Investigating pre‐analytical requirements for serum and plasma based infrared spectro‐diagnostic

Infrared spectroscopy is a rapid, easy‐to‐operate, label‐free and therefore cost‐effective technique. Many studies performed on biofluids (eg, serum, plasma, urine, sputum, bile and cerebrospinal fluid) have demonstrated its promising application as a clinical diagnostic tool. Given all these characteristics, infrared spectroscopy appears to be an ideal candidate to be implemented into the clinics. However, before considering its translation, a clear effort is needed to standardise protocols for biofluid spectroscopic analysis. To reach this goal, careful investigations to identify and track errors that can occur during the pre‐analytical phase is a crucial step. Here, we report for the first time, results of investigations into pre‐analytical factors that can affect the quality of the spectral data acquired on serum and plasma, such as the impact of long‐term freezing time storage of samples as well as the month‐to‐month reproducibility of the spectroscopic analysis. The spectral data discrimination has revealed to be majorly impacted by a residual water content variation in serum and plasma dried samples.      

Vapour pressure deficit during growth has little impact on genotypic differences of transpiration efficiency at leaf and whole‐plant level: an example from Populus nigra L.

Poplar genotypes differ in transpiration efficiency (TE) at leaf and whole‐plant level under similar conditions. We tested whether atmospheric vapour pressure deficit (VPD) affected TE to the same extent across genotypes. Six Populus nigra genotypes were grown under two VPD. We recorded (1) ¹³C content in soluble sugars; (2) ¹⁸O enrichment in leaf water; (3) leaf‐level gas exchange; and (4) whole‐plant biomass accumulation and water use. Whole‐plant and intrinsic leaf TE and ¹³C content in soluble sugars differed significantly among genotypes. Stomatal conductance contributed more to these differences than net CO₂ assimilation rate. VPD increased water use and reduced whole‐plant TE. It increased intrinsic leaf‐level TE due to a decline in stomatal conductance. It also promoted higher ¹⁸O enrichment in leaf water. VPD had no genotype‐specific effect. We detected a deviation in the relationship between ¹³C in leaf sugars and ¹³C predicted from gas exchange and the standard discrimination model. This may be partly due to genotypic differences in mesophyll conductance, and to its lack of sensitivity to VPD. Leaf‐level ¹³C discrimination was a powerful predictor of the genetic variability of whole‐plant TE irrespective of VPD during growth.     

Genes involved in the regulation of vascular homeostasis determine renal survival rate in patients with chronic glomerulonephritis

Chronic glomerulonephritis (CGN) is one of the most severe kidney diseases. Genes of vascular reactivity are thought to play an important role in development and progression of CGN. In this study, we analyzed association of genes of vascular homeostasis with hypertension and renal survival of CGN patients. The study sample included 238 patients with CGN and 304 healthy subjects of population control. Ten polymorphisms of ten genes of vascular homeostasis were genotyped through polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) analysis and TaqMan assays. Association of the genotypes with renal survival was analyzed by the Kaplan–Meier estimator. Genotypes 311SC and 311SS of the PON2 gene, (− 1166)AC and (− 1166)CC of the AGTR1 gene, (+ 46)AA of the ADRB2 gene, and 198KK and 198KN of the EDN1 gene were associated with decreased rate of renal survival of the patients. Polymorphisms S311C PON2, (− 1166)A/C AGTR1, (+ 46)G/A ADRB2, and K198N EDN1 were associated with the accelerated decline in kidney function in the CGN patients.     

Visualization and correction of automated segmentation,tracking and lineaging from 5-D stem cell image sequences

Background

Neural stem cells are motile and proliferative cells that undergo mitosis, dividing to produce daughter cells and ultimately generating differentiated neurons and glia. Understanding the mechanisms controlling neural stem cell proliferation and differentiation will play a key role in the emerging fields of regenerative medicine and cancer therapeutics. Stem cell studies in vitro from 2-D image data are well established. Visualizing and analyzing large three dimensional images of intact tissue is a challenging task. It becomes more difficult as the dimensionality of the image data increases to include time and additional fluorescence channels. There is a pressing need for 5-D image analysis and visualization tools to study cellular dynamics in the intact niche and to quantify the role that environmental factors play in determining cell fate.

Results

We present an application that integrates visualization and quantitative analysis of 5-D (x,y,z,t,channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks.

Conclusions

By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. We combine unsupervised image analysis algorithms with an interactive visualization of the results. Our validation interface allows for each data set to be corrected to 100% accuracy, ensuring that downstream data analysis is accurate and verifiable. Our tool is the first to combine all of these aspects, leveraging the synergies obtained by utilizing validation information from stereo visualization to improve the low level image processing tasks.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-328) contains supplementary material, which is available to authorized users.     

Losing the beat: deficits in temporal coordination

Tapping or clapping to an auditory beat, an easy task for most individuals, reveals precise temporal synchronization with auditory patterns such as music, even in the presence of temporal fluctuations. Most models of beat-tracking rely on the theoretical concept of pulse: a perceived regular beat generated by an internal oscillation that forms the foundation of entrainment abilities. Although tapping to the beat is a natural sensorimotor activity for most individuals, not everyone can track an auditory beat. Recently, the case of Mathieu was documented (Phillips-Silver et al. 2011 Neuropsychologia 49, 961–969. (doi:10.1016/j.neuropsychologia.2011.02.002)). Mathieu presented himself as having difficulty following a beat and exhibited synchronization failures. We examined beat-tracking in normal control participants, Mathieu, and a second beat-deaf individual, who tapped with an auditory metronome in which unpredictable perturbations were introduced to disrupt entrainment. Both beat-deaf cases exhibited failures in error correction in response to the perturbation task while exhibiting normal spontaneous motor tempi (in the absence of an auditory stimulus), supporting a deficit specific to perception–action coupling. A damped harmonic oscillator model was applied to the temporal adaptation responses; the model''s parameters of relaxation time and endogenous frequency accounted for differences between the beat-deaf cases as well as the control group individuals.     

Diel vertical migration of the loosejaw dragonfishes (Stomiiformes: Stomiidae: Malacosteinae): a new analysis for rare pelagic taxa

The diel vertical migration (DVM) of three genera of the stomiid subfamily Malacosteinae (Photostomias, Aristostomias and Malacosteus) was analysed from capture records of nearly 300 specimens in the Atlantic Ocean. To account for broad temporal and geographic scales encountered in this study, local time of capture was transformed to a corrected time representing position in a solar day. Species of Photostomias and Aristostomias undertake asynchronous DVMs characterized by a residence in the mesopelagic zone during the day and separate migrating and non‐migrating subpopulations at night. Species of Photostomias displayed an asynchronous DVM pattern characterized by a residence in the lower mesopelagic zone (>500 m) during the day and a segregated distribution at night. Specimens of Photostomias guernei captured at night in the mesopelagic were nearly identical in size to those captured in the epipelagic; however, day epipelagic specimens were stratified by size. In species of Aristostomias, few specimens were caught in the mesopelagic zone during the day and only small specimens were captured in the mesopelagic zone at night, indicating that sampling depth may not have been adequate to capture the bulk of mesopelagic daytime residents and the entire size range of the non‐migrating night‐time residents. In contrast, Malacosteus niger was distributed below 600 m, did not regularly migrate to the epipelagic zone and was stratified across the 700 m isobath. From these data, relationships between DVM patterns, morphology and foraging ecology are inferred and biases and applications of this method are discussed.     

Unraveling the finding of 1/<Emphasis Type="Italic">f</Emphasis><Superscript><Emphasis Type="Italic">β</Emphasis></Superscript> noise in self-paced and synchronized tapping: a unifying mechanistic model

1/f ( beta ) noise has been revealed in both self-paced and synchronized tapping sequences, without being consistently taken into consideration for the modeling of underlying timing mechanisms. In this study we characterize variability, short-range, and long-range correlation properties of asynchronies and inter-tap intervals collected in a synchronization tapping experiment, attesting statistically the presence of 1/f ( beta ) noise in asynchronies. We verify that the linear phase correction model of synchronization tapping in its original formulation cannot account for the empirical long-range correlation properties. On the basis of previous accounts of 1/f ( beta ) noise in the literature on self-paced tapping, we propose an extension of the original synchronization model by modeling the timekeeping process as a source of 1/f ( beta ) fluctuations. Simulations show that this '1/f-AR synchronization model' accounts for the statistical properties of empirical series, including long-range correlations, and provides an unifying mechanistic account of 1/f ( beta ) noise in self-paced and synchronization tapping. This account opens the original synchronization framework to further investigations of timing mechanisms with regard to the serial correlation properties in performed time intervals.     

Mapping large-scale distribution of submerged aquatic vegetation coverage using remote sensing

This study investigated the potential of using remote sensing for mapping and monitoring of submerged aquatic vegetation (SAV) on a large scale. The spectral characteristics of SAV with varied coverage were measured using a portable spectroradiometer on a man-made lake at the Chongming International Wetland Park, Shanghai, China. A good relationship between the coverage of SAV and their field spectral characteristics was established and the reflectance of SAV increased with its increasing coverage. A regression analysis was then carried out between the coverage and the reflectance at the wavelengths of four QuickBird bands. After making an atmospheric correction from a synchronous QuickBird image for the study site, the image digital number (DN) was converted into the ground reflectance. The reflectance image was then deduced into a distribution map of SAV coverage by using the results of the regression functions between the coverage of SAV and the reflectance rate measured in situ. An accuracy assessment indicated that this approach could be used to quickly monitor the distribution and growth situation of SAV. The implications of this observation, in terms of the ability of remote sensing to estimate and monitor the distribution and dynamics of SAV on a large scale are discussed.     

Investigation of the status quo of massive blood transfusion in China

The aim of this study was to provide an overview of massive transfusion in Chinese hospitals, identify the important indications for massive transfusion and corrective therapies based on clinical evidences and supporting experimental studies, and propose guidelines for the management of massive transfusion. This multi-region, multi-center retrospective study involved a Massive Blood Transfusion Coordination Group composed of 50 clinical experts specializing in blood transfusion, cardiac surgery, anesthesiology, obstetrics, general surgery, and medical statistics from 20 tertiary general hospitals across five regions in China. Data were collected for all patients, who received ≥ 10 U red blood cell transfusion within 24 hours in the participating hospitals from January 1 2009 to December 31 2010, including patient’s demographics, pre-, peri-, and post-operative clinical characteristics, laboratory test results before, during, and after transfusion, and patient mortality at post-transfusion and discharge. We also designed an in vitro hemodilution model to investigate the changes of blood coagulation indices during massive transfusion and the correction of coagulopathy through supplement blood components under different hemodilutions. The experimental data in combination with the clinical evidences were used to determine the optimal proportion and timing for blood component supplementation during massive transfusion. Based on the findings from the present study, together with an extensive review of domestic and international transfusion-related literature and consensus feedback from the 50 experts, we drafted the guidelines on massive blood transfusion that may help Chinese hospitals to develop standardized protocols for massive blood transfusion.