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1.  Schwannoma of the brachial plexus; report of two cases involving the C7 root 
Brachial plexus schwannomas are rare tumors. They are benign nerve sheath tumors and only about 5% of Schwannoma arise from the brachial plexus. They pose a great challenge to surgeons due to their rare occurrence and complex anatomical location. We present two cases who presented with a supraclavicular swelling, that were proven to be schwannoma on histopathology.
doi:10.1186/1749-7221-8-12
PMCID: PMC3953679  PMID: 24180468
Brachial plexus tumors; Schwannoma; Supraclavicular swelling
2.  Phalloplasty: The dream and the reality 
Phalloplasty has come a long way as Plastic Surgery has evolved over the years. The complication ridden multistage tube pedicles popularized by Gillis were, with the advent of microsurgery, replaced by radial forearm flaps. The composite osteo-cutaneous version of this flap promised ‘All for one and one for all’ assuring both a reliable urinary conduit and a phallus stiffener. Prelamination and prefabrication to make the neo-urethra came with the promise of reducing both fistula and strictures but that did not happen and flap failure rates increased. Penile stiffeners of various types have been introduced; the artificial ones were associated with high infection and failure rates and are best inserted after the neo-penis regains some sensitivity. With the introduction of perforator flaps the Anterolateral thigh flap in its sensate pedicled form has started replacing the Radial forearm free flap as the first choice flap because of a hidden donor area and lack of microsurgical expertise requirement. Being sensate it tolerates a stiffener better. It is now possible to reconstruct an aesthetically pleasing glans as well, thus meeting both the aesthetic and functional desires of the patient. Complications encountered in this reconstructive effort include flap failure, urethral fistula, urethral stricture and stiffener related problems.
doi:10.4103/0970-0358.118606
PMCID: PMC3901910  PMID: 24501465
Gender reassignment; penile reconstruction; phalloplasty
3.  Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367 
Journal of Bacteriology  2012;194(12):3282-3283.
Mycobacterium xenopi is a slow-growing, thermophilic, water-related Mycobacterium species. Like other nontuberculous mycobacteria, M. xenopi more commonly infects humans with altered immune function, such as chronic obstructive pulmonary disease patients. It is considered clinically relevant in a significant proportion of the patients from whom it is isolated. We report here the whole genome sequence of M. xenopi type strain RIVM700367.
doi:10.1128/JB.00482-12
PMCID: PMC3370862  PMID: 22628510
4.  Complete Genome Sequence of Mycobacterium phlei Type Strain RIVM601174 
Journal of Bacteriology  2012;194(12):3284-3285.
Mycobacterium phlei is a rapidly growing nontuberculous Mycobacterium species that is typically nonpathogenic, with few reported cases of human disease. Here we report the whole genome sequence of M. phlei type strain RIVM601174.
doi:10.1128/JB.00485-12
PMCID: PMC3370867  PMID: 22628511
5.  READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation 
Bioinformatics  2012;29(3):391-392.
Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material).
Availability: http://cbrc.kaust.edu.sa/readscan
Contact: arnab.pain@kaust.edu.sa or raeece.naeem@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/bts684
PMCID: PMC3562070  PMID: 23193222
6.  Herd risk factors associated with sero-prevalence of Maedi-Visna in the Manitoba sheep population 
The Canadian Veterinary Journal  2010;51(4):385-390.
Disease associated with Maedi-Visna infection results in substantial economic losses in affected sheep producing areas of the world. A survey was conducted to estimate herd and individual seroprevalence in the province of Manitoba and evaluate risk factors for seropositive herds. Of 2207 sheep sampled from 77 selected sheep flocks, the animal level seroprevalence was 2.47% and herd level seroprevalence was 25.10%. The herd-level factors of presence of clinical skin disease, herd size of > 70, history of musculoskeletal/lameness abnormalities, and the purchase of new stock (> 50) in the last 1 to 5 y, showed significant associations with seropositive herd status. The study documented a remarkable stability of low seroprevalence in the province over a 20-year period in the absence of a systematic disease control program.
PMCID: PMC2839827  PMID: 20592827
7.  Hmrbase: a database of hormones and their receptors 
BMC Genomics  2009;10:307.
Background
Hormones are signaling molecules that play vital roles in various life processes, like growth and differentiation, physiology, and reproduction. These molecules are mostly secreted by endocrine glands, and transported to target organs through the bloodstream. Deficient, or excessive, levels of hormones are associated with several diseases such as cancer, osteoporosis, diabetes etc. Thus, it is important to collect and compile information about hormones and their receptors.
Description
This manuscript describes a database called Hmrbase which has been developed for managing information about hormones and their receptors. It is a highly curated database for which information has been collected from the literature and the public databases. The current version of Hmrbase contains comprehensive information about ~2000 hormones, e.g., about their function, source organism, receptors, mature sequences, structures etc. Hmrbase also contains information about ~3000 hormone receptors, in terms of amino acid sequences, subcellular localizations, ligands, and post-translational modifications etc. One of the major features of this database is that it provides data about ~4100 hormone-receptor pairs. A number of online tools have been integrated into the database, to provide the facilities like keyword search, structure-based search, mapping of a given peptide(s) on the hormone/receptor sequence, sequence similarity search. This database also provides a number of external links to other resources/databases in order to help in the retrieving of further related information.
Conclusion
Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission, DrugPedia linkage etc. Hmrbase is available online for public from .
doi:10.1186/1471-2164-10-307
PMCID: PMC2720991  PMID: 19589147
8.  Phylogeography of mtDNA haplogroup R7 in the Indian peninsula 
Background
Human genetic diversity observed in Indian subcontinent is second only to that of Africa. This implies an early settlement and demographic growth soon after the first 'Out-of-Africa' dispersal of anatomically modern humans in Late Pleistocene. In contrast to this perspective, linguistic diversity in India has been thought to derive from more recent population movements and episodes of contact. With the exception of Dravidian, which origin and relatedness to other language phyla is obscure, all the language families in India can be linked to language families spoken in different regions of Eurasia. Mitochondrial DNA and Y chromosome evidence has supported largely local evolution of the genetic lineages of the majority of Dravidian and Indo-European speaking populations, but there is no consensus yet on the question of whether the Munda (Austro-Asiatic) speaking populations originated in India or derive from a relatively recent migration from further East.
Results
Here, we report the analysis of 35 novel complete mtDNA sequences from India which refine the structure of Indian-specific varieties of haplogroup R. Detailed analysis of haplogroup R7, coupled with a survey of ~12,000 mtDNAs from caste and tribal groups over the entire Indian subcontinent, reveals that one of its more recently derived branches (R7a1), is particularly frequent among Munda-speaking tribal groups. This branch is nested within diverse R7 lineages found among Dravidian and Indo-European speakers of India. We have inferred from this that a subset of Munda-speaking groups have acquired R7 relatively recently. Furthermore, we find that the distribution of R7a1 within the Munda-speakers is largely restricted to one of the sub-branches (Kherwari) of northern Munda languages. This evidence does not support the hypothesis that the Austro-Asiatic speakers are the primary source of the R7 variation. Statistical analyses suggest a significant correlation between genetic variation and geography, rather than between genes and languages.
Conclusion
Our high-resolution phylogeographic study, involving diverse linguistic groups in India, suggests that the high frequency of mtDNA haplogroup R7 among Munda speaking populations of India can be explained best by gene flow from linguistically different populations of Indian subcontinent. The conclusion is based on the observation that among Indo-Europeans, and particularly in Dravidians, the haplogroup is, despite its lower frequency, phylogenetically more divergent, while among the Munda speakers only one sub-clade of R7, i.e. R7a1, can be observed. It is noteworthy that though R7 is autochthonous to India, and arises from the root of hg R, its distribution and phylogeography in India is not uniform. This suggests the more ancient establishment of an autochthonous matrilineal genetic structure, and that isolation in the Pleistocene, lineage loss through drift, and endogamy of prehistoric and historic groups have greatly inhibited genetic homogenization and geographical uniformity.
doi:10.1186/1471-2148-8-227
PMCID: PMC2529308  PMID: 18680585
9.  Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs 
BMC Bioinformatics  2007;8:337.
Background
In past number of methods have been developed for predicting subcellular location of eukaryotic, prokaryotic (Gram-negative and Gram-positive bacteria) and human proteins but no method has been developed for mycobacterial proteins which may represent repertoire of potent immunogens of this dreaded pathogen. In this study, attempt has been made to develop method for predicting subcellular location of mycobacterial proteins.
Results
The models were trained and tested on 852 mycobacterial proteins and evaluated using five-fold cross-validation technique. First SVM (Support Vector Machine) model was developed using amino acid composition and overall accuracy of 82.51% was achieved with average accuracy (mean of class-wise accuracy) of 68.47%. In order to utilize evolutionary information, a SVM model was developed using PSSM (Position-Specific Scoring Matrix) profiles obtained from PSI-BLAST (Position-Specific Iterated BLAST) and overall accuracy achieved was of 86.62% with average accuracy of 73.71%. In addition, HMM (Hidden Markov Model), MEME/MAST (Multiple Em for Motif Elicitation/Motif Alignment and Search Tool) and hybrid model that combined two or more models were also developed. We achieved maximum overall accuracy of 86.8% with average accuracy of 89.00% using combination of PSSM based SVM model and MEME/MAST. Performance of our method was compared with that of the existing methods developed for predicting subcellular locations of Gram-positive bacterial proteins.
Conclusion
A highly accurate method has been developed for predicting subcellular location of mycobacterial proteins. This method also predicts very important class of proteins that is membrane-attached proteins. This method will be useful in annotating newly sequenced or hypothetical mycobacterial proteins. Based on above study, a freely accessible web server TBpred http://www.imtech.res.in/raghava/tbpred/ has been developed.
doi:10.1186/1471-2105-8-337
PMCID: PMC2147037  PMID: 17854501

Results 1-9 (9)