Popliteal Fossa Sarcomas

PURPOSE OF THE STUDY Soft tissue sarcomas of the popliteal fossa are extremely rare tumors of mesenchymal origin accounting for 3%-5% of all extremity sarcomas. However, data regarding the tumor type, neurovascular involvement, and administration of radiation therapy before or after resection are limited. This study aimed to report on popliteal fossa sarcomas analyzing data from two institutions based on a relatively large patient sample. MATERIAL AND METHODS Twenty-four patients (80%; 9 men and 15 women) with a popliteal fossa soft tissue sarcoma were included in this study. The reviewed patient data included sex, age, duration of complaints, interval to diagnosis, radiology, pre- and postoperative biopsy, tumor histology, surgery type, complications, and pre- and postoperative oncologic and functional outcomes. The minimum follow-up was 24 months. RESULTS The mean age of the patients was 48 ± 21.23 (range 3-72) years at the time of diagnosis. The mean follow-up was 41.79 ± 16.97 (range 24-120) months. The most common histological diagnoses were synovial sarcoma (6 patients), hemangiopericytoma (2 patients), soft tissue osteosarcoma (2 patients), unidentified fusiform cell sarcoma (2 patients), and myxofibrosarcoma (2 patients). Local recurrence after limb salvage was observed in six patients (26%). At the latest followup, 2 patients died of the disease, 2 patients were still alive with progressive lung disease and soft tissue metastasis, and the remaining 20 patients were free from the disease. CONCLUSIONS Microscopically positive margins may not be an absolute indication for amputation. Also, negative margins do not provide a guarantee that local recurrence will not occur. Lymph node or distant metastasis may be predictive factors for local recurrence rather than positive margins. Key words: fossa poplitea, sarcoma.

Aortoenteric fistulas - our experiences with surgeons' nightmare

BACKGROUND

Aortoenteric fistula (AEF) is a rare medical emergency, but one of the most difficult and threatening complications of gastrointestinal (GI) bleeding.

METHODS

A retrospective observational study was performed on patients hospitalised with GI bleeding and a definitive AEF diagnosis. We collected operative reports and medical records of patients operated on with an AEF diagnosis. The literature data and our data were analysed and discussed.

RESULTS

We admitted eight patients who were definitively diagnosed with AEF after reviewing our hospital records. All patients were male except one. Their ages ranged from 28 to 82, with a mean of 64. All but two patients had secondary AEF (SAEF). Four SAEF cases had open aortic surgery and three had a history of endovascular procedure. The main complaints of the patients on admission were poor general condition, abdominal pain, and GI bleeding. Melena was found in all patients. Hematemesis and hematochezia were other significant GI bleeding findings. Infected grafts were removed in all but one patient; extra-anatomical bypass surgery and bowel repairs were performed. One patient underwent endovascular repair. In all patients, the 30-day in-hospital mortality rate was 50%.

CONCLUSION

In patients presenting with GI bleeding, an aortoenteric fistula should be considered. The outcome depends on early diagnosis, the patient's medical status, the severity of infection, and the anatomic location of the affected aorta. A multidisciplinary approach, appropriate treatment planning and close follow-up after treatment lead to positive outcomes.

A new radiographic acetabular cup anteversion measurement method in total hip arthroplasty: a clinical study

BACKGROUND

The acetabular cup positioning is one of the most crucial steps affecting stability and wear rates in total hip arthroplasty. Different methods have been described for determining the anteversion of the acetabular cup in the literature. But there is still not a widely accepted method to assess the acetabular anteversion radiography. The aim of this study is to measure the acetabular anteversion angle on a single pelvis AP radiography with our method which was proven with an experimental study before.

MATERIALS AND METHODS

A total of 15 patients (8 males, 7 females) who underwent total hip arthroplasty and have had a pelvis computed tomography scans in our outpatient clinic were evaluated retrospectively. The anteversion angle was calculated in all of pelvis CT scans. For radiological measurement, the formula defined by the authors in an experimental model previously was used.

RESULTS

Statistically significant difference was not determined between radiographic and CT-based measurements (p = 0.207; p > 0.05). A statistically significant agreement was observed at a level of 98.8% between radiographic and CT-based measurements (ICC = 0.988; 95% CI 0.966-0.996; p < 0.01).

CONCLUSION

Assessment of the acetabular cup anteversion is very important to predict the possible complications after total hip arthroplasty. Although many methods have been defined for this purpose, each of these has advantages and disadvantages. In particular, with computed tomography method, the patient is exposed to excessive radiation, whereas we think that our method is a preferred method due to features not requiring additional equipment, low radiation exposure, being simple, cost-effectiveness, easily applicable and almost 100% accurate.

Increased risk of genetic and epigenetic instability in human embryonic stem cells associated with specific culture conditions

The self-renewal and differentiation capacities of human pluripotent stem cells (hPSCs) make them a promising source of material for cell transplantation therapy, drug development, and studies of cellular differentiation and development. However, the large numbers of cells necessary for many of these applications require extensive expansion of hPSC cultures, a process that has been associated with genetic and epigenetic alterations. We have performed a combinatorial study on both hESCs and hiPSCs to compare the effects of enzymatic vs. mechanical passaging, and feeder-free vs. mouse embryonic fibroblast feeder substrate, on the genetic and epigenetic stability and the phenotypic characteristics of hPSCs. In extensive experiments involving over 100 continuous passages, we observed that both enzymatic passaging and feeder-free culture were associated with genetic instability, higher rates of cell proliferation, and persistence of OCT4/POU5F1-positive cells in teratomas, with enzymatic passaging having the stronger effect. In all combinations of culture conditions except for mechanical passaging on feeder layers, we noted recurrent deletions in the genomic region containing the tumor suppressor gene TP53, which was associated with decreased mRNA expression of TP53, as well as alterations in the expression of several downstream genes consistent with a decrease in the activity of the TP53 pathway. Among the hESC cultures, we also observed culture-associated variations in global gene expression and DNA methylation. The effects of enzymatic passaging and feeder-free conditions were also observed in hiPSC cultures. Our results highlight the need for careful assessment of the effects of culture conditions on cells intended for clinical therapies.

Specific lectin biomarkers for isolation of human pluripotent stem cells identified through array-based glycomic analysis

Rapid and dependable methods for isolating human pluripotent stem cell (hPSC) populations are urgently needed for quality control in basic research and in cell-based therapy applications. Using lectin arrays, we analyzed glycoproteins extracted from 26 hPSC samples and 22 differentiated cell samples, and identified a small group of lectins with distinctive binding signatures that were sufficient to distinguish hPSCs from a variety of non-pluripotent cell types. These specific biomarkers were shared by all the 12 human embryonic stem cell and the 14 human induced pluripotent stem cell samples examined, regardless of the laboratory of origin, the culture conditions, the somatic cell type reprogrammed, or the reprogramming method used. We demonstrated a practical application of specific lectin binding by detecting hPSCs within a differentiated cell population with lectin-mediated staining followed by fluorescence microscopy and flow cytometry, and by enriching and purging viable hPSCs from mixed cell populations using lectin-mediated cell separation. Global gene expression analysis showed pluripotency-associated differential expression of specific fucosyltransferases and sialyltransferases, which may underlie these differences in protein glycosylation and lectin binding. Taken together, our results show that protein glycosylation differs considerably between pluripotent and non-pluripotent cells, and demonstrate that lectins may be used as biomarkers to monitor pluripotency in stem cell populations and for removal of viable hPSCs from mixed cell populations.

Equivalence of conventionally-derived and parthenote-derived human embryonic stem cells

Background

As human embryonic stem cell (hESC) lines can be derived via multiple means, it is important to determine particular characteristics of individual lines that may dictate the applications to which they are best suited. The objective of this work was to determine points of equivalence and differences between conventionally-derived hESC and parthenote-derived hESC lines (phESC) in the undifferentiated state and during neural differentiation.

Methodology/Principal Findings

hESC and phESC were exposed to the same expansion conditions and subsequent neural and retinal pigmented epithelium (RPE) differentiation protocols. Growth rates and gross morphology were recorded during expansion. RTPCR for developmentally relevant genes and global DNA methylation profiling were used to compare gene expression and epigenetic characteristics. Parthenote lines proliferated more slowly than conventional hESC lines and yielded lower quantities of less mature differentiated cells in a neural progenitor cell (NPC) differentiation protocol. However, the cell lines performed similarly in a RPE differentiation protocol. The DNA methylation analysis showed similar general profiles, but the two cell types differed in methylation of imprinted genes. There were no major differences in gene expression between the lines before differentiation, but when differentiated into NPCs, the two cell types differed in expression of extracellular matrix (ECM) genes.

Conclusions/Significance

These data show that hESC and phESC are similar in the undifferentiated state, and both cell types are capable of differentiation along neural lineages. The differences between the cell types, in proliferation and extent of differentiation, may be linked, in part, to the observed differences in ECM synthesis and methylation of imprinted genes.

Friedreich's ataxia induced pluripotent stem cells model intergenerational GAA⋅TTC triplet repeat instability

The inherited neurodegenerative disease Friedreich's ataxia (FRDA) is caused by GAA⋅TTC triplet repeat hyperexpansions within the first intron of the FXN gene, encoding the mitochondrial protein frataxin. Long GAA⋅TTC repeats cause heterochromatin-mediated gene silencing and loss of frataxin in affected individuals. We report the derivation of induced pluripotent stem cells (iPSCs) from FRDA patient fibroblasts by transcription factor reprogramming. FXN gene repression is maintained in the iPSCs, as are the global gene expression signatures reflecting the human disease. GAA⋅TTC repeats uniquely in FXN in the iPSCs exhibit repeat instability similar to patient families, where they expand and/or contract with discrete changes in length between generations. The mismatch repair enzyme MSH2, implicated in repeat instability in other triplet repeat diseases, is highly expressed in pluripotent cells and occupies FXN intron 1, and shRNA silencing of MSH2 impedes repeat expansion, providing a possible molecular explanation for repeat expansion in FRDA.

DNA methylation in embryonic stem cells

Embryonic stem cells (ESCs) are pluripotent, self-renewing cells. These cells can be used in applications such as cell therapy, drug development, disease modeling, and the study of cellular differentiation. Investigating the interplay of epigenetics, genetics, and gene expression in control of pluripotence and differentiation could give important insights on how these cells function. One of the best known epigenetic factors is DNA methylation, which is a major mechanism for regulation of gene expression. This phenomenon is mostly seen in imprinted genes and X-chromosome inactivation where DNA methylation of promoter regions leads to repression of gene expression. Differential DNA methylation of pluripotence-associated genes such as Nanog and Oct4/Pou5f1 has been observed between pluripotent and differentiated cells. It is clear that tight regulation of DNA methylation is necessary for normal development. As more associations between aberrant DNA methylation and disease are reported, the demand for high-throughput approaches for DNA methylation analysis has increased. In this article, we highlight these methods and discuss recent DNA methylation studies on ESCs.

Dissection of the abdominal aorta in a child with Takayasu's arteritis

Takayasu's arteritis is a chronic inflammatory disease that primarily involves the aorta and its main branches. Varying degrees of narrowing, occlusion, or dilatation develop in the involved vessel segments. However, dissection of the aorta is quite rare in this disease, and it may develop particularly after angioplasty. We report a very rare case of Takayasu's arteritis with dissection of the abdominal aorta just distal to the origin of the inferior mesenteric artery in a 9-year-old girl. She was treated conservatively with close follow-up. At the end of 1 year's follow-up, the dissection of the aorta did not show progression, and new lesions were not identified. To our knowledge, this patient is the youngest child presented with arterial dissection as the initial manifestation of the disease.

Parallel protein secondary structure prediction based on neural networks

Protein secondary structure prediction has a fundamental influence on today's bioinformatics research. In this work, binary and tertiary classifiers of protein secondary structure prediction are implemented on Denoeux belief neural network (DBNN) architecture. Hydrophobicity matrix, orthogonal matrix, BLOSUM62 and PSSM (position specific scoring matrix) are experimented separately as the encoding schemes for DBNN. The experimental results contribute to the design of new encoding schemes. New binary classifier for Helix versus not Helix ( approximately H) for DBNN produces prediction accuracy of 87% when PSSM is used for the input profile. The performance of DBNN binary classifier is comparable to other best prediction methods. The good test results for binary classifiers open a new approach for protein structure prediction with neural networks. Due to the time consuming task of training the neural networks, Pthread and OpenMP are employed to parallelize DBNN in the hyperthreading enabled Intel architecture. Speedup for 16 Pthreads is 4.9 and speedup for 16 OpenMP threads is 4 in the 4 processors shared memory architecture. Both speedup performance of OpenMP and Pthread is superior to that of other research. With the new parallel training algorithm, thousands of amino acids can be processed in reasonable amount of time. Our research also shows that hyperthreading technology for Intel architecture is efficient for parallel biological algorithms.

A new seed selection algorithm that maximizes local structural similarity in proteins

The PHI-BLAST algorithm for protein sequence alignment takes a query sequence and searches a protein database for a small seed or region of high similarity and extends this alignment to produce the total alignment for sequences. Clearly, the success of this approach depends on the quality of the seeds. We propose an algorithm that maximizes the likelihood of seeds sharing the same local structure in both the query and known sequences. This was tested on the 2290 protein sequences in the PISCES database. Our new algorithm results in an effective a priori estimate of seed structural quality.

Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property

Information about local protein sequence motifs is very important to the analysis of biologically significant conserved regions of protein sequences. These conserved regions can potentially determine the diverse conformation and activities of proteins. In this work, recurring sequence motifs of proteins are explored with an improved K-means clustering algorithm on a new dataset. The structural similarity of these recurring sequence clusters to produce sequence motifs is studied in order to evaluate the relationship between sequence motifs and their structures. To the best of our knowledge, the dataset used by our research is the most updated dataset among similar studies for sequence motifs. A new greedy initialization method for the K-means algorithm is proposed to improve traditional K-means clustering techniques. The new initialization method tries to choose suitable initial points, which are well separated and have the potential to form high-quality clusters. Our experiments indicate that the improved K-means algorithm satisfactorily increases the percentage of sequence segments belonging to clusters with high structural similarity. Careful comparison of sequence motifs obtained by the improved and traditional algorithms also suggests that the improved K-means clustering algorithm may discover some relatively weak and subtle sequence motifs, which are undetectable by the traditional K-means algorithms. Many biochemical tests reported in the literature show that these sequence motifs are biologically meaningful. Experimental results also indicate that the improved K-means algorithm generates more detailed sequence motifs representing common structures than previous research. Furthermore, these motifs are universally conserved sequence patterns across protein families, overcoming some weak points of other popular sequence motifs. The satisfactory result of the experiment suggests that this new K-means algorithm may be applied to other areas of bioinformatics research in order to explore the underlying relationships between data samples more effectively.

Congestive heart failure associated with chronic venous insufficiency and leg ulcers secondary to an arteriovenous fistula caused by a shotgun wound 15 years ago

We present a 65-year-old man who had a significant arteriovenous fistula between the right arteria profunda femoralis and vena profunda femoralis. He had evidence of chronic venous insufficiency and chronic leg ulcers on his right leg, and he had clinical findings of congestive heart failure. An arteriovenous fistula was responsible for all of clinical situation that had been caused by a shotgun wound 15 years ago. Using ultrasonography, after palpating a marked thrill and mass during physical examination, established the diagnosis of arteriovenous fistula. Angiography was performed both to delineate the suspected vascular anatomy and to show the coronary arteries. The patient was operated on and no complication was experienced during or after the procedure. Dramatic improvement was seen in the clinical picture just after surgery, and heart size markedly reduced both on chest X-ray and echocardiographic examination.

Intra- and perioral shooting fatalities

Determination of the manner of death in the case of intra- and perioral firearm wounds can be difficult especially if death scene investigation is unclear and inadequate. In this study, we investigated some characteristics of these firearm wounds which were autopsied in Istanbul. During the 5-year period from 1991 through 1995, there were 15 intra- and perioral firearm fatalities investigated. In all the cases, only one shot was fired into the mouth. They constituted 1% of all the firearm fatalities. The mean age of the victims was 27 years and males constituted 73.3% of the victims. Most of the wounds were caused by handguns. Homicides accounted for 53.3% of these deaths. Three of 15 cases could not be identified as intraoral firearm wounds by general practitioners during the scene investigations.

Comparison between semiquantitative interictal Tc-99m HMPAO SPECT and clinical parameters in children with partial seizures

The aim of the present study was to correlate between clinical parameters (age, age of onset, frequency and duration of seizures) and semiquantitative interictal SPECT parameters in children with partial seizures. We obtained 30 patients who had hypoperfusion in interictal SPECT, retrospectively. All patients underwent a detailed clinical examination, electroencephalography (EEG) investigation and brain computerized tomography (CT) and/or magnetic resonance imaging (MRI). Single photon emission computerized tomography (SPECT) studies were evaluated visually and by calculating semiquantitative parameters (the degree (asymmetry index, AI) and extent (number of ROI) of hypoperfusion). Visual analysis detected ipsilateral hypoperfusion in 23 (76%) patients with a unilateral focus and contralateral hypoperfusion in seven patients. We found an inverse correlation between the age at onset of seizure (r = -0.40, P = 0.025), frequency of seizures(but positive correlation; r = 0.77, P = 0.000) and AI. Number of ROIs showed a moderate correlation with the frequency of seizures (r = 0.67, P = 0.000), while correlation of the age at onset of seizures was not significant. This study performed in pediatric patients also suggested that either SPECT parameters may be used for correlating with clinical parameters.

Deaths among homeless people in Istanbul

The number of the homeless people in Istanbul, one of the largest cities in the world, is at present unknown. There has been no previous study in Turkey on cases and causes of death occurring among these individuals. In this paper, documents and autopsy reports of the Mortuary Section of the Council of Forensic Medicine, Istanbul, covering the period January 1st, 1991-December 31st, 1995, were reviewed. We established that there were 126 cases of death among homeless individuals in Istanbul during this period, 120 of them being males (95%), four (3%) females, and two (2%) transsexuals. Ninety-four corpses were found outdoors, 32 indoors. No personal documents, such as identity cards, were found in 110 individuals (87%), whereas only 16 individuals could be identified. Most deaths occurred in the age group of 41-50 years. One hundred and three of the cases (82%) died in the cold season between October and April. The deaths of 98 cases were attributable to natural causes, whereas the remaining 28 cases died from unnatural causes. Respiratory tract diseases occupied the first rank among cases of death from natural causes (44%). Alcohol abuse and other infections were further striking factors contributing to the fatal outcome. This is the first retrospective study on this topic in Turkey. However, more detailed and anterospectively programmed studies on this subject, a growing social problem, should be carried out.

Firearm fatalities in Edirne, 1984-1997

During the 14-year period from 1984 to 1997 there were 85 firearm fatalities investigated by the Department of Forensic Medicine and the Department of Pathology in Edirne, Turkey. We determined the characteristics of these 85 firearm deaths which comprised 17.03% of all medicolegal autopsies. The overall incidence was 1.58 per 100,000 population. The median age was 35.5 years. Fifty-four percent of the victims were aged between 20 and 40 years. Males constituted 82% of the victims. The most frequent manner of death was homicide (68.3%). Handguns accounted for 62.4% of the weapons used. The most common sites for the firearm entrance wounds were both head-neck-nape (32.8%) and chest (32%). In conclusion, our study shows that, in spite of legal restrictions, illegal access to firearms is easy and deaths by firearms are still increasing.