A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds

BACKGROUND: Microarrays provide a means to simultaneously examine the gene expression of the entire transcriptome in a single sample. Many studies have highlighted the need for novel software and statistical approaches to assess the measured gene expression. Less attention has been directed toward whether genes considered undetectable by microarray can be detected by other strategies or whether these genes can provide accurate gene expression determinations. In the kidney this is a concern for genes such as cytokines which dramatically influence the immune response but are often considered low abundance genes produced by a small number of cells. RESULTS: Using both publicly available and our own microarray datasets we analyzed the detection p-value and detection call values for 81 human kidney samples run on the U133A or U133Plus2.0 Affymetrix microarrays (Affymetrix, Santa Clara, CA). For the cytokine genes, the frequency of detection in each sample group (normal, transplant and renal cell carcinoma) was examined and revealed that a majority of cytokine related genes are not detectable in human kidney by microarray. Using a subset of 29 Mayo transplant samples, a group of seven transplant-related cytokines and eight non-cytokine genes were evaluated by real-time PCR (rt-PCR). For these 15 genes we compared the impact of decreasing microarray detection frequency with the changes in gene expression observed by both microarray and rt-PCR. We found that as microarray detection frequency decreased the correlation between microarray and rt-PCR data also decreased. CONCLUSION: We conclude that, when analyzing microarray data from human kidney samples, genes generally expressed at low abundance (i.e. cytokines) should be evaluated with more sensitive approaches such as rt-PCR. In addition, our data suggest that the use of detection frequency cutoffs for inclusion or exclusion of microarray data may be appropriate when comparing microarray and rt-PCR gene expression data and p-value calculations

Particle tunneling through a polarizable insulator

The tunneling probability between two leads connected by a molecule, a chain, a film, or a bulk polarizable insulator is investigated within a model of an electron tunneling from lead A to a state higher in energy, describing the barrier, and from there to lead B. To describe the possibility of energy exchange with excitations of the molecule or the insulator we couple the intermediate state to a single oscillator or to a spectrum of these, respectively. In the single-oscillator case we find for weak coupling that the tunneling is weakly suppressed by a Debye-Waller-type factor. For stronger coupling the oscillator gets 'stiff' and we observe a suppression of tunneling since the effective barrier is increased. The probability for the electron to excite the oscillator increases with the coupling. In the case of a film, or a bulk barrier the behavior is qualitatively the same as in the single oscillator case. An insulating chain, as opposed to a film or a bulk connecting the two leads,shows an 'orthogonality catastrophe' similar to that of an electronic transition in a Fermi gas.Comment: 4 pages, 1 figur

Global Neurosurgery: The Unmet Need

Globally, the lack of access to basic surgical care causes 3 times as much deaths as HIV/AIDS, tuberculosis, and malaria combined. The magnitude of this unmet need has been described recently, and the numbers are startling. Major shifts in global health agenda have highlighted access to essential and emergency surgery as a high priority. A broad examination of the current global neurosurgical efforts to improve access has revealed some strengths, particularly in the realm of training; however, the demand grossly outstrips the supply; most people in low-income countries do not have access to basic surgical care, either due to lack of availability or affordability. Projects that help create a robust and resilient health system within low- and middle-income countries require urgent implementation. In this context, concurrent scale-up of human resources, investments in capacity building, local data collection, and analysis for accurate assessment are essential. In addition, through process of collaboration and consensus building within the neurosurgical community, a unified voice of neurosurgery is necessary to effectively advocate for all those who need neurosurgical care wherever, whenever

Selective dorsal rhizotomy for treatment of spasticity after hemispherectomy in children: A case report

Performing a hemispherotomy or hemispherectomy is known to treat medically intractable epilepsy successfully, yet contralateral hemiparesis and increased muscle tone follow the epilepsy surgery. Spasticity and coexisting dystonia presumably cause the increased muscle tone in the lower extremity on the opposite side of epilepsy surgery. However, the extent of the role of spasticity and dystonia in high muscle tone is unknown. A selective dorsal rhizotomy is performed to reduce spasticity. If a selective dorsal rhizotomy is performed in the affected patient and muscle tone is reduced, the high muscle tone is not due to dystonia. Two children, who previously underwent a hemispherectomy or hemispherotomy, had a selective dorsal rhizotomy (SDR) performed in our clinic. Both children underwent orthopedic surgery to treat heel cord contractures. To study the extent of the role of spasticity and dystonia in high muscle tone, the mobility of the two children was examined pre- and post-SDR. The children had follow-ups 12 months and 56 months after SDR to study long-term effects. Before SDR, both children showed signs of spasticity. The SDR procedure removed spasticity, and muscle tone in the lower extremity became normal. Importantly, dystonia did not surface after SDR. Patients started independent walking less than two weeks after SDR. Sitting, standing, walking, and balance improved. They could walk longer distances while experiencing less fatigue. Running, jumping, and other more vigorous physical activities became possible. Notably, one child showed voluntary foot dorsiflexion that was absent before SDR. The other child showed improvement in voluntary foot dorsiflexion that was present before SDR. Both children maintained the progress at the 12 and 56-month follow-up visits. The SDR procedure normalized muscle tone and improved ambulation by removing spasticity. The high muscle tone following the epilepsy surgery was not due to dystonia

Clinical and kidney structural characteristics of living kidney donors with nephrolithiasis and their long-term outcomes

Background: Nephrolithiasis in living kidney donors is concerning due to the potential impact on long-term postdonation kidney function. Methods: We performed a cohort study of living kidney donors from 2 centers with a baseline computed tomography scan and implantation renal biopsy. Donors (\u3e5 y since donation) completed a follow-up survey or underwent chart review to assess eGFR and incident hypertension. Stone formers were classified as symptomatic if they had a past symptomatic episode or asymptomatic if only incidental radiographic kidney stones were identified during donor evaluation. We compared baseline clinical, imaging, and biopsy characteristics by stone former status including review of metabolic evaluations in stone formers. Long-term risks of renal complications (low eGFR and hypertension) by stone former status were evaluated. Results: There were 12 symptomatic and 76 asymptomatic stone formers among 866 donors. Overall, baseline clinical characteristics and implantation biopsy findings were similar between stone formers and non-stone formers. After a median follow-up of 10 y, stone former status was not associated with eGFR \u3c60 mL/min/1.73 m2, eGFR \u3c45 mL/min/1.73 m Conclusions: Both asymptomatic and symptomatic SF have favorable histology findings at baseline. Long-term kidney outcomes were favorable in select stone formers with no evident increased long-term risk for decreased kidney function or hypertension after donation

Total energy differences between SiC polytypes revisited

The total energy differences between various SiC polytypes (3C, 6H, 4H, 2H, 15R and 9R) were calculated using the full-potential linear muffin-tin orbital method using the Perdew-Wang-(91) generalized gradient approximation to the exchange-correlation functional in the density functional method. Numerical convergence versus k-point sampling and basis set completeness are demonstrated to be better than 1 meV/atom. The parameters of several generalized anisotropic next-nearest-neighbor Ising models are extracted and their significance and consequences for epitaxial growth are discussed.Comment: 8 pages, 3 figures, Latex, uses epsfig and revte

A Survey of Air-to-Ground Propagation Channel Modeling for Unmanned Aerial Vehicles

In recent years, there has been a dramatic increase in the use of unmanned aerial vehicles (UAVs), particularly for small UAVs, due to their affordable prices, ease of availability, and ease of operability. Existing and future applications of UAVs include remote surveillance and monitoring, relief operations, package delivery, and communication backhaul infrastructure. Additionally, UAVs are envisioned as an important component of 5G wireless technology and beyond. The unique application scenarios for UAVs necessitate accurate air-to-ground (AG) propagation channel models for designing and evaluating UAV communication links for control/non-payload as well as payload data transmissions. These AG propagation models have not been investigated in detail when compared to terrestrial propagation models. In this paper, a comprehensive survey is provided on available AG channel measurement campaigns, large and small scale fading channel models, their limitations, and future research directions for UAV communication scenarios

Detailed Inspection of Metal Implants

Detailed visual inspection of metal hips is the first step in retrieval analysis. In this study a systematic visual inspection protocol was developed to quantify bearing surface changes and their associations with material loss was investigated. Simple and multiple linear regression models found that moderate surface scratching, discolouration, haziness and the size of visible wear scars were all significantly associated with material loss (R2 = 5% - 73%, p<0.05). Visual inspection is not a substitute for measurement of material loss but an understanding of bearing surface changes may offer unique clues as to the mechanisms of failure of retrieved hips

Combining best evidence: A novel method to calculate the alcohol-attributable fraction and its variance for injury mortality

<p>Abstract</p> <p>Background</p> <p>The alcohol-attributable fraction for injury mortality is defined as the proportion of fatal injury that would disappear if consumption went to zero. Estimating this fraction has previously been based on a simplistic view of drinking and associated risk. This paper develops a new way to calculate the alcohol-attributable fraction for injury based on different dimensions of drinking, mortality data, experimental data, survey research, new risk scenarios, and by incorporating different distributions of consumption within populations. For this analysis, the Canadian population in 2005 was used as the reference population.</p> <p>Methods</p> <p>Binge drinking and average daily consumption were modeled separately with respect to the calculation of the AAF. The acute consumption risk was calculated with a probability-based method that accounted for both the number of binge drinking occasions and the amount of alcohol consumed per occasion. The average daily consumption was computed based on the prevalence of daily drinking at various levels. These were both combined to get an overall estimate. 3 sensitivity analyses were performed using different alcohol consumption parameters to test the robustness of the model. Calculation of the variance to generate confidence limits around the point estimates was accomplished via Monte Carlo resampling methods on randomly generated AAFs that were based on the distribution and prevalence of drinking in the Canadian population.</p> <p>Results</p> <p>Overall, the AAFs decrease with age and are significantly lower for women than men across all ages. As binge drinking increases, the injury mortality AAF also increases. Motor vehicle collisions show the largest relative increases in AAF as alcohol consumption is increased, with over a 100% increase in AAF from the lowest to highest consumption category. Among non-motor vehicle collisions, the largest change in total AAF occurred both for homicide and other intentional injuries at about a 15% increase in the AAF from the lowest to the highest binge consumption scenarios.</p> <p>Conclusions</p> <p>This method combines the best available evidence to generate new alcohol-attributable fractions for alcohol-attributable injury mortality. Future research is needed to refine the risk function for non-motor vehicle injury types and to investigate potential interactions between binge drinking and average volume of alcohol consumption.</p

The HY5-PIF regulatory module coordinates light and temperature control of photosynthetic gene transcription

The ability to interpret daily and seasonal alterations in light and temperature signals is essential for plant survival. This is particularly important during seedling establishment when the phytochrome photoreceptors activate photosynthetic pigment production for photoautotrophic growth. Phytochromes accomplish this partly through the suppression of phytochrome interacting factors (PIFs), negative regulators of chlorophyll and carotenoid biosynthesis. While the bZIP transcription factor long hypocotyl 5 (HY5), a potent PIF antagonist, promotes photosynthetic pigment accumulation in response to light. Here we demonstrate that by directly targeting a common promoter cis-element (G-box), HY5 and PIFs form a dynamic activation-suppression transcriptional module responsive to light and temperature cues. This antagonistic regulatory module provides a simple, direct mechanism through which environmental change can redirect transcriptional control of genes required for photosynthesis and photoprotection. In the regulation of photopigment biosynthesis genes, HY5 and PIFs do not operate alone, but with the circadian clock. However, sudden changes in light or temperature conditions can trigger changes in HY5 and PIFs abundance that adjust the expression of common target genes to optimise photosynthetic performance and growth