A High-Throughput Solver for Marginalized Graph Kernels on GPU

We present the design and optimization of a linear solver on General Purpose GPUs for the efficient and high-throughput evaluation of the marginalized graph kernel between pairs of labeled graphs. The solver implements a preconditioned conjugate gradient (PCG) method to compute the solution to a generalized Laplacian equation associated with the tensor product of two graphs. To cope with the gap between the instruction throughput and the memory bandwidth of current generation GPUs, our solver forms the tensor product linear system on-the-fly without storing it in memory when performing matrix-vector dot product operations in PCG. Such on-the-fly computation is accomplished by using threads in a warp to cooperatively stream the adjacency and edge label matrices of individual graphs by small square matrix blocks called tiles, which are then staged in registers and the shared memory for later reuse. Warps across a thread block can further share tiles via the shared memory to increase data reuse. We exploit the sparsity of the graphs hierarchically by storing only non-empty tiles using a coordinate format and nonzero elements within each tile using bitmaps. Besides, we propose a new partition-based reordering algorithm for aggregating nonzero elements of the graphs into fewer but denser tiles to improve the efficiency of the sparse format.We carry out extensive theoretical analyses on the graph tensor product primitives for tiles of various density and evaluate their performance on synthetic and real-world datasets. Our solver delivers three to four orders of magnitude speedup over existing CPU-based solvers such as GraKeL and GraphKernels. The capability of the solver enables kernel-based learning tasks at unprecedented scales

Simple staining method for differentiating live and dead marine zooplankton in field samples

We describe and evaluate a method for the use of neutral red staining to differentiate live and dead zooplankton in marine field samples. The protocol can be easily incorporated into shipboard zooplankton sampling. The use of neutral red in laboratory studies is common, but its application for quantifying natural live/dead zooplankton composition under field conditions has not been evaluated in detail. We tested the accuracy and precision of the method for a range of salinities and temperatures, and for common estuarine zooplankton groups. Detailed descriptions of staining intensities and patterns are provided. In addition, we evaluated potential artifact mortality due to collection and sample handling. The method produced accurate results under conditions tested, and artifact mortality was negligible using the recommended protocol. Neutral red staining is ideal for quantification of zooplankton carcasses in field samples, which will allow for more systematic study of in situ zooplankton mortality and related processes

How Well Can You Tailor the Charge of Lipid Vesicles?

Knowledge and control of surface charge or potential is important for tailoring colloidal interactions. In this work, we compare widely used zeta potential (ζ) measurements of charged lipid vesicle surface potential to direct measurements using the surface force apparatus (SFA). Our measurements show good agreement between the two techniques. On varying the fraction of anionic lipids dimyristoylphosphatidylserine (DMPS) or dimyristoylphosphatidylglycerol (DMPG) mixed with zwitterionic dimyristoylphosphatidylcholine (DMPC) from 0 to 100 mol % we observed a near-linear increase in membrane surface charge or potential up to 20-30 mol % charged lipids beyond which charge saturation occurred in physiological (high) salt conditions. Similarly, in low salt concentrations, a linear increase in charge/potential was found but only up to ∼5-10 mol % charged lipids beyond which the surface charge or potential leveled off. While a lower degree of ionization is expected due to the lower dielectric constant (ε ∼ 4) of the lipid acyl chain environment, increasing intramembrane electrostatic repulsion between neighboring charged lipid head groups at higher charge loading contributes to charge suppression. Measured potentials in physiological salt solutions were consistent with predictions using the Gouy-Chapman-Stern-Grahame (GCSG) model of the electrical double layer with Langmuir binding of counterions, but in low salt conditions, the model significantly overestimated the surface charge/potential. The much lower ionization in low salt (maximum ∼1-2% of total lipids ionized) instead was consistent with counterion condensation at the bilayer surface which limited the charge that could be obtained. The strong interplay between membrane composition, lipid headgroup ionization, electrolyte concentration, and solution pH complicates exact prediction and tuning of membrane surface charge for applications. However, the theoretical frameworks used here can provide guidelines to understand this interplay and establish a range of achievable potentials for a system and predict the response to triggers like pH and salt concentration changes

Dead in the water: The fate of copepod carcasses in the York River estuary, Virginia

Using laboratory and field experiments we investigated three fates of copepod carcass organic matter in the York River estuary, Virginia: ingestion by planktivores (necrophagy), microbial decomposition, and removal by gravitational settling in the presence of turbulence (sinking). The ctenophore Mnemiopsis leidyi ingested live copepods and carcasses indiscriminately in feeding experiments. Microbial decomposition led to ca. 50% of carcass dry weight loss within 8 h after death. Carcass settling velocities in still water were ca. 0.1 cm s(-1), implying short residence time (hours) in the shallow estuary. However, turbulent mixing kept carcasses in suspension much of the time, reducing sinking losses. Rates of carcass organic matter removal were combined in a simple mathematical model predicting the fate of estuarine copepod carcasses. When sinking was considered, it removed a large fraction of carcass organic matter (\u3e= 58% for copepodites, \u3e= 35% for nauplii), with most of the remainder being removed by microbial decomposition. In the absence of sinking losses, necrophagy became proportionally more important in removing carcass organic matter (\u3e= 49%, except in summer)

Survival and recovery of Phaeocystis antarctica (Prymnesiophyceae) from prolonged darkness and freezing

The colony-forming haptophyte Phaeocystis antarctica is an important primary producer in the Ross Sea, and must survive long periods of darkness and freezing temperature in this extreme environment. We conducted experiments on the responses of P. antarctica-dominated phytoplankton assemblages to prolonged periods of darkness and freezing. Chlorophyll and photosynthetic capacity of the alga declined nonlinearly and independently of each other in the dark, and darkness alone would potentially reduce photosynthetic capacity by only 60 per cent over 150 days (approximately the length of the Antarctic winter in the southern Ross Sea). The estimated reduction of colonial mucous carbon is higher than that of colonial cell carbon, suggesting metabolism of the colonial matrix in the dark. The alga quickly resumed growth upon return to light. Phaeocystis antarctica also survived freezing, although longer freezing durations lengthened the lag before growth resumption. Particulate dimethylsulfoniopropionate relative to chlorophyll increased upon freezing and decreased upon darkness. Taken together, the abilities of P. antarctica to survive freezing and initiate growth quickly after darkness may provide it with the capability to survive in both the ice and the water column, and help explain its repeated dominance in austral spring blooms in the Ross Sea and elsewhere in the Southern Ocean

Gap junctions regulate vessel diameter in chick chorioallantoic membrane vasculature by both tone‐dependent and structural mechanisms

Objective: In this study, we examined the impact of gap junction blockade on chick chorioallantoic membrane microvessels. Methods: Expression of Cx37, Cx40/42, and Cx43 in chick chorioallantoic membrane tissue was studied by PCR, Western blot, and confocal immunofluorescence microscopy. Vessel diameter changes occurring under gap junction blockade with carbenoxolone (175 µmol/L), palmitoleic acid (100 µmol/L), 43GAP27 (1 mmol/L) were analyzed by intravital microscopy. To analyze vascular tone, chick chorioallantoic membrane vessels were exposed to a vasodilator cocktail consisting of acetylcholine (10 μmol/L), adenosine (100 μmol/L), papaverine (200 μmol/L), and sodium nitroprusside (10 μmol/L). Results: In chick chorioallantoic membrane lysates, Western blot analysis revealed the expression of Cx40 and Cx43. Immunofluorescence in intact chick chorioallantoic membrane vasculature showed only Cx43, limited to arterial vessel walls. Upon gap junction blockade (3 hours) arterial and venous diameters decreased to 0.50 ± 0.03 and 0.36 ± 0.06 (carbenoxolone), 0.72 ± 0.08 and 0.63 ± 0.15 (palmitoleic acid) and 0.77 ± 0.004 and 0.58 ± 0.05 (GAP27), relative to initial values. Initially, diameter decrease was dominated by increasing vascular tone. After 6 hours, however, vessel tone was reduced, suggesting structural network remodeling. Conclusions: Our findings suggest a major role for connexins in mediating acute and chronic diameter changes in developing vascular networks

Human α2β1HI CD133+VE epithelial prostate stem cells express low levels of active androgen receptor

Stem cells are thought to be the cell of origin in malignant transformation in many tissues, but their role in human prostate carcinogenesis continues to be debated. One of the conflicts with this model is that cancer stem cells have been described to lack androgen receptor (AR) expression, which is of established importance in prostate cancer initiation and progression. We re-examined the expression patterns of AR within adult prostate epithelial differentiation using an optimised sensitive and specific approach examining transcript, protein and AR regulated gene expression. Highly enriched populations were isolated consisting of stem (α(2)β(1)(HI) CD133(+VE)), transiently amplifying (α(2)β(1)(HI) CD133(-VE)) and terminally differentiated (α(2)β(1)(LOW) CD133(-VE)) cells. AR transcript and protein expression was confirmed in α(2)β(1)(HI) CD133(+VE) and CD133(-VE) progenitor cells. Flow cytometry confirmed that median (±SD) fraction of cells expressing AR were 77% (±6%) in α(2)β(1)(HI) CD133(+VE) stem cells and 68% (±12%) in α(2)β(1)(HI) CD133(-VE) transiently amplifying cells. However, 3-fold lower levels of total AR protein expression (peak and median immunofluorescence) were present in α(2)β(1)(HI) CD133(+VE) stem cells compared with differentiated cells. This finding was confirmed with dual immunostaining of prostate sections for AR and CD133, which again demonstrated low levels of AR within basal CD133(+VE) cells. Activity of the AR was confirmed in prostate progenitor cells by the expression of low levels of the AR regulated genes PSA, KLK2 and TMPRSS2. The confirmation of AR expression in prostate progenitor cells allows integration of the cancer stem cell theory with the established models of prostate cancer initiation based on a functional AR. Further study of specific AR functions in prostate stem and differentiated cells may highlight novel mechanisms of prostate homeostasis and insights into tumourigenesis

Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood

Background Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization. Methods Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT), 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS) and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms. Results Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder). Conclusion The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.Boryana S Stamova, Michelle Apperson, Wynn L Walker, Yingfang Tian, Huichun Xu, Peter Adamczy, Xinhua Zhan, Da-Zhi Liu, Bradley P Ander, Isaac H Liao, Jeffrey P Gregg, Renee J Turner, Glen Jickling, Lisa Lit and Frank R Shar

The design and protocol of heat-sensitive moxibustion for knee osteoarthritis: a multicenter randomized controlled trial on the rules of selecting moxibustion location

<p>Abstract</p> <p>Background</p> <p>Knee osteoarthritis is a major cause of pain and functional limitation. Complementary and alternative medical approaches have been employed to relieve symptoms and to avoid the side effects of conventional medication. Moxibustion has been widely used to treat patients with knee osteoarthritis. Our past researches suggested heat-sensitive moxibustion might be superior to the conventional moxibustion. Our objective is to investigate the effectiveness of heat-sensitive moxibustion compared with conventional moxibustion or conventional drug treatment.</p> <p>Methods</p> <p>This study consists of a multi-centre (four centers in China), randomised, controlled trial with three parallel arms (A: heat-sensitive moxibustion; B: conventional moxibustion; C: conventional drug group). The moxibustion locations are different from A and B. Group A selects heat-sensitization acupoint from the region consisting of Yin Lingquan(SP9), Yang Lingquan(GB34), Liang Qiu(ST34), and Xue Hai (SP10). Meanwhile, fixed acupoints are used in group B, that is Xi Yan (EX-LE5) and He Ding (EX-LE2). The conventional drug group treats with intra-articular Sodium Hyaluronate injection. The outcome measures above will be assessed before the treatment, the 30 days of the last moxibustion session and 6 months after the last moxibustion session.</p> <p>Discussion</p> <p>This trial will utilize high quality trial methodologies in accordance with CONSORT guidelines. It will provide evidence for the effectiveness of moxibustion as a treatment for moderate and severe knee osteoarthritis. Moreover, the result will clarify the rules of heat-sensitive moxibustion location to improve the therapeutic effect with suspended moxibustion, and propose a new concept and a new theory of moxibustion to guide clinical practices.</p> <p>Trial Registration</p> <p>The trial is registered at Controlled Clinical Trials: ChiCTR-TRC-00000600.</p

A tale of two societies : The doing of qualitative comparative research in Hong Kong and Britain

This article explores the challenges and opportunities for methodological innovation arising from an exploratory, cross-national, qualitative study of women’s lives in Hong Kong and Britain. We begin by briefly outlining the aims of our study and its original research design, based on life history interviews with young adult women and their mothers in each location.We then turn to a discussion of how this was modified as we recruited participants and conducted the interviews, including the use of vignettes. We aim to be transparent about some of the problems of implementing a symmetrical approach to generating qualitative data in very different socio-cultural settings compounded by the practical difficulties of geographical distance between team members. We argue for a flexible approach that takes account of local cultural sensibilities rather than trying to follow rigidly identical procedures, recognising also that, in any qualitative research team, there will be differences in approach that affect the data produced. We highlight some of the insights yielded by the problems we encountered and, in particular, an accidental innovation that occurred through an ad hoc decision to conduct focus groups with the young women, which we call ‘cross-cultural data feedback’. This innovation involved our participants in contributing to cross cultural comparison and also brought taken-for-granted assumptions in each setting into sharp relief, as well as sensitising us to issues that proved important in analysing our data. This leads us to raise issues of interpreting and analysing data from differing socio-cultural locations and translating between cultures. We conclude with some recommendations including the potential for the future development of our method of cross-cultural data feedback