Venous Thromboembolism is Associated With Lack of Vitamin D Supplementation in Patients With Spinal Cord Injury and Low Vitamin D Levels.

BACKGROUND: The role of vitamin D in the pathogenesis of venous thromboembolism (VTE) and prevalence of low vitamin D (LVitD) in spinal cord injury (SCI) has motivated vitamin D testing and supplementation. This is an exploratory study of data collected at a time before the routine clinical practice of vitamin D supplementation, allowing for evaluation of the natural history of vitamin D levels in patients with SCI. OBJECTIVE: To determine if vitamin D supplementation in persons with SCI and LVitD levels is associated with decreased prevalence of VTE. DESIGN: Retrospective cohort study. SETTING: Rehabilitation Center at a Level I Trauma Center. PARTICIPANTS: Patients with SCI admitted to acute inpatient rehabilitation (N = 282). MAIN OUTCOME MEASURES: VTE prevalence in patients with LVitD levels, grouped by presence or absence of vitamin D supplementation. RESULTS: Of the acute inpatient SCI population, 80% (227/282) of patients demonstrated vitamin D levels <30 ng/mL (LVitD). Although the incidence of VTE was almost double in the LVitD group, 19% (43/227) of the patients in the LVitD group had VTE versus 9% (5/55) of patients with vitamin D levels ≥30 ng/mL (normal VitD [NVitD]); this difference was not statistically significant (P = .108, Cramer's V = .104). When the role of vitamin D supplementation was analyzed, individuals in the LVitD group who received no vitamin D supplementation (LVitDSuppNegative) had a higher incidence of VTE (statistically significant) compared to the LVitD group with vitamin D supplementation (LVitDSuppPositive) (24% [42/178] vs. 2% [1/49]) (P < .001, Cramer's V = .226). In post hoc exploratory analyses, the VTE rate of patients in the LVitDSuppNegative group was noted to be significantly higher than that in all other patient groups combined (P < .001, Cramer's V = .229). A binary logistic regression model incorporating clinical covariates also showed this grouping to be significant. CONCLUSION: A significant association appears to exist between lack of vitamin D supplementation and VTE occurrence in persons with acute SCI and LVitD levels. LEVEL OF EVIDENCE: III.

Differential expression of degradome components in cutaneous squamous cell carcinomas.

Although the cure rate for cutaneous squamous cell carcinoma is high, the diverse spectrum of squamous cell carcinoma has made it difficult for early diagnosis, particularly the aggressive tumors that are highly associated with mortality. Therefore, molecular markers are needed as an adjunct to current staging methods for diagnosing high-risk lesions, and stratifying those patients with aggressive tumors. To identify such biomarkers, we have examined a comprehensive set of 200 histologically defined squamous cell carcinoma and normal skin samples by using a combination of microarray, QRT-PCR and immunohistochemistry analyses. A characteristic and distinguishable profile including matrix metalloproteinase (MMP) as well as other degradome components was differentially expressed in squamous cell carcinoma compared with normal skin samples. The expression levels of some of these genes including matrix metallopeptidase 1 (MMP1), matrix metallopeptidase 10 (MMP10), parathyroid hormone-like hormone (PTHLH), cyclin-dependent kinase inhibitor 2A (CDKN2A), A disintegrin and metalloproteinase with thrombospondin motifs 1 (ADAMTS1), FBJ osteosarcoma oncogene (FOS), interleukin 6 (IL6) and reversion-inducing-cysteine-rich protein with kazal motifs (RECK) were significantly differentially expressed (P≤0.02) in squamous cell carcinoma compared with normal skin. Furthermore, based on receiver operating characteristic analyses, the mRNA and protein levels of MMP1 are significantly higher in aggressive tumors compared with non-aggressive tumors. Given that MMPs represent the most prominent family of proteinases associated with tumorigenesis, we believe that they may have an important role in modulating the tumor microenvironment of squamous cell carcinoma.

MetaMiner (CF): a disease-oriented bioinformatics analysis environment.

MetaMiner (CF) is a data analysis platform for a broad range of CF researchers including wet lab biologists, bioinformaticians, clinicians, and chemists. To understand disease mechanisms and gain insight into complex biological actions, analysis of even simple gene interactions often requires integration of a variety of separate data resources such as literature, 3D molecular models, metabolic pathways, ontologies, small molecules, and drugs. Large-scale data sets from high-throughput screening assays, microarrays, and other data intensive procedures present an even greater challenge in data handling and analysis which now requires interdisciplinary teams of scientists with strikingly diverse backgrounds including computer scientists, statisticians, biologists, and clinicians. To address the issues raised by the complexity of analysis and resource limitations of many research laboratories, MetaMiner (CF) was developed by GeneGo under direction and funding of Cystic Fibrosis Foundation Therapeutics. The platform was designed to provide the CF community with a single tool for analyzing experimental data in a disease-centered environment. To that end, the most important biological and chemical experimental data available today in cystic fibrosis research have been assembled and integrated with data analysis and visualization tools to highlight the key pathways leading to and perturbed by the disease. GeneGo developers assembled and edited CF-specific content and designed the disease-specific interface under the guidance and review of a team of leading cystic fibrosis experts. Updates and revisions will be processed quarterly under the direction of the CF Foundation Therapeutics.

Mortality in late post-traumatic seizures.

The objective of this study was to examine the mortality rates in individuals with traumatic brain injury (TBI) who were classified as having experienced late post-traumatic seizures (LPTS) in the first 2 years post-TBI compared to those who were seizure-free (non-LPTS). Participants were a pooled sample (n = 508) from two studies which enrolled individuals with TBI who were injured between March 31, 1992 and December 20, 1999. The first sample was made up of individuals enrolled in a study of risk factors for LPTS development; the second sample was composed of individuals enrolled in the TBI National Database from a single rehabilitation center. Seventy-one (14%) participants had LPTS, of which 27% had died at 8-15 years post-injury, as compared to 10% of non-LPTS participants. Individuals with LPTS died at a younger age (54.1 versus 67.7 years; p = 0.01), but there were no statistically significant differences in either time from date of injury to death or highest GCS score in the first 24 h. Causes of death were variable and not specifically related to epilepsy. Of those with LPTS, risk factors for death include advanced age at time of injury and presence of subdural hematoma. The higher mortality rate and death at younger age with variable causes in TBI individuals with LPTS warrant close medical evaluation and monitoring of these individuals, particularly accessibility and compliance with ongoing general medical care, and education of primary care colleagues of the unique needs of this at-risk population.

Make it better but don't change anything.

With massive amounts of data being generated in electronic format, there is a need in basic science laboratories to adopt new methods for tracking and analyzing data. An electronic laboratory notebook (ELN) is not just a replacement for a paper lab notebook, it is a new method of storing and organizing data while maintaining the data entry flexibility and legal recording functions of paper notebooks. Paper notebooks are regarded as highly flexible since the user can configure it to store almost anything that can be written or physically pasted onto the pages. However, data retrieval and data sharing from paper notebooks are labor intensive processes and notebooks can be misplaced, a single point of failure that loses all entries in the volume. Additional features provided by electronic notebooks include searchable indices, data sharing, automatic archiving for security against loss and ease of data duplication. Furthermore, ELNs can be tasked with additional functions not commonly found in paper notebooks such as inventory control. While ELNs have been on the market for some time now, adoption of an ELN in academic basic science laboratories has been lagging. Issues that have restrained development and adoption of ELN in research laboratories are the sheer variety and frequency of changes in protocols with a need for the user to control notebook configuration outside the framework of professional IT staff support. In this commentary, we will look at some of the issues and experiences in academic laboratories that have proved challenging in implementing an electronic lab notebook.

Respiratory epithelial gene expression in patients with mild and severe cystic fibrosis lung disease.

Despite having identical cystic fibrosis transmembrane conductance regulator genotypes, individuals with DeltaF508 homozygous cystic fibrosis (CF) demonstrate significant variability in severity of pulmonary disease. This investigation used high-density oligonucleotide microarray analysis of nasal respiratory epithelium to investigate the molecular basis of phenotypic differences in CF by (1) identifying differences in gene expression between DeltaF508 homozygotes in the most severe 20th percentile of lung disease by forced expiratory volume in 1 s and those in the most mild 20th percentile of lung disease and (2) identifying differences in gene expression between DeltaF508 homozygotes and age-matched non-CF control subjects. Microarray results from 23 participants (12 CF, 11 non-CF) met the strict quality control guidelines and were used for final data analysis. A total of 652 of the 11,867 genes identified as present in 75% of the samples were significantly differentially expressed in one of the three disease phenotypes: 30 in non-CF, 53 in mild CF, and 569 in severe CF. An analysis of genes differentially expressed by severity of CF lung disease demonstrated significant upregulation in severe CF of genes involved in protein ubiquination (P < 0.04), mitochondrial oxidoreductase activity (P < 0.01), and lipid metabolism (P < 0.03). Analysis of genes with decreased expression in patients with CF compared with control subjects demonstrated significant downregulation of genes involved in airway defense (P < 0.047) and protein metabolism (P < 0.048). This study suggests that differences in CF lung phenotype are associated with differences in expression of genes involving airway defense, protein ubiquination, and mitochondrial oxidoreductase activity and identifies specific new candidate modifiers of the CF phenotype.

Polycystin 2 interacts with type I inositol 1,4,5-trisphosphate receptor to modulate intracellular Ca2+ signaling.

Autosomal dominant polycystic kidney disease, a common cause of renal failure, arises from mutations in either the PKD1 or the PKD2 gene. The precise function of both PKD gene products polycystins (PCs) 1 and 2 remain controversial. PC2 has been localized to numerous cellular compartments, including the endoplasmic reticulum, plasma membrane, and cilia. It is unclear what pools are the most relevant to its physiological function as a putative Ca2+ channel. We employed a Xenopus oocyte Ca2+ imaging system to directly investigate the role of PC2 in inositol 1,4,5-trisphosphate (IP3)-dependent Ca2+ signaling. Cytosolic Ca2+ signals were recorded following UV photolysis of caged IP3 in the absence of extracellular Ca2+. We demonstrated that overexpression of PC2, as well as type I IP3 receptor (IP3R), significantly prolonged the half-decay time (t1/2) of IP3-induced Ca2+ transients. However, overexpressing the disease-associated PC2 mutants, the point mutation D511V, and the C-terminally truncated mutation R742X did not alter the t1/2. In addition, we found that D511V overexpression significantly reduced the amplitude of IP3-induced Ca2+ transients. Interestingly, overexpression of the C terminus of PC2 not only significantly reduced the amplitude but also prolonged the t1/2. Co-immunoprecipitation assays indicated that PC2 physically interacts with IP3R through its C terminus. Taken together, our data suggest that PC2 and IP3R functionally interact and modulate intracellular Ca2+ signaling. Therefore, mutations in either PC1 or PC2 could result in the misregulation of intracellular Ca2+ signaling, which in turn could contribute to the pathology of autosomal dominant polycystic kidney disease.

Gene expression profile analysis of 4-phenylbutyrate treatment of IB3-1 bronchial epithelial cell line demonstrates a major influence on heat-shock proteins.

Most individuals with cystic fibrosis (CF) carry one or two mutations that result in a maturation defect of the full-length CFTR protein. The DeltaF508 mutation results in a mutant protein that is degraded by the proteosome instead of progressing to the apical membrane where it functions as a cAMP-regulated chloride channel. 4-Phenylbutyrate (PBA) modulates heat-shock protein expression and promotes trafficking of DeltaF508, thus permitting maturation and membrane insertion. The goal of this study was to gain insight into the genetic mechanism of PBA action through a large-scale analysis of gene expression. The Affymetrix genome-spanning U133 microarray set was used to compare mRNA expression levels in untreated IB3-1 cell line cultures with cultures treated with 1 mM PBA for 12 and 24 h. The most notable changes in mRNA levels were transient elevations in heat-shock proteins. The majority of genes downregulated throughout the application period were functionally associated with control of gene expression. Another set of genes increased in expression starting at 24 h, suggesting these are downstream effects of altered gene expression initiated by PBA. More than one-third of the genes in this late expressing set were identified as having potential significance in understanding the pathology of CF. Our results demonstrate the usefulness of gene expression profile analysis in understanding the consequences of PBA treatment and provide insights in how this drug exerts its effect on the trafficking of CFTR.

The association of early computed tomography scan findings and ambulation, self-care, and supervision needs at rehabilitation discharge and at 1 year after traumatic brain injury.

OBJECTIVE: To ascertain the association between early computed tomography (CT) scan findings and the need for assistance with ambulation, activities of daily living (ADLs), and supervision at rehabilitation discharge and at 1 year after traumatic brain injury (TBI). DESIGN: Prospective longitudinal design. SETTING: Seventeen Traumatic Brain Injury Model Systems (TBIMS) centers. PARTICIPANTS: A total of 1,839 adults with TBI admitted to TBIMS trauma centers with subsequent acute rehabilitation; 849 were followed to 1 year after injury. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Accumulated CT scan pathology from the first week after injury; FIM instrument and Disability Rating Scale at rehabilitation discharge and 1 year after injury; and Supervision Rating Scale at 1 year. RESULTS: Chi-square analyses showed that individuals with a midline shift greater than 5mm (lateral compression) were more likely to require the assistance of another person at discharge from acute rehabilitation with ambulation (29% vs 17%-19%, P=.02), toileting (47% vs 33%-38%, P=.05), lower-body dressing (57% vs 39%-46%, P=.015), bladder continence (32% vs 19%-23%, P=.03), and overall supervision (53% vs 44%, P=.0006) than patients with a midline shift of lesser degree. At 1 year, 57% of patients with a midline shift greater than 5mm on acute CT scans were being supervised in the home versus 30% to 39% of those with a shift of lesser degree (P=.003); there were no significant differences in the percentages of those needing assistance for ambulation or ADLs. The association of subdural hematoma with ambulation, self-care, and supervision needs was related to the degree of midline shift but not to the presence of subdural hematoma. Individuals with subcortical contusions were more likely to require assistance at rehabilitation discharge for ambulation (32% vs 18%, P<.0001), lower-body dressing (61% vs 44%), toileting (52% vs 35%), bladder continence (34% vs 22%), and overall supervision (61% vs 44%) than those without subcortical contusions (P<.0001). At 1 year, individuals with acute subcortical contusions were more likely to need assistance with ambulation (15% vs 8%, P=.004) and stair climbing (15% vs 9%, P=.03). Those with bilateral frontal (54% vs 46%, P=.009) or bilateral temporal (58% vs 46%, P=.03) contusions were more likely to need assistance with overall supervision at rehabilitation discharge, compared with those with unilateral or no cortical contusions. CONCLUSIONS: The presence of either a midline shift greater than 5mm or a subcortical contusion on acute CT scans is associated with a greater need of assistance with ambulation, ADLs, and global supervision at rehabilitation discharge. Patients with bilateral cortical contusions require more global supervision at rehabilitation discharge but no more supervision for ambulation and ADLs. These findings may aid health care professionals and potential caregivers in planning for rehabilitation and supervision needs after rehabilitation discharge and, to a lesser extent, at 1 year after TBI.