Une nouvelle approche computationnelle pour la découverte des sites de fixation de facteurs de transcription à l’ADN, adaptée aux données de ChIP-chip et de ChIP-séquençage

Les facteurs de transcription sont des protéines spécialisées qui jouent un rôle important dans différents processus biologiques tel que la différenciation, le cycle cellulaire et la tumorigenèse. Ils régulent la transcription des gènes en se fixant sur des séquences d’ADN spécifiques (éléments cis-régulateurs). L’identification de ces éléments est une étape cruciale dans la compréhension des réseaux de régulation des gènes. Avec l’avènement des technologies de séquençage à haut débit, l’identification de tout les éléments fonctionnels dans les génomes, incluant gènes et éléments cis-régulateurs a connu une avancée considérable. Alors qu’on est arrivé à estimer le nombre de gènes chez différentes espèces, l’information sur les éléments qui contrôlent et orchestrent la régulation de ces gènes est encore mal définie. Grace aux techniques de ChIP-chip et de ChIP-séquençage il est possible d’identifier toutes les régions du génome qui sont liées par un facteur de transcription d’intérêt. Plusieurs approches computationnelles ont été développées pour prédire les sites fixés par les facteurs de transcription. Ces approches sont classées en deux catégories principales: les algorithmes énumératifs et probabilistes. Toutefois, plusieurs études ont montré que ces approches génèrent des taux élevés de faux négatifs et de faux positifs ce qui rend difficile l’interprétation des résultats et par conséquent leur validation expérimentale. Dans cette thèse, nous avons ciblé deux objectifs. Le premier objectif a été de développer une nouvelle approche pour la découverte des sites de fixation des facteurs de transcription à l’ADN (SAMD-ChIP) adaptée aux données de ChIP-chip et de ChIP-séquençage. Notre approche implémente un algorithme hybride qui combine les deux stratégies énumérative et probabiliste, afin d’exploiter les performances de chacune d’entre elles. Notre approche a montré ses performances, comparée aux outils de découvertes de motifs existants sur des jeux de données simulées et des jeux de données de ChIP-chip et de ChIP-séquençage. SAMD-ChIP présente aussi l’avantage d’exploiter les propriétés de distributions des sites liés par les facteurs de transcription autour du centre des régions liées afin de limiter la prédiction aux motifs qui sont enrichis dans une fenêtre de longueur fixe autour du centre de ces régions. Les facteurs de transcription agissent rarement seuls. Ils forment souvent des complexes pour interagir avec l’ADN pour réguler leurs gènes cibles. Ces interactions impliquent des facteurs de transcription dont les sites de fixation à l’ADN sont localisés proches les uns des autres ou bien médier par des boucles de chromatine. Notre deuxième objectif a été d’exploiter la proximité spatiale des sites liés par les facteurs de transcription dans les régions de ChIP-chip et de ChIP-séquençage pour développer une approche pour la prédiction des motifs composites (motifs composés par deux sites et séparés par un espacement de taille fixe). Nous avons testé ce module pour prédire la co-localisation entre les deux demi-sites ERE qui forment le site ERE, lié par le récepteur des œstrogènes ERα. Ce module a été incorporé à notre outil de découverte de motifs SAMD-ChIP.

Robot Motion Vision by Fixation

In many motion-vision scenarios, a camera (mounted on a moving vehicle) takes images of an environment to find the "motion'' and shape. We introduce a direct-method called fixation for solving this motion-vision problem in its general case. Fixation uses neither feature-correspondence nor optical-flow. Instead, spatio-temporal brightness gradients are used directly. In contrast to previous direct methods, fixation does not restrict the motion or the environment. Moreover, fixation method neither requires tracked images as its input nor uses mechanical tracking for obtaining fixated images. The experimental results on real images are presented and the implementation issues and techniques are discussed.

A practical method for lingual retainer fixation before direct bonding: Clinical suggest

The retention phase is initiated after orthodontic treatment completion to prevent orthodontic relapse. There are several techniques, direct and indirect, available for placing bonded lingual retainers, but none of them is considered as a standard clinical protocol. The best choice should be the association of simplicity and efficiency. This article presents a practical method sequence for fixation of the lingual retainer before direct bonding. © 2009 Elsevier Ltd and the Japanese Orthodontic Society.

Block Bone Graft Fixation ( Onlay): A Modification of the Surgical Technique

Several reconstructive methods of the alveolar ridge have been reported to make possible future rehabilitations with implants. Many of these methods come from studies done in animals, mainly rats. With this clinical practice based on scientific evidence, any experimental procedure that can be undertaken in real life is fundamental. Thus, any research that emulates as closely as possible those techniques used in humans are important. This study describes the modification of the technique for block bone graft fixation (onlay) in rats using the lag screw-type technique, normally used in clinical procedures for grafts in humans. The conclusion was that the execution of the described procedures minimizes interference of blood flow in the area because of the maintenance of the muscle insertion in the buckle aspect of the most anterior region of the mandible, providing better stability to the graft and better contact interface of the graft and receptor bed.

Primary stability in cementless total hip replacement: measurement techniques and aided-surgery

Primary stability of stems in cementless total hip replacements is recognized to play a critical role for long-term survival and thus for the success of the overall surgical procedure. In Literature, several studies addressed this important issue. Different approaches have been explored aiming to evaluate the extent of stability achieved during surgery. Some of these are in-vitro protocols while other tools are coinceived for the post-operative assessment of prosthesis migration relative to the host bone. In vitro protocols reported in the literature are not exportable to the operating room. Anyway most of them show a good overall accuracy. The RSA, EBRA and the radiographic analysis are currently used to check the healing process of the implanted femur at different follow-ups, evaluating implant migration, occurance of bone resorption or osteolysis at the interface. These methods are important for follow up and clinical study but do not assist the surgeon during implantation. At the time I started my Ph.D Study in Bioengineering, only one study had been undertaken to measure stability intra-operatively. No follow-up was presented to describe further results obtained with that device. In this scenario, it was believed that an instrument that could measure intra-operatively the stability achieved by an implanted stem would consistently improve the rate of success. This instrument should be accurate and should give to the surgeon during implantation a quick answer concerning the stability of the implanted stem. With this aim, an intra-operative device was designed, developed and validated. The device is meant to help the surgeon to decide how much to press-fit the implant. It is essentially made of a torsional load cell, able to measure the extent of torque applied by the surgeon to test primary stability, an angular sensor that measure the relative angular displacement between stem and femur, a rigid connector that enable connecting the device to the stem, and all the electronics for signals conditioning. The device was successfully validated in-vitro, showing a good overall accuracy in discriminating stable from unstable implants. Repeatability tests showed that the device was reliable. A calibration procedure was then performed in order to convert the angular readout into a linear displacement measurement, which is an information clinically relevant and simple to read in real-time by the surgeon. The second study reported in my thesis, concerns the evaluation of the possibility to have predictive information regarding the primary stability of a cementless stem, by measuring the micromotion of the last rasp used by the surgeon to prepare the femoral canal. This information would be really useful to the surgeon, who could check prior to the implantation process if the planned stem size can achieve a sufficient degree of primary stability, under optimal press fitting conditions. An intra-operative tool was developed to this aim. It was derived from a previously validated device, which was adapted for the specific purpose. The device is able to measure the relative micromotion between the femur and the rasp, when a torsional load is applied. An in-vitro protocol was developed and validated on both composite and cadaveric specimens. High correlation was observed between one of the parameters extracted form the acquisitions made on the rasp and the stability of the corresponding stem, when optimally press-fitted by the surgeon. After tuning in-vitro the protocol as in a closed loop, verification was made on two hip patients, confirming the results obtained in-vitro and highlighting the independence of the rasp indicator from the bone quality, anatomy and preserving conditions of the tested specimens, and from the sharpening of the rasp blades. The third study is related to an approach that have been recently explored in the orthopaedic community, but that was already in use in other scientific fields. It is based on the vibration analysis technique. This method has been successfully used to investigate the mechanical properties of the bone and its application to evaluate the extent of fixation of dental implants has been explored, even if its validity in this field is still under discussion. Several studies have been published recently on the stability assessment of hip implants by vibration analysis. The aim of the reported study was to develop and validate a prototype device based on the vibration analysis technique to measure intra-operatively the extent of implant stability. The expected advantages of a vibration-based device are easier clinical use, smaller dimensions and minor overall cost with respect to other devices based on direct micromotion measurement. The prototype developed consists of a piezoelectric exciter connected to the stem and an accelerometer attached to the femur. Preliminary tests were performed on four composite femurs implanted with a conventional stem. The results showed that the input signal was repeatable and the output could be recorded accurately. The fourth study concerns the application of the device based on the vibration analysis technique to several cases, considering both composite and cadaveric specimens. Different degrees of bone quality were tested, as well as different femur anatomies and several levels of press-fitting were considered. The aim of the study was to verify if it is possible to discriminate between stable and quasi-stable implants, because this is the most challenging detection for the surgeon in the operation room. Moreover, it was possible to validate the measurement protocol by comparing the results of the acquisitions made with the vibration-based tool to two reference measurements made by means of a validated technique, and a validated device. The results highlighted that the most sensitive parameter to stability is the shift in resonance frequency of the stem-bone system, showing high correlation with residual micromotion on all the tested specimens. Thus, it seems possible to discriminate between many levels of stability, from the grossly loosened implant, through the quasi-stable implants, to the definitely stable one. Finally, an additional study was performed on a different type of hip prosthesis, which has recently gained great interest thus becoming fairly popular in some countries in the last few years: the hip resurfacing prosthesis. The study was motivated by the following rationale: although bone-prosthesis micromotion is known to influence the stability of total hip replacement, its effect on the outcome of resurfacing implants has not been investigated in-vitro yet, but only clinically. Thus the work was aimed at verifying if it was possible to apply to the resurfacing prosthesis one of the intraoperative devices just validated for the measurement of the micromotion in the resurfacing implants. To do that, a preliminary study was performed in order to evaluate the extent of migration and the typical elastic movement for an epiphyseal prosthesis. An in-vitro procedure was developed to measure micromotions of resurfacing implants. This included a set of in-vitro loading scenarios that covers the range of directions covered by hip resultant forces in the most typical motor-tasks. The applicability of the protocol was assessed on two different commercial designs and on different head sizes. The repeatability and reproducibility were excellent (comparable to the best previously published protocols for standard cemented hip stems). Results showed that the procedure is accurate enough to detect micromotions of the order of few microns. The protocol proposed was thus completely validated. The results of the study demonstrated that the application of an intra-operative device to the resurfacing implants is not necessary, as the typical micromovement associated to this type of prosthesis could be considered negligible and thus not critical for the stabilization process. Concluding, four intra-operative tools have been developed and fully validated during these three years of research activity. The use in the clinical setting was tested for one of the devices, which could be used right now by the surgeon to evaluate the degree of stability achieved through the press-fitting procedure. The tool adapted to be used on the rasp was a good predictor of the stability of the stem. Thus it could be useful for the surgeon while checking if the pre-operative planning was correct. The device based on the vibration technique showed great accuracy, small dimensions, and thus has a great potential to become an instrument appreciated by the surgeon. It still need a clinical evaluation, and must be industrialized as well. The in-vitro tool worked very well, and can be applied for assessing resurfacing implants pre-clinically.

Mesh shrinkage and pain in laparoscopic ventral hernia repair: a randomized clinical trial comparing suture versus tack mesh fixation

Mesh fixation during laparoscopic ventral hernia repair can be performed using transfascial sutures or metal tacks. The aim of the present study is to compare mesh shrinkage and pain between two different techniques of mesh fixation in a prospective randomized trial.

Comminuted fractures of the radial head and neck: is fixation to the shaft necessary?

Mason type III fractures of the radial head are treated by open reduction and internal fixation, resection or prosthetic joint replacement. When internal fixation is performed, fixation of the radial head to the shaft is difficult and implant-related complications are common. Furthermore, problems of devascularisation of the radial head can result from fixation of the plate to the radial neck. In a small retrospective study, the treatment of Mason type III fractures with fixation of the radial neck in 13 cases (group 2) was compared with 12 cases where no fixation was performed (group 1). The mean clinical and radiological follow-up was four years (1 to 9). The Broberg-Morrey index showed excellent results in both groups. Degenerative radiological changes were seen more frequently in group 2, and removal of the implant was necessary in seven of 13 cases. Post-operative evaluation of these two different techniques revealed similar ranges of movement and functional scores. We propose that anatomical reconstruction of the radial head without metalwork fixation to the neck is preferable, and the outcome is the same as that achieved with the conventional technique. In addition degenerative changes of the elbow joint may develop less frequently, and implant removal is not necessary.

The effect of cementing technique on structural fixation of pegged glenoid components in total shoulder arthroplasty

Although loosening of cemented glenoid components is one of the major complications of total shoulder arthroplasty, there is little information about factors affecting initial fixation of these components in the scapular neck. This study was performed to assess the characteristics of structural fixation of pegged glenoid components, if inserted with two different recommended cementing techniques. Six fresh-frozen shoulder specimens and two types of glenoid components were used. The glenoids were prepared according to the instructions and with the instrumentation of the manufacturer. In 3 specimens, the bone cement was inserted into the peg receiving holes (n = 12) and applied to the back surface of the glenoid component with a syringe. In the other 3 specimens, the cement was inserted into the holes (n = 15) by use of pure finger pressure: no cement was applied on the backside of the component. Micro-computed tomography scans with a resolution of 36 microm showed an intact cement mantle around all 12 pegs (100%) when a syringe was used. An incomplete cement plug was found in 7 of 15 pegs (47%) when the finger-pressure technique was used. Cement penetration into the cancellous bone was deeper in osteopenic bone. Application of bone cement on the backside of the glenoid prosthesis improved seating by filling out small spaces between bone and polyethylene resulting from irregularities after reaming or local cement extrusion from a drill hole. The fixation of a pegged glenoid component is better if the holes are filled with cement under pressure by use of a syringe and if cement is applied to the back of the glenoid component than if cement is inserted with pure finger pressure and no cement is applied to the back surface of the component.

Sexual function after sacrospinous fixation for vaginal vault prolapse: bad or mad?

BACKGROUND: The main indication for sacrospinous ligament suspension is to correct either total procidentia, a posthysterectomy vaginal vault prolapse with an associated weak cardinal uterosacral ligament complex, or a posthysterectomy enterocele. This study aimed to evaluate sexual function and anatomic outcome for patients after sacrospinous ligament suspension. METHODS: For this study, 52 patients who had undergone sacrospinous ligament fixation during the preceding 5 years were asked to complete the Female Sexual Function Index (FSFI) questionnaire. The patients were vaginally examined using the ICS POP score, and the results were compared with their preoperative status. For statistical analysis, GraphPad for Windows, version 4.0, was used. RESULTS: The 52 patients were examined during a follow-up period of 38 months. No major intraoperative complications were noted. Recurrence of symptomatic apical descent was noted in 6% of the patients and de novo prolapse in 13.5%. Only one patient was symptomatic. Three patients experienced de novo dyspareunia, which resolved in two cases after stitch removal. Sexual function was good, rating higher than three points for each of the domains including satisfaction, lubrication, desire, orgasm, and pain. CONCLUSION: Sacrospinous ligament fixation still is a valuable option for the treatment of vaginal vault prolapse. Sexual function is satisfactory, with few cases of de novo dyspareunia.

Visual Fixation for 3D Video Stabilization

Visual fixation is employed by humans and some animals to keep a specific 3D location at the center of the visual gaze. Inspired by this phenomenon in nature, this paper explores the idea to transfer this mechanism to the context of video stabilization for a handheld video camera. A novel approach is presented that stabilizes a video by fixating on automatically extracted 3D target points. This approach is different from existing automatic solutions that stabilize the video by smoothing. To determine the 3D target points, the recorded scene is analyzed with a stateof- the-art structure-from-motion algorithm, which estimates camera motion and reconstructs a 3D point cloud of the static scene objects. Special algorithms are presented that search either virtual or real 3D target points, which back-project close to the center of the image for as long a period of time as possible. The stabilization algorithm then transforms the original images of the sequence so that these 3D target points are kept exactly in the center of the image, which, in case of real 3D target points, produces a perfectly stable result at the image center. Furthermore, different methods of additional user interaction are investigated. It is shown that the stabilization process can easily be controlled and that it can be combined with state-of-theart tracking techniques in order to obtain a powerful image stabilization tool. The approach is evaluated on a variety of videos taken with a hand-held camera in natural scenes.

Minimal-invasive percutaneous reduction and transsacral screw fixation for U-shaped fractures

STUDY DESIGN Technical note and case series. OBJECTIVE To introduce an innovative minimal-invasive surgical procedure reducing surgery time and blood loss in management of U-shaped sacrum fractures. SUMMARY OF BACKGROUND Despite their seldom appearance, U-shaped fractures can cause severe neurological deficits and surgical management difficulties. According to the nature of the injury normally occurring in multi-injured patients after a fall from height, a jump, or road traffic accident, U-shaped fractures create a spinopelvic dissociation and hence are highly unstable. In the past, time-consuming open procedures like large posterior constructs or shortening osteotomies with or without decompression were the method of choice, sacrificing spinal mobility. Insufficient restoration of sacrococcygeal angle and pelvic incidence with conventional techniques may have adverse long-term effects in these patients. METHODS In a consecutive series of 3 patients, percutaneous reduction of the fracture with Schanz pins inserted in either the pedicles of L5 or the S1 body and the posterior superior iliac crest was achieved. The Schanz pins act as lever, allowing a good manipulation of the fracture. The reduction is secured by a temporary external fixator to permit optimal restoration of pelvic incidence and sacral kyphosis. Insertion of 2 transsacral screws allow fixation of the restored spinopelvic alignment. RESULTS Anatomic alignment of the sacrum was possible in each case. Surgery time ranged from 90 to 155 minutes and the blood loss was <50 mL in all 3 cases. Two patients had very good results in the long term regarding maintenance of pelvic incidence and sacrococcygeal angle. One patient with previous cauda equina decompression had loss of correction after 6 months. CONCLUSIONS Percutaneous reduction and transsacral screw fixation offers a less invasive method for treating U-shaped fractures. This can be advantageous in treatment of patients with multiple injuries.

Anterior fixation of unstable pelvic ring fractures using the modified Stoppa approach: mid-term results are independent on patients' age

PURPOSE Open surgical management of unstable pelvic ring injuries has been discussed controversially compared to percutaneous techniques in terms of surgical site morbidity especially in older patients. Thus, we assessed the impact of age on the outcome following fixation of unstable pelvic ring injuries through the modified Stoppa approach. METHODS Out of a consecutive series of 92 patients eligible for the study, 63 patients (mean age 50 years, range 19-78) were evaluated [accuracy of reduction, complications, failures, Majeed-Score, Oswestry Disability Questionnaire (ODI), Mainz Pain Staging System (MPSS)] at a mean follow-up of 3.3 years (range 1.0-7.9). Logistic multivariate regression analysis was performed to assess the outcome in relation to increasing patient age and/or Injury Severity Score (ISS). RESULTS Out of 63 patients, in 36 an "anatomic" reduction was achieved. Ten postoperative complications occurred in eight patients. In five patients, failure of fixation was noted at the anterior and/or posterior pelvic ring. In 49 patients, an "excellent" or "good" Majeed-Score was obtained; the mean ODI was 14 % (range 0-76 %); 50 patients reported either no or only minor chronic pelvic pain (MPSS). Only an increasing ISS conferred an increased likelihood of the occurrence of a non-anatomical reduction, a "poor" or "fair" Majeed-Score, or an ODI >20 %. CONCLUSIONS Increasing age did not impact the analysed parameters. Open reduction and internal fixation of the anterior pelvic ring through a modified Stoppa approach in unstable pelvic ring injuries did not result in an unfavourable outcome with increasing age of patients.

N2 fixation in marine heterotrophic bacteria: dynamics of environmental and molecular regulation.

Molecular and immunological techniques were used to examine N2 fixation in a ubiquitous heterotrophic marine bacterium, the facultative anaerobic Vibrio natriegens. When batch cultures were shifted from aerobic N-replete to anaerobic N-deplete conditions, transcriptional and post-translational regulation of N2 fixation was observed. Levels of nifHDK mRNA encoding the nitrogenase enzyme were highest at 140 min postshift and undetectable between 6 and 9 h later. Immunologically determined levels of nitrogenase enzyme (Fe protein) were highest between 6 and 15 h postshift, and nitrogenase activity peaked between 6 and 9 h postshift, declining by a factor of 2 after 12-15 h. Unlike their regulation in cyanobacteria, Fe protein and nitrogenase activity were present when nifHDK mRNA was absent in V. natriegens, indicating that nitrogenase is stored and stable under anaerobic conditions. Both nifHDK mRNA and Fe protein disappeared within 40 min after cultures were shifted from N2-fixing conditions (anaerobic, N-deplete) to non- N2-fixing conditions (aerobic, N-enriched) but reappeared when shifted to conditions favoring N2 fixation. Thus, unlike other N2-fixing heterotrophic bacteria, nitrogenase must be resynthesized after aerobic exposure in V. natriegens. Immunological detection based on immunoblot (Western) analysis and immunogold labeling correlated positively with nitrogenase activity; no localization of nitrogenase was observed. Because V. natriegens continues to fix N2 for many hours after anaerobic induction, this species may play an important role in providing "new" nitrogen in marine ecosystems.

Postoperative analgesic effect, of preoperatively administered dexamethasone, after operative fixation of fractured neck of femur: randomised, double blinded controlled study.

Background: Fractured neck of femur is a common cause of hospital admission in the elderly and usually requires operative fixation. In a variety of clinical settings, preoperative glucocorticoid administration has improved analgesia and decreased opioid consumption. Our objective was to define the postoperative analgesic efficacy of single dose of dexamethasone administered preoperatively in patients undergoing operative fixation of fractured neck of femur. Methods: Institutional ethical approval was granted and written informed consent was obtained from each patient. Patients awaiting for surgery at Cork University Hospital were recruited between July 2009 and August 2012. Participating patients, scheduled for surgery were randomly allocated to one of two groups (Dexamethasone or Placebo). Patients in the dexamethasone group received a single dose of intravenous dexamethasone 0.1 mg kg -1 immediately preoperatively. Patients in the placebo group received the same volume of normal saline. Patients underwent operative fixation of fractured neck of femur using standardised spinal anaesthesia and surgical techniques. The primary outcome was pain scores at rest 6 h after the surgery. Results: Thirty seven patients were recruited and data from thirty patients were analysed. The groups were similar in terms of patient characteristics. Pain scores at rest 6 h after the surgery (the principal outcome) were lesser in the dexamethasone group compared with the placebo group [0.8(1.3) vs. 3.9(2.9), mean(SD) p = 0.0004]. Cumulative morphine consumption 24 h after the surgery was also lesser in the dexamethasone group [7.7(8.3) vs. 15.1(9.4), mean(SD) mg, p = 0.04]. Conclusions: A single dose of intravenous dexamethasone 0.1 mg kg -1 administered before operative fixation of fractured neck of femur improve significantly the early postoperative analgesia. Trial registration: ClinicalTrials.gov identifier: NCT01550146, date of registration: 07/03/2012