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1.  Atypical language lateralization: an fMRI study in patients with cerebral lesions  
Functional Neurology  2013;28(1): 55 - 61 .
Summary
Differences in the lateralization of language processes between healthy subjects and patients with neurological complaints other than epilepsy have been less documented than those between healthy subjects and epilepsy patients. Moreover, the contribution of factors such as the location and type of lesion in determining interhemispheric shift of language function is poorly understood.
Sixty-seven patients who underwent presurgical evaluations at the Medical Imaging Center of the Imam Khomeini University Hospital, Tehran, and the same number of healthy controls, were recruited. The laterality index (LI) of language activation, calculated from two separate functional magnetic resonance imaging tasks, was compared between the patients and the age-/gender-/handedness-matched controls.
Chi square testing showed that the percentages of subjects with “typical” and “atypical” language dominance in the patient group were significantly different from the percentages recorded in the matched healthy controls for both tasks (p<0.005). Lesion type, lesion location, lesion hemisphere, presenting symptom and patient gender had no statistically significant effect on the hemispheric LI (p>0.05). In a logistic regression model including all potential determinants of atypical LI, age emerged as the only independent predictor (p<0.05, odds ratio=0.9).
Abnormal language lateralization is found in patients with a variety of cerebral lesions and with a diversity of clinical manifestations. In our selected population, symptom duration, lesion hemisphere and anatomical site of the lesion were not found to impact significantly on the development of an abnormal LI while patient age can independently predict the presence of an atypical LI.
PMCID: PMC3812717  PMID: 23731916
brain lesion ;  functional magnetic resonance imaging ;  language lateralization
2.  Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease 
PLoS ONE  2012;7(6):e37919.
The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (∼2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ∼90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.
doi:10.1371/journal.pone.0037919
PMCID: PMC3366996  PMID: 22675498
4.  Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences 
BMC Genomics  2011;12(Suppl 2):S4.
Background
A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels.
Results
We propose that better classification results can be obtained by tuning the taxonomic classifier to each matching length, reference gene, and taxonomic level. We present a novel taxonomic classifier MetaPhyler (http://metaphyler.cbcb.umd.edu), which uses phylogenetic marker genes as a taxonomic reference. Results on simulated datasets demonstrate that MetaPhyler outperforms other tools commonly used in this context (CARMA, Megan and PhymmBL). We also present interesting results by analyzing a real metagenomic dataset.
Conclusions
We have introduced a novel taxonomic classification method for analyzing the microbial diversity from whole-metagenome shotgun sequences. Compared with previous approaches, MetaPhyler is much more accurate in estimating the phylogenetic composition. In addition, we have shown that MetaPhyler can be used to guide the discovery of novel organisms from metagenomic samples.
doi:10.1186/1471-2164-12-S2-S4
PMCID: PMC3194235  PMID: 21989143
5.  Alignment and clustering of phylogenetic markers - implications for microbial diversity studies 
BMC Bioinformatics  2010;11:152.
Background
Molecular studies of microbial diversity have provided many insights into the bacterial communities inhabiting the human body and the environment. A common first step in such studies is a survey of conserved marker genes (primarily 16S rRNA) to characterize the taxonomic composition and diversity of these communities. To date, however, there exists significant variability in analysis methods employed in these studies.
Results
Here we provide a critical assessment of current analysis methodologies that cluster sequences into operational taxonomic units (OTUs) and demonstrate that small changes in algorithm parameters can lead to significantly varying results. Our analysis provides strong evidence that the species-level diversity estimates produced using common OTU methodologies are inflated due to overly stringent parameter choices. We further describe an example of how semi-supervised clustering can produce OTUs that are more robust to changes in algorithm parameters.
Conclusions
Our results highlight the need for systematic and open evaluation of data analysis methodologies, especially as targeted 16S rRNA diversity studies are increasingly relying on high-throughput sequencing technologies. All data and results from our study are available through the JGI FAMeS website http://fames.jgi-psf.org/.
doi:10.1186/1471-2105-11-152
PMCID: PMC2859756  PMID: 20334679
6.  Are the distributions of variations of circle of Willis different in different populations? – Results of an anatomical study and review of literature 
BMC Neurology  2006;6:22.
Background
Previous studies have proposed correlation between variants of the cerebral arterial circle (also known as circle of Willis) and some cerebrovascular diseases. Differences in the incidence of these diseases in different populations have also been investigated. The study of variations in the anatomy of the cerebral arterial circle may partially explain differences in the incidence of some of the cerebrovascular diseases in different ethnic or racial groups.
While many studies have investigated the variations in the anatomy of each segment of the cerebral arterial circle, few have addressed the variants of the cerebral arterial circle as a whole. Similarly, the frequency of occurrence of such variants in different ethnic or racial groups has not been compared.
Methods
102 brains of recently deceased Iranian males were dissected, in order to observe variations in the anatomy of the cerebral arterial circle. The dissection process was recorded on film and digitized. One resized picture from each dissection, showing complete circle has been made available online. The variations of the circle as whole and segmental variations were compared with previous studies.
Results
On the whole, the frequencies of the different variants of the entire cerebral arterial circle and segmental variations were comparable with previous studies.
More specifically variants with uni- and bilateral hypoplasia of posterior communicating arteries were the most common in our study, similar to the previous works. No hypoplasia of the precommunicating part of the left anterior cerebral artery (A1), aplasia of A1 or the precommunicating part of the posterior cerebral artery (P1) was seen. In 3% both right and left posterior communcating arteries were absent.
Conclusion
The anatomical variations found in the cerebral arterial circle of the Iranian males in the current study were not significantly different to those of more diverse populations reported in the literature. While taking into account potential confounding factors, the authors conclude that based on available studies, there is no evidence suggesting that the distributions of the variations of cerebral arterial circle differ in different populations.
doi:10.1186/1471-2377-6-22
PMCID: PMC1543654  PMID: 16796761
7.  Childhood trauma fatality and resource allocation in injury control programs in a developing country 
BMC Public Health  2006;6:117.
Background
Only a few studies have addressed the trimodal distribution of childhood trauma fatalities in lesser developed countries. We conducted this study to evaluate pre-hospital, Emergency Department (ED) and in-hospital distribution of childhood injury-related death for each mechanism of injury in Tehran, Iran. This information will be used for the efficient allocation of the limited injury control resources in the city.
Methods
We used Tehran's Legal Medicine Organization (LMO) database. This is the largest and the most complete database that receives information about trauma fatalities from more than 100 small and large hospitals in Tehran. We reviewed all the medical records and legal documents of the deceased registered in LMO from September 1999 to September 2000. Demographic and injury related characteristics of the children 15 years old or younger were extracted from the records.
Results
Ten percent of the 4,233 trauma deaths registered in LMO occurred among children 15 years old or younger. Motor vehicle crashes (MVCs) (50%), burns (18%), falls (6%) and poisonings (6%) were the most common mechanisms of unintentional fatal injuries. Prehospital, emergency department and hospital deaths comprised 42%, 20% and 37% of the trauma fatalities, respectively. While, more than 80% of fatal injuries due to poisoning and drowning occurred in prehospital setting, 92% of burn-related fatalities happened after hospital admission.
Conclusion
Injury prevention is the single most important solution for controlling trauma fatalities due to poisoning and drowning. Improvements in the quality of care in hospitals and intensive care units might substantially alleviate the magnitude of the problem due to burns. Improvements in prehospital and ED care might significantly decrease MVC and falls-related fatalities.
doi:10.1186/1471-2458-6-117
PMCID: PMC1471786  PMID: 16670023
8.  Prophylactic antibiotic for prevention of posttraumatic meningitis after traumatic pneumocephalus: design and rationale of a placebo-controlled randomized multicenter trial [ISRCTN71132784] 
Trials  2006;7:2.
Background
The purpose of this study is to compare the efficacy of prophylactic antibiotic for prevention of meningitis in acute traumatic pneumocephalus patients.
Methods
In this prospective, randomized controlled clinical trial, 200 selected head injury patients with traumatic pneumocephalus are randomly assigned to receive intravenous antibiotics (2 grams Ceftriaxone twice a day), oral antibiotics (Azithromycin) or placebo for at least 7 days after trauma. The patients will be followed for one month posttrauma.
Conclusion
The authors hope that this study helps clarifying the effectiveness and indications of antibiotics in prevention of meningitis in traumatic pneumocephalus after head injury and in specific subgroup of these patients.
doi:10.1186/1745-6215-7-2
PMCID: PMC1402327  PMID: 16542035
9.  Play dough as an educational tool for visualization of complicated cerebral aneurysm anatomy 
Background
Imagination of the three-dimensional (3D) structure of cerebral vascular lesions using two-dimensional (2D) angiograms is one of the skills that neurosurgical residents should achieve during their training. Although ongoing progress in computer software and digital imaging systems has facilitated viewing and interpretation of cerebral angiograms enormously, these facilities are not always available.
Methods
We have presented the use of play dough as an adjunct to the teaching armamentarium for training in visualization of cerebral aneurysms in some cases.
Results
The advantages of play dough are low cost, availability and simplicity of use, being more efficient and realistic in training the less experienced resident in comparison with the simple drawings and even angiographic views from different angles without the need for computers and similar equipment. The disadvantages include the psychological resistance of residents to the use of something in surgical training that usually is considered to be a toy, and not being as clean as drawings or computerized images.
Conclusion
Although technology and computerized software using the patients' own imaging data seems likely to become more advanced in the future, use of play dough in some complicated cerebral aneurysm cases may be helpful in 3D reconstruction of the real situation.
doi:10.1186/1472-6920-5-15
PMCID: PMC1274244  PMID: 15885141
10.  Comparison of artificial neural network and logistic regression models for prediction of mortality in head trauma based on initial clinical data 
Background
In recent years, outcome prediction models using artificial neural network and multivariable logistic regression analysis have been developed in many areas of health care research. Both these methods have advantages and disadvantages. In this study we have compared the performance of artificial neural network and multivariable logistic regression models, in prediction of outcomes in head trauma and studied the reproducibility of the findings.
Methods
1000 Logistic regression and ANN models based on initial clinical data related to the GCS, tracheal intubation status, age, systolic blood pressure, respiratory rate, pulse rate, injury severity score and the outcome of 1271 mainly head injured patients were compared in this study. For each of one thousand pairs of ANN and logistic models, the area under the receiver operating characteristic (ROC) curves, Hosmer-Lemeshow (HL) statistics and accuracy rate were calculated and compared using paired T-tests.
Results
ANN significantly outperformed logistic models in both fields of discrimination and calibration but under performed in accuracy. In 77.8% of cases the area under the ROC curves and in 56.4% of cases the HL statistics for the neural network model were superior to that for the logistic model. In 68% of cases the accuracy of the logistic model was superior to the neural network model.
Conclusions
ANN significantly outperformed the logistic models in both fields of discrimination and calibration but lagged behind in accuracy. This study clearly showed that any single comparison between these two models might not reliably represent the true end results. External validation of the designed models, using larger databases with different rates of outcomes is necessary to get an accurate measure of performance outside the development population.
doi:10.1186/1472-6947-5-3
PMCID: PMC551612  PMID: 15713231
11.  Bilateral asynchronous acute epidural hematoma : a case report 
Background
Bilateral extradural hematomas have only rarely been reported in the literature. Even rarer are cases where the hematomas develop sequentially, one after removal of the other. Among 187 cases of operated epidural hematomas during past 4 years in our hospital, we found one case of sequentially developed bilateral epidural hematoma.
Case Presentation
An 18-year-old conscious male worker was admitted to our hospital after a fall. After deterioration of his consciousness, an emergency brain CT scan showed a right temporoparietal epidural hematoma. The hematoma was evacuated, but the patient did not improve afterwards. Another CT scan showed contralateral epidural hematoma and the patient was reoperated. Postoperatively, the patient recovered completely.
Conclusions
This case underlines the need for monitoring after an operation for an epidural hematoma and the need for repeat brain CT scans if the patient does not recover quickly after removal of the hematoma, especially if the first CT scan has been done less than 6 hours after the trauma. Intraoperative brain swelling can be considered as a clue for the development of contralateral hematoma.
doi:10.1186/1471-227X-3-1
PMCID: PMC317469  PMID: 14697100
bialteral; epidual; hematoma
12.  Spinal subdural hematoma revealing hemophilia A in a child: A case report 
Background
Intraspinal bleeding especially in the form of subdural hematoma is rare in hemophiliacs. In the present case, we report a neglected hemophilic A child with such a problem and discuss its management options.
Case Presentation
A 9-year old hemophilic A boy presented with quadriparesis, confusion and meningismus after a fall 4 days previously. There was no sign of direct trauma to his back. His CT Scan and MRI showed spinal extramedullary hematoma extended from C5 to L2. We corrected the factor VIII level, but two days later, the patient's lower limbs weakened to 1/5 proximally as well as distally. We performed a laminectomy from T11 to L2, according to the level of the maximal neurological deficit and recent deterioration course. The subdural hematoma was evacuated. The hematoma in other spinal levels was managed conservatively. In the week following the operation, the patient's neurological status approached normal.
Conclusion
This case calls attention to the clinical manifestation, radiological features and management options of the rarely reported intraspinal hematoma in hemophilic children. Although this case has been managed operatively for its hematoma in the thoracolumbar region, at the same time it can be considered a successful case of conservative management of intraspinal hematoma in the cervicothoracic region. Both conservative and surgical management could be an option in managing these patients considering their neurological course.
doi:10.1186/1471-2326-3-2
PMCID: PMC194670  PMID: 12904268
Hematoma; Hemophilia; Spine; Subdural.
13.  Vestibular schwannoma with contralateral facial pain – case report 
BMC Neurology  2003;3:2.
Background
Vestibular schwannoma (acoustic neuroma) most commonly presents with ipsilateral disturbances of acoustic, vestibular, trigeminal and facial nerves. Presentation of vestibular schwannoma with contralateral facial pain is quite uncommon.
Case presentation
Among 156 cases of operated vestibular schwannoma, we found one case with unusual presentation of contralateral hemifacial pain.
Conclusion
The presentation of contralateral facial pain in the vestibular schwannoma is rare. It seems that displacement and distortion of the brainstem and compression of the contralateral trigeminal nerve in Meckel's cave by the large mass lesion may lead to this atypical presentation. The best practice in these patients is removal of the tumour, although persistent contralateral pain after operation has been reported.
doi:10.1186/1471-2377-3-2
PMCID: PMC153508  PMID: 12659656

Results 1-13 (13)