lncRNADetector: a bioinformatics pipeline for long non-coding RNA identification and MAPslnc: a repository of medicinal and aromatic plant lncRNAs.

Long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs and potent regulatory elements in the living cells. High throughput RNA sequencing analyses have generated a tremendous amount of transcript sequence data. A large proportion of these transcript sequences does not code for proteins and are known as non-coding RNAs. Among them, lncRNAs are a unique class of transcripts longer than 200 nucleotides with diverse biological functions and regulatory mechanisms. Recent emerging studies and next-generation sequencing technologies show a substantial amount of lncRNAs within the plant genome, which are yet to be identified. The computational identification of lncRNAs from these transcripts is a challenging task due to the involvement of a series of filtering steps. We have developed lncRNADetector, a bioinformatics pipeline for the identification of novel lncRNAs, especially from medicinal and aromatic plant (MAP) species. The lncRNADetector has been utilized to analyse and identify more than 88,459 lncRNAs from 21 species of MAPs. To provide a knowledge resource for the plant research community towards elucidating the diversity of biological roles of lncRNAs, the information generated about MAP lncRNAs (post-filtering steps) through lncRNADetector has been stored and organized in MAPslnc database (MAPslnc, https://lncrnapipe.cimap.res.in). The lncRNADetector web server and MAPslnc database have been developed in order to facilitate researchers for accurate identification of lncRNAs from the next-generation sequencing data of different organisms for downstream studies. To the best of our knowledge no such MAPslnc database is available till date.

Pathological, ultrasonographic, and electrophysiological characterization of clinically diagnosed cases of pure neuritic leprosy.

A subset of neuritic form of leprosy, called pure neuritic leprosy (PNL), seen in a minority of leprosy patients, is characterized by peripheral neuropathy without skin lesions and an absence of acid-fast bacilli on skin smears. Patients with PNL are often started on drug therapy without confirmation of diagnosis. We, therefore, did a prospective study of clinically diagnosed PNL patients with correlation of ultrasonographic and biopsy findings. A total of 100 consecutive patients with PNL, diagnosed according to the consensus case definition, were included in the study. All patients underwent nerve conduction study, peripheral nerve ultrasonography, and sural nerve biopsy. Multiple mononeuropathies were present in 75% of cases, mononeuropathy in 18%, and polyneuropathy in the remaining 7%. Compared to clinical examination, ultrasonographic assessment of the peripheral nerves was not only better at the detection of thickening but also helped in characterization of their fascicular architecture, echogenicity, and vascularity. A total of 32 cases were confirmed on nerve biopsy, out of which 75% had demonstrable lepra bacilli. Cranial nerve involvement, presence of trophic ulcers, and bilateral thickening of the great auricular nerve were significantly associated with the positivity of lepra bacilli. A significant improvement in the disability score happened after multidrug therapy. A comprehensive electrophysiologic, ultrasonographic, and histological evaluation may be helpful in establishing a diagnosis of PNL with greater confidence, while ruling out other non-leprosy diagnoses.

Jejunal stricture: a rare complication of chemotherapy in pediatric gastrointestinal B-cell non-Hodgkin lymphoma.

The use of intensive chemotherapy has led to remarkable improvements in the treatment of high-grade B-cell Non-Hodgkin lymphoma (NHL); however, it is associated with significant side effects such as myelosuppression and mucositis. Gastrointestinal NHL rarely leads to the development of aneurysmal dilatation of the bowel, as desmoplastic reaction is not a feature of NHL. Strictures and fibrosis are not a manifestation of NHL involvement. Here, we report a child with primary gastrointestinal B-cell NHL who presented with jejunal stricture developing as a sequela of severe chemotherapy-induced mucositis. The patient improved with surgical resection of stricture and end-to-end anastomosis.

Glioneuronal tumor with neuropil-like islands: a new entity.

Glioneuronal tumor with neuropil-like islands (GTNI) is a distinctive and rare tumor characterized by both glial and neuronal differentiation. However, unlike other mixed glioneuronal tumors, which are characterized by a favorable prognosis, this neoplasm has been found to be potentially aggressive. We report here a case arising in a 60-year old male patient who presented with seizures, forgetfulness and right-sided hemiparesis, due to a left frontal lobe tumor. Unlike most cases described in the literature, the present tumor was unique in its radiological appearance, which was cystic. On microscopic evaluation, the glial component was chiefly gemistocytic punctuated by neuropil-like islands. Strong nuclear immunolabeling of p53 and absence of 1p/19q deletion by fluorescence in situ hybridization assay were consistent with those in previous reports.

Assessment of 1p/19q status by fluorescence in situ hybridization assay: A comparative study in oligodendroglial, mixed oligoastrocytic and astrocytic tumors.

BACKGROUND: Due to overlapping histomorphological features, difference in clinical behavior and treatment response, establishing potential molecular markers to facilitate diagnosis of various genetic subtypes of diffuse gliomas is essential. AIM: To analyze 1p/19q status in diffuse gliomas and correlate it with epidermal growth factor receptor (EGFR) and p53 protein expression. MATERIALS AND METHODS: 1p/19q status in 43 cases was evaluated by fluorescence in situ hybridization assay. Glial fibrillary acidic protein (GFAP), EGFR and p53 were assessed by immunohistochemistry. RESULTS: Glial fibrillary acidic protein immunopositivity was observed in oligodendrogliomas within minigemistocytes and gliofibrillary oligodendrocytes as perinuclear homogenous blobs. It also highlighted the intermingled reactive astrocytes. Astrocytomas and the astrocytic component of oligoastrocytomas showed a diffuse fibrillary type of staining. 1p and/or 19q loss was seen in 65% (13/20) of oligodendrogliomas and 66.6% (5/9) of mixed oligoastrocytomas. There was one case each of pediatric oligodendroglioma and mixed oligoastrocytoma, none of which showed 1p/19q loss. None of the astrocytomas including two pediatric cases showed this alteration (P < 0.05). p53 was expressed in 57.1% of astrocytomas (8/14), 33% of mixed oligoastrocytomas (3/9) and 10% of oligodendrogliomas (2/20). Majority of oligodendrogliomas (85%; 17/20) and oligodendroglial areas in mixed oligoastrocytomas (77.7%; 7/9) showed a membranous lace-like immunopositivity with EGFR. In contrast, all astrocytomas (Grade II and III) were EGFR negative. CONCLUSION: Loss of 1p/19q is strongly associated with oligodendroglial phenotype, while astrocytic tumors are more likely to show p53 over-expression. p53 expression and 1p/19q status appear to be mutually exclusive.

Effects of soil amendments on the bioavailability of heavy metals from zinc mine tailings.

A study was conducted to test the effects of soil amendments on the bioavailability of heavy metals in a zinc mine tailings containing soil to plants, using the Indian mustard plant (Brassica juncea) as a test organism. Zinc mine tailing containing soil was amended with humus soil (HS) and phosphatic clay (PC). The zinc mine tailing containing soil (ZMTS) was characterized for heavy metals. It was mixed with PC and HS, and four mixtures were prepared. The first mixture contained ZMTS, and served as a control. The second mixture contained ZMTS and PC in the ratio of 1:1 (w/w). The third mixture contained ZMTS and HS in the ratio of 1:1(w/w). The fourth mixture containing ZMTS, PC and HS in the ratio of (2:1:1) (w/w). A slight increase in the bioavailability of Pb, Cu, Zn and Mn was noticed with increase in the incubation time from 14 to 42 days. The bioavailability of Pb, Cu, Zn and Mn from ZMTS alone in Brassica plant was in the range of 94-99% up to 42 days. Addition of PC and HS to the ZMTS soil reduced the bioavailabilities of Pb by (15%), of Cu by (20%), of Zn by (20%) and of Mn by (25%) in the mustard plant. The data showed that PC in the presence of HS had a high affinity for the heavy metals in the order of Pb, Cu, Zn and Mn.

Delayed Diagnosis of Dopa responsive Dystonia in Two Siblings.

BACKGROUND: Dopa responsive dystonia is characterized by progressive disabling dystonia, diurnal variation and a dramatic response to Levodopa. CASE CHARACTERISTICS: Two siblings presented with regression of motor milestones and hypertonia in lower limbs. History of diurnal variation was present in elder sibling. OUTCOME: Both responded dramatically to Levodopa. The genomic DNA analysis of elder sibling revealed a novel mutation. MESSAGE: A trial of Levodopa should be considered in a child with motor regression with diurnal variation, in the presence of extrapyramidal features.

Macrodactyly and fibrous hamartoma in a child with tuberous sclerosis complex.

A 10-year-old boy with tuberous sclerosis complex and macrodactyly of the right index and middle fingers is described. He also had a fibrous hamartoma at the front of the right wrist. The association of fibrous hamartoma and macrodactyly has not been previously described in tuberous sclerosis complex.

Right atrial myxoma with glandular differentiation: A rare entity in pediatric age group.

Cardiac myxomas (CMs) account for nearly half of the primary cardiac tumors in the elderly. They arise from sub-endocardial "reserve" or lepidic" cells, which may show divergent differentiation. We describe a CM with glandular differentiation in the right atrium of a 10-year-old child who presented with respiratory distress on exertion, of 2 months duration. On echocardiography, two large interconnected masses measuring 34×30 mm and 20×17 mm were seen to arise from the free wall of the right atrium. Cut surface of the excised mass was myxoid with areas of calcification. On microscopy, there were typical features of a myxoma with prominent glandular differentiation and characteristic immunophenotype. The case is being reported due to its rarity in pediatric age group as well as its glandular differentiation, which must be recognized as a spectrum of histomorphologic diversity and must not be mistaken for a metastatic adenocarcinoma.

Intracranial inflammatory pseudotumor: report of a rare case.

Inflammatory pseudotumors (IPs) arising in the CNS (IP-CNS) are quite rare. We report here a case of IP in a 5-year-old boy. Intraoperatively there was a well-defined extra-axial lesion in the right frontobasal region with CSF all around. There was no dural attachment. The tumor was removed piece-meal. On pathological examination, the lesion was well circumscribed and comprised of spindled cells in a collagenous background with sprinkling of inflammatory cells. The case was worked up considering the possibilities of low grade glioma, lymphoplasmacyte-rich meningioma, fungal/tubercular infection or inflammatory pseudotumors. Appropriate immunohistochemical stains were performed to rule out the rare possibility of lymphoma or plasmacytoma. The spindled cells were diffusely immunopositive for vimentin and only occasional cells were positive for smooth muscle actin (SMA). The cells did not show anaplastic lymphoma kinase-1 immunopositivity. Based on the above morphological and immunohistochemical analysis, a diagnosis of inflammatory pseudotumor was rendered.