Miracle-dz/UniFAR-FTUs huggingface dataset:
Silencing of CCR4-NOT complex subunits affects heart structure and function

ABSTRACT The identification of genetic variants that predispose individuals to cardiovascular disease and a better understanding of their targets would be highly advantageous. Genome-wide association studies have identified variants that associate with QT-interval length (a measure of myocardial repolarization). Three of the strongest associating variants (single-nucleotide polymorphisms) are located in the putative promotor region of CNOT1, a gene encoding the central CNOT1 subunit of CCR4-NOT: a multifunctional, conserved complex regulating gene expression and mRNA stability and turnover. We isolated the minimum fragment of the CNOT1 promoter containing all three variants from individuals homozygous for the QT risk alleles and demonstrated that the haplotype associating with longer QT interval caused reduced reporter expression in a cardiac cell line, suggesting that reduced CNOT1 expression might contribute to abnormal QT intervals. Systematic siRNA-mediated knockdown of CCR4-NOT components in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) revealed that silencing CNOT1 and other CCR4-NOT genes reduced their proliferative capacity. Silencing CNOT7 also shortened action potential duration. Furthermore, the cardiac-specific knockdown of Drosophila orthologs of CCR4-NOT genes in vivo (CNOT1/Not1 and CNOT7/8/Pop2) was either lethal or resulted in dilated cardiomyopathy, reduced contractility or a propensity for arrhythmia. Silencing CNOT2/Not2, CNOT4/Not4 and CNOT6/6L/twin also affected cardiac chamber size and contractility. Developmental studies suggested that CNOT1/Not1 and CNOT7/8/Pop2 are required during cardiac remodeling from larval to adult stages. To summarize, we have demonstrated how disease-associated genes identified by GWAS can be investigated by combining human cardiomyocyte cell-based and whole-organism in vivo heart models. Our results also suggest a potential link of CNOT1 and CNOT7/8 to QT alterations and further establish a crucial role of the CCR4-NOT complex in heart development and function. This article has an associated First Person interview with the first author of the paper. Summary: Genome-wide association studies combined with in vitro human cardiac cell assays and a model organism suitable for heart studies in vivo connect CNOT1, CNOT7 and overall the CCR4-NOT complex to human heart disease and morbidity.
Spatio-temporal modelling of Glossina palpalis gambiensis and Glossina tachinoides apparent densities in fragmented ecosystems of Burkina Faso

Here we propose two novel approaches to space-time analysis derived from space-time geostatistics in a kriging framework. The approaches were developed through analysis of a dataset recording the Apparent Density of Glossina palpalis gambiensis and Glossina tachinoides (Diptera: Glossinidae) in three riparian sites in Burkina Faso over 15 months between 2006 and 2007. This site is fragmented due to human activity in the area. The first approach, Space Time Ordinary Kriging, does not consider the effect of fragmentation. It is used as a benchmark to test the increased explanatory power of the second method, which does account for fragmentation. The second method, Regression Space Time Simple Kriging, is a distinct improvement over the first approach because it allows for a spatial trend in the mean trap catch; this trend is related to, and later predicted from, environmental co-variates. The results indicate the presence of space and time effects on tsetse distribution, dependent on the size of the habitat fragmentation patches. These effects occur at relatively small geographic scales within a season. Whilst such variation has long been suspected, the new methods presented here are able to quantify this variation precisely, so that seasonal and spatial comparisons can now be made both within and between species.
The effect of surgical trauma on circulating free DNA levels in cancer patients—implications for studies of circulating tumor DNA

Detection of circulating tumor DNA (ctDNA) post‐treatment is an emerging marker of residual disease. ctDNA constitutes only a minor fraction of the cell‐free DNA (cfDNA) circulating in cancer patients, complicating ctDNA detection. This is exacerbated by trauma‐induced cfDNA. To guide optimal blood sample timing, we investigated the duration and magnitude of surgical trauma‐induced cfDNA in patients with colorectal or bladder cancer. DNA levels were quantified in paired plasma samples collected before and up to 6 weeks after surgery from 436 patients with colorectal cancer and 47 patients with muscle‐invasive bladder cancer. To assess whether trauma‐induced cfDNA fragments are longer than ordinary cfDNA fragments, the concentration of short (< 1 kb) and long (> 1 kb) fragments was determined for 91 patients. Previously reported ctDNA data from 91 patients with colorectal cancer and 47 patients with bladder cancer were used to assess how trauma‐induced DNA affects ctDNA detection. The total cfDNA level increased postoperatively—both in patients with colorectal cancer (mean threefold) and bladder cancer (mean eightfold). The DNA levels were significantly increased up to 4 weeks after surgery in both patient cohorts (P = 0.0005 and P ≤ 0.0001). The concentration of short, but not long, cfDNA fragments increased postoperatively. Of 25 patients with radiological relapse, eight were ctDNA‐positive and 17 were ctDNA‐negative in the period with trauma‐induced DNA. Analysis of longitudinal samples revealed that five of the negative patients became positive shortly after the release of trauma‐induced cfDNA had ceased. In conclusion, surgery was associated with elevated cfDNA levels, persisting up to 4 weeks, which may have masked ctDNA in relapse patients. Trauma‐induced cfDNA was of similar size to ordinary cfDNA. To mitigate the impact of trauma‐induced cfDNA on ctDNA detection, it is recommended that a second blood sample collected after week 4 is analyzed for patients initially ctDNA negative.
Effect of ageing on antiretroviral drug pharmacokinetics using clinical data combined with modelling and simulation

The impact of ageing on antiretroviral pharmacokinetics remains uncertain, leading to missing dosing recommendations for elderly people living with human immunodeficiency virus (HIV: PLWH). The objective of this study was to investigate whether ageing leads to clinically relevant pharmacokinetic changes of antiretrovirals that would support a dose adjustment based on the age of the treated PLWH.
Role of Rhizobacteria and Arbuscular Mycorrhizae on Enhancing Nutrient Absorption Efficiency of Sweet Sorghum (Sorghum bicolor L. Moench)

Chemical fertilizer use efficiency can be defined in agronomic terms with widely varying results. In general, getting as much of nutrient as possible into the harvested portion of a crop is the concept of efficient nutrient use. Tracking recovery of applied nutrients is key component to measure nutrient efficiency. Field experiments were conducted to assess the effects of inoculating sweet sorghum (Sorghum bicolor L. Moench) with rhizobacteria and arbuscular mycorrhizal fungus (AMF) in various concentrations of chemical fertilizers. Two spesies of rhizobacteria (Mycobacterium senegalense 73MDL dan Bacillus firmus 80JR) were compared in the presence or absence of AMF (Gigaspora sp. 40MDL and Glomus sp. 38MDL) and adding various concentrations of chemical fertilizers. Biomass production, sugar content and plant uptake of phosphorus, potassium and nitrogen were analyzed. Rhizobacterial inoculation alone had significant effects on plant height and P content at p<0.01, while on biomass production, sugar content, P and K uptake at p<0.05. Mycorrhizal inoculation alone had significant effects on biomass production and N content at p<0.01, while on sugar content at p<0.05. Interaction of rhizobacteria and AMF could increase biomass production, K uptake and absorption efficiency of N. Overall, inoculation of rhizobacteria, AMF and chemical fertilizers could increase biomass production, sugar content, P and K uptake and absorption efficiency of N. Finally, using rhizobacteria and AMF as biofertilizer had potential to improve efficiency of chemical fertilizers use, which is expected to reduce cost of sweet sorghum production.
Maternal and neo‐natal weight in the grasscutter Thyronomys swinderianus (Temminck) in Ghana*

Summary Neonatal weight and maternal weight at parturition in forty-six captive grasscutters and weights of embryos in sixty-six full-term pregnancies and their maternal weights were analysed. The captive sample with a regular food supply showed no apparent correlation between litter weight as a percentage of maternal weight and neonatal weight, nor between litter size and mean litter weight. These variables were, however, negatively correlated (P<0. 1) in samples of wild animals. Both samples showed a strong positive correlation between maternal weight and litter size, litter size and litter weight, and litter weight as a percentage of maternal weight and litter size. But whereas maternal weight was significantly positively correlated with litter weight in captivity (P<0.01) there was no apparent correlation in the wild. There was a strong negative, significant correlation in the wild. There was a strong negative, significant correlation between maternal weight and mean litter weight in the wild but in captivity, the strong correlation was positively significant. There is great variation in the weights of young and embryos both in litter mates and from litter to litter. Embryos implanted at the cervical end of the uterine horn tended to be heavier than those implanted at the ovarian end. RESUMEE On a analyse les poids des nouveau-nes et de la mere lors de la parturition chez quar-ante-six aulacodes captifs et les poids des embryons a terme et de leur mere dans soixante-six cas de gestation. Chez l'echantillon captif nourri regulierement, on ne constate pas de correlation apparente entre le poids de la portee exprime en pourcentage du poids maternel et neonatal, ni entre la taille et le poids moyen de la portee. Ces variables cependant presente une correlation negative (P<0.1) parmi les echantillons d'animaux sauvages. Les deux echantillons presentent une bonne correlation positive entre le poids de la mere et la taille de la portee, la taille et le poids de la portie, le poids de la portee exprime en pourcentage du poids maternel et la taille de la portee. Mais le ou le poids maternel presente une correation positive significative avec le poids de la portee en captivite (P<0.01), it n'y a aucune correlation apparente sur le terraine. It y a une nette correlation significativement negative entre le poids maternel et le poids moyen de la portet sur le terrain, mais en captivite cette nette correlation est significativement positive.
Application of Bio-Organic Fertilizer Significantly Affected Fungal Diversity of Soils

Cotton verticillium wilt (Verticillium dahliae Kleb.) is a very destructive disease. In this study, we evaluated a Bacillus subtilis enhanced bio-organic fertilizer (BOF) for control of the disease and for its effect on rhizosphere microbiota. Greenhouse pot experiments were conducted during three cotton (Gossypium hirsutum L.) growing seasons with serial treatments of BOF or unenhanced organic fertilizer (OF). Consistent control of cotton verticillium wilt was obtained in the three trials. The complete BOF treatment, in which both nursery cups with healthy soils and transplanted pots with diseased soils were amended with BOF, was the most effective in reducing the counts of pathogenic V. dabliae and of total fungi in the cotton rhizosphere. The complete BOF treatment was also the most effective in reducing disease incidence. Rhizosphere soil DNA was extracted at harvest and the 5' end (370 base pairs) of the fungal 18S rRNA gene was amplified by using the primer pair NS1 and GCFung (fungus specific). Seventy-one bands were recognized in denaturing gradient gel electrophoresis (DGGE) gels and excised for sequencing, but only 35 bands were successfully sequenced during the study. Nonmetric multidimensional scaling analysis of DGGE patterns showed that the complete BOF treatments were not close to any other treatment. Ribotypes related to four Ascomycota and two Basidiomycota fungi were detected in the untreated but not in the BOF-amended soil. The results suggest that the complete BOF treatment could effectively control cotton verticillium wilt by significantly improving fungal structure in rhizosphere soils.
Which groups affected by Potentially Traumatic Events (PTEs) are most at risk for a lack of social support? A prospective population-based study on the 12-month prevalence of PTEs and risk factors for a lack of post-event social support

Objectives Little is known about the 12-month prevalence of potentially traumatic events (PTEs) and to what extent the type of PTE is a risk factor for post-event lack of social support. In addition, it is largely unknown if pre-event mental health problems and loneliness, and demographics are risk factors for a lack of support. Aim of the present prospective study is to fill these gaps in evidence-based knowledge. Methods A survey was conducted among a large random sample of the Dutch adult population (i.e. the longitudinal LISS panel) in March-April 2018, and linked with pre-event mental health and loneliness data from surveys conducted in 2016 (n = 5,879). We distinguished four forms of perceived social support: emotional and esteem support, and social recognition and general disapproval. Results Loss of a significant other and/or colleague (28%) was the most prevalent 12-month PTE. The 12-month prevalence of violence, accidents and/or, and theft-related events was 13%. Multivariate logistic regression analyses revealed no differences in lack of emotional and esteem support, or in lack of recognition across non-death PTEs and death-related PTEs. However, victims of threat and physical (sexual) violence more often faced disapproval than those affected by burglary and accidents. Results furthermore showed that pre-event mental health problems, pre-event loneliness and stress during the PTE were important independent predictors of forms of support and acknowledgment. Affected individuals with a non-Western background more often lacked support and acknowledgment. Conclusions Many adults are confronted with a PTE during a year. In general, pre-event factors and stress during the event are better predictors of a perceived lack of support and acknowledgment than type of event. Early screening programs should especially assess pre-event mental health and loneliness, besides levels of stress during the event, to identify affected people who are at risk for a lack of social support and acknowledgment.
Fine-scale layer of hydromedusae is revealed by video plankton recorder (VPR) in a semi-enclosed bay in northern Norway

High resolution images of zooplankton organisms were recorded in situ using a digital autonomous video plankton recorder (VPR) in a semi-enclosed bay in northern Norway. Data from vertical VPR profiles was used to estimate the depth distribution and abundance of zooplankton along a bay-wide grid. Images were recorded simultaneously with hydrographical data, and the spa- tial distribution of different organisms was related to several water column characteristics, such as chlorophyll a, density, and buoyancy frequencies. In June, unusually high abundances of hydrome- dusae (Rathkea octopunctata and Obelia sp.) were located in a fine-scale layer of a few metres thick- ness. This layer could be associated with relatively high buoyancy frequencies, reflecting a density gradient present throughout the entire sampling area. Aggregation of hydromedusae around density discontinuities may have enabled retention of medusae in the bay. Ctenophores and appendiculari- ans were distributed above the medusae layer, while peaks of copepod abundance were found out- side the layer boundaries. We suggest that the bloom of R. octopunctata was initially caused by liber- ation of new medusae from successful benthic hydroid colonies, and that proliferation of this species was sustained by asexual, manubrial budding in the medusae stage.
Age Differences in COVID-19 Risk Perceptions and Mental Health: Evidence From a National U.S. Survey Conducted in March 2020

Abstract Objectives Theories of aging posit that older adult age is associated with less negative emotions, but few studies have examined age differences at times of novel challenges. As COVID-19 spread in the United States, this study therefore aimed to examine age differences in risk perceptions, anxiety, and depression. Method In March 2020, a nationally representative address-based sample of 6,666 U.S. adults assessed their perceived risk of getting COVID-19, dying if getting it, getting quarantined, losing their job (if currently working), and running out of money. They completed a mental health assessment for anxiety and depression. Demographic variables and precrisis depression diagnosis had previously been reported. Results In regression analyses controlling for demographic variables and survey date, older adult age was associated with perceiving larger risks of dying if getting COVID-19, but with perceiving less risk of getting COVID-19, getting quarantined, or running out of money, as well as less depression and anxiety. Findings held after additionally controlling for precrisis reports of depression diagnosis. Discussion With the exception of perceived infection-fatality risk, U.S. adults who were relatively older appeared to have a more optimistic outlook and better mental health during the early stages of the pandemic. Interventions may be needed to help people of all ages maintain realistic perceptions of the risks, while also managing depression and anxiety during the COVID-19 crisis. Implications for risk communication and mental health interventions are discussed.
CARBON BALANCE OF A BOREAL BOG DURING A YEAR WITH AN EXCEPTIONALLY DRY SUMMER

Northern peatlands are important terrestrial carbon stores, and they show large spatial and temporal variation in the atmospheric exchange of CO2 and CH4. Thus, annual carbon balance must be studied in detail in order to predict the climatic responses of these ecosystems. Closed-chamber methods were used to study CO2 and CH4 in hollow, Sphagnum angustifolium lawn, S. fuscum lawn, and hummock microsites within an om- brotrophic S. fuscum bog. Micrometeorological tower measurements were used as a ref- erence for the CH4 efflux from the bog. Low precipitation during May-August in 1994 (84 mm below the long-term average for the same period) and a warm July-August period caused the water table to drop by more than 15 cm below the peat surface in the hollows and to 48 cm below the surface in high hummocks. Increased annual total respiration exceeded gross production and resulted in a net C loss of 4-157 g/m2 in the different microsites. Drought probably caused irreversible desiccation in some lawns of S. angus- tifolium and S. balticum and in S. fuscum in the hummocks, while S. balticum growing in hollows retained its moisture and even increased its photosynthetic capacity during the July-August period. Seasonal (12 May-4 October) CH4 emissions ranged from 2 g CH4- C/M2 in drier S. fuscum hummocks and lawns to 7 and 14 g/m2 in wetter S. angustifolium- S. balticum lawns and hollows, respectively. Aerodynamic gradient measurements at the tower showed slightly higher CH4 flux rates than the average estimates for the whole bog obtained by closed-chamber methods. Winter C efflux comprised 30 g C02-C/m2 and 1 g CH4-C/m2 out of a total loss of 90 g C/M2 on average in the bog, and there was an estimated annual loss of 7 g C/M2 by leaching. This study shows how delicately the boreal bog's C balance in different microsites depends on climatic variations, especially the distribution of precipitation. It also confirms that severe C losses can occur in boreal bogs during extended summer droughts, even in years with annual temperatures close to the long-term average and with precipitation clearly greater than the long-term average.
Antibacterial Effect of the Natural Polymer ε-Polylysine Against Oral Pathogens Associated with Periodontitis and Caries

Antimicrobials are important adjuncts in the treatment of caries and periodontitis. However, increased bacterial resistance and hypersensitivity reactions to commonly used antimicrobials have led to an increasing demand for safe and natural substances. The objective of this study was to investigate the antibacterial effects of ε-polylysine against oral pathogens Streptococcus mutans and Porphyromonas gingivalis. Broth dilution assay, scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) analyses were performed to explore the antibacterial effect of ε-polylysine against S. mutans strain ATCC25175 and P. gingivalis strain ATCC332277. For the test solution, ε-polylysine was added to the bacterial suspension to prepare 0.125%, 0.25%, 0.5% and 1% ε-polylysine solutions diluted in broth medium. All four concentrations demonstrated complete inhibition of S. mutans and significantly reduced viable cell counts of P. gingivalis after 24 h. From starting inoculum of 9.15 log CFU/mL, P. gingivalis cell counts reduced to 4.01 log CFU/mL in the 0.125% ε-polylysine treatment group. SEM, CLSM, and the LIVE/DEAD bacterial assay of ε-polylysine application on P. gingivalis biofilm-dentin specimens revealed bacterial cell membrane disruption and irregular cell morphologies. The results indicated satisfactory antibacterial efficacy of ε-polylysine against P. gingivalis and S. mutans in liquid medium and as an application on biofilm-dentin specimens.
Isolation and Characterization of a New Vitamin C Producing Enzyme (L-Gulono-γ-lactone Dehydrogenase) of Bacterial Origin

For the first time we found that the bacterial strain Gluconobacter oxydans DSM 4025 produced L-ascorbic acid from L-gulono-γ-lactone and therefore we isolated and purified the enzyme L-gulono-γ-lactone dehydrogenase catalyzing the oxidation reaction.G. oxydans DSM 4025 produced 8.57 and 13.9 mg of L-ascorbic acid per ml from 70.3 and 89.3 mg of L-gulono-γ-lactone per ml in the growing and resting cell systems, respectively.The enzyme was isolated from the soluble fraction of the cells of G. oxydans DSM 4025 by DEAE-cellulose, Q-Sepharose, hydroxylapatite, and Sephacryl S-300 column chromatographies. The molecular weight of the enzyme was 110, 000 and it consisted of three kinds of subunits of 61, 000, 32, 500, and 16, 5000. L-Gulono-γ-lactone was oxidized to L-ascorbic acid very rapidly in the presence of dyes, such as 2, 6-dichlorophenolindophenol or phenazine methosulfate, but oxygen was not available as an electron acceptor. The absorption spectrum of the reduced form of the native enzyme showed maxim.