julilili42/papers huggingface dataset:
Patterns of recent natural selection on genetic loci associated with sexually differentiated human body size and shape phenotypes
2020-06-19

Abstract Levels of sex differences for human body size and shape phenotypes are hypothesized to have adaptively reduced following the agricultural transition as part of an evolutionary response to relatively more equal divisions of labor and new technology adoption. In this study, we tested this hypothesis by studying genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat percentage, and waist circumference. We first analyzed genome-wide association (GWAS) results for UK Biobank individuals (∼197,000 females and ∼167,000 males) to identify a total of 119,023 single nucleotide polymorphisms (SNPs) significantly associated with at least one of the studied phenotypes in females, males, or both sexes (P&lt;5×10 -8 ). From these loci we then identified 3,016 SNPs (2.5%) with significant differences in the strength of association between the female- and male-specific GWAS results at a low false-discovery rate (FDR&lt;0.001). Genes with known roles in sexual differentiation are significantly enriched for co-localization with one or more of these SNPs versus SNPs associated with the phenotypes generally but not with sex differences (2.93-fold enrichment; permutation test; P=0.0041). We also confirmed that the identified variants are disproportionately associated with greater phenotype effect sizes in the sex with the stronger association value. We then used the singleton density score statistic, which quantifies recent (within the last ∼3,000 years; post-agriculture adoption in Britain) changes in the frequencies of alleles underlying polygenic traits, to identify a signature of recent positive selection on alleles associated with greater body fat percentage in females (permutation test; P=0.0038; FDR=0.0380), directionally opposite to that predicted by the sex differentiation reduction hypothesis. Otherwise, we found no evidence of positive selection for sex difference-associated alleles for any other trait. Overall, our results challenge the longstanding hypothesis that sex differences adaptively decreased following subsistence transitions from hunting and gathering to agriculture. Author Summary There is uncertainty regarding the evolutionary history of human sex differences for quantitative body size and shape phenotypes. In this study we identified thousands of genetic loci that differentially impact body size and shape trait variation between females and males using a large sample of UK Biobank individuals. After confirming the biological plausibility of these loci, we used a population genomics approach to study the recent (over the past 3,000 years) evolutionary histories of these loci in this population. We observed significant increases in the frequencies of alleles associated with greater body fat percentage in females. This result is contradictory to longstanding hypotheses that sex differences have adaptively decreased following subsistence transitions from hunting and gathering to agriculture.
Solid accretion onto planetary cores in radiative disks
2020-06-19

\\nThe solid accretion rate, which is necessary to grow gas giant planetary cores within the disk lifetime, has been a major constraint for theories of planet formation. We tested the solid accretion rate efficiency on planetary cores of different masses embedded in their birth disk by means of 3D radiation-hydrodynamics, where we followed the evolution of a swarm of embedded solids of different sizes. We found that by using a realistic equation of state and radiative cooling, the disk at 5 au is able to efficiently cool and reduce its aspect ratio. As a result, the pebble isolation mass is reached before the core grows to 10 M⊕, thus fully stopping the pebble flux and creating a transition disk. Moreover, the reduced isolation mass halts the solid accretion before the core reaches the critical mass, leading to a barrier to giant planet formation, and this explains the large abundance of super-Earth planets in the observed population. \\n
Observations of Buried Lake Drainage on the Antarctic Ice Sheet
2020-06-20

Abstract Between 1992 and 2017, the Antarctic Ice Sheet (AIS) lost ice equivalent to 7.6 ± 3.9 mm of sea level rise. AIS mass loss is mitigated by ice shelves that provide a buttress by regulating ice flow from tributary glaciers. However, ice‐shelf stability is threatened by meltwater ponding, which may initiate, or reactivate preexisting, fractures, currently poorly understood processes. Here, through ground penetrating radar (GPR) analysis over a buried lake in the grounding zone of an East Antarctic ice shelf, we present the first field observations of a lake drainage event in Antarctica via vertical fractures. Concurrent with the lake drainage event, we observe a decrease in surface elevation and an increase in Sentinel‐1 backscatter. Finally, we suggest that fractures that are initiated or reactivated by lake drainage events in a grounding zone will propagate with ice flow onto the ice shelf itself, where they may have implications for its stability.
Pedotransfer Function for the Brunswick Soil Hydraulic Property Model and Comparison to the van Genuchten‐Mualem Model
2020-06-20

Abstract Modeling soil hydraulic properties requires an effective representation of capillary and noncapillary storage and conductivity. This is made possible by using physically comprehensive yet flexible soil hydraulic property models. Such a model (Brunswick [BW] model) was introduced by Weber et al. (2019, https://doi.org/10.1029/2018WR024584 ), and it overcomes some core deficiencies present in the widely used van Genuchten‐Mualem (VGM) model. We first compared the performance of the BW model to that of the VGM model in its ability to describe water retention and hydraulic conductivity data on a set of measurements of 402 soil samples with textures covering the entire range of classes. Second, we developed a simple transfer function to predict BW parameters based on VGM parameters. Combined with our new function, any existing pedotransfer function for the prediction of the VGM parameters can be extended to predict BW model parameters. Based on information criteria, the smaller variance of the residuals, and a 40% reduction in mean absolute error in the hydraulic conductivity over all samples, the BW model clearly outperforms VGM. This is possible as the BW model explicitly accounts for hydraulic properties of dry soils. With the new pedotransfer function developed in this study, better descriptions of water retention and hydraulic conductivities are possible. We are convinced that this will strengthen the utility of the new model and enable improved field‐scale simulations, climate change impact assessments on water, energy and nutrient fluxes, as well as crop productivity in agroecosystems by soil‐crop and land‐surface modeling. The models and the pedotransfer function are included in an R package spsh (https://cran.r‐project.org/package=spsh).
Tissue-autonomous phenylpropanoid production is essential for establishment of root barriers
2020-06-20

ABSTRACT Plants deposit polymeric barriers in their root cell walls to protect against external stress and facilitate selective nutrient uptake. The compounds that make up these barriers originate from the fatty acid- and phenylpropanoid biosynthetic pathways. Although the machinery responsible for production of the barrier constituents is well-char-acterized, our pathway models lack spatiotemporal resolution – especially in roots - and the source tissue is often not clear due to the apoplastic nature of barriers. Insights into how the individual root tissues or cells contribute to forming apoplastic barriers is important for elucidation of their ultrastructure, function and development. Manipulation of the associated biosynthesis is delicate, as mutants often display pleiotropic phenotypes due to the broad role of the underlying metabolites. Here, we address these issues by creating a genetic tool that allows in vivo repression of the phenylpropanoid pathway with both spatial and temporal control. We provide strong evidence that tissue-auton-omous production of phenylpropanoids is essential for establishment of the endodermal Casparian strip. Moreover, we find that in order to maintain deposition and attachment of a coherent suberin matrix to the cell wall, cells require continuous production of aromatic constituents. This process is especially crucial in the suberized endodermis where we find that repression of phenylpropanoid production leads to active removal of suberin.
Germanium nanospheres for ultraresolution picotensiometry of kinesin motors
2020-06-20

Kinesin motors are essential for transport of cellular cargo along cytoskeletal microtubule filaments. How motors step, detach, and cooperate is still unclear. To dissect the molecular motion of kinesin-1, we have developed germanium nanospheres as ultraresolution optical trapping probes. We found that single motors took 4-nm-center-of-mass steps. Furthermore, motors never detached from microtubules under native hindering load conditions. Instead, motors slid on microtubules with microsecond-long, 8-nm steps and remained in this slip state before detaching or reengaging in directed motion. Surprisingly, reengagement and, thus, rescue of directed motion was prevailing. We argue that teams of motors may be synchronized through this slip state and rescues need to be accounted for to understand long-range transport. One Sentence Summary Optical trapping of high-refractive-index semiconductor nanoparticles shows how motors detach and walk with 4-nm steps.
Die Närrin als konstitutiver Störfaktor in Jörg Wickrams Goldtfaden (1557)
2020-06-20

Jörg Wickram’s novel Der Goldtfaden deals with courtly communication in the form of an unusual constellation of its participants. It is a complex system of norms that is binding for all members of the court and becomes problematic if an outsider joins the act. Communication situations are presented in a variety of media, some of which succeed through fortunate coincidence, while others fail due to existing conventions and their disregard. Above all, the figure of the fool plays an essential role, which is constitutive for the entire text.
Time to make a change: A call for more experimental research on key mechanisms in anorexia nervosa
2020-06-21

&lt;p&gt;Anorexia nervosa (AN) is a life‐threatening eating disorder, characterised by persistent pathological weight loss behaviours and an intense fear of weight gain and food consumption. Although there is an abundance of scientific theories on the neurobiological, psychological and sociocultural factors thought to be involved in the maintenance of AN, there is little experimental research testing these ideas. The need for theory firmly grounded in empirical evidence becomes strikingly clear when we consider that current treatments for patients with AN are limited in their effectiveness, and relapse after treatment is common.&lt;/p&gt;
Arbuscular mycorrhizal fungi alleviate negative effects of arsenic‐induced stress on crop plants: A meta‐analysis
2020-06-21

Societal Impact Statement The inoculation with arbuscular mycorrhizal (AM) fungi shows great potential to increase the tolerance of host plants toward toxic arsenic. In many Asian countries and elsewhere, crops are increasingly being irrigated with arsenic‐contaminated groundwater, which causes loss of yield and the risk that arsenic enters the food chain. Greenhouse cultivation experiments demonstrated that AM fungi are able to increase the arsenic tolerance in crop plants, but the results are highly variable. This meta‐analysis demonstrates that AM fungi significantly reduce the arsenic concentration, and at the same time, positively modify the nutrient supply and the biomass in host crops that are grown under arsenic stress. Thus, the inoculation with AM fungi represents a promising approach to alleviate the negative effects of arsenic on crop growth, which deserves to be developed in future studies. Summary Recent greenhouse experiments showed that the inoculation of crop plants with arbuscular mycorrhizal (AM) fungi does not only improve plant nutrition but also shows great potential to increase the host plants’ tolerance toward the toxic metalloid arsenic (As). This approach could alleviate negative effects of crop plants grown under As stress, which causes substantial loss of yield and the risk of As entering the food chain. This is especially relevant in Asian countries and elsewhere where As subsequently accumulates in soil due to irrigation with As‐polluted groundwater. Overall effects of AM fungi symbiosis on seven crop plants grown under As stress were assessed by a meta‐analysis that included 299 studies obtained from 27 independent publications. Biomass, concentrations of As and phosphorus (P), and P/As ratios in plant tissue were used to evaluate the effects of AM fungi in host crops. Inoculation with AM fungi reduced As concentrations in tissue of host plants by 19% on average, while it increased the P/As ratio and biomass at the same time by 64% and 53%, respectively. With the exception of Helianthus annuus , AM effects were highly significant in all crop plants. The meta‐analysis results illustrate that AM fungi are able to significantly reduce As concentration, and at the same time, positively modify the nutrient supply and the biomass in host crops. These promising results strongly encourage the implementation of field trials as a next step toward the development of AM fungi‐based approaches to alleviate the negative effects of As stress on crop growth.
First evidence for continuous circulation of hepatitis A virus subgenotype IIA in Central Africa
2020-06-21

Abstract Although a high seroprevalence of antibodies against hepatitis A virus (HAV) has been estimated in Central Africa, the current status of both HAV infections and seroprevalence of anti‐HAV antibodies remains unclear due to a paucity of surveillance data available. We conducted a serological survey during 2015‐2017 in Gabon, Central Africa, and confirmed a high seroprevalence of anti‐HAV antibodies in all age groups. To identify the currently circulating HAV strains and to reveal the epidemiological and genetic characteristics of the virus, we conducted molecular surveillance in a total of 1007 patients presenting febrile illness. Through HAV detection and sequencing, we identified subgenotype IIA (HAV‐IIA) infections in the country throughout the year. A significant prevalence trend emerged in the young child population, presenting several infection peaks which appeared to be unrelated to dry or rainy seasons. Whole‐genome sequencing and phylogenetic analyses revealed local HAV‐IIA evolutionary events in Central Africa, indicating the circulation of HAV‐IIA strains of a region‐specific lineage. Recombination analysis of complete genome sequences revealed potential recombination events in Gabonese HAV strains. Interestingly, Gabonese HAV‐IIA possibly acquired the 5’‐untranslated region (5’‐UTR) of the rare subgenotype HAV‐IIB in recent years, suggesting the present existence of HAV‐IIB in Central Africa. These findings indicate a currently stable HAV‐IIA circulation in Gabon, with a high risk of infections in children aged under 5 years. Our findings will enhance the understanding of the current status of HAV infections in Central Africa and provide new insight into the molecular epidemiology and evolution of HAV genotype II.
Difficulties of Popular Density Functionals to Describe the Conformational Isomerism in Iodoacetic Acid
2020-06-21

Matrix isolation studies in solid argon and neon at 4.2 K reveal that iodoacetic acid initially only exists as its ground state (<i>c</i>,<i>x</i>) conformer with an almost perpendicular I-C-C═O dihedral angle, but UV irradiation in the 240-255 nm range leads to population of the 0.8 kcal mol<sup>-1</sup> less stable (<i>c</i>,<i>c</i>) isomer. The latter structure exhibits a close 3.23 Å contact of the iodine and carbonyl oxygen atoms decidedly below the sum of their van der Waals radii (3.50 Å). Increasing the matrix temperature by only a few Kelvin triggers the thermal back reaction of (<i>c</i>,<i>c</i>) to (<i>c</i>,<i>x</i>) and leads to an estimated upper limit of 0.38 kcal mol<sup>-1</sup> for the associated torsional barrier. While wave function methods including completely uncorrelated Hartree-Fock theory have no problem to identify (<i>c</i>,<i>c</i>) as a proper minimum, many popular density functionals fail to describe the C-C torsional potential in <i>cis</i>-iodoacetic acid qualitatively correct. We assessed the performance of 12 density functionals of different levels of sophistication, namely, the BLYP, PBE, TPSS, B3LYP, BHandHLYP, PBE0, M06-2X, CAM-B3LYP, ωB97X-D3, B2-PLYP, B2GP-PLYP, and DSD-PBEP86 methods, against accurate extrapolated CCSD(T)/CBS(T-Q)//MP2/def2-TZVPP energies and found that almost all of them yield acceptable relative energies. Still, even some of the best performers fail to find a reasonably deep minimum in the region of the (<i>c</i>,<i>c</i>) conformer, and addition of the empirical D3-dispersion correction does not remedy the qualitative shortcoming. Instead, inclusion of a sufficient amount of (long-range) exact exchange and likely a proper treatment of medium-range correlation effects all along the torsional coordinate play an important role in the proper description of the sub-van der Waals iodine-oxygen contact. More modern, recommended functionals do not suffer from the described shortcoming.
The impact of life events and transitions on physical activity: A scoping review
2020-06-22

Life events and transitions can be conceptualized as natural interventions that occur across the life course and that are oftentimes associated with changes in PA behavior. Our study indicates that, despite some emerging trends, similar events do not necessarily have similar impacts on PA across individuals. It also shows that the research landscape is characterized by a lack of conceptual clarity and by disparate methodologies, making it difficult to synthesize results across studies.
Systematic review: non-adherence and non-persistence in intravitreal treatment
2020-06-22

Abstract Purpose Intravitreal injection of VEGF inhibitors has become the standard of care for different macular diseases within the last years resulting in improved visual outcomes. Under real-life conditions, however, the necessity for frequent retreatments and reexaminations poses a burden for patients and treatment centers. Non-adherence and non-persistence to intravitreal treatment may lead to inferior clinical outcomes, and knowledge of contributing factors is crucial to improve adherence. This systematic review analyzes current literature for potential factors involved in non-adherence and non-persistence. Methods A systematic search was conducted in PubMed and Embase including three different aspects of intravitreal injection therapy: (1) diseases with intravitreal injections as treatment, (2) intravitreal injection, and (3) aspects of therapy adherence or therapy persistence. Data from identified quantitative studies were further extracted and grouped according to WHO criteria (condition, socio-economy, therapy, patient, and health system). The methodological quality of identified studies was graded. Identified qualitative studies (i.e., interviews) were descriptively analyzed and their findings narratively reported. Results Twenty-four publications were included. In 16 of those publications, a quantitative data analysis was conducted, analyzing factors associated with non-adherence. Worse visual acuity at baseline and unfavorable development of visual acuity, higher age, and greater distance to the treatment center were associated with non-adherence, while there was inconsistent evidence for an association of comorbidity. In qualitative studies, high follow-up/treatment burden, fear and anxiety, disappointed patient expectations, and lack of motivation to continue treatment were reported as reasons for non-persistence. Conclusions Knowledge of potential barriers in IVT treatment may improve adherence and potentially clinical results. Improvements can be achieved particularly in the healthcare complex (organizational improvements) and the “patient” complex by establishing realistic expectations. Recurrent education of the patient may be necessary.
Involvement of top-down networks in the perception of facial emotions: A magnetoencephalographic investigation
2020-06-22

Conscious perception of the emotional valence of faces has been proposed to involve top-down and bottom-up information processing. Yet, the underlying neuronal mechanisms of these two processes and the implementation of their cooperation is still unclear. According to the global workspace model, higher level cognitive processing of visual emotional stimuli relies on both bottom-up and top-down processing. Using masking stimuli in a visual backward masking paradigm with delays at the perceptual threshold, at which stimuli can only partly be detected, suggests that only top-down processing differs between correctly and incorrectly perceived stimuli, while bottom-up visual processing is not compromised and comparable for both conditions. Providing visual stimulation near the perceptual threshold in the backward masking paradigm thus enabled us to compare differences in top-down modulation of the visual information of correctly and incorrectly recognized facial emotions in 12 healthy individuals using magnetoencephalography (MEG). For correctly recognized facial emotions, we found a right-hemispheric fronto-parietal network oscillating in the high-beta and low-gamma band and exerting top-down control as determined by the causality measure of phase slope index (PSI). In contrast, incorrect recognition was associated with enhanced coupling in the gamma band between left frontal and right parietal regions. Our results indicate that the perception of emotional face stimuli relies on the right-hemispheric dominance of synchronized fronto-parietal gamma-band activity.
The predictive and prognostic significance of cell‐free DNA concentration in melanoma
2020-06-22

Abstract Background Melanoma is the leading cause of skin cancer‐related deaths worldwide. While there have been significant improvements in the treatment of advanced melanoma in the past decade, biomarker development lagged behind. Objectives The majority of liquid biopsy biomarkers rely on the analyses of oncogenic mutations; however, about 20% of melanoma patients are wild type. Therefore, validation of universal predictive and prognostic biomarkers is urgently needed. Methods We analysed plasma samples in a discovery cohort ( n = 20) and expansion cohort ( n = 166) of metastatic melanoma patients and healthy donors ( n = 116). Total plasma circulating cell‐free DNA (cfDNA) concentrations were measured on the Qubit ® platform using assays for single‐(ss) and double (ds)‐stranded DNA, DNA spectrophotometry and RNase P qPCR. We explored the diagnostic, predictive and prognostic potential of cfDNA concentration by bio‐statistical methods and established a cfDNA threshold for risk stratification. Results Our selected best method was Qubit ® dsDNA assay which quantified higher plasma cfDNA concentrations in melanoma patients than in healthy controls (AUC 72%). Measurement of baseline cfDNA concentration revealed that high cfDNA was associated with presence of metastases and higher AJCC stage ( P &lt; 0.05). Furthermore, high baseline cfDNA was an indicator of shorter overall survival in patients with oncogenic mutations (HR 2.12, P = 0.0008), and in wild‐type patients (HR 5.55, P &lt; 0.0001). Conclusions We provide evidence that total cfDNA can be used as a biomarker for melanoma irrespective of the tumour genotype and can provide information on tumour load, risk of progression and risk of death.