Sharing FAIR monitoring program data improves discoverability and reuse.

Data resulting from environmental monitoring programs are valuable assets for natural resource managers, decision-makers, and researchers. These data are often collected to inform specific reporting needs or decisions with a specific timeframe. While program-oriented data and related publications are effective for meeting program goals, sharing well-documented data and metadata allows users to research aspects outside initial program intentions. As part of an effort to integrate data from four long-term large-scale US aquatic monitoring programs, we evaluated the original datasets against the FAIR (Findable, Accessible, Interoperable, Reusable) data principles and offer recommendations and lessons learned. Differences in data governance across these programs resulted in considerable effort to access and reuse the original datasets. Requirements, guidance, and resources available to support data publishing and documentation are inconsistent across agencies and monitoring programs, resulting in various data formats and storage locations that are not easily found, accessed, or reused. Making monitoring data FAIR will reduce barriers to data discovery and reuse. Programs are continuously striving to improve data management, data products, and metadata; however, provision of related tools, consistent guidelines and standards, and more resources to do this work is needed. Given the value of these data and the significant effort required to access and reuse them, actions and steps intended on improving data documentation and accessibility are described.

A pilot study of darbepoetin alfa for prophylactic neuroprotection in aortic surgery.

BACKGROUND: Descending aortic (DA) surgery poses a high risk for spinal and cerebral infarction and routine use of lumbar drains allows for measurement of CSF markers of neurologic injury. Erythropoiesis medications have extensive preclinical data demonstrating neuroprotection. We hypothesized that prophylactic darbepoetin alfa (DARB) given before surgery reduces neurologic injury in patients undergoing DA repair. METHODS AND RESULTS: We performed a prospective adaptive dose-finding trial of prophylactic DARB ( www.clinicaltrials.gov NCT00647998) that terminated prematurely following publication of an erythropoietin stroke study showing possible harm. Enrollment halted before dose adjustments; nine patients each received 1 mg/kg IV DARB immediately before surgery. A prospective cohort of nine untreated patients was subsequently obtained for comparison. The primary outcome of death or neurologic impairment at discharge occurred in 1/9 (11 %) DARB patients and 3/9 (33 %) controls (p = 0.58). There were no statistical differences in changes of CSF biomarkers from baseline to 48 h comparing DARB patients to controls: S100ß, median 214 versus 260 ng/ml (p = 0.69); glial fibrillary acidic protein (GFAP), median 0.022 versus 0.58 ng/ml (p = 0.45). In patients with early perioperative neurologic ischemia, there were greater changes in CSF biomarkers, compared to those without ischemia: S100ß, median 2301 versus 124 ng/ml (p = 0.04); GFAP, median 31.78 versus 0.31 ng/ml (p = 0.34). CONCLUSIONS: There were no significant effects of prophylactic DARB on clinical outcome or CSF markers of neurologic injury in this pilot study, although all point estimates favored treatment. DA repair is a promising model of prophylactic neuroprotection.

Evidence for a new paradigm for ultraviolet exposure: a universal schedule that is skin phototype independent.

BACKGROUND: The Food and Drug Administration has published guidelines for manufacturer-recommended exposure schedules for ultraviolet (UV) tanning, intended to limit acute and delayed damage from UV exposure. These guidelines recommend that exposure schedules be adjusted for skin phototype. However, it has been shown that the dose necessary to produce tanning is similar for phototypes 2-4. METHODS: We observed tanning in phototypes 2 and 3 from repeated UV exposures over a 5-week period. Pigmentation was evaluated visually, instrumentally, and through Fontana-Masson staining of biopsies. RESULTS: The resultant pigmentation was equal or greater in phototype 3 compared with phototype 2 - both visually and instrumentally - measured on day 31 of the exposure protocol. The amount of melanin measured in biopsies taken 24 h postexposure was also greater in phototype 3 compared with phototype 2. CONCLUSION: Published data on tanning in phototypes 4 and 5 support our findings that higher phototypes can develop pigmentation more efficiently than lower phototypes. Therefore, a universal exposure schedule (based on sensitivity of phototype 2) can be used for all phototypes that are expected to engage in indoor tanning. This approach will result in a reduction of the UV burden for skin phototypes 3 and above.

Genetic and functional analysis of human P2X5 reveals a distinct pattern of exon 10 polymorphism with predominant expression of the nonfunctional receptor isoform.

P2X5 is a member of the P2X family of ATP-gated nonselective cation channels, which exist as trimeric assemblies. P2X5 is believed to trimerize with another member of this family, P2X1. We investigated the single-nucleotide polymorphism (SNP) at the 3' splice site of exon 10 of the human P2X5 gene. As reported previously, presence of a T at the SNP location results in inclusion of exon 10 in the mature transcript, whereas exon 10 is excluded when a G is present at this location. Our genotyping of human DNA samples reveals predominance of the G-bearing allele, which was exclusively present in DNA samples from white American, Middle Eastern, and Chinese donors. Samples from African American donors were polymorphic, with the G allele more frequent. Reverse transcription-polymerase chain reaction analysis of lymphocytes demonstrated a 100% positive correlation between genotype and P2X5 transcript. Immunostaining of P2X1/P2X5 stably coexpressing cell lines showed full-length P2X5 to be expressed at the cell surface and the exon 10-deleted isoform to be cytoplasmic. Fluorometric imaging-based pharmacological characterization indicated a ligand-dependent increase in intracellular calcium in 1321N1 astrocytoma cells transiently expressing full-length P2X5 but not the exon 10-deleted isoform. Likewise, electrophysiological analysis showed robust ATP-evoked currents when full-length but not the exon 10-deleted isoform of P2X5 was expressed. Taken together, our findings indicate that most humans express only a nonfunctional isoform of P2X5, which is in stark contrast to what is seen in other vertebrate species in which P2X5 has been studied, from which only the full-length isoform is known.

CaSm (LSm-1) overexpression in lung cancer and mesothelioma is required for transformed phenotypes.

CaSm (cancer-associated Sm-like) was originally identified based on elevated expression in pancreatic cancer and in several cancer-derived cell lines. It encodes a 133-amino acid protein that contains two Sm motifs found in the common snRNP proteins and the LSm (like-Sm) family of proteins. Lung tumors and mesotheliomas express high levels of CaSm mRNA and protein compared with adjacent nontumor and normal lung tissue, measured by immunohistochemistry, qRT-PCR, and Western blot analyses. In addition, several human lung cancer- and mesothelioma-derived cell lines have elevated CaSm expression. Two cell lines, transfected with and expressing antisense CaSm RNA, demonstrate altered transformed phenotypes, reducing their ability to form colonies in soft agar and tumors in SCID mice. Furthermore, RNAi-mediated reduction of CaSm RNA and protein is associated with inhibition of cellular growth. These data support the model that elevated CaSm expression in epithelial tissue contributes to the transformed state. Cell lines expressing exogenous CaSm also exhibit transformed characteristics, including increased anchorage-independent colony formation and tumor growth. Thus, the results of loss of function and gain of function studies presented both indicate that CaSm functions as an oncogene in the promotion of cellular transformation and cancer progression.

Immortalization and transformation of primary human airway epithelial cells by gene transfer.

One critical step in the development of a cancerous cell is its acquisition of an unlimited replicative lifespan, the process termed immortalization. Experimental model systems designed to study cellular transformation ex vivo have relied to date on the in vitro selection of a subpopulation of cells that have become immortalized through treatment with chemical or physical mutagens and the selection of rare clonal variants. In this study, we describe the direct immortalization of primary human airway epithelial cells through the successive introduction of the Simian Virus 40 Early Region and the telomerase catalytic subunit hTERT. Cells immortalized in this way are now responsive to malignant transformation by an introduced H-ras or K-ras oncogene. These immortalized human airway epithelial cells, which have been created through the stepwise introduction of genetic alterations, provide a novel experimental model system with which to study further the biology of the airway epithelial cell and to dissect the molecular basis of lung cancer pathogenesis.

Vertebroplasty increases compression of adjacent IVDs and vertebrae in osteoporotic spines.

BACKGROUND CONTEXT: Approximately 25% of vertebroplasty patients experience subsequent fractures within 1 year of treatment, and vertebrae adjacent to the cemented level are up to three times more likely to fracture than those further away. The increased risk of adjacent fractures postaugmentation raises concerns that treatment of osteoporotic compression fractures with vertebroplasty may negatively impact spine biomechanics. PURPOSE: To quantify the biomechanical effects of vertebroplasty on adjacent intervertebral discs (IVDs) and vertebral bodies (VBs). STUDY DESIGN: A biomechanics study was conducted using cadaveric thoracolumbar spinal columns from elderly women (age range, 51-98 years). METHODS: Five level motion segments (T11-L3) were assigned to a vertebroplasty treated or untreated control group (n=10/group) such that bone mineral density (BMD), trabecular architecture, and age were similar between groups. Compression fractures were created in the L1 vertebra of all specimens, and polymethylmethacrylate bone cement was injected into the fractured vertebra of vertebroplasty specimens. All spine segments underwent cyclic axial compression for 115,000 cycles. Microcomputed tomography imaging was performed before and after cyclic loading to quantify compression in adjacent VBs and IVDs. RESULTS: Cyclic loading increased strains 3% on average in the vertebroplasty group when compared with controls after 115,000 cycles. This global strain manifested locally as approximately fourfold more compression in the superior VB (T12) and two- to fourfold higher axial and circumferential deformations in the superior IVD (T12-L1) of vertebroplasty-treated specimens when compared with untreated controls. Low BMD and high cement fill were significant factors that explained the increased strain in the vertebroplasty-treated group. CONCLUSIONS: These data indicate that vertebroplasty alters spine biomechanics resulting in increased compression of adjacent VB and IVD in severely osteoporotic women and may be the basis for clinical reports of adjacent fractures after vertebroplasty.

Conditioning of transcranial magnetic stimulation: evidence of sensory-induced responding and prepulse inhibition.

BACKGROUND: Transcranial magnetic stimulation (TMS) is a non-invasive method for stimulating the human cortex. Classical conditioning is a phenomenon of developed associations between stimuli. Our primary objective was to determine whether TMS effects could be conditioned. Prepulse inhibition represents another relationship between two stimuli, and a secondary assessment was performed to explore this relationship. METHODS: An auditory-visual conditioning stimulus (CS) was paired with the TMS unconditioned stimulus (US) over motor cortex producing a motor-evoked potential (MEP) unconditioned response (UR). Two versions of the CS-US pairing paradigms were tested, one with a short intertrial interval (ITI) and another with a long ITI. The short ITI paradigm had more CS-US pairings and shorter session duration than the long ITI paradigm. Tests for conditioned responses (CRs) were performed following CS-US pairing (CS+/US+), by presenting the CS alone (CS+/US-). Reverse testing was also performed after CS-US pairing (CS+/US+) in separate sessions, by presenting the US alone (CS-/US+). RESULTS: Evidence for CRs was found only with the short ITI paradigm. The magnitudes of CRs were smaller than TMS-induced MEPs, and the CRs were found only in a percentage of tests. Prepulse inhibition was robustly evident for the long ITI paradigm, but not for the short ITI paradigm. CONCLUSIONS: We have found evidence that classical conditioning principles can be applied to brain stimulation in humans. These findings provide a method for exploring brain and behavioral relationships in humans, as well as suggesting approaches to enhance therapeutic uses of TMS or other forms of brain stimulation.

Bayesian Adaptation of the Summary ROC Curve Method for Meta-analysis of Diagnostic Test Performance.

Meta-analytic methods for diagnostic test performance, Bayesian methods in particular, have not been well developed. The most commonly used method for meta-analysis of diagnostic test performance is the Summary Receiver Operator Characteristic (SROC) curve approach of Moses, Shapiro and Littenberg. In this paper, we provide a brief summary of the SROC method, then present a case study of a Bayesian adaptation of their SROC curve method that retains the simplicity of the original model while additionally incorporating uncertainty in the parameters, and can also easily be extended to incorporate the effect of covariates. We further derive a simple transformation which facilitates prior elicitation from clinicians. The method is applied to two datasets: an assessment of computed tomography for detecting metastases in non-small-cell lung cancer, and a novel dataset to assess the diagnostic performance of endoscopic ultrasound (EUS) in the detection of biliary obstructions relative to the current gold standard of endoscopic retrograde cholangiopancreatography (ERCP).

Complement activation in the peripheral nervous system following the spinal nerve ligation model of neuropathic pain.

Neuroinflammatory and neuroimmune mechanisms, as exemplified by infiltrating immune cells and activation of resident endothelial/glial cells, respectively, are known to be involved in the establishment and maintenance of chronic pain. An immune system pathway that may be involved in the activation of both immune and glial cells is complement. The complement pathway is made up of a large number of distinct plasma proteins which react with one another to opsonize pathogens and induce a series of inflammatory responses to help fight infection. Cleaved products and complexes produced by complement activation are responsible for a range of effects including mediation of immune infiltration, activation of phagocytes, opsonization/lysis of pathogens and injured cells, and production of vasoactive amines such as histamine and serotonin. Gene-expression microarray-analysis performed on the rat spinal nerve ligation (SNL) model of neuropathic pain revealed that multiple complement components including the C1 inhibitor, C1q alpha, beta, and gamma, C1r, C1s, C2, C3, C4, C7, and factors B, D, H, and P, were up-regulated while DAF was down-regulated. Regulation of C3 and DAF was confirmed by real-time RT-PCR and in situ hybridization. To test the hypothesis that complement plays a role in neuropathic pain, SNL rats were treated with cobra venom factor (CVF) to deplete plasma of complement component C3. Pain behavior was significantly attenuated in SNL rats treated with CVF as was complement activity at the ipsilateral dorsal root ganglia. Our results suggest the complement pathway might be a novel target for the development of neuropathic pain therapeutics.

A BDNF infusion into the medial prefrontal cortex suppresses cocaine seeking in rats.

The medial prefrontal cortex (mPFC) is critical for reinstatement of cocaine seeking and is the main source of brain-derived neurotrophic factor (BDNF) to striatal regions of the brain relapse circuitry. To test the hypothesis that BDNF in the mPFC regulates cocaine-seeking behavior, rats were trained to press a lever for cocaine infusions (0.2 mg/inf, 2 h/day) paired with light+tone conditioned stimulus (CS) presentations on 10 consecutive days. After the last self-administration session, rats received a single infusion of BDNF (0.75 microg/0.5 microL/side) into the mPFC; this manipulation produced protracted effects on cocaine-seeking behavior (non-reinforced lever pressing). BDNF pretreatment administered after the last session attenuated cocaine seeking 22 h later and, remarkably, it also blocked cocaine-induced suppression of phospho-extracellular-regulated kinase and elevated BDNF immunoreactivity in the nucleus accumbens. The same pretreatment also suppressed cocaine-seeking behavior elicited by response-contingent CS presentations after 6 days of forced abstinence or extinction training, as well as a cocaine challenge injection (10 mg/kg, i.p.) after extinction training. However, BDNF infused into the mPFC had no effect on food-seeking behavior. Furthermore, BDNF infused on the sixth day of abstinence failed to alter responding, suggesting that the regulatory influence of BDNF is time limited. The suppressive effects of BDNF infused into the mPFC on cocaine seeking indicate that BDNF regulates cortical pathways implicated in relapse to drug seeking and that corticostriatal BDNF adaptations during early abstinence diminish compulsive drug seeking.