PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data.

Enrichment of Methylocystis dominant mixed culture from rice field for PHB production.

Presence of methanotrophs in diverse environmental habitats helps to reduce emissions of greenhouse gas like methane. Isolation and culture of undiscovered wealth of methanotrophic organisms can help in exploitation of these organisms in value added products. The present study focuses on the enrichment of methanotroph dominated mixed microbial community by use of three stage strategy of revival, proliferation, and segregation. During the enrichment process amplicon sequencing of 16 s rRNA V3-V4 region showed relative abundance of mixed culture comprising single methanotrophic species of Methylocystis genus (88.92%) along with only three other species. Methylocystis dominant mixed culture (MMI-11) was observed to produce polyhydroxyalkanoates (PHA). During studies to identify favourable culture conditions, nitrate was found to be preferred nitrogen source for growth and PHA production. Cell growth ability to produce PHA was also evaluated at 14 L fermentor by supplying gas using continuous bubbling and through pressurization in the headspace. The mixed methanotrophic culture was found to accumulate maximum of 22.20% polyhydroxybutyrate (PHB) under nitrate limited condition. The molecular weight of PHB was found to be 2.221 × 105 g mol-1 with polydispersity of 1.82.

Prognostic factors for loco-regional failure in early stage (I and II) squamous cell carcinoma of the gingivobuccal complex.

The objective of the article is to study the prognostic indicators of loco-regional failure in patients with early stage cancers of the gingivobuccal complex (GBC) treated at a single institution. The study design is based on retrospective chart review. A review of 2,275 patients diagnosed with GBC was conducted from January 1997 to December 1999, wherein 207 patients who fulfilled our inclusion criteria were analyzed. Univariate analysis, multivariate analysis, and disease-free survival are reported. During a median follow-up of 2.85 years there were 85 (43%) loco-regional failures of which 64% could be salvaged. As much as 80% of all failures occurred within the first 24 months and the mean survival for patients with recurrences was 9.6 months. Two and five-year disease-free survival for the entire cohort was 65% and 52%, respectively. Nodal metastasis, soft tissue infiltration, and pathological bone involvement correlated with poor disease-free survival on multivariate analysis. Early stage tumors of the GBC as evaluated clinically are often upstaged pathologically due to a high rate of occult nodal metastasis and local failure as they tend to invade bone and infiltrate adjacent soft tissue. Consequently, we recommend aggressive surgical therapy as we would recommend for advanced stage cancers of the GBC which includes a wide three-dimensional resection to account for soft tissue and bony infiltrations and adjuvant therapy in the presence of adverse features since salvage rates for recurrent tumors are poor.

Quality of life in head and neck cancer survivors: a cross-sectional survey.

PURPOSE: Head and neck cancer (HNC) survivors have substantial psychological distress in addition to treatment-related side effects. This study examines the long-term quality of life (QOL) of HNC survivors in a busy tertiary care center. MATERIAL AND METHODS: A prospective, cross-sectional survey was conducted studying 212 HNC survivors 1 year after completion of their treatment at a tertiary cancer center. Quality of life assessments were performed using the 2 standardized health-related QOL questionnaires: The European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core-30 and The Quality of Life Questionnaire Head and Neck Cancer Module. RESULTS: The overall global QOL rating for the study cohort was satisfactory. The European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core-30 scores showed that the domains where most patients faired poorly included financial difficulties (54%), appetite loss (36%), fatigue (33%), and cough (30%). The Quality of Life Questionnaire Head and Neck Cancer Module scale identified the domains with poor scores to be dry mouth (64%), dental problems (42%), sticky saliva (40%), cough (39%), and problems with mouth opening (32%). Patients with early-stage tumors and those treated with surgery alone had significantly better QOL scores when compared with advanced stage tumors and patients receiving either radiation alone or multimodality treatment, respectively. CONCLUSIONS: Quality of life questionnaires provide a medium for patients to effectively communicate with their physician in a busy tertiary care facility and provide an insight into the physical, psychological, and social problems affecting our patients which can then direct future interventions.

Extensive tubercular neck lymphadenopathy in a man with early-stage tongue cancer.

BACKGROUND: A 66-year-old Asian man presented with a tongue ulcer and without palpable metastases to the neck nodes. A thorough clinical examination of the head and neck region did not reveal any other primary lesion. To assess the status of the neck, PET-CT imaging was advised. INVESTIGATIONS: Physical examination, punch biopsy, PET-CT imaging, blood tests, chest radiograph, fine-needle aspiration biopsy, tumor biopsy, neck incision, tuberculin test, sputum culture and histopathology. DIAGNOSIS: Carcinoma of the tongue of pathologic stage T2 N0 M0, with tubercular lymphadenitis and no nodal metastases. MANAGEMENT: Surgical excision and multidrug antitubercular therapy.

Squamous cell carcinoma of the superior gingival-buccal complex.

Squamous cell carcinoma of the superior gingival-buccal complex are rare and few English-language data have been published on their biological behaviour. Reported in this paper are the clinical behaviour and treatment outcomes of squamous cell carcinoma of the upper gingival-buccal complex. We reviewed the charts of 110 patients with squamous cell carcinoma restricted to the upper gingiva, superior gingival-buccal sulcus and adjoining buccal mucosa, seen between 1997 and 2001. Separate outcome analyses were carried out among 86 patients who had undergone surgery, and 24 patients treated by radiotherapy or chemo-radiation. Disease-free survival at 2 and 5 years was 48.9% and 36%, respectively, and was independent of epicentre of disease. Five-year, disease-free survival was 48.8% and 0% for surgical treatment and non-surgical treatment groups. T stage (p=0.024) and extra-capsular spread of disease (p=0.036) were independent predictors of disease-free survival on multivariate analysis. Adequate surgical resection and adjuvant treatment, in the first instance, offers the best chance of disease control.

Selective neck dissection (I-III) for node negative and node positive necks.

Selective neck dissection (I-III) for oral cancers offers similar regional control rates with less morbidity as compared with modified radical neck dissection. Charts of 414 patients with oral cancer, who underwent selective neck dissection (I-III) during 1994-2001, were analysed retrospectively. Seventy nine percent of the patients had a primary tumour in the gingivo-buccal complex. Cancer of tongue showed a trend towards higher regional failure (12.3%) as compared to gingivo-buccal cancers (6.5%). Primary tumour was staged as T1-8%, T2-47%, T3-19% and T4-26%. Sixty five percent of the patients were clinically node negative. Isolated neck failure was observed in 4.8% of patients at 2 years and in 5.8% at 5 years. De-differentiation of primary tumour and perineural spread were associated with regional failures. Eighty three percent of the neck recurrences were in the ipsilateral neck and only 16% of these were at levels IV or V. In all, 30% of all regional failures were outside the field of dissection.

Small cell carcinoma of the esophagus: the Tata Memorial Hospital experience.

BACKGROUND: Small cell carcinoma of the esophagus is a rare disease, characterized by aggressive progression. It has a high incidence of metastatic disease at presentation and a poor overall prognosis. Treatment protocols are not well established because of the paucity of cases and a lack of large studies. METHODS: We performed a retrospective review of all patients with small cell carcinoma of the esophagus diagnosed at the Tata Memorial Hospital between 1985 and 2001. We retrieved and analyzed data regarding demographic details, diagnosis, staging, type of treatment, and overall survival. RESULTS: Eighteen patients with a mean age of 62 years (range 48 to 80 years) diagnosed as having small cell carcinoma of the esophagus were analyzed. The group included 13 men and 5 women. Seven of the 18 patients (39%) presented with metastatic disease including 5 patients (28%) with liver metastases. Four patients were treated with surgery, with or without chemotherapy or radiotherapy. Three patients were treated with combination chemoradiotherapy, 2 patients with chemotherapy alone, and 5 patients with radiotherapy alone. Four patients with advanced disease and poor general condition were not offered any treatment. The overall median survival of our patients was 6 months. Patients treated with surgery and chemotherapy had a better overall survival. CONCLUSIONS: Small cell carcinoma of the esophagus should be regarded as a systemic disease with a high distant failure rate. Treatment strategies hence must incorporate systemic chemotherapy along with radical surgery or radiotherapy as part of a multimodality approach.

Thoracic duct cyst of the mediastinum.

Thoracic duct cysts of the mediastinum are extremely rare. The etiology may be related to a congenital or degenerative weakness in the wall of the thoracic duct. They are generally asymptomatic but may sometimes cause pressure effects on adjacent structures. Imaging studies are supportive but not diagnostic. Excision of these cysts is required for diagnosis and to prevent complications. We describe a 49-year old man who presented to us with hoarseness and a fixed right vocal cord. Computed tomography (CT) showed a cystic posterior mediastinal mass in the right paratracheal region. We performed a posterolateral thoracotomy and found the cyst arising from the thoracic duct and contained chylous fluid with a high lipid concentration. We dissected the cyst from the surrounding structures and excised it. Histopathology revealed a cyst lined by a single layer of endothelial cells. He is asymptomatic now one year after surgery.

Prospective analysis of reasons for non-enrollment in a phase III randomized controlled trial.

AIM: This study aims to provide information on the accrual rate and to identify the reasons for non-enrollment of oral cancer patients into a clinical trial. SETTING AND DESIGN: Prospective study conducted at the Tertiary Cancer Centre (India). MATERIALS AND METHODS: Patients eligible and screened for the oral cancer adjuvant therapy (OCAT) were logged prospectively and reasons for non-enrollment were documented which were broadly divided into patient and trial related. STATISTICAL ANALYSIS USED: Demographic characteristics of the non-enrolees were compared with the enrolled. Factors predicting non-enrollment were analyzed using multivariate logistic regression test. RESULTS: A total of 1335 patients with locally advanced cancer of the oral cavity were screened of whom 498 (37%) could be enrolled. Among non enrolled 837 patients, 182 (22%) had the trial-related reasons and 655 (78%) had patient-related reasons. Most important patient-related reasons were patients' preference of taking treatment closer to their native place (26.2%), lack of interest (16.8%) in trial participation. Anticipated poor compliance to treatment (5.9%) and follow-up (6.6%), inability to start treatment in time (6.2%) were important trial-related reasons for non-enrollment. Multivariate analysis identified the genders (female), education (illiterate), occupation (laborer) and non availability of support system in the city as significant predictors of non-enrollment. CONCLUSIONS: Both trial design and patient factors were important causes of non enrollment in eligible patients. Patients' need for being closer to home and refusal to participate were the most common reasons for non-enrollment.

Elective neck dissection for the management of the N0 neck in early cancer of the oral tongue: need for a randomized controlled trial.

BACKGROUND: The aim of this study is to determine the need for a randomized controlled trial in order to define the role of an elective neck dissection (END) in the treatment of early tongue cancers. METHODS: We present a large retrospective analysis of patients with T1-2 N0 squamous cell cancers of the oral anterior tongue treated at a single institution. A total of 359 eligible patients with early tongue cancers were divided into 2 groups: END and wait and watch (WW). An analysis for survival outcomes and prognostic factors was conducted. RESULTS: The estimated 3- and 5-year disease-free survival for the END group was 76% and 74% versus 71% and 68% for the WW group, respectively (p = .53). The 3- and 5-year overall survival (OS) rate for the END group was 69% and 60% versus 62% and 60% for the WW group, respectively (p = .24). Tumor grade and perineural invasion were independent predictors of recurrence. CONCLUSION: END did not impact disease-free or OS. Current literature still remains divided on this issue emphasizing the need for a randomized controlled trial.

Verrucous carcinoma of the oral cavity: A clinical and pathological study of 101 cases.

This paper studies the clinical and pathological predictors of local recurrence and disease-free survival (DFS) in patients with oral verrucous carcinoma (OVC) treated surgically, through a retrospective chart review. Three hundred and two patients with OVC were identified from January 1990 to December 2000, of which, 101 surgically treated patients who fulfilled our inclusion criteria were analyzed. A univariate analysis (UVA) of important prognostic factors, patterns of recurrence, and DFS is reported. Seventy-nine patients were male (M:F ratio, 3.6:1) and the mean age at presentation was 53.9 years (range, 23-90 years). The median follow up was 4.61 years (range, 0.51-14.3 years). The incidence of tobacco chewing, smoking, and alcohol intake was 77%, 42%, and 10%, respectively. Thirty-four patients (33.7%) had either leukoplakia or submucous fibrosis (SMF) on oral cavity examination. Early-stage tumors accounted for 39.7%; while 60.4% were late-stage tumors. On UVA, tumor location, presence of a premalignant lesion, smoking, and positive margins were statistically significant. Sixty-eight percent (19/28) recurred locally. The salvage rate for recurrent tumors was 66.7% (16/28) with a median post-recurrence survival of 16 months (range, 10-83 months). The five year DFS with surgical therapy was 77.6%. OVC has an excellent prognosis with surgical treatment. The significance of positive margins emphasizes the need for adequate surgical resection. Additionally, the presence of either leukoplakia or SMF and tumor location in the upper alveolar-palatal complex is associated with worse outcomes. Neck dissection, if considered, may be limited to a supra-omohyoid neck dissection (SOHND).

Squamous cell carcinoma of the gingivobuccal complex: predictors of locoregional failure in stage III-IV cancers.

The purpose of our study was to analyze the indicators of loco-regional failure in a large cohort of patients with gingivobuccal complex tumors treated at a single institution. A retrospective review of 2275 patients diagnosed with tumors of the gingivobuccal complex was conducted from January 1997 to December 1999; 642 patients who fulfilled our inclusion criteria were analyzed. A univariate analysis, multivariate analysis, and disease-free survival are reported. During a median follow up of 2.51 years, there were 228 (35.5%) recurrences with a median post-recurrence survival of 2.7 months. The incidence of occult neck metastasis was 29%. The 2- and 5-year DFS rates were 63.8% and 53.3%, respectively. On multivariate analysis, tumor depth and metastatic lymphadenopathy were found to be independent prognostic factors for disease-free survival. Advanced gingivobuccal cancers fail loco-regionally. Cervical metastasis and tumor depth influence disease-free survival. Elective neck dissection due to a high incidence of occult neck disease is recommended.

Validation and assessment of voice-related quality of life in Indian patients undergoing total laryngectomy and primary tracheoesophageal puncture.

BACKGROUND: Voice-related quality of life (V-RQOL) has never been studied in Indian patients. This study was planned to validate and assess V-RQOL in patients using tracheoesophageal puncture (TEP). METHODS: A cross-sectional study was undertaken to validate V-RQOL questionnaire by testing reliability, validity, and responsiveness. V-RQOL was assessed in patients undergoing total laryngectomy with primary TEP. RESULTS: One hundred thirty-two patients filled 188 questionnaires. Analysis was carried out on 122 patients. Reliability and validity of questionnaire were tested by Cronbach's alpha (.84-.91) and item-scale correlation (.67-.86). Median V-RQOL-Total score was 76.2 indicating excellent V-RQOL. Higher scores were observed in patients less than 50 years (82.5 vs 72.5, p = .08). There was no effect of time interval between laryngectomy and assessment of questionnaire on the V-RQOL scores. CONCLUSION: V-RQOL questionnaire can be used reliably to assess V-RQOL, which is found to be excellent in Indian patients undergoing TEP.

Buccal plate excision for buccal paramandibular spread.

Cancer of buccal gingival sulcus lie in close proximity to mandible but tend to invade bone late in the course of disease. Segmental mandibulectomy advocated for these tumors results in cosmetic disfigurement and functional impairment. We, for the first time, describe a mandibular preservation alternative, in form of buccal cortical plate excision, for these tumors.

Advanced squamous cell carcinoma of lower gingivobuccal complex: patterns of spread and failure.

BACKGROUND: Carcinoma of the gingivobuccal complex is commonly associated with the use of smokeless tobacco known as "quid." METHODS: We conducted a retrospective chart review of 511 patients with advanced cancer of gingivobuccal complex surgically treated during 1994 to 1995. We evaluated patterns of disease failure in these patients and correlated disease-free survival with various prognostic factors. RESULTS: During a median follow-up of 46 months, 159 locoregional recurrences and 11 distant metastases were detected in 148 patients. Seventy-nine percent of the recurrences appeared within 18 months of surgery, and the median survival for patients with recurrent disease was less than 4 months. Two-year and 5-year disease-free survival rates were 64% and 57%, respectively. On multivariate analysis, disease-free survival showed significant correlation with skin involvement and extracapsular spread. CONCLUSIONS: Gingivobuccal cancers usually fail locoregionally. Soft tissue infiltration and extracapsular spread of nodal disease influence disease-free survival.

A novel technique of raising a pectoralis major myocutaneous flap through the skin paddle incision alone.

A good reconstruction should not only be functionally and aesthetically sound at the recipient site but also cause least possible cosmetic aberration of the donor site. The pectoralis major myocutaneous (PMMC) flap continues to be one of the most commonly used flap for head and neck reconstruction in this part of the world. Conventionally, once the skin paddle over the pectoralis major muscle is marked, a line is drawn joining the outer edge of the skin flap extending to the apex of the anterior axillary skin fold or midclavicular point to expose the underlying pectoralis major muscle and harvest the flap. We intend to suggest a novel technique, in which the pectoralis major muscle is exposed by raising the skin around the skin paddle incision alone without making any further extension.

Reconstruction of early lower gingivo buccal complex lesions using floor of mouth advancement augmented with hyoglossus release.

The surgical treatment in early cancers of the lower gingivobuccal (GB) complex involves wide resection of the buccal mucosa and GB sulcus with or without marginal mandibulectomy. To reconstruct this defect we endeavour to describe a method of advancement of the lateral floor of mouth and tongue to provide pliable, vascularised tissue to bridge the mucosal defect and achieve tension free, primary closure whilst preserving maximum tongue mobility and maintaining adequate mouth opening, thus offering an elegant and simple solution to the problems of reconstruction in early lesions of the lower gingivo buccal complex.