Can Zipf's law be adapted to normalize microarrays?

BACKGROUND: Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented. RESULTS: Using pairwise comparisons using MA plots (log ratio vs. log intensity), we compared this novel method to previously published normalization techniques, namely global normalization to the mean, the quantile method, and a variation on the loess normalization method designed specifically for boutique microarrays. Results indicated that, for single channel microarrays, the quantile method was superior with regard to eliminating intensity-dependent effects (banana curves), but Zipf's law normalization does minimize this effect by rotating the data distribution such that the maximal number of data points lie on the zero of the log ratio axis. For two channel boutique microarrays, the Zipf's law normalizations performed as well as, or better than existing techniques. CONCLUSION: Zipf's law normalization is a useful tool where the Quantile method cannot be applied, as is the case with microarrays containing functionally specific gene sets (boutique arrays)

Disrupted reward processing in Parkinson's disease and its relationship with dopamine state and neuropsychiatric syndromes: a systematic review and meta-analysis

Background: Neuropsychiatric symptoms are common in Parkinson’s disease (PD) and predict poorer outcomes. Reward processing dysfunction is a candidate mechanism for the development of psychiatric symptoms including depression and impulse control disorders (ICDs). We aimed to determine whether reward processing is impaired in PD and its relationship with neuropsychiatric syndromes and dopamine replacement therapy. // Methods: The Ovid MEDLINE/PubMed, Embase and PsycInfo databases were searched for articles published up to 5 November 2020. Studies reporting reward processing task performance by patients with PD and healthy controls were included. Summary statistics comparing reward processing between groups were converted to standardised mean difference (SMD) scores and meta-analysed using a random effects model. // Results: We identified 55 studies containing 2578 participants (1638 PD and 940 healthy controls). Studies assessing three subcomponent categories of reward processing tasks were included: option valuation (n=12), reinforcement learning (n=37) and reward response vigour (n=6). Across all studies, patients with PD on medication exhibited a small-to-medium impairment versus healthy controls (SMD=0.34; 95% CI 0.14 to 0.53), with greater impairments observed off dopaminergic medication in within-subjects designs (SMD=0.43, 95% CI 0.29 to 0.57). Within-subjects subcomponent analysis revealed impaired processing off medication on option valuation (SMD=0.57, 95% CI 0.39 to 0.75) and reward response vigour (SMD=0.36, 95% CI 0.13 to 0.59) tasks. However, the opposite applied for reinforcement learning, which relative to healthy controls was impaired on-medication (SMD=0.45, 95% CI 0.25 to 0.65) but not off-medication (SMD=0.28, 95% CI −0.03 to 0.59). ICD was the only neuropsychiatric syndrome with sufficient studies (n=13) for meta-analysis, but no significant impairment was identified compared tonon-ICD patients (SMD=−0.02, 95% CI −0.43 to 0.39). // Conclusion: Reward processing disruption in PD differs according to subcomponent and dopamine medication state, and warrants further study as a potential treatment target and mechanism underlying associated neuropsychiatric syndromes

Acute fuelling and recovery practices of academy soccer players: implications for growth, maturation, and physical performance

Academy soccer players frequently train in the evening (i.e. 1700-2000 h), hence limited time to nutritionally prepare and recover due to schooling, travel and sleep schedules. Accordingly, we assessed timing and quantity of energy intake in the pre-training and post-training period. Over a 3-day in-season training period, male players (n=48; n=8 from under (U) 12, 13, 14, 15/16, 18 and 23 players) from an English Premier League academy self-reported dietary intake and physical activity levels (via the remote food photography method and activity diary, respectively) in the four hours pre- and post-training. Timing of pre-training energy intake ranged from 40 ± 28 mins (U15/U16 players) to 114 ± 71 mins (U18) before training and mean carbohydrate (CHO) intake ranged from 0.8±0.4 g.kg-1 (U23) to 1.5±0.9 g.kg-1 (U12). Timing of post-training energy intake ranged from 39 ± 27 mins (U14) to 70 ± 84 mins (U23) and mean CHO intake ranged from 1.6±0.8 g.kg-1 (U12) to 0.9±0.5 g.kg-1 (U14). In contrast to CHO, all age groups consumed sufficient protein intake in the post-training period (i.e. > 0.3 g.kg-1). We conclude academy soccer players habitually practice sub-optimal fuelling and recovery strategies, the consequence of which could impair growth, maturation and physical performance

The Nrf2 inhibitor brusatol is a potent antitumour agent in an orthotopic mouse model of colorectal cancer

© Evans et al. Nrf2 is a transcription factor that regulates cellular stress response and irinotecan-metabolising pathways. Its aberrant activity has been reported in a number of cancers, although relatively few studies have explored a role for Nrf2 in colorectal cancer (CRC). This study assessed the expression of Nrf2 in patient CRC tissues and explored the effect of Nrf2 modulation alone, or in combination with irinotecan, in human (HCT116) and murine (CT26) cell lines in vitro and in an orthotopic syngeneic mouse model utilising bioluminescent imaging. Using a tissue microarray, Nrf2 was found to be overexpressed (p < 0.01) in primary CRC and metastatic tissue relative to normal colon, with a positive correlation between Nrf2 expression in matched primary and metastatic samples. In vitro experiments in CRC cell lines revealed that Nrf2 siRNA and brusatol, which is known to inhibit Nrf2, decreased viability and sensitised cells to irinotecan toxicity. Furthermore, brusatol effectively abrogated CRC tumour growth in subcutaneously and orthotopicallyallografted mice, resulting in an average 8-fold reduction in luminescence at the study end-point (p=0.02). Our results highlight Nrf2 as a promising drug target in the treatment of CRC

Effects of 10 days of separate heat and hypoxic exposure on heat acclimation and temperate exercise performance.

Adaptations to heat and hypoxia are typically studied in isolation but are often encountered in combination. Whether the adaptive response to multiple stressors affords the same response as when examined in isolation is unclear. We examined 1) the influence of overnight moderate normobaric hypoxia on the time course and magnitude of adaptation to daily heat exposure and 2) whether heat acclimation (HA) was ergogenic and whether this was influenced by an additional hypoxic stimulus. Eight males [V̇o2max = 58.5 (8.3) ml·kg-1·min-1] undertook two 11-day HA programs (balanced-crossover design), once with overnight normobaric hypoxia (HAHyp): 8 (1) h per night for 10 nights [[Formula: see text] = 0.156; SpO2 = 91 (2)%] and once without (HACon). Days 1, 6, and 11 were exercise-heat stress tests [HST (40°C, 50% relative humidity, RH)]; days 2-5 and 7-10 were isothermal strain [target rectal temperature (Tre) ~38.5°C], exercise-heat sessions. A graded exercise test and 30-min cycle trial were undertaken pre-, post-, and 14 days after HA in temperate normoxia (22°C, 55% RH; FIO2 = 0.209). HA was evident on day 6 (e.g., reduced Tre, mean skin temperature (T̄sk), heart rate, and sweat [Na+], P < 0.05) with additional adaptations on day 11 (further reduced T̄sk and heart rate). HA increased plasma volume [+5.9 (7.3)%] and erythropoietin concentration [+1.8 (2.4) mIU/ml]; total hemoglobin mass was unchanged. Peak power output [+12 (20) W], lactate threshold [+15 (18) W] and work done [+12 (20) kJ] increased following HA. The additional hypoxic stressor did not affect these adaptations. In conclusion, a separate moderate overnight normobaric hypoxic stimulus does not affect the time course or magnitude of HA. Performance may be improved in temperate normoxia following HA, but this is unaffected by an additional hypoxic stressor

Early epigenetic downregulation of microRNA-192 expression promotes pancreatic cancer progression

Pancreatic ductal adenocarcinoma (PDAC) is characterized by very early metastasis, suggesting the hypothesis that metastasis-associated changes may occur prior to actual tumor formation. In this study, we identified miR-192 as an epigenetically regulated suppressor gene with predictive value in this disease. miR-192 was downregulated by promoter methylation in both PDAC and chronic pancreatitis, the latter of which is a major risk factor for the development of PDAC. Functional studies in vitro and in vivo in mouse models of PDAC showed that overexpression of miR-192 was sufficient to reduce cell proliferation and invasion. Mechanistic analyses correlated changes in miR-192 promoter methylation and expression with epithelial–mesenchymal transition. Cell proliferation and invasion were linked to altered expression of the miR-192 target gene SERPINE1 that is encoding the protein plasminogen activator inhibitor-1 (PAI-1), an established regulator of these properties in PDAC cells. Notably, our data suggested that invasive capacity was altered even before neoplastic transformation occurred, as triggered by miR-192 downregulation. Overall, our results highlighted a role for miR-192 in explaining the early metastatic behavior of PDAC and suggested its relevance as a target to develop for early diagnostics and therapy. Cancer Res; 76(14); 4149–59. ©2016 AACR

Acute fuelling and recovery practices of academy soccer players: implications for growth, maturation, and physical performance.

Considering that academy soccer players frequently train in the evening (i.e. 17:00-20:00 h), there is often limited time to nutritionally prepare and recover due to schooling, travel and sleep schedules. Accordingly, we assessed the timing and quantity of dietary intake of academy soccer players in the pre-training and post-training period. Over a 3-day in-season training period, male adolescent players (n=48; n=8 from under (U) 12, 13, 14, 15/16, 18 and 23 players) from an English Premier League academy self-reported their dietary intake and physical activity levels (via the remote food photography method and activity diary, respectively) in the four hours before and after training. External training load was also quantified via GPS. Timing of pre-training energy intake ranged from 40 ± 28 mins (U15/U16 players) to 114 ± 71 mins (U18) before training and mean carbohydrate (CHO) intake ranged from 0.8±0.4 g.kg-1 (U23) to 1.5±0.9 g.kg-1 (U12). Timing of post-training energy intake ranged from 39 ± 27 mins (U14) to 70 ± 84 mins (U23) and mean CHO intake ranged from 1.6±0.8 g.kg-1 (U12) to 0.9±0.5 g.kg-1 (U14). In contrast to sub-optimal CHO intakes, all age groups consumed sufficient protein intake in the post-training period (i.e. > 0.3 g.kg-1). We conclude academy soccer players habitually practice sub-optimal acute fuelling and recovery strategies, the consequence of which could impair growth, maturation and physical performance. Player and stakeholder education and behaviour change interventions should therefore target specific behaviours that lead to increased CHO intake before, during and after training

Somatic mutations in exocrine pancreatic tumors: association with patient survival.

KRAS mutations are major factors involved in initiation and maintenance of pancreatic tumors. The impact of different mutations on patient survival has not been clearly defined. We screened tumors from 171 pancreatic cancer patients for mutations in KRAS and CDKN2A genes. Mutations in KRAS were detected in 134 tumors, with 131 in codon 12 and only 3 in codon 61. The GGT>GAT (G12D) was the most frequent mutation and was present in 60% (80/134). Deletions and mutations in CDKN2A were detected in 43 tumors. Analysis showed that KRAS mutations were associated with reduced patient survival in both malignant exocrine and ductal adenocarcinomas (PDAC). Patients with PDACs that had KRAS mutations showed a median survival of 17 months compared to 30 months for those without mutations (log-rank P = 0.07) with a multivariate hazard ratio (HR) of 2.19 (95%CI 1.09-4.42). The patients with G12D mutation showed a median survival of 16 months (log-rank-test P = 0.03) and an associated multivariate HR 2.42 (95%CI 1.14-2.67). Although, the association of survival in PDAC patients with CDKN2A aberrations in tumors was not statistically significant, the sub-group of patients with concomitant KRAS mutations and CDKN2A alterations in tumors were associated with a median survival of 13.5 months compared to 22 months without mutation (log-rank-test P = 0.02) and a corresponding HR of 3.07 (95%CI 1.33-7.10). Our results are indicative of an association between mutational status and survival in PDAC patients, which if confirmed in subsequent studies can have potential clinical application

Temporal variance of disturbance did not affect diversity and structure of a marine fouling community in north-eastern New Zealand

Natural heterogeneity in ecological parameters, like population abundance, is more widely recognized and investigated than variability in the processes that control these parameters. Experimental ecologists have focused mainly on the mean intensity of predictor variables and have largely ignored the potential to manipulate variances in processes, which can be considered explicitly in experimental designs to explore variation in causal mechanisms. In the present study, the effect of the temporal variance of disturbance on the diversity of marine assemblages was tested in a field experiment replicated at two sites on the northeast coast of New Zealand. Fouling communities grown on artificial settlement substrata experienced disturbance regimes that differed in their inherent levels of temporal variability and timing of disturbance events, while disturbance intensity was identical across all levels. Additionally, undisturbed assemblages were used as controls. After 150 days of experimental duration, the assemblages were then compared with regard to their species richness, abundance and structure. The disturbance effectively reduced the average total cover of the assemblages, but no consistent effect of variability in the disturbance regime on the assemblages was detected. The results of this study were corroborated by the outcomes from simultaneous replicate experiments carried out in each of eight different biogeographical regions around the world