Zherlock: an open source data analysis software

Zherlock is an open source software that provides state-of-the-art data analysis tools to the user in an intuitive and flexible way. It is a front-end to different numerical "engines" to produce a seamless integration of algorithms written in different computer languages. Of particular interest is creating an interface to high-level scientific languages such as Octave (a Matlab clone) and R (an S-PLUS clone) to enable efficient porting of new data analytical methods. Zherlock uses advanced scientific visualization tools in 2-D and 3-D and has been extended to work on virtual reality (VR) systems. Central to Zherlock is a visual programming environment (VPE) which enables diagram based programming. These diagrams consist of nodes and connection lines where each node is an operator or a method and lines describe the flow of data between nodes. A VPE is chosen for Zherlock because it forms an effective way to control the processing pipeline in complex data analyses. The VPE is similar in functionality to other programs such as IRIS Explorer, AVS or LabVIEW.

[Are titanium implants superior to gold implants in the tympanic cavity?]

BACKGROUND

Gold implants in reconstructive surgery of the middle ear have proved to work sufficiently: That applies to tympanic cavity conditions without signs of chronic inflammation as also to the bacterially infected middle ear. For some years titanium implants are also in the use and established as well. The biocompatibility of titanium, the clinical and the audiological results are satisfactory. When using gold-prostheses in stapes surgery however, the still unsolved problem of occasional deafness has to be considered.

PATIENTS

The clinical and functional results of middle ear surgery were examined retrospectively. There was no preselection of patients. 53 patients underwent middle ear surgery with titanium prostheses, 42 patients with gold prostheses.

RESULTS

Due to their material properties and due to their delicate shape titanium prostheses (PORP, TORP) can be inserted into the tympanic cavity more simply and with better fit. The audiological results of gold and titanium prostheses are comparable. The extruding rate of the gold prostheses is substantial, whereas the extruding rate of titanium is negligible.

CONCLUSION

The functional results of both materials are comparable. Due to the high extruding rates of gold prostheses titanium is clearly superior.

[Mechanical ileus caused by a Provox voice prosthesis -- an "iatrogenic" enteral complication in voice prosthesis rehabilitation of laryngectomees]

BACKGROUND

During the exchange of a defect Provox-I voice prosthesis followed by an insertion of a Provox-II voice prosthesis the esophageal part of the prosthesis often is pushed into the esophagus, as the enteral passage of the prosthesis was thought to be less traumatic for the voice shunt in comparison to a complete extraction of the stiff esophageal flange through the tracheostoma. This procedure is also recommended in the users video of the ATOS company.

CASE

A laryngectomized patient, in whom the change of the voice prosthesis was carried out pushing the esophageal flange of the prosthesis into the esophagus, developed a mechanical ileus, as the voice prosthesis got stuck in Bauhin's valve. This resulted in the necessity of a laparatomy for removal of the voice prosthesis.

CONCLUSION

During the replacement of the Provox voice prosthesis it is necessary in all cases that the esophageal remnant of the voice prosthesis either is pulled out of the tracheoesophageal shunt via the tracheostoma or removed with a guide-wire transorally.

[Functional long-term results following hemipharyngo-hemilaryngectomy and microvascular reconstruction using the radial forearm flap]

BACKGROUND

The surgical treatment of advanced hypopharyngeal carcinomas with infiltration of the laryngeal skeleton often includes total laryngectomy for functional reasons, although tumor infiltration is limited to only one half of the larynx. When not only the infiltrated half of the thyroid cartilage but also the cricoid cartilage of the involved side has to be removed, in spite of adequate reconstruction using local or pedicled flaps (f. e. pectoralis major flap) persistent dysphagia and aspiration prevent oral food intake and closure of the tracheostoma. These functional disturbances are increased by the negative effects of postoperative radiotherapy, which has to be applied in most of the cases for oncological reasons. The routine use of free, microvascularly anastomosed flaps for reconstruction of defects following removal of extended carcinomas of the mouth, the tongue or the oropharynx as well as in total pharyngolaryngectomy led to considerable improvements in functional rehabilitation of swallowing and speech. An improved functional outcome is also reported following partial resections of the hypopharynx and reconstruction by means of these thin and pliable transplants (f. e. replacement of the entire posterior hypopharyngeal wall).

METHOD

Since 1991 in 30 patients with a T3 or T4 squamous cell carcinoma of the piriform sinus a complete hemipharyngo-hemilaryngectomy including resection of the involved thyroid and cricoid cartilage was carried out. For reconstruction a radial forearm flap was dissected with two separate epithelial islands: The smaller island was used to create an epithelialized endolarynx, which allows complete closure of the glottis by the healthy vocal chord. With the bigger second island the hypopharynx was replaced, creating a highly mobile, adaptable neo-piriform-sinus, which was suspended to the ipsilateral half of the hyoid bone. Parts of the both islands were sutured together to create a new aryepiglottic fold. The laryngeal skeleton intentionally was not reconstructed.

RESULTS

One year evaluation revealed 25 of the 30 patients swallowing normal diet and being decannulated. 4 patients could take up a soft diet, 1 patient with a severe stricture at the entrance to the esophagus however had to be laryngectomized for functional reasons. Most of the patients judged their postoperative voice as satisfactory, although there was a different impairment of the voice (quite normal up to a marked hoarseness). During follow-up (up to 10 years) 4 patients developed a local recurrence, in 3 cases a secondary metastasis after neck dissection occurred. In 3 patients a second primary was detected (oropharynx 2, esophagus 1), 3 patients died with lung metastases.

CONCLUSION

Rehabilitation of normal swallowing and a satisfying voice restoration without a permanent tracheostoma following complete hemipharyngo-hemilaryngectomy can obviously be improved by the use of microvascular transplants (here radial forearm flap) in comparison to other surgical techniques. The necessary radical extirpation of these extended carcinomas also is guaranteed like in total laryngectomy, so that in spite of the advanced tumor stage an organ preserving surgery can be offered. A prolonged course of swallowing rehabilitation however has to be taken into consideration.

A highly specific one-step PCR - assay for the rapid discrimination of enteropathogenic Yersinia enterocolitica from pathogenic Yersinia pseudotuberculosis and Yersinia pestis

Based on differences within the yopT-coding region of Yersinia. enterocolitica, Y pseudotuberculosis and Y pestis, a rapid and sensitive one-step polymerase chain reaction assay with high specificity for pathogenic Y enterocolitica was developed. By this method pathogenic isolates of Y enterocolitica can be easily identified and discriminated from other members of this genus. The entire coding sequence of the yopT effector gene of Y. pseudotuberculosis Y36 was determined.

[Tracheostomy valve with integrated cough flap for improving hands-free speech in laryngectomized patients--development and clinical applications]

BACKGROUND

Following successful voice restoration after laryngectomy either by a voice prosthesis, a surgical shunt or microvascular laryngoplasty, a further goal in rehabilitation is the insertion of a tracheostoma valve, which enables the patient to speak without using his fingers for closure of the tracheostoma. One important disadvantage of the tracheostoma valves, which are available today, is the necessity of removal of the valve in case of coughing, because the valve could be thrown from the stoma by the strong air flow during coughing. As many laryngectomies suffer from chronic bronchitis, this coughing problem is one of the reasons why only few patients could be provided with this useful aid.

METHOD

At the department of biomedical engineering of the faculty of medicine at the university of Groningen, the Netherlands, 1994 two prototypes of a tracheostoma valve with an integrated cough lid were developed. These devices contain two separate valve systems: the normal speaking valve and a special coughing valve, which opens at a certain air flow and closes automatically after the coughing attack. Thus no manipulations are necessary during coughing, the patient can speak undisturbed. The ADEVA company (Lübeck, Germany) undertook the industrial production of this new type of tracheostoma valve creating different modifications of the prototype #2.

PATIENTS

In four series with 6-8 patients per group the modified tracheostoma valves were tested clinically and the occurring faults or lack of correct function eliminated by small changes in the production.

RESULTS

Meanwhile a suitable model for routine use is available, which was tested in 30 patients so far. This suitability was achieved by improvements in the valve mechanism, the valve seal and the adjustment mechanisms for the individual pressure level of the speaking and the coughing valve.

CONCLUSION

The newly developed tracheostoma valve with integrated coughing lid (Window, ADEVA-medical Company, Lübeck, Germany) provides further improvement in speech rehabilitation of laryngectomies. The low acceptance of tracheostoma valves, which enable the patient to speak without using his fingers for closure of the tracheostoma, possibly may be raised by this new aid.

[Thrombosis of the basilar artery--a rare differential sudden deafness diagnosis and vestibular failure]

BACKGROUND

Occlusion of basilar artery is a rare and life-threatening event. A quick and safe diagnosis and initiation of adequate therapy are decisive. For the ENT-specialist it is important to know that this thrombosis, which runs a lethal course in many cases, can develop with a disturbance of hearing and/or vestibular function as initial symptoms.

PATIENTS

Reported are four cases of thrombosis of the basilar or vertebral artery. Two out of four patients contacted the ENT emergency unit because of symptoms of acute vestibular neuritis, one patient was previously diagnosed with sudden deafness by a local ENT-specialist, one patient was treated for hypertension induced epistaxis in one of our wards. Only one patient initially presented additional neurological symptoms, causing suspicion for a brainstem lesion as well. However these symptoms were only noticed on close examination. By immediate anticoagulation therapy (with Heparin) progress of thrombosis could be avoided. The patient showed a complete recovery and was free of any symptoms two years after thrombosis. Two of the other two patients developed a delayed onset of neurological symptoms next to the initial symptoms of vestibular and cochlear affection (within 24 hours), therefore diagnosis of thrombosis was late and despite of immediate anticoagulation therapy (with Heparin) both patients died. The one patient treated for hypertension induced epistaxis developed only discrete symptoms of basilar artery thrombosis, nevertheless he was diagnosed and treated immediately. He made a complete recovery and was dismissed two weeks later.

CONCLUSIONS

It is therefore necessary to carefully control and sometimes correct diagnosis in cases of sudden deafness and acute vestibular neuritis. Especially additional neurological symptoms indicate the necessity of a MRI-angiogram or CT-(angiography)scan to exclude thrombosis of the basilar artery.

Aflatoxin B1-induced mitotic recombination in L5178Y mouse lymphoma cells

Aflatoxin B1 is a human hepatocarcinogen. It is also a known point mutagen in bacteria and mammalian cells. This mutagenic activity may be at least partly responsible for its carcinogenic activity. However, recent studies show that aflatoxin B1 induces mitotic recombination in the yeast Saccharomyces cerevisiae. Because numerous reports have implicated mitotic recombination in mechanisms leading to carcinogenesis and because no one has shown that aflatoxin B1 induces recombination in mammalian cells, we decided to examine the ability of aflatoxin B1 to induce recombination in a mammalian cell line. We used a combination of methods, analysis for loss of heterozygosity and whole chromosome in situ hybridization, to identify mechanisms of chromosome mutation, including mitotic recombination in the mammalian L5178Y mouse lymphoma cell system. Our experiments revealed that mitotic recombination caused approximately 60% or more of the aflatoxin B1-induced mutagenic lesions in this cell system. Thus, mitotic recombination plays an important role in aflatoxin B1-induced mutagenesis in mammalian cells and possibly in chemically induced mutagenesis and carcinogenesis. This work suggests that multiple genetic lesions may be involved in aflatoxin B1-induced pathology.

Free-flap reconstruction for laryngeal preservation after partial laryngectomy in patients with extended tumors of the oropharynx and hypopharynx

Partial laryngeal resection often results in major aspiration problems, making larynx preservation during surgical removal of tumors of the oropharynx and hypopharynx impossible. However, free flaps can be used to reconstruct perilaryngeal tissue, thus preserving the larynx and ensuring a better quality of life for patients. We present the results of forearm free-flap reconstruction of the supraglottis in 22 patients who underwent resections of extended squamous cell carcinomas of the oropharynx and hypopharynx. A total of 9 patients had T3 lesions and 13 had T4 lesions. All patients were additionally treated with radiation therapy alone (to 70 Gy) or in combination with chemotherapy (Cisplatin; 5-fluorouracil). The mean follow-up was 2.4 years. In four patients, tracheostomy could be closed. Five patients suffered from severe aspiration, one of whom had to undergo a laryngectomy. Six patients had mild aspiration and 7 patients had no aspiration, but extensive edema made decanulation impossible. A total of 13 patients were free of disease, 4 patients died of disease, 1 patient died as the result of a second primary cancer and 1 patient died of other causes. Three patients are alive with persistent tumor. Although the majority of patients experienced a better quality of life as a result of larynx preservation, aspiration has remained a problem following treatment.

[Outcome after resection of extensive oropharyngeal carcinomas and defect coverage by microvascular anastomosis of a radialis flap]

BACKGROUND

Extensive tumors of the oropharynx require an open approach and plastic reconstruction for good oncologic and functional results.

PATIENTS AND METHODS

From January 1988 through December 1996 at the Department of Otolaryngology, Head and Neck Surgery, of the University of Würzburg, 62 patients with extensive tumors of the oropharynx underwent surgical treatment (T2 = 6, T3 = 24, T4 = 32). In 40 patients, the resection was performed via a median mandibulotomy approach, in 22 patients using a lateral pharyngotomy. All patients underwent postoperative radiotherapy up to 70 Gy.

RESULTS

Using the Kaplan-Meier method, the five-year survival was 80% for T2, 52% for T3, and 22% for T4. Four patients (7%) presented with a second primary carcinoma, and one also had a third carcinoma. Seven patients who died of T3- and T4-tumors had distant metastases, among them 5 patients who were free of local disease. A regular oral diet was possible on average 14 days postoperatively. All patients underwent tracheostomy. Ninety percent of them were decanulated one year postoperatively.

CONCLUSIONS

Resection of extensive carcinomas of the oropharynx and microvascular reconstruction produces good oncological and functional results. The best access to extensive tumors is provided by a mandibulotomy. The advantage of this excellent approach outweighs an increasing morbidity in occasional cases.

Cytotoxic and genotoxic effects of paclitaxel (Taxol) and radiation in a squamous cell carcinoma cell line of the larynx

Paclitaxel (Taxol) is an antimicrotubular agent which blocks the cells in the G2/M phase of the cell cycle. Because of this mechanism it is presumed that this drug could function as a radiation sensitizer. The cytotoxic and genotoxic effects of paclitaxel and a combination of paclitaxel and radiation were studied in the human laryngeal carcinoma cell line HLac 79. The growth of the cells was significantly reduced at concentrations of paclitaxel as low as 10 nM. Flow cytometry data showed a G2/M block after exposure to paclitaxel. Radiation at 12 and 24 h after drug treatment exerted an additive but no radiation sensitizing effect. As genotoxic effect paclitaxel induced multinucleated cells, possibly in a synergistic manner, at low concentrations (10 nM) and radiation doses up to 3 Gy.

[Voice prostheses with sound-producing metal reed element--an experimental study and initial clinical results]

BACKGROUND

Following total laryngectomy the voice is produced by esophageal speech as well as with voice prostheses by vibrations of pharyngeal mucosal folds. This pharyngeal sound normally has a significantly lower fundamental frequency than the healthy voice (men about 120 Hz, women about 240 Hz, pharyngeal voice about 70 Hz), which is a handicap especially for female laryngectomy patients. In order to improve the postlaryngectomy voice, a new type of voice prostheses containing an integrated sound-producing metallic reed element was developed (ADEVA Company, Lübeck, Germany).

METHODS/PATIENTS

Thirty-five of these new sound-producing voice prostheses were tested in vitro for different prosthesis-specific physical parameters (pressure, flow, sound pressure, flow resistance, frequency range). In 15 voice prosthesis speakers, a sound-producing prosthesis was introduced during a routine outpatient visit. Besides measurement of the above mentioned physical parameters in patients with conventional and sound-producing prostheses, the resulting voice as also evaluated by means of a video recording.

RESULTS

In vitro all prostheses with the metallic reed element produced a clear sound. Flow resistance of the prostheses was slightly elevated by the reed element. Insertion of the prostheses was hindered by the reed element. Period of uninterrupted sound production was prolonged after insertion of a sound-producing prosthesis and patients could speak on a lower pressure level, but the sound of the reed element was permanently distinguishable only in 6 of 15 patients.

CONCLUSIONS

In principle a variation of the pharyngeal voice by means of a sound producing element, which is integrated into a voice prosthesis, is possible. The current design of the metallic reed element tested is not yet suitable for routine clinical use: 1. The reed element is too sensitive and is easily damaged during insertion, so the insertion device has to be improved. 2. The sound producing element is blocked by small amounts of tracheal secretions, so that this element should be replaceable separately without requiring removal of the silicone value (if possible by the patient himself). Prior to insertion of the sound producing voice prosthesis the maximum air flow through the shunt should be measured to determine if the patient can produce the necessary air flow for activation of the reed element. A further improvement for these special types of voice prostheses would be a sound producing element, which generates a variable frequency of sound. Limiting the patient to only one fundamental frequency creates a monotone, which does not sound naturally. Initial progress toward a sound-producing voice prostheses has been made. This should be followed by the necessary improvements in order to improve the feasibility of this design for routine clinical use.

[Indications and risks of manual lymph drainage in head-neck tumors]

BACKGROUND

Secondary lymphedema of the head and neck can develop as a result of obstruction of lymphatic channels following the surgical removal of lymph nodes and fibrosis due to irradiation. This can be treated with manual lymphatic drainage. An increase of tumor recurrence due to this therapy is at controversial discussion.

PATIENTS

In a retrospective study 191 patients treated for head and neck cancer were questioned on occurrence of lymphedema and therapy with manual lymphatic drainage.

RESULTS

100 patients had received lymphatic drainage, whereas 91 patients belonged to the group without lymphatic drainage therapy. In 37 cases a tumor recurrence or local metastases were reported, 18 of whom had received lymphatic drainage and 19 belonged to the control group. Among these 37 patients neither the group with lymphatic drainage nor the control group differed significantly concerning stage of cancer, histopathological grading, the in sano/non in sano resection of the primary tumor and a lymphangiosis carcinomatosa. An increased recurrence rate among patients who underwent a lymphatic drainage therapy could not be found.

CONCLUSION

A lymphatic drainage therapy for patients presenting with lymphedema after the oncological therapy does not increase the rate of local recurrencies. Moreover it improves the quality of life after the cancer therapy. As only few data are available for cases with non in sano surgery and tumors with lymphangiosis carcinomatosa these cases should be excluded from a lymphatic drainage therapy. A spreading of occult tumor cells in these patients might be possible.

Geological record and reconstruction of the late Pliocene impact of the Eltanin asteroid in the Southern Ocean

In 1995, an expedition on board the research vessel FS Polarstern explored the impact site of the Eltanin asteroid in the Southern Ocean, the only known asteroid impact into a deep ocean basin. Analyses of the geological record of the impact region place the event in the late Pliocene (approximately 2.15 Myr) and constrain the size of the asteroid to be >1 km. The explosive force inferred for this event places it at the threshold of impacts believed to have global consequences, and its study should therefore provide a baseline for the reconstruction and modelling of similar events, which are common on geological timescales.