k(pol)) and the apparent dissociation constant (K(d,app)) were measured with dATP, Rp-dATPalphaS, and Sp-dATPalphaS in the presence of Mg(2+), Mn(2+), or Cd(2+). The results indicate that wild type (WT) polymerase (Pol) beta can incorporate both Sp- and Rp-dATPalphaS in the presence of Mg(2+), but Sp is the preferred isomer. The stereoselectivity, defined as (k(pol)/K(d))(Sp)/(k(pol)/K(d))(Rp) (abbreviated Sp/Rp ratio), is 57.5 in the presence of Mg(2+). When Mg(2+) was substituted with Mn(2+) and Cd(2+), the Sp/Rp ratio decreased to 7.6 and 21, respectively. These results are discussed in relation to the crystal structures of various Pol beta complexes, as well as previous steady-state kinetic studies of other DNA polymerases. In addition, the D276R mutant was designed to introduce a potential extra hydrogen bonding interaction between the arginine side chain and the pro-Sp oxygen of the alpha-phosphate of dNTP. The kinetic data of the D276R mutant showed a pronounced relaxation of stereoselectivity of dATPalphaS (Sp/Rp ratio = 1.5, 3.7, and 1.5 for Mg(2+), Mn(2+), and Cd(2+), respectively). Furthermore, the D276R mutant showed a 5-fold enhanced reactivity toward Rp-dATPalphaS relative to WT Pol beta, suggesting that this mutant Pol beta can be used to incorporate Rp-dNTPalphaS into DNA oligomers.

Mechanism of phosphatidylinositol-specific phospholipase C: origin of unusually high nonbridging thio effects

Phosphatidylinositol-specific phospholipase C (PI-PLC) has been proposed previously to employ a catalytic mechanism highly reminiscent of that of ribonuclease A (RNase A). Both catalytic sites are comprised of two histidine side chains acting as a general base-general acid pair and a phosphate-activating residue: an arginine in the case of PI-PLC and a lysine in RNase A. Despite these structural similarities, the PI-PLC reaction is slowed 10(5)-fold upon substitution of one of the phosphate nonbridging oxygen atoms with sulfur, whereas a much smaller effect is observed in the analogous RNase A reaction. Here, we report a systematic study of this property in PI-PLC, conducted by means of site-directed chemical modification of a cysteine residue replacing the arginine at position 69. The results show that mutant enzymes featuring bidentate side chains at this position display significantly higher activity, higher thio effects, and greater stereoselectivity than do those with monodentate side chains. The results suggest that the bidentate nature of Arg69 is the origin of the large thio effects and stereoselectivity in PI-PLC. We propose that in addition to binding the phosphate, the function of arginine 69 is to bring the phosphate group and the 2-OH group of inositol into proximity and to induce proper alignment for nucleophilic attack, and possibly to lower the pK(a) of the 2-OH. The results presented here could be important to mechanisms of phosphoryl transfer enzymes in general, suggesting that a major part of thio effects observed in enzymatic phosphoryl transfer reactions can originate from factors other than direct interaction between a side chain and a phosphate group, and caution the use of the absolute magnitude of the thio effect as an indicator of the strength of such interactions.

Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes

The catalytic reaction mediated by DNA polymerases is known to require two Mg(II) ions, one associated with dNTP binding and the other involved in metal ion catalysis of the chemical step. Here we report a functional intermediate structure of a DNA polymerase with only one metal ion bound, the DNA polymerase beta-DNA template-primer-chromium(III).2'-deoxythymidine 5'-beta,gamma-methylenetriphosphate [Cr(III).dTMPPCP] complex, at 2.6 A resolution. The complex is distinct from the structures of other polymerase-DNA-ddNTP complexes in that the 3'-terminus of the primer has a free hydroxyl group. Hence, this structure represents a fully functional intermediate state. Support for this contention is provided by the observation of turnover in biochemical assays of crystallized protein as well as from the determination that soaking Pol beta crystals with Mn(II) ions leads to formation of the product complex, Pol beta-DNA-Cr(III).PCP, whose structure is also reported. An important feature of both structures is that the fingers subdomain is closed, similar to structures of other ternary complexes in which both metal ion sites are occupied. These results suggest that closing of the fingers subdomain is induced specifically by binding of the metal-dNTP complex prior to binding of the catalytic Mg(2+) ion. This has led us to reevaluate our previous evidence regarding the existence of a rate-limiting conformational change in Pol beta's reaction pathway. The results of stopped-flow studies suggest that there is no detectable rate-limiting conformational change step.

Involvement of the Arg-Asp-His catalytic triad in enzymatic cleavage of the phosphodiester bond

Phosphatidylinositol-specific phospholipase C (PI-PLC) catalyzes the cleavage of the P-O bond in phosphatidylinositol via intramolecular nucleophilic attack of the 2-hydroxyl group of inositol on the phosphorus atom. Our earlier stereochemical and site-directed mutagenesis studies indicated that this reaction proceeds by a mechanism similar to that of RNase A, and that the catalytic site of PI-PLC consists of three major components analogous to those observed in RNase A, the His32 general base, the His82 general acid, and Arg69 acting as a phosphate-activating residue. In addition, His32 is associated with Asp274 in forming a catalytic triad with inositol 2-hydroxyl, and His82 is associated with Asp33 in forming a catalytic diad. The focus of this work is to provide a global view of the mechanism, assess cooperation between various catalytic residues, and determine the origin of enzyme activation by the hydrophobic leaving group. To this end, we have investigated kinetic properties of Arg69, Asp33, and His82 mutants with phosphorothioate substrate analogues which feature leaving groups of varying hydrophobicity and pK(a). Our results indicate that interaction of the nonbridging pro-S oxygen atom of the phosphate group with Arg69 is strongly affected by Asp33, and to a smaller extent by His82. This result in conjunction with those obtained earlier can be rationalized in terms of a novel, dual-function triad comprised of Arg69, Asp33, and His82 residues. The function of this triad is to both activate the phosphate group toward the nucleophilic attack and to protonate the leaving group. In addition, Asp33 and His82 mutants displayed much smaller degrees of activation by the fatty acid-containing leaving group as compared to the wild-type (WT) enzyme, and the level of activation was significantly reduced for substrates featuring the leaving group with low pK(a) values. These results strongly suggest that the assembly of the above three residues into the fully catalytically competent triad is controlled by the hydrophobic interactions of the enzyme with the substrate leaving group.