Ensembl 2009.

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).

Ensembl 2008.

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein-DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Ensembl 2007.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.

Study of quadrant high-dose intraoperative radiation therapy for early-stage breast cancer.

BACKGROUND: Partial breast irradiation has been tested in limited pilot studies and shown to provide acceptable cosmesis, minimal toxicity and adequate local control. The aim of this study was to determine the feasibility of using quadrant high-dose intraoperative radiation therapy (IORT) for the treatment of early-stage breast cancer. METHODS: Fifty-two women with early-stage breast cancer were treated with breast-conserving therapy and IORT between October 2002 and January 2006. The first 18 women received a radiation dose of 20 Gy. The protocol was then amended and the remaining 34 women were treated with 18 Gy. Each patient was evaluated after surgery, and at 3, 6 and 12 months; complications, toxicity and cosmetic outcomes were recorded by the breast surgeon. RESULTS: Women treated with 18 Gy appeared to have a more favourable cosmetic outcome compared with the earlier treatment group. At last follow-up, none of the women treated on the protocol had a breast recurrence. CONCLUSION: Experience suggests that this IORT technique is feasible, although further follow-up is necessary to assess its therapeutic value.

Diffusion and perfusion MRI to differentiate treatment-related changes including pseudoprogression from recurrent tumors in high-grade gliomas with histopathologic evidence.

BACKGROUND AND PURPOSE: Treatment-related changes and recurrent tumors often have overlapping features on conventional MR imaging. The purpose of this study was to assess the utility of DWI and DSC perfusion imaging alone and in combination to differentiate treatment-related effects and recurrent high-grade gliomas. MATERIALS AND METHODS: We retrospectively identified 68 consecutive patients with high-grade gliomas treated by surgical resection followed by radiation therapy and temozolomide, who then developed increasing enhancing mass lesions indeterminate for treatment-related changes versus recurrent tumor. All lesions were diagnosed by histopathology at repeat surgical resection. ROI analysis was performed of the enhancing lesion on the ADC and DSC maps. Measurements made by a 2D ROI of the enhancing lesion on a single slice were recorded as ADCLesion and rCBVLesion, and measurements made by the most abnormal small fixed diameter ROI as ADCROI and rCBVROI. Statistical analysis was performed with Wilcoxon rank sum tests with P = .05. RESULTS: Ten of the 68 patients (14.7%) had treatment-related changes, while 58 patients (85.3%) had recurrent tumor only (n = 19) or recurrent tumor mixed with treatment effect (n = 39). DWI analysis showed higher ADCLesion in treatment-related changes than in recurrent tumor (P = .003). DSC analysis revealed lower relative cerebral blood volume (rCBV)Lesion and rCBVROI in treatment-related changes (P = .003 and P = .011, respectively). Subanalysis of patients with suspected pseudoprogression also revealed higher ADCLesion (P = .001) and lower rCBVLesion (P = .028) and rCBVROI (P = .032) in treatment-related changes. Applying a combined ADCLesion and rCBVLesion model did not outperform either the ADC or rCBV metric alone. CONCLUSIONS: Treatment-related changes showed higher diffusion and lower perfusion than recurrent tumor. Similar correlations were found for patients with suspected pseudoprogression.

Validation of a nutritional screen in children with respiratory syncytial virus admitted to an intensive care complex.

OBJECTIVE: We sought to validate a nutritional screen that was easy to perform and accurate in identifying pediatric patients at risk for adverse clinical outcomes based on their nutritional status. METHODS: Twenty-five consecutive patients admitted to our pediatric intensive care complex between July 1992 and July 1993 with a primary diagnosis of respiratory syncytial virus infection were evaluated. Nutritional screen parameters included historical (disease and condition), growth (anthropometrics), and laboratory (hemoglobin, lymphocyte count, and albumin) data. Outcome measures included days in the hospital, days of mechanical ventilation, days not fed enterally, and days receiving oxygen. RESULTS: Regression analysis indicated that a score of 5 or less signified a low risk of adverse outcome and a score of greater than 5 signified a high risk. Eleven of 25 patients had low scores, and 14 of 25 had high scores. All outcome measures differed significantly between the low- and high-risk groups: median number of days in the hospital, 7 and 13.5, respectively; median number of days of ventilation, 0 and 8.5, respectively; median number of days without enteral feeding, 3 and 8.5, respectively; and median number of days receiving oxygen, 4 and 20, respectively. CONCLUSIONS: Our nutritional screen identifies patients in the pediatric intensive care complex with respiratory syncytial virus at increased risk for adverse outcome. This screen may be useful in identifying pediatric patients at risk for adverse clinical outcomes from other medical diagnoses.

Short report: penile lymphoma following local injections for erectile dysfunction.

We report a case of high grade lymphoma which appeared at the site of prior injections of medications into the shaft of the penis for erectile dysfunction. We discuss the possible mechanisms of causation for this unusual form of lymphoma.

The optokinetic cervico reflex during simulated helicopter flight.

INTRODUCTION: The optokinetic cervico reflex (OKCR) is a recently hypothesized, visually driven reflex that serves to stabilize the image of the external horizon on the retina during roll maneuvers in high-performance aircraft. Although reported anecdotally, head tilt during helicopter flight has not been studied formally. Such research is required to determine the full impact and significance that it may have on the flying performance of a rotary-wing aviator. OBJECTIVE: The aim of this study was to investigate the relationship between horizon position and the perception of orientation and, thus, to generate vital information to assess whether OKCR plays an important role in spatial disorientation. HYPOTHESIS: Pilots of rotary-wing aircraft will exhibit the OKCR. METHODS: A UH-60 flight simulator study, with 20 volunteer pilots participating, was performed to examine the effects of this reflex during day flight and during flight with night vision goggles (NVGs). RESULTS: The results confirm that the OKCR occurs during simulated helicopter flight, both with and without NVGs. As with previous studies, head roll increased during flight under visual meteorological conditions in relation to an increasing aircraft roll angle up to a maximum sustainable level and then remained constant. Head roll did not occur during flight under instrument meteorological conditions. CONCLUSION: The presence of the OKCR will impact rotary-wing operations. Various aspects are discussed, and recommendations are made for future research.

Falls risk factors in an acute-care setting: a retrospective study.

Research findings have been contradictory regarding risk factors for falls in the acute-care setting. Identification of factors that place individuals at risk of falling in this setting are a priority because falls result in high morbidity and mortality and thus increased healthcare costs. The purpose of this study was to extend knowledge beyond the known risk factors of age and medical diagnosis by comparing the characteristics of 301 adults who fell while hospitalized with a matched sample of adults who did not fall while hospitalized. A descriptive, retrospective, comparative design was used. The fall and non-fall group were matched on age and primary medical diagnosis at the time of discharge. Data were collected from hospital incident reports and medical records. Logistic regression for matched groups identified 5 risk factors, as follows. Incontinence. The odds of falling were 11.3 (CI = 3.85, 33.05) times greater for those who were incontinent than for those who were not incontinent. Long hospital stay. The odds of falling were 9.9 (CI = 4.89, 19.88) times greater for those hospitalized 19 days or longer than for those hospitalized less than 19 days. Dependency for ambulation. The odds of falling were 6 (CI = 2.83, 12.84) times greater for those who were dependent for ambulation than for those who were independent. Independency for hygiene. The odds of falling were 2.5 (CI = 1.23, 4.88) times greater for those who were independent for hygiene than for those who were dependent. Lack of regular exercise. The odds of falling were twice as high (CI = 1.00, 3.82) for those who did not exercise regularly as for those who exercised regularly. These findings suggest that ongoing assessment may be more important than the admission assessment in identifying risk factors for falls in the acute-care setting. No 2 studies have found exactly the same set of risk factors, although some findings are consistent across studies. This suggests that those risk factors that are consistent across studies may identify persons who are at the greatest risk for falls and that other risk factors for falls are specific to a patient population.

Lasers in vascular surgery.

The adoption of laser-assisted balloon angioplasty (LABA) has been advocated because of two advantages it may have over conventional balloon techniques. First, it has been suggested that more patients and lesions are amenable to LABA. Second, use of the laser has been said to produce higher long-term patency rates. There is already evidence that laser devices can supplement the complement of balloon and wires used in recanalizing peripheral vascular lesions that previously could not be treated. The skilled nursing management required by the patient with atherosclerotic peripheral vascular disease is based on the nursing process principles of assessment, planning, implementation, and evaluation combined with the technical understanding and knowledge of the LABA procedure in the operating room.

Patterns of relapse and prognosis after bevacizumab failure in recurrent glioblastoma.

BACKGROUND: Bevacizumab has recently been approved by the US Food and Drug Administration for recurrent glioblastoma (GBM). However, patterns of relapse, prognosis, and outcome of further therapy after bevacizumab failure have not been studied systematically. METHODS: We identified patients at Memorial Sloan-Kettering Cancer Center with recurrent GBM who discontinued bevacizumab because of progressive disease. RESULTS: There were 37 patients (26 men with a median age of 54 years). The most common therapies administered concurrently with bevacizumab were irinotecan (43%) and hypofractionated reirradiation (38%). The median overall survival (OS) after progressive disease on bevacizumab was 4.5 months; 34 patients died. At the time bevacizumab was discontinued for tumor progression, 17 patients (46%) had an increase in the size of enhancement at the initial site of disease (local recurrence), 6 (16%) had a new enhancing lesion outside of the initial site of disease (multifocal), and 13 (35%) had progression of predominantly nonenhancing tumor. Factors associated with shorter OS after discontinuing bevacizumab were lower performance status and nonenhancing pattern of recurrence. Additional salvage chemotherapy after bevacizumab failure was given to 19 patients. The median progression-free survival (PFS) among these 19 patients was 2 months, the median OS was 5.2 months, and the 6-month PFS rate was 0%. CONCLUSIONS: Contrast enhanced MRI does not adequately assess disease status during bevacizumab therapy for recurrent glioblastoma (GBM). A nonenhancing tumor pattern of progression is common after treatment with bevacizumab for GBM and is correlated with worse survival. Treatments after bevacizumab failure provide only transient tumor control.

FDG-PET scanning for detection and staging of extranodal marginal zone lymphomas of the MALT type: a report of 42 cases.

BACKGROUND: Although reports have suggested that FDG-PET scans were not useful for staging of extranodal marginal zone lymphomas (MZL), experience at our center suggests otherwise. Thus we reviewed the findings of FDG-PET scans in patients with extranodal MZL seen at our center. PATIENTS AND METHODS: A database of 175 patients with histologically-confirmed diagnoses of extranodal MZL was reviewed. Forty-two patients who had had FDG-PET scans for initial staging were identified. All information was obtained by retrospective review of medical records and PET scans. RESULTS: Thirty-four (81%) patients had focal tracer uptake within verified tumor sites, six (14%) patients did not, and two (5%) patients had indeterminate uptake. Seven of the 34 (21%) patients with uptake within verified tumor sites had uptake in regional lymph nodes and four patients were upstaged due to FDG-PET findings. Eight patients also obtained post-treatment FDG-PET scans. In five of those eight, the repeated FDG-PET scan indicated a complete response, and in three there was an indeterminate or mixed response. CONCLUSION: FDG-PET scans carried out for initial staging of extranodal MZL detected disease in a high proportion of patients. This study suggests that imaging with FDG-PET scans is useful for both initial staging and follow-up of patients with extranodal MZL.

Intraoperative advances: laparoscopic cholecystectomy.

The introduction of laparoscopic cholecystectomy in general surgery is an exciting technology because of the success that has been produced using the procedure. The noninvasive surgical approach was introduced at a time when medicine needed a new advancement in the plan of care for the surgical patient. The less invasive procedure, shorter hospital stay, and faster recovery are just a few of the reasons why laparoscopic cholecystectomy is a procedure that is now gaining popularity in the ambulatory surgery setting.