Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation

BACKGROUND: Gene microarray technology provides the ability to study the regulation of thousands of genes simultaneously, but its potential is limited without an estimate of the statistical significance of the observed changes in gene expression. Due to the large number of genes being tested and the comparatively small number of array replicates (e.g., N = 3), standard statistical methods such as the Student's t-test fail to produce reliable results. Two other statistical approaches commonly used to improve significance estimates are a penalized t-test and a Z-test using intensity-dependent variance estimates. RESULTS: The performance of these approaches is compared using a dataset of 23 replicates, and a new implementation of the Z-test is introduced that pools together variance estimates of genes with similar minimum intensity. Significance estimates based on 3 replicate arrays are calculated using each statistical technique, and their accuracy is evaluated by comparing them to a reliable estimate based on the remaining 20 replicates. The reproducibility of each test statistic is evaluated by applying it to multiple, independent sets of 3 replicate arrays. Two implementations of a Z-test using intensity-dependent variance produce more reproducible results than two implementations of a penalized t-test. Furthermore, the minimum intensity-based Z-statistic demonstrates higher accuracy and higher or equal precision than all other statistical techniques tested. CONCLUSION: An intensity-based variance estimation technique provides one simple, effective approach that can improve p-value estimates for differentially regulated genes derived from replicated microarray datasets. Implementations of the Z-test algorithms are available at

A new in vitro model to evaluate differential responses of endothelial cells to simulated arterial shear stress wave forms.

In the circulation, flow-responsive endothelial cells (ECs

Dissociation and its biological and clinical associations in functional neurological disorder: : systematic review and meta-analysis

BackgroundStudies have reported elevated rates of dissociative symptoms and comorbid dissociative disorders in functional neurological disorder (FND); however, a comprehensive review is lacking.AimsTo systematically review the severity of dissociative symptoms and prevalence of comorbid dissociative disorders in FND and summarise their biological and clinical associations.MethodWe searched Embase, PsycInfo and MEDLINE up to June 2021, combining terms for FND and dissociation. Studies were eligible if reporting dissociative symptom scores or rates of comorbid dissociative disorder in FND samples. Risk of bias was appraised using modified Newcastle–Ottawa criteria. The findings weresynthesised qualitatively and dissociative symptom scores were included in a meta-analysis (PROSPERO CRD42020173263).ResultsSeventy-five studies were eligible (FND n = 3940; control n = 3073), most commonly prospective case–control studies (k = 54). Dissociative disorders were frequently comorbid in FND. Psychoform dissociation was elevated in FND compared with healthy (g = 0.90, 95% CI 0.66–1.14, I2 = 70%) and neurologicalcontrols (g = 0.56, 95% CI 0.19–0.92, I2 = 67%). Greater psychoform dissociation was observed in FND samples with seizure symptoms versus healthy controls (g = 0.94, 95% CI 0.65–1.22, I2 = 42%) and FND samples with motor symptoms (g = 0.40, 95% CI −0.18 to 1.00, I2 = 54%). Somatoform dissociation was elevated in FND versus healthy controls (g = 1.80, 95% CI 1.25–2.34,I2 = 75%). Dissociation in FND was associated with more severe functional symptoms, worse quality of life and brain alterations.ConclusionsOur findings highlight the potential clinical utility of assessing patients with FND for dissociative symptomatology. However, fewer studies investigated FND samples with motor symptoms and heterogeneity between studies and risk of bias were high. Rigorous investigation of the prevalence, features and mechanistic relevance of dissociation in FND is needed

Prevalence of anti-sperm antibodies, risk factors associated and their impact on spermatobioscopy in infertile men

Background: The first immunological correlation with male infertility was reported in 1954 by Wilson and Rumke with the identification of anti-sperm antibodies. The prevalence of anti-sperm antibodies in infertile men varies from 9%-36%, the main cause being the loss of the blood-testicular barrier and otherwise the association with chronic inflammation. It has been shown that immune infertility is found in 15% of patients with varicocele.Methods: A transversal comparative study was carried out with 360 infertile men who were tested for anti-sperm antibodies between January 2011 and July 2018. Two groups were integrated; Group 1, infertile men with positive anti-sperm antibodies >50%, group 2, infertile men with negative anti-sperm <50%. Seminogram parameters were evaluated according to the WHO 5th edition and associated risk factors with anti-sperm antibodies.Results: 360 infertile men were evaluated during the study, 42 were excluded because they did not meet the inclusion criteria, the prevalence of anti-sperm antibodies was 14.5%. Group 1; n=46 (14.5%) and group 2, n=272 (85.5%), the clinical characteristics and the hormonal profile were compared at study admission without significant difference. There was a significant decrease in progressive motility in group 1 (38.7±23.8) vs group 2 (50.1±18.9) p=0.03. Analyzing the risk factors, varicocele was found to be significant 23.7%, OR 2.14 (1.27-3.61) p=0.004 as well as retractable testicle 26.4%, OR 2.13 (1.23-3.70) p= 0.008.Conclusions: The affectation of motility was confirmed, which leads to the suspect varicocele and retractable testicle as risk factors

Acute Stress in Health Workers during Two Consecutive EpidemicWaves of COVID-19

The COVID-19 pandemic has provoked generalized uncertainty around the world, with health workers experiencing anxiety, depression, burnout, insomnia, and stress. Although the effects of the pandemic on mental health may change as it evolves, the majority of reports have been web-based, cross-sectional studies. We performed a study assessing acute stress in frontline healthworkers during two consecutive epidemic waves. After screening for trait anxiety/depression and dissociative experiences, we evaluated changes in acute stress, considering resilience, state anxiety, burnout, depersonalization/derealization symptoms, and quality of sleep as cofactors. During the first epidemic wave (April 2020), health workers reported acute stress related to COVID-19, which was related to state anxiety. After the first epidemic wave, acute stress decreased, with no increase during the second epidemic wave (December 2020), and further decreased when vaccination started.During the follow-up (April 2020 to February 2021), the acute stress score was related to bad quality of sleep. However, acute stress, state anxiety, and burnout were all related to trait anxiety/depression, while the resilience score was invariant through time. Overall, the results emphasize the relevance of mental health screening before, during

Carbon dioxide fluxes across the Sierra de Guadarrama, Spain

Understanding the spatial and temporal variation in soil respiration within small geographic areas is essential to accurately assess the carbon budget on a global scale. In this study, we investigated the factors controlling soil respiration in an altitudinal gradient in a southern Mediterranean mixed pine&#8211;oak forest ecosystem in the north face of the Sierra de Guadarrama in Spain. Soil respiration was measured in five Pinus sylvestris L. plots over a period of 1 year by means of a closed dynamic system (LI-COR 6400). Soil temperature and water content were measured at the same time as soil respiration. Other soil physico-chemical and microbiological properties were measured during the study. Measured soil respiration ranged from 6.8 to 1.4 lmol m-2 s-1, showing the highest values at plots situated at higher elevation. Q10 values ranged between 1.30 and 2.04, while R10 values ranged between 2.0 and 3.6. The results indicate that the seasonal variation of soil respiration was mainly controlled by soil temperature and moisture. Among sites, soil carbon and nitrogen stocks regulate soil respiration in addition to soil temperature and moisture. Our results suggest that application of standard models to estimate soil respiration for small geographic areas may not be adequate unless other factors are considered in addition to soil temperature

Emergence of qualia from brain activity or from an interaction of proto-consciousness with the brain: which one is the weirder? Available evidence and a research agenda

This contribution to the science of consciousness aims at comparing how two different theories can explain the emergence of different qualia experiences, meta-awareness, meta-cognition, the placebo effect, out-of-body experiences, cognitive therapy and meditation-induced brain changes, etc. The first theory postulates that qualia experiences derive from specific neural patterns, the second one, that qualia experiences derive from the interaction of a proto-consciousness with the brain\u2019s neural activity. From this comparison it will be possible to judge which one seems to better explain the different qualia experiences and to offer a more promising research agenda

KLF2 Is a Novel Transcriptional Regulator of Endothelial Proinflammatory Activation

The vascular endothelium is a critical regulator of vascular function. Diverse stimuli such as proinflammatory cytokines and hemodynamic forces modulate endothelial phenotype and thereby impact on the development of vascular disease states. Therefore, identification of the regulatory factors that mediate the effects of these stimuli on endothelial function is of considerable interest. Transcriptional profiling studies identified the Kruppel-like factor (KLF)2 as being inhibited by the inflammatory cytokine interleukin-1β and induced by laminar shear stress in cultured human umbilical vein endothelial cells. Overexpression of KLF2 in umbilical vein endothelial cells robustly induced endothelial nitric oxide synthase expression and total enzymatic activity. In addition, KLF2 overexpression potently inhibited the induction of vascular cell adhesion molecule-1 and endothelial adhesion molecule E-selectin in response to various proinflammatory cytokines. Consistent with these observations, in vitro flow assays demonstrate that T cell attachment and rolling are markedly attenuated in endothelial monolayers transduced with KLF2. Finally, our studies implicate recruitment by KLF2 of the transcriptional coactivator cyclic AMP response element–binding protein (CBP/p300) as a unifying mechanism for these various effects. These data implicate KLF2 as a novel regulator of endothelial activation in response to proinflammatory stimuli

Parasite histones are toxic to brain endothelium and link blood barrier breakdown and thrombosis in cerebral malaria

Microvascular thrombosis and blood–brain barrier (BBB) breakdown are key components of cerebral malaria (CM) pathogenesis in African children and are implicated in fatal brain swelling. How Plasmodium falciparum infection causes this endothelial disruption and why this occurs, particularly in the brain, is not fully understood. In this study, we have demonstrated that circulating extracellular histones, equally of host and parasite origin, are significantly elevated in CM patients. Higher histone levels are associated with brain swelling on magnetic resonance imaging. On postmortem brain sections of CM patients, we found that histones are colocalized with P falciparum–infected erythrocytes sequestered inside small blood vessels, suggesting that histones might be expelled locally during parasite schizont rupture. Histone staining on the luminal vascular surface colocalized with thrombosis and leakage, indicating a possible link between endothelial surface accumulation of histones and coagulation activation and BBB breakdown. Supporting this, patient sera or purified P falciparum histones caused disruption of barrier function and were toxic to cultured human brain endothelial cells, which were abrogated with antihistone antibody and nonanticoagulant heparin. Overall, our data support a role for histones of parasite and host origin in thrombosis, BBB breakdown, and brain swelling in CM, processes implicated in the causal pathway to death. Neutralizing histones with agents such as nonanticoagulant heparin warrant exploration to prevent brain swelling in the development or progression of CM and thereby to improve outcomes