ResearchPad - research-and-analysis-methods https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Estimating the potential impact of behavioral public health interventions nationally while maintaining agreement with global patterns on relative risks]]> https://www.researchpad.co/article/elastic_article_13880 This paper introduces a novel method to evaluate the local impact of behavioral scenarios on disease prevalence and burden with representative individual level data while ensuring that the model is in agreement with the qualitative patterns of global relative risk (RR) estimates. The method is used to estimate the impact of behavioral scenarios on the burden of disease due to ischemic heart disease (IHD) and diabetes in the Turkish adult population.MethodsDisease specific Hierarchical Bayes (HB) models estimate the individual disease probability as a function of behaviors, demographics, socio-economics and other controls, where constraints are specified based on the global RR estimates. The simulator combines the counterfactual disease probability estimates with disability adjusted life year (DALY)-per-prevalent-case estimates and rolls up to the targeted population level, thus reflecting the local joint distribution of exposures. The Global Burden of Disease (GBD) 2016 study meta-analysis results guide the analysis of the Turkish National Health Surveys (2008 to 2016) that contain more than 90 thousand observations.FindingsThe proposed Qualitative Informative HB models do not sacrifice predictive accuracy versus benchmarks (logistic regression and HB models with non-informative and numerical informative priors) while agreeing with the global patterns. In the Turkish adult population, Increasing Physical Activity reduces the DALYs substantially for both IHD by 8.6% (6.4% 11.2%), and Diabetes by 8.1% (5.8% 10.6%), (90% uncertainty intervals). Eliminating Smoking and Second-hand Smoke predominantly decreases the IHD burden 13.1% (10.4% 15.8%) versus Diabetes 2.8% (1.1% 4.6%). Increasing Fruit and Vegetable Consumption, on the other hand, reduces IHD DALYs by 4.1% (2.8% 5.4%) while not improving the Diabetes burden 0.1% (0% 0.1%).ConclusionWhile the national RR estimates are in qualitative agreement with the global patterns, the scenario impact estimates are markedly different than the attributable risk estimates from the GBD analysis and allow evaluation of practical scenarios with multiple behaviors. ]]> <![CDATA[Ultrasound prediction of Zika virus-associated congenital injury using the profile of fetal growth]]> https://www.researchpad.co/article/elastic_article_13878 Zika virus (ZIKV) is a mosquito-transmitted flavivirus, recently linked to microcephaly and central nervous system anomalies following infection in pregnancy. Striking findings of disproportionate growth with a smaller than expected head relative to body length have been observed more commonly among fetuses with exposure to ZIKV in utero compared to pregnancies without ZIKV infection regardless of other signs of congenital infection including microcephaly. This study’s objective was to determine the diagnostic accuracy of femur-sparing profile of intrauterine growth restriction for the identification of ZIKV-associated congenital injuries on postnatal testing. A retrospective cohort study of pregnant women with possible or confirmed ZIKV infection between January 1, 2016 and December 31, 2017 were included. Subjects were excluded if no prenatal ultrasound was available. A femur-sparing profile of growth restriction determined using INTERGROWTH-21st sonographic standard for head circumference to femur length (HC: FL). Congenital injuries were determined postnatally by imaging, comprehensive eye exam and standard newborn hearing screen. A total of 111 pregnant women diagnosed with ZIKV infection underwent fetal ultrasound and 95 neonates had complete postnatal evaluation. Prenatal microcephaly was detected in 5% of fetuses (6/111). Postnatal testing detected ZIKV-associated congenital injuries in 25% of neonates (24/95). A HC: FL Z-score ≤ -1.3 had a 52% specificity (95% CI 41–63%), 82% negative predictive value (NPV, 95% CI 73–88%) for the detection of ZIKV-associated congenital injuries in the neonatal period. A more stringent threshold with a Z-score ≤ -2 was associated with a 90% specificity (95% CI 81–95%), 81% NPV (95% CI 77–85%). Excluding cases of fetal microcephaly, HC: FL (Z-score ≤ -2) demonstrated a similar specificity (89%, 95% CI 81–95%) with superior NPV (87%, 95% CI 84–90%). The sonographic recognition of a normally proportioned fetus may be useful prenatally to exclude a wider spectrum of ZIKV-associated congenital injuries detected postnatally.

]]>
<![CDATA[Evaluation of residue management practices on barley residue decomposition]]> https://www.researchpad.co/article/elastic_article_13875 Optimizing barley (hordeum vulgare L.) production in Idaho and other parts of the Pacific Northwest (PNW) should focus on farm resource management. The effect of post-harvest residue management on barley residue decomposition has not been adequately studied. Thus, the objective of this study was to determine the effect of residue placement (surface vs. incorporated), residue size (chopped vs. ground-sieved) and soil type (sand and sandy loam) on barley residue decomposition. A 50-day(d) laboratory incubation experiment was conducted at a temperature of 25°C at the Aberdeen Research and Extension Center, Aberdeen, Idaho, USA. Following the study, a Markov-Chain Monte Carlo (MCMC) modeling approach was applied to investigate the first-order decay kinetics of barley residue. An accelerated initial flush of residue carbon(C)-mineralization was measured for the sieved (Day 1) compared to chopped (Day 3 to 5) residues for both surface incorporated applications. The highest evolution of carbon dioxide (CO2)-C of 8.3 g kg-1 dry residue was observed on Day 1 from the incorporated-sieved application for both soils. The highest and lowest amount of cumulative CO2-C released and percentage residue decomposed over 50-d was observed for surface-chopped (107 g kg-1 dry residue and 27%, respectively) and incorporated-sieved (69 g kg-1 dry residue and 18%, respectively) residues, respectively. There were no significant differences in C-mineralization from barley residue based on soil type or its interactions with residue placement and size (p >0.05). The largest decay constant k of 0.0083 d-1 was calculated for surface-chopped residue where the predicted half-life was 80 d, which did not differ from surface sieved or incorporated chopped. In contrast, incorporated-sieved treatments only resulted in a k of 0.0054 d-1 and would need an additional 48 d to decompose 50% of the residue. Future residue decomposition studies under field conditions are warranted to verify the residue C-mineralization and its impact on residue management.

]]>
<![CDATA[Decyl caffeic acid inhibits the proliferation of colorectal cancer cells in an autophagy-dependent manner <i>in vitro</i> and <i>in vivo</i>]]> https://www.researchpad.co/article/elastic_article_13874 The treatment of human colorectal cancer (CRC) cells through suppressing the abnormal survival signaling pathways has recently become a significant area of focus. In this study, our results demonstrated that decyl caffeic acid (DC), one of the novel caffeic acid derivatives, remarkedly suppressed the growth of CRC cells both in vitro and in vivo. The inhibitory effects of DC on CRC cells were investigated in an in vitro cell model and in vivo using a xenograft mouse model. CRC cells were treated with DC at various dosages (0, 10, 20 and 40 μM), and cell survival, the apoptotic index and the autophagy level were measured using an MTT assay and flow cytometry analysis, respectively. The signaling cascades in CRC were examined by Western blot assay. The anti-cancer effects of DC on tumor growth were examined by using CRC HCT-116 cells implanted in an animal model. Our results indicated that DC differentially suppressed the growth of CRC HT-29 and HCT-116 cells through an enhancement of cell-cycle arrest at the S phase. DC inhibited the expression of cell-cycle regulators, which include cyclin E and cyclin A proteins. The molecular mechanisms of action were correlated to the blockade of the STAT3 and Akt signaling cascades. Strikingly, a high dosage of DC prompted a self-protection action through inducing cell-dependent autophagy in HCT-116 cells. Suppression of autophagy induced cell death in the treatment of DC in HCT-116 cells. DC seemed to inhibit cell proliferation of CRC differentially, and the therapeutic advantage appeared to be autophagy dependent. Moreover, consumption of DC blocked the tumor growth of colorectal adenocarcinoma in an experimental animal model. In conclusion, our results suggested that DC could act as a therapeutic agent through the significant suppression of tumor growth of human CRC cells.

]]>
<![CDATA[The two types of society: Computationally revealing recurrent social formations and their evolutionary trajectories]]> https://www.researchpad.co/article/elastic_article_13873 Comparative social science has a long history of attempts to classify societies and cultures in terms of shared characteristics. However, only recently has it become feasible to conduct quantitative analysis of large historical datasets to mathematically approach the study of social complexity and classify shared societal characteristics. Such methods have the potential to identify recurrent social formations in human societies and contribute to social evolutionary theory. However, in order to achieve this potential, repeated studies are needed to assess the robustness of results to changing methods and data sets. Using an improved derivative of the Seshat: Global History Databank, we perform a clustering analysis of 271 past societies from sampling points across the globe to study plausible categorizations inherent in the data. Analysis indicates that the best fit to Seshat data is five subclusters existing as part of two clearly delineated superclusters (that is, two broad “types” of society in terms of social-ecological configuration). Our results add weight to the idea that human societies form recurrent social formations by replicating previous studies with different methods and data. Our results also contribute nuance to previously established measures of social complexity, illustrate diverse trajectories of change, and shed further light on the finite bounds of human social diversity.

]]>
<![CDATA[<i>In silico</i> analyses identify lncRNAs: WDFY3-AS2, BDNF-AS and AFAP1-AS1 as potential prognostic factors for patients with triple-negative breast tumors]]> https://www.researchpad.co/article/elastic_article_13870 Long non-coding RNAs (lncRNAs) are characterized as having 200 nucleotides or more and not coding any protein, and several been identified as differentially expressed in several human malignancies, including breast cancer.MethodsHere, we evaluated lncRNAs differentially expressed in triple-negative breast cancer (TNBC) from a cDNA microarray data set obtained in a previous study from our group. Using in silico analyses in combination with a review of the current literature, we identify three lncRNAs as potential prognostic factors for TNBC patients.ResultsWe found that the expression of WDFY3-AS2, BDNF-AS, and AFAP1-AS1 was associated with poor survival in patients with TNBCs. WDFY3-AS2 and BDNF-AS are lncRNAs known to play an important role in tumor suppression of different types of cancer, while AFAP1-AS1 exerts oncogenic activity.ConclusionOur findings provided evidence that WDFY3-AS2, BDNF-AS, and AFAP1-AS1 may be potential prognostic factors in TNBC development. ]]> <![CDATA[What makes an effective grants peer reviewer? An exploratory study of the necessary skills]]> https://www.researchpad.co/article/elastic_article_13869 This exploratory mixed methods study describes skills required to be an effective peer reviewer as a member of review panels conducted for federal agencies that fund research, and examines how reviewer experience and the use of technology within such panels impacts reviewer skill development. Two specific review panel formats are considered: in-person face-to-face and virtual video conference. Data were collected through interviews with seven program officers and five expert peer review panelists, and surveys from 51 respondents. Results include the skills reviewers’ consider necessary for effective review panel participation, their assessment of the relative importance of these skills, how they are learned, and how review format affects skill development and improvement. Results are discussed relative to the peer review literature and with consideration of the importance of professional skills needed by successful scientists and peer reviewers.

]]>
<![CDATA[Low LEF1 expression is a biomarker of early T-cell precursor, an aggressive subtype of T-cell lymphoblastic leukemia]]> https://www.researchpad.co/article/elastic_article_13868 Early T-cell precursor (ETP) is the only subtype of acute T-cell lymphoblastic leukemia (T-ALL) listed in the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia. Patients with ETP tend to have worse disease outcomes. ETP is defined by a series of immune markers. The diagnosis of ETP status can be vague due to the limitation of the current measurement. In this study, we performed unsupervised clustering and supervised prediction to investigate whether a molecular biomarker can be used to identify the ETP status in order to stratify risk groups. We found that the ETP status can be predicted by the expression level of Lymphoid enhancer binding factor 1 (LEF1) with high accuracy (AUC of ROC = 0.957 and 0.933 in two T-ALL cohorts). The patients with ETP subtype have a lower level of LEF1 comparing to the those without ETP. We suggest that incorporating the biomarker LEF1 with traditional immune-phenotyping will improve the diagnosis of ETP.

]]>
<![CDATA[Crystal structure of <i>Thermus thermophilus</i> methylenetetrahydrofolate dehydrogenase and determinants of thermostability]]> https://www.researchpad.co/article/elastic_article_13865 The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for the thermostability of this enzyme. The description of rotamer distributions by Gini coefficients and Kullback–Leibler (KL) divergence both revealed significant correlations with temperature. The emerging view seems to indicate that a static salt bridge/charged residue network plays a fundamental role in the temperature resistance of Thermus thermophilus MTHFD by enhancing both electrostatic interactions and entropic energy dispersion. Furthermore, this analysis uncovered a relationship between residue mutations and evolutionary pressure acting on thermophilic organisms and thus could be of use for the design of future thermostable enzymes.

]]>
<![CDATA[TIM, a targeted insertional mutagenesis method utilizing CRISPR/Cas9 in <i>Chlamydomonas reinhardtii</i>]]> https://www.researchpad.co/article/elastic_article_13864 Generation and subsequent analysis of mutants is critical to understanding the functions of genes and proteins. Here we describe TIM, an efficient, cost-effective, CRISPR-based targeted insertional mutagenesis method for the model organism Chlamydomonas reinhardtii. TIM utilizes delivery into the cell of a Cas9-guide RNA (gRNA) ribonucleoprotein (RNP) together with exogenous double-stranded (donor) DNA. The donor DNA contains gene-specific homology arms and an integral antibiotic-resistance gene that inserts at the double-stranded break generated by Cas9. After optimizing multiple parameters of this method, we were able to generate mutants for six out of six different genes in two different cell-walled strains with mutation efficiencies ranging from 40% to 95%. Furthermore, these high efficiencies allowed simultaneous targeting of two separate genes in a single experiment. TIM is flexible with regard to many parameters and can be carried out using either electroporation or the glass-bead method for delivery of the RNP and donor DNA. TIM achieves a far higher mutation rate than any previously reported for CRISPR-based methods in C. reinhardtii and promises to be effective for many, if not all, non-essential nuclear genes.

]]>
<![CDATA[Barriers and facilitating factors in the prevention of diabetes type 2 and gestational diabetes in vulnerable groups: A scoping review]]> https://www.researchpad.co/article/elastic_article_13859 Type 2 diabetes mellitus (T2DM) and gestational diabetes (GDM) are globally on the rise, accompanied by comorbidities and associated health costs. Increased physical activity, healthy nutrition, and weight loss have shown the potential to prevent T2DM/GDM. Despite this, reaching vulnerable groups remains a key challenge. The aim of this scoping review was to identify barriers and facilitating factors in the prevention of T2DM/GDM in vulnerable groups.MethodsWe conducted a systematic literature search in May 2018, updated in September 2019, in several databases (e.g. PubMed, Embase) to identify barriers and facilitating factors in the prevention of T2DM/GDM in vulnerable groups. Two reviewers independently screened the results. Extracted data was charted, categorized, and summarized.ResultsWe included 125 articles. Ninety-eight studies were extracted, and eight categories of barriers and facilitating factors were formed. The most common categories of barriers were limited knowledge, family/friends, and economic factors, and the most common categories of facilitating factors were family/friends, social support, and knowledge.ConclusionThis scoping review identified various barriers and facilitating factors in vulnerable groups. Preventive interventions should consider these barriers and facilitating factors in developing preventive interventions or in adapting existing ones. ]]> <![CDATA[Warm, lively, rough? Assessing agreement on aesthetic effects of artworks]]> https://www.researchpad.co/article/elastic_article_13856 The idea that simple visual elements such as colors and lines have specific, universal associations—for example red being warm—appears rather intuitive. Such associations have formed a basis for the description of artworks since the 18th century and are still fundamental to discourses on art today. Art historians might describe a painting where red is dominant as “warm,” “aggressive,” or “lively,” with the tacit assumption that beholders would universally associate the works’ certain key forms with specific qualities, or “aesthetic effects”. However, is this actually the case? Do we actually share similar responses to the same line or color? In this paper, we tested whether and to what extent this assumption of universality (sharing of perceived qualities) is justified. We employed—for the first time—abstract artworks as well as single elements (lines and colors) extracted from these artworks in an experiment in which participants rated the stimuli on 14 “aesthetic effect” scales derived from art literature and empirical aesthetics. To test the validity of the assumption of universality, we examined on which of the dimensions there was agreement, and investigated the influence of art expertise, comparing art historians with lay people. In one study and its replication, we found significantly lower agreement than expected. For the whole artworks, participants agreed on the effects of warm-cold, heavy-light, and happy-sad, but not on 11 other dimensions. Further, we found that the image type (artwork or its constituting elements) was a major factor influencing agreement; people agreed more on the whole artwork than on single elements. Art expertise did not play a significant role and agreement was especially low on dimensions usually of interest in empirical aesthetics (e.g., like-dislike). Our results challenge the practice of interpreting artworks based on their aesthetic effects, as these effects may not be as universal as previously thought.

]]>
<![CDATA[A network analysis of research productivity by country, discipline, and wealth]]> https://www.researchpad.co/article/elastic_article_13855 Research productivity has been linked to a country’s intellectual and economic wealth. Further analysis is needed to assess the association between the distribution of research across disciplines and the economic status of countries.MethodsBy using 55 years of data, spanning 1962 to 2017, of Elsevier publications across a large set of research disciplines and countries globally, this manuscript explores the relationship and evolution of relative research productivity across different disciplines through a network analysis. It also explores the associations of those with economic productivity categories, as measured by the World Bank economic classification. Additional analysis of discipline similarities is possible by exploring the cross-country evolution of those disciplines.ResultsResults show similarities in the relative importance of research disciplines among most high-income countries, with larger idiosyncrasies appearing among the remaining countries. This group of high-income countries shows similarities in the dynamics of the relative distribution of research productivity over time, forming a stable research productivity cluster. Lower income countries form smaller, more independent and evolving clusters, and differ significantly from each other and from higher income countries in the relative importance of their research emphases. Country-based similarities in research productivity profiles also appear to be influenced by geographical proximity.ConclusionsThis new form of analyses of research productivity, and its relation to economic status, reveals novel insights to the dynamics of the economic and research structure of countries. This allows for a deeper understanding of the role a country’s research structure may play in shaping its economy, and also identification of benchmark resource allocations across disciplines for developing countries. ]]> <![CDATA[Aging-associated sinus arrest and sick sinus syndrome in adult zebrafish]]> https://www.researchpad.co/article/elastic_article_13853 Because of its powerful genetics, the adult zebrafish has been increasingly used for studying cardiovascular diseases. Considering its heart rate of ~100 beats per minute at ambient temperature, which is very close to human, we assessed the use of this vertebrate animal for modeling heart rhythm disorders such as sinus arrest (SA) and sick sinus syndrome (SSS). We firstly optimized a protocol to measure electrocardiogram in adult zebrafish. We determined the location of the probes, implemented an open-chest microsurgery procedure, measured the effects of temperature, and determined appropriate anesthesia dose and time. We then proposed an PP interval of more than 1.5 seconds as an arbitrary criterion to define an SA episode in an adult fish at ambient temperature, based on comparison between the current definition of an SA episode in humans and our studies of candidate SA episodes in aged wild-type fish and Tg(SCN5A-D1275N) fish (a fish model for inherited SSS). With this criterion, a subpopulation of about 5% wild-type fish can be considered to have SA episodes, and this percentage significantly increases to about 25% in 3-year-old fish. In response to atropine, this subpopulation has both common SSS phenotypic traits that are shared with the Tg(SCN5A-D1275N) model, such as bradycardia; and unique SSS phenotypic traits, such as increased QRS/P ratio and chronotropic incompetence. In summary, this study defined baseline SA and SSS in adult zebrafish and underscored use of the zebrafish as an alternative model to study aging-associated SSS.

]]>
<![CDATA[Not sick enough to worry? "Influenza-like" symptoms and work-related behavior among healthcare workers and other professionals: Results of a global survey]]> https://www.researchpad.co/article/elastic_article_13852 Healthcare workers (HCWs) and non-HCWs may contribute to the transmission of influenza-like illness (ILI) to colleagues and susceptible patients by working while sick (presenteeism). The present study aimed to explore the views and behavior of HCWs and non-HCWs towards the phenomenon of working while experiencing ILI.MethodsThe study was a cross-sectional online survey conducted between October 2018 and January 2019 to explore sickness presenteeism and the behaviour of HCWs and non-HCWs when experiencing ILI. The survey questionnaire was distributed to the members and international networks of the International Society of Antimicrobial Chemotherapy (ISAC) Infection Prevention and Control (IPC) Working Group, as well as via social media platforms, including LinkedIn, Twitter and IPC Blog.ResultsIn total, 533 respondents from 49 countries participated (Europe 69.2%, Asia-Pacific 19.1%, the Americas 10.9%, and Africa 0.8%) representing 249 HCWs (46.7%) and 284 non-HCWs (53.2%). Overall, 312 (58.5%; 95% confidence interval [CI], 56.2–64.6) would continue to work when sick with ILI, with no variation between the two categories. Sixty-seven (26.9%) HCWs and forty-six (16.2%) non-HCWs would work with fever alone (p<0 .01) Most HCWs (89.2–99.2%) and non-HCWs (80%-96.5%) would work with “minor” ILI symptoms, such as sore throat, sinus cold, fatigue, sneezing, runny nose, mild cough and reduced appetite.ConclusionA future strategy to successfully prevent the transmission of ILI in healthcare settings should address sick-leave policy management, in addition to encouraging the uptake of influenza vaccine. ]]> <![CDATA[Comparability of modern contraceptive use estimates between a face-to-face survey and a cellphone survey among women in Burkina Faso]]> https://www.researchpad.co/article/elastic_article_13849 The proliferation of cell phone ownership in Sub-Saharan Africa (SSA) presents the opportunity to collect public health indicators at a lower cost compared to face-to-face (FTF) surveys. This analysis assesses the equivalence of modern contraceptive prevalence estimates between a nationally representative FTF survey and a cell phone survey using random digit dialing (RDD) among women of reproductive age in Burkina Faso.MethodsWe analyzed data from two surveys conducted in Burkina Faso between December 2017 and May 2018. The FTF survey conducted by Performance Monitoring and Accountability (PMA2020) comprised a nationally representative sample of 3,556 women of reproductive age (15–49 years). The RDD survey was conducted using computer-assisted telephone interviewing and included 2,379 women of reproductive age.ResultsCompared to FTF respondents, women in the RDD sample were younger, were more likely to have a secondary degree and to speak French. RDD respondents were more likely to report using modern contraceptive use (40%) compared to FTF respondents (26%) and the difference remained unchanged after applying post-stratification weights to the RDD sample (39%). This difference surpassed the equivalence margin of 4%. The RDD sample also produced higher estimates of contraceptive use than the subsample of women who owned a phone in the FTF sample (32%). After adjusting for women’s sociodemographic factors, the odds of contraceptive use were 1.9 times higher (95% CI: 1.6–2.2) in the RDD survey compared to the FTF survey and 1.6 times higher (95% CI: 1.3–1.8) compared to FTF phone owners.ConclusionsModern contraceptive prevalence in Burkina Faso is over-estimated when using a cell phone RDD survey, even after adjusting for a number of sociodemographic factors. Further research should explore causes of differential estimates of modern contraceptive use by survey modes. ]]> <![CDATA[Fruit and vegetable consumption in Europe according to gender, educational attainment and regional affiliation—A cross-sectional study in 21 European countries]]> https://www.researchpad.co/article/elastic_article_13846 The purpose of the present study was to examine fruit and vegetable consumption according to gender, educational attainment and regional affiliation in Europe.DesignCross-sectional study.Setting21 European countries.Participants37 672 adults participating in the 7th round of the European Social Survey.Main outcome measuresFruit and vegetable consumption was measured using two single frequency questions. Responses were dichotomized into low (<once a day) and high (≥once a day) consumption. The association between consumption of fruit and vegetables and gender, educational level, regional affiliation was examined using logistic regression analyses.ResultsOverall, females showed increased odds of consuming fruit (OR 1.71 (95%CI:1.62, 1.79) and vegetable (1.59 (1.51, 1.67)) compared to males and high educated participants showed increased odds of consuming fruit (1.53 (1.43, 1.63)) and vegetables (1.86 (1.74, 2.00)) compared to low educated participants. Our results also showed that participants living in Eastern Europe had the lowest odds of consuming fruit and vegetables, whereas participants from Southern- and Northern Europe had the highest odds of consuming fruit and vegetables, respectively. Results from interaction analyses confirmed the positive association between fruit and vegetable consumption and educational level, although for some European regions, decreased odds of fruit and vegetables was observed among medium educated participants compared to those with low education.ConclusionsOverall, the present study showed that being female and having a high education were associated with increased consumption of fruit and vegetables. However, the direction and strength of these relationships depends on regional affiliations. ]]> <![CDATA[Quantitative live imaging of Venus::BMAL1 in a mouse model reveals complex dynamics of the master circadian clock regulator]]> https://www.researchpad.co/article/elastic_article_13838 Cell-autonomous circadian clocks are transcriptional/translational feedback loops that co-ordinate almost all mammalian physiology and behaviour. Although their genetic basis is well understood, we are largely ignorant of the natural behaviour of clock proteins and how they work within these loops. This is particularly true for the essential transcriptional activator BMAL1. To address this, we created and validated a mouse carrying a fully functional knock-in allele that encodes a fluorescent fusion of BMAL1 (Venus::BMAL1). Quantitative live imaging in tissue explants and cells, including the central clock of the suprachiasmatic nucleus (SCN), revealed the circadian expression, nuclear-cytoplasmic mobility, fast kinetics and surprisingly low molecular abundance of endogenous BMAL1, providing significant quantitative insights into the intracellular mechanisms of circadian timing at single-cell resolution.

]]>
<![CDATA[Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis]]> https://www.researchpad.co/article/elastic_article_13837 In single-cell RNA-seq (scRNA-seq) experiments, the number of individual cells has increased exponentially, and the sequencing depth of each cell has decreased significantly. As a result, analyzing scRNA-seq data requires extensive considerations of program efficiency and method selection. In order to reduce the complexity of scRNA-seq data analysis, we present scedar, a scalable Python package for scRNA-seq exploratory data analysis. The package provides a convenient and reliable interface for performing visualization, imputation of gene dropouts, detection of rare transcriptomic profiles, and clustering on large-scale scRNA-seq datasets. The analytical methods are efficient, and they also do not assume that the data follow certain statistical distributions. The package is extensible and modular, which would facilitate the further development of functionalities for future requirements with the open-source development community. The scedar package is distributed under the terms of the MIT license at https://pypi.org/project/scedar.

]]>
<![CDATA[Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra]]> https://www.researchpad.co/article/elastic_article_13836 One of the most striking features of the human electroencephalogram (EEG) is the presence of neural oscillations in the range of 8-13 Hz. It is well known that attenuation of these alpha oscillations, a process known as alpha blocking, arises from opening of the eyes, though the cause has remained obscure. In this study we infer the mechanism underlying alpha blocking by fitting a neural population model to EEG spectra from 82 different individuals. Although such models have long held the promise of being able to relate macroscopic recordings of brain activity to microscopic neural parameters, their utility has been limited by the difficulty of inferring these parameters from fits to data. Our approach involves fitting eyes-open and eyes-closed EEG spectra in a way that minimizes unnecessary differences in model parameters between the two states. Surprisingly, we find that changes in just one parameter, the level of external input to the inhibitory neurons in cortex, is sufficient to explain the attenuation of alpha oscillations. This indicates that opening of the eyes reduces alpha activity simply by increasing external inputs to the inhibitory neurons in the cortex.

]]>