Neural complexity: a graph theoretic interpretation.

One of the central challenges facing modern neuroscience is to explain the ability of the nervous system to coherently integrate information across distinct functional modules in the absence of a central executive. To this end, Tononi et al. [Proc. Natl. Acad. Sci. USA. 91, 5033 (1994)] proposed a measure of neural complexity that purports to capture this property based on mutual information between complementary subsets of a system. Neural complexity, so defined, is one of a family of information theoretic metrics developed to measure the balance between the segregation and integration of a system's dynamics. One key question arising for such measures involves understanding how they are influenced by network topology. Sporns et al. [Cereb. Cortex 10, 127 (2000)] employed numerical models in order to determine the dependence of neural complexity on the topological features of a network. However, a complete picture has yet to be established. While De Lucia et al. [Phys. Rev. E 71, 016114 (2005)] made the first attempts at an analytical account of this relationship, their work utilized a formulation of neural complexity that, we argue, did not reflect the intuitions of the original work. In this paper we start by describing weighted connection matrices formed by applying a random continuous weight distribution to binary adjacency matrices. This allows us to derive an approximation for neural complexity in terms of the moments of the weight distribution and elementary graph motifs. In particular, we explicitly establish a dependency of neural complexity on cyclic graph motifs.

Prostate cancer in BRCA2 germline mutation carriers is associated with poorer prognosis.

BACKGROUND: The germline BRCA2 mutation is associated with increased prostate cancer (PrCa) risk. We have assessed survival in young PrCa cases with a germline mutation in BRCA2 and investigated loss of heterozygosity at BRCA2 in their tumours. METHODS: Two cohorts were compared: one was a group with young-onset PrCa, tested for germline BRCA2 mutations (6 of 263 cases had a germline BRAC2 mutation), and the second was a validation set consisting of a clinical set from Manchester of known BRCA2 mutuation carriers (15 cases) with PrCa. Survival data were compared with a control series of patients in a single clinic as determined by Kaplan-Meier estimates. Loss of heterozygosity was tested for in the DNA of tumour tissue of the young-onset group by typing four microsatellite markers that flanked the BRCA2 gene, followed by sequencing. RESULTS: Median survival of all PrCa cases with a germline BRCA2 mutation was shorter at 4.8 years than was survival in controls at 8.5 years (P=0.002). Loss of heterozygosity was found in the majority of tumours of BRCA2 mutation carriers. Multivariate analysis confirmed that the poorer survival of PrCa in BRCA2 mutation carriers is associated with the germline BRCA2 mutation per se. CONCLUSION: BRCA2 germline mutation is an independent prognostic factor for survival in PrCa. Such patients should not be managed with active surveillance as they have more aggressive disease.

Neural complexity and structural connectivity.

Tononi [Proc. Natl. Acad. Sci. U.S.A. 91, 5033 (1994)] proposed a measure of neural complexity based on mutual information between complementary subsystems of a given neural network, which has attracted much interest in the neuroscience community and beyond. We develop an approximation of the measure for a popular Gaussian model which, applied to a continuous-time process, elucidates the relationship between the complexity of a neural system and its structural connectivity. Moreover, the approximation is accurate for weakly coupled systems and computationally cheap, scaling polynomially with system size in contrast to the full complexity measure, which scales exponentially. We also discuss connectivity normalization and resolve some issues stemming from an ambiguity in the original Gaussian model.

Use of the ISO 9308-1 procedure for the detection of E. coil in water utilizing two incubation temperatures and two confirmation procedures and comparison with defined substrate technology.

Disinfected and non-disinfected samples have been used to determine the accuracy of the ISO procedure (ISO 9308-1) for detection of E. coli in drinking water. Samples were analysed using the ISO procedure at both 36 and 44 degrees C and using the defined substrate technology method Colilert-18/Quanti-Tray (Colilert-18). Utilizing the confirmation procedure described in ISO 9308-1, large numbers of false positive E. coli results were obtained using the ISO primary isolation procedure at 36 degrees C. However, when glucuronidase production was used as the confirmation procedure, the 'confirmed' count of E. coli was lowest with ISO 9308-1 performed at 36 degrees C. When TTC medium was incubated at 36 degrees C confirmation using production of indole at 44 degrees C resulted in 29% more 'E. coli' being recovered than when confirmation was performed using production of glucuronidase. When 44 degrees C was used as the primary isolation temperature the difference between the number of 'confirmed' E. coli identified using the two confirmation procedures was less than 1% and was not significant. Identification of isolates which 'confirmed' when using production of indole at 44 degrees C as the test method but which failed to produce beta-D-glucuronidase, showed that the majority of these isolates were Klebsiella oxytoca.

Soil erosion and significance for carbon fluxes in a mountainous Mediterranean-climate watershed.

In topographically complex terrains, downslope movement of soil organic carbon (OC) can influence local carbon balance. The primary purpose of the present analysis is to compare the magnitude of OC displacement by erosion with ecosystem metabolism in such a complex terrain. Does erosion matter in this ecosystem carbon balance? We have used the Revised Universal Soil Loss Equation (RUSLE) erosion model to estimate lateral fluxes of OC in a watershed in northwestern Mexico. The watershed (4900 km2) has an average slope of 10 degrees +/- 9 degrees (mean +/- SD); 45% is >10 degrees, and 3% is >30 degrees. Land cover is primarily shrublands (69%) and agricultural lands (22%). Estimated bulk soil erosion averages 1350 Mg x km(-2) x yr(-1). We estimate that there is insignificant erosion on slopes < 2 degrees and that 20% of the area can be considered depositional. Estimated OC erosion rates are 10 Mg x km(-2) x yr(-1) for areas steeper than 2 degrees. Over the entire area, erosion is approximately 50% higher on shrublands than on agricultural lands, but within slope classes, erosion rates are more rapid on agricultural areas. For the whole system, estimated OC erosion is approximately 2% of net primary production (NPP), increasing in high-slope areas to approximately 3% of NPP. Deposition of eroded OC in low-slope areas is approximately 10% of low-slope NPP. Soil OC movement from erosional slopes to alluvial fans alters the mosaic of OC metabolism and storage across the landscape.

Differential regulation of protein phosphatase-1(I) by neurabin.

Neurabin is a brain-specific actin and protein phosphatase-1 (PP-1) binding protein that inhibits the purified catalytic subunit of protein phosphatase-1 (PP-1(C)). However, endogenous PP-1 exists primarily as multimeric complexes of PP-1(C) bound to various regulatory proteins that determine its activity, substrate specificity, subcellular localization and function. The major form of endogenous PP-1 in brain is protein phosphatase-1(I) (PP-1(I)), a Mg(2+)/ATP-dependent form of PP-1 that consists of PP-1(C), the inhibitor-2 regulatory subunit, an activating protein kinase and other unidentified proteins. We have identified four PP-1(I) holoenzyme fractions (PP-1(IA), PP-1(IB), PP-1(IC), and PP-1(ID)) in freshly harvested pig brain separable by poly-L-lysine chromatography. Purified recombinant neurabin (amino acid residues 1-485) inhibited PP-1(IB) (IC(50)=1.1 microM), PP-1(IC) (IC(50)=0.1 microM), and PP-1(ID) (IC(50)=0.2 microM), but activated PP-1(IA) by up to threefold (EC(50)=40 nM). The PP-1(IA) activation domain was localized to neurabin(1-210). Our results indicate a novel mechanism of PP-1 regulation by neurabin as both an inhibitor and an activator of distinct forms of PP-1(I) in brain.

Spatially embedded random networks.

Many real-world networks analyzed in modern network theory have a natural spatial element; e.g., the Internet, social networks, neural networks, etc. Yet, aside from a comparatively small number of somewhat specialized and domain-specific studies, the spatial element is mostly ignored and, in particular, its relation to network structure disregarded. In this paper we introduce a model framework to analyze the mediation of network structure by spatial embedding; specifically, we model connectivity as dependent on the distance between network nodes. Our spatially embedded random networks construction is not primarily intended as an accurate model of any specific class of real-world networks, but rather to gain intuition for the effects of spatial embedding on network structure; nevertheless we are able to demonstrate, in a quite general setting, some constraints of spatial embedding on connectivity such as the effects of spatial symmetry, conditions for scale free degree distributions and the existence of small-world spatial networks. We also derive some standard structural statistics for spatially embedded networks and illustrate the application of our model framework with concrete examples.

Modelling the evolution of genetic regulatory networks.

An evolutionary model of genetic regulatory networks is developed, based on a model of network encoding and dynamics called the Artificial Genome (AG). This model derives a number of specific genes and their interactions from a string of (initially random) bases in an idealized manner analogous to that employed by natural DNA. The gene expression dynamics are determined by updating the gene network as if it were a simple Boolean network. The generic behaviour of the AG model is investigated in detail. In particular, we explore the characteristic network topologies generated by the model, their dynamical behaviours, and the typical variance of network connectivities and network structures. These properties are demonstrated to agree with a probabilistic analysis of the model, and the typical network structures generated by the model are shown to lie between those of random networks and scale-free networks in terms of their degree distribution. Evolutionary processes are simulated using a genetic algorithm, with selection acting on a range of properties from gene number and degree of connectivity through periodic behaviour to specific patterns of gene expression. The evolvability of increasingly complex patterns of gene expression is examined in detail. When a degree of redundancy is introduced, the average number of generations required to evolve given targets is reduced, but limits on evolution of complex gene expression patterns remain. In addition, cyclic gene expression patterns with periods that are multiples of shorter expression patterns are shown to be inherently easier to evolve than others. Constraints imposed by the template-matching nature of the AG model generate similar biases towards such expression patterns in networks in initial populations, in addition to the somewhat scale-free nature of these networks. The significance of these results on current understanding of biological evolution is discussed.

ATM polymorphisms as risk factors for prostate cancer development.

The risk of prostate cancer is known to be elevated in carriers of germline mutations in BRCA2, and possibly also in carriers of BRCA1 and CHEK2 mutations. These genes are components of the ATM-dependent DNA damage signalling pathways. To evaluate the hypothesis that variants in ATM itself might be associated with prostate cancer risk, we genotyped five ATM variants in DNA from 637 prostate cancer patients and 445 controls with no family history of cancer. No significant differences in the frequency of the variant alleles at 5557G>A (D1853N), 5558A>T (D1853V), ivs38-8t>c and ivs38-15g>c were found between the cases and controls. The 3161G (P1054R) variant allele was, however, significantly associated with an increased risk of developing prostate cancer (any G vs CC OR 2.13, 95% CI 1.17-3.87, P=0.016). A lymphoblastoid cell line carrying both the 3161G and the 2572C (858L) variant in the homozygote state shows a cell cycle progression profile after exposure to ionising radiation that is significantly different to that seen in cell lines carrying a wild-type ATM gene. These results provide evidence that the presence of common variants in the ATM gene, may confer an altered cellular phenotype, and that the ATM 3161C>G variant might be associated with prostate cancer risk.

Influence of an injury reduction program on injury and fitness outcomes among soldiers.

OBJECTIVE: This study evaluated the influence of a multiple injury control intervention on injury and physical fitness outcomes among soldiers attending United States Army Ordnance School Advanced Individual Training. METHODS: The study design was quasiexperimental involving a historical control group (n = 2559) that was compared to a multiple intervention group (n = 1283). Interventions in the multiple intervention group included modified physical training, injury education, and a unit based injury surveillance system (UBISS). The management responsible for training independently formed an Injury Control Advisory Committee that examined surveillance reports from the UBISS and recommended changes to training. On arrival at school, individual soldiers completed a demographics and lifestyle questionnaire and took an army physical fitness test (APFT: push-ups, sit-ups, and two mile run). Injuries among soldiers were tracked by a clinic based injury surveillance system that was separate from the UBISS. Soldiers completed a final APFT eight weeks after arrival at school. RESULTS: Cox regression (survival analysis) was used to examine differences in time to the first injury while controlling for group differences in demographics, lifestyle characteristics, and physical fitness. The adjusted relative risk of a time loss injury was 1.5 (95% confidence interval 1.2 to 1.8) times higher in the historical control men and 1.8 (95% confidence interval 1.1 to 2.8) times higher in the historical control women compared with the multiple intervention men and women, respectively. After correcting for the lower initial fitness of the multiple intervention group, there were no significant differences between the multiple intervention and historical control groups in terms of improvements in push-ups, sit-ups, or two mile run performance. CONCLUSIONS: This multiple intervention program contributed to a reduction in injuries while improvements in physical fitness were similar to a traditional physical training program previously used at the school.

CHEK2 variants in susceptibility to breast cancer and evidence of retention of the wild type allele in tumours.

We have recently shown that the CHEK2*1100delC mutation acts as a low penetrance breast cancer susceptibility allele. To investigate if other CHEK2 variants confer an increased risk of breast cancer, we have screened an affected individual with breast cancer from 68 breast cancer families. Five of these individuals were found to harbour germline variants in CHEK2. Three carried the 1100delC variant (4%). One of these three individuals also carried the missense variant, Arg180His. In the other two individuals, missense variants, Arg117Gly and Arg137Gln, were identified. These two missense variants reside within the Forkhead-associated domain of CHEK2, which is important for the function of the expressed protein. None of these missense variants were present in 300 healthy controls. Microdissected tumours with a germline mutation showed loss of the mutant allele suggesting a mechanism for tumorigenesis other than a loss of the wild type allele. This study provides further evidence that sequence variation in CHEK2 is associated with an increased risk of breast cancer, and implies that tumorigenesis in association with CHEK2 mutations does not involve loss of the wild type allele.

Conserved signals and machinery for RNA transport in Drosophila oogenesis and embryogenesis.

Localization of cytoplasmic messenger RNA transcripts is widely used to target proteins within cells. For many transcripts, localization depends on cis-acting elements within the transcripts and on microtubule-based motors; however, little is known about other components of the transport machinery or how these components recognize specific RNA cargoes. Here, we show that in Drosophila the same machinery and RNA signals drive specific accumulation of maternal RNAs in the early oocyte and apical transcript localization in blastoderm embryos. We demonstrate in vivo that Egalitarian (Egl) and Bicaudal D (BicD), maternal proteins required for oocyte determination, are selectively recruited by, and co-transported with, localizing transcripts in blastoderm embryos, and that interfering with the activities of Egl and BicD blocks apical localization. We propose that Egl and BicD are core components of a selective dynein motor complex that drives transcript localization in a variety of tissues.

The molecular phenotype of heparan sulfate in the Hs2st-/- mutant mouse.

Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. We previously described the phenotype of mice with a gene-trap mutation in Hs2st, encoding the key HS 2-O-sulfotransferase enzyme in HS polymer modification. In contrast to the early developmental failure of embryos lacking HS, the onset of abnormalities in the Hs2st(-/-) mice occurs only after midgestation, the most dramatic being the complete failure of kidney development. Uronate 2-O-sulfates were not detected in the mutant HS, indicating a complete loss of function of Hs2st. However, the domain structure of the mutant HS is conserved, and compensatory increases in N- and 6-O-sulfation maintain the overall charge density. The apparent affinities of the mutant HS for hepatocyte growth factor/scatter factor and fibronectin were unchanged but were reduced for fibroblast growth factor-1 and -2. Surprisingly, the Hs2st(-/-) cells were able to mount an apparently normal signaling response to fibroblast growth factor-1 and -2 as well as to hepatocyte growth factor/scatter factor.

A gene trap insertion reveals that amyloid precursor protein expression is a very early event in murine embryogenesis.

Although it is known that aberrant processing of amyloid precursor protein (APP) in the adult is associated with Alzheimer's disease, the normal roles of APP in neuronal and embryonic development are not clear yet. As part of a gene trap screen undertaken to identify genes coding for secreted proteins involved in mouse gastrulation, we have obtained a mouse line in which the gene encoding APP is mutated by insertion of the lacZ reporter gene. This study shows that App expression is detected as early as gastrulation. In addition, although widely distributed at later stages, APP expression appears dynamically regulated during development.

Biomechanical evaluation of two halo pin designs, with, and without, intact periosteum.

The presence of periosteum has been hypothesized to adversely affect halo pin penetration and performance (Voor, 1992. Ph.D. Dissertation, Tulane University, New Orleans, LA). However, biomechanical testing of halo pins has historically been conducted on bone specimens with periosteum removed. This may have lead to an unrealistic measure of biomechanical pin performance. Our study compares the biomechanical performance of two halo pin designs on bovine bone specimens with, and without, intact periosteum. The two pin designs included in this study were the conventional pin (Bremer Medical) with conical tip, and a newly released trochar-style pin (DePuy AcroMed). Results showed the mean peak load before failure of the trochar-style pin (mean +/- 95% confidence interval: 656+/-29 N) to be significantly higher than the conventional pin (517+/-53 N) on bone with intact periosteum (p = 0.001). With the periosteum removed, the mean peak load of the trochar-style pin (655+/-99 N) remained statistically the same (p = 0.987), while the mean peak load of the conventional pin (634+/-65 N) increased significantly (p = 0.026). Variation of the data of the conventional pin significantly decreased from 32 to 19% on removal of periosteum (sigma = 165-103 N, respectively, p = 0.0967), while variation of the trochar-style remained statistically the same at 30-29% (sigma = 193-188 N, respectively, p = 0.954). These results show that the trochar-style pin may be biomechanically superior to the conventional pin for vertical forces experienced during immobilization. The performance of this new pin style may also not be significantly affected by overlying soft tissue. Use of this new pin style may, therefore, improve overall stability and fixation of the halo apparatus.

The effect of season and vitamin D supplementation on bone mineral density in healthy women: a double-masked crossover study.

Vitamin D status is known to be an important determinant of bone mineral density (BMD). There is a significant seasonal variation in serum vitamin D, and some studies have reported an associated seasonal variation in BMD. The present study was devised to investigate whether a seasonal variation in BMD could be detected in healthy normal subjects, along with associated variations in serum parathyroid hormone (PTH), intestinal calcium absorption and biochemical markers of bone turnover. A second aim was to investigate whether, if such variations were identified, they could be suppressed by vitamin D supplementation. The subjects were 70 healthy female volunteers (mean age 47.2 years, range 24-70 years) recruited into a double-masked crossover study and followed over 2 years. During the first year 35 subjects received a daily oral supplement containing 800 IU (20 micrograms) cholecalciferol (group 1) and 35 subjects received a placebo preparation (group 2). During the second year the treatment each group received was reversed. Lumbar spine (L1-L4), left proximal femur and total body BMD were measured by DXA at 3-month intervals. Serum 25-hydroxyvitamin D (25-OHD), serum PTH, bone markers (bone-specific ALP (BSAP) and urinary crosslinks (DYPD/creatinine)) and calcium absorption were also measured at each visit. Cholecalciferol treatment increased serum 25-OHD by 25.4 nmol/l (p < 0.001), while a reciprocal decrease in serum PTH of 6.6 ng/l (p = 0.011) was seen in subjects in the lowest quartile of baseline serum 25-OHD. The treatment had no significant effect on spine, femur or total body BMD, calcium absorption or bone markers. When Fourier analysis was used to analyze the data for seasonal effect (defined as twice the amplitude of the 1-year period variation) a highly significant effect for 25-OHD of 18 nmol/l (p < 0.001) was found. However, no effect was found for BMD, PTH, calcium absorption or bone markers. The analysis set a 95% confidence limit to the seasonal effect of less than 0.6% for spine, total hip and total body BMD. It was concluded that in the population of healthy women studied there was no evidence of seasonal variation in spine, femur or total body BMD, serum PTH, calcium absorption or bone markers. Vitamin D supplementation was found to have no effect on BMD.

Rb dephosphorylation and suppression of E2F activity in human breast tumor cells exposed to a pharmacological concentration of estradiol.

This report characterizes the influence of a pharmacological concentration of estradiol on growth arrest and cell death in MCF-7 breast tumor cells, with a focus on elements of the Rb-E2F cell-cycle regulatory pathway. Continuous exposure of MCF-7 breast tumor cells to 100 microM estradiol produces a marked reduction in the G1 and S phase populations and a corresponding increase in the G2/M population within 24 h; after 48 h, accumulation of cells in G1 becomes evident while after 72 h the cells appear to be equally distributed between the G1 and G2/M phases. The accumulation of cells in G1 is temporally associated with dephosphorylation of the Rb protein and suppression of E2F activity. Estradiol also produces an initial burst of cell death with loss of approximately 40% of the tumor cell population within 24 h; however, there is no tangible evidence for the occurrence of apoptosis based on terminal transferase end-labeling of DNA, DNA fragmentation analysis by alkaline unwinding, cell-cycle analysis or cell morphology. In addition to the lack of caspase-3 in MCF-7 cells, the absence of apoptosis could be related, at least in part, to the fact that estradiol promotes a rapid reduction in levels of the E2F-1 and Myc proteins. Overall, these studies are consistent with the concept that alterations in the levels and/or activity of the E2F family of proteins as well as proteins interacting with the E2F family may influence the nature of the antiproliferative and cytotoxic responses of the breast tumor cell.

Enhanced S phase delay and inhibition of replication of an undamaged shuttle vector in UVC-irradiated xeroderma pigmentosum variant.

Xeroderma pigmentosum variant (XP-V) cells are defective in bypass replication of UVC-induced thymine dimers in DNA because they lack a novel DNA polymerase (polymerase eta). In this study the effects of UVC on S phase cells were compared in fibroblasts derived from normal donors (IDH4) and XP-V patients (CTag) and immortalized by expression of the SV40 large T antigen. These transformed fibroblasts did not activate the G(1) checkpoint or inhibit replicon initiation when damaged by UVC or gamma-rays. The transformed XP-V cells (CTag) retained the increased sensitivity to UVC-induced inhibition of DNA strand growth previously observed with their diploid counterpart. Cell cycle progression analyses showed that CTag cells displayed a stronger S phase delay than transformed fibroblasts from normal individuals (IDH4) after treatment with only 2 J/m(2) UVC. Low doses of UVC also caused a lag in CTag cell proliferation. The extent of replication of an episomal DNA (pSV011), not previously exposed to radiation, was measured after the host cells were irradiated with 1-3 J/m(2) UVC. Replication of pSV011 was barely affected in irradiated IDH4 cells. Plasmid replication was inhibited by 50% in irradiated CTag cells and this inhibition could not be accounted for by increased killing of host cells by UVC. These results suggest that even in transformed cells UVC induces DNA damage responses that are reflected in transient cell cycle arrest, delay in proliferation and inhibition of episomal DNA replication. These responses are enhanced in CTag cells, presumably because of their bypass replication defect. The accumulation of replication complexes blocked at thymine dimers and extended single-stranded regions in chromosomal DNA might sequester replication factors that are needed for plasmid and chromosomal replication. Alternatively, aberrant replication structures might activate a signal transduction pathway that down-regulates DNA synthesis.

Formative evaluation of a computer-assisted learning program in pharmacology for nursing students.

Previous literature on evaluation of computer-assisted learning (CAL) programs has generally not emphasized the importance of evaluation during the design and development phases. A tendency toward an objective model of evaluation rather than a naturalistic model has also meant that there is little consideration given to the context in which students learn. The aim of this study was to demonstrate the benefits of using a combination of objective and naturalistic models when undertaking a formative evaluation of a computer-assisted learning program. During the design and development phases, the program, Pharmacology Resource for Nurses (PRN), was evaluated using observation of student pairs, student questionnaires, and student focus group interviews to address the complex issues underlying program effectiveness. This study confirmed the importance and value of collecting a variety of evaluation data in order to produce a useful learning program for students.