julilili42/papers huggingface dataset:
The genetic interaction of REVOLUTA and WRKY53 links plant development, senescence, and immune responses
2021-07-27

Abstract In annual plants, tight coordination of successive developmental events is of primary importance to optimize performance under fluctuating environmental conditions. The recent finding of the genetic interaction of WRKY53 , a key senescence-related gene with REVOLUTA , a master regulator of early leaf patterning, raises the question of how early and late developmental events are connected. Here, we investigated the developmental and metabolic consequences of an alteration of the REVOLUTA and WRKY53 gene expression, from seedling to fruiting. Our results show that REVOLUTA critically controls late developmental phases and reproduction while inversely WRKY53 determines vegetative growth at early developmental stages. We further show that these regulators of distinct developmental phases frequently, but not continuously, interact throughout ontogeny and demonstrated that their genetic interaction is mediated by the salicylic acid (SA). Moreover, we showed that REVOLUTA and WRKY53 are keys regulatory nodes of development and plant immunity thought their role in SA metabolic pathways, which also highlights the role of REV in pathogen defence. Together, our findings demonstrate how late and early developmental events are tightly intertwined by molecular hubs. These hubs interact with each other throughout ontogeny, and participate to the interplay between plant development and immunity.
Influence of pre-analytical sample preparation on drug concentration measurements in peritoneal tissue: an ex-vivo study
2021-07-27

Abstract Objectives Biopsy morphology (surface/depth ratio) and sample processing might affect pharmacological measurements in peritoneal tissue. Methods This is an ex-vivo study on inverted bovine urinary bladders (IBUB). We compared cisplatin (CIS) and doxorubicin (DOX) concentration in 81 standardized transmural punch biopsies of different diameters (6 and 12 mm). Then, we assessed the effect of dabbing the peritoneal surface before analysis. After automatized tissue homogenization with ceramic beads followed by lyophilisation, DOX concentration was quantified by high-performance liquid chromatography (HPLC), CIS concentration by atomic absorption spectroscopy. Experiments were performed in triplicate; the analysis was blinded to the sample origin. Comparisons were performed using non-parametric tests. Results Concentrations are given in mean (CI 5–95%). Results were reproducible between experiments (for CIS p=0.783, for DOX p=0.235) and between different localizations within the IBUB (for CIS p=0.032, for DOX p=0.663). Biopsy diameter had an influence on CIS tissue concentration (6 mm biopsies: 23.2 (20.3–26.1), vs. 12 mm biopsies: 8.1 (7.2–9.2) ng/mg, p&lt;0.001) but not on DOX: (0.46, 0.29–0.62) vs. 0.43 (0.33–0.54) ng/mg respectively, p=0.248). Dabbing the peritoneal surface reduced DOX tissue concentration (dry biopsies: 0.28 (0.12–0.43) vs. wet biopsies: 0.64 (0.35–0.93) ng/mg, p=0.025) but not CIS (23.5 (19.0–28.0) vs. 22.9 (18.9–26.9) ng/mg, respectively, p=0.735). Conclusions Measurements of drug concentration in peritoneal tissue can be influenced by the biopsy’s surface/depth ratio and after drying the biopsy’s surface . This influence can reach a factor three, depending on the drug tested . The biopsy technique and the pre-analytical sample preparation should be standardized to ensure reliable pharmacological measurements in peritoneal tissue.
The Cancer Therapy-Related Clonal Hematopoiesis Driver Gene Ppm1d Promotes Inflammation and Non-Ischemic Heart Failure in Mice
2021-07-28

Rationale: Cancer therapy can be associated with short- and long-term cardiac dysfunction. Patients with cancer often exhibit therapy-related clonal hematopoiesis (t-CH), an aggressive form of clonal hematopoiesis that can result from somatic mutations in genes encoding regulators of the DNA-damage response (DDR) pathway. Gain-of-function mutations in exon 6 of the protein phosphatase Mg2+/Mn2+ dependent 1D ( PPM1D ) gene are the most frequently mutated DNA-damage response gene associated with t-CH. Whether t-CH can contribute to cardiac dysfunction is unknown. Objective: We evaluated the causal and mechanistic relationships between Ppm1d -mediated t-CH and nonischemic heart failure in an experimental system. Methods and Results: To test whether gain-of-function hematopoietic cell mutations in Ppm1d can increase susceptibility to cardiac stress, we evaluated cardiac dysfunction in a mouse model where clonal hematopoiesis-associated mutations in exon 6 of Ppm1d were produced by CRISPR-Cas9 technology. Mice transplanted with hematopoietic stem cells containing the mutated Ppm1d gene exhibited augmented cardiac remodeling following the continuous infusion of Ang II (angiotensin II). Ppm1d -mutant macrophages were impaired in DDR pathway activation and displayed greater DNA damage, higher reactive oxygen species generation, and an augmented proinflammatory profile with elevations in IL (interleukin)-1β and IL-18. The administration of an NLRP3 (NLR family pyrin domain containing 3) inflammasome inhibitor to mice reversed the cardiac phenotype induced by the Ppm1d -mutated hematopoietic stem cells under conditions of Ang II–induced stress. Conclusions: A mouse model of Ppm1d -mediated t-CH was more susceptible to cardiac stress. Mechanistically, disruption of the DDR pathway led to elevations in inflammatory cytokine production, and the NLRP3 inflammasome was shown to be essential for this augmented cardiac stress response. These data indicate that t-CH involving activating mutations in PPM1D can contribute to the cardiac dysfunction observed in cancer survivors, and that anti-inflammatory therapy may have utility in treating this condition.
Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development
2021-07-28

Epithelial ovarian cancer (EOC) is the most lethal disease of the female reproductive tract, and although most patients respond to the initial treatment with platinum (cPt)-based compounds, relapse is very common. We investigated the role of epigenetic changes in cPt-sensitive and -resistant EOC cell lines and found distinct differences in their enhancer landscape. Clinical data revealed that two genes (JAK1 and FGF10), which gained large enhancer clusters in resistant EOC cell lines, could provide novel biomarkers for early patient stratification with statistical independence for JAK1. To modulate the enhancer remodeling process and prevent the acquisition of cPt resistance in EOC cells, we performed a chromatin-focused RNAi screen in the presence of cPt. We identified subunits of the Nucleosome Remodeling and Deacetylase (NuRD) complex as critical factors sensitizing the EOC cell line A2780 to platinum treatment. Suppression of the Methyl-CpG Binding Domain Protein 3 (MBD3) sensitized cells and prevented the establishment of resistance under prolonged cPt exposure through alterations of H3K27ac at enhancer regions, which are differentially regulated in cPt-resistant cells, leading to a less aggressive phenotype. Our work establishes JAK1 as an independent prognostic marker and the NuRD complex as a potential target for combinational therapy.
Acoustic velocity measurements for detecting the crystal orientation fabrics of a temperate ice core
2021-07-28

Abstract. The crystal orientation fabric (COF) in ice cores provides detailed information, such as grain size and distribution and the orientation of the crystals in relation to the large-scale glacier flow. These data are relevant for a profound understanding of the dynamics and deformation history of glaciers and ice sheets. The intrinsic, mechanical anisotropy of the ice crystals causes an anisotropy of the polycrystalline ice of glaciers and affects the velocity of acoustic waves propagating through the ice. Here, we employ such acoustic waves to obtain the seismic anisotropy of ice core samples and compare the results with calculated acoustic velocities derived from COF analyses. These samples originate from an ice core from Rhonegletscher (Rhone Glacier), a temperate glacier in the Swiss Alps. Point-contact transducers transmit ultrasonic P waves with a dominant frequency of 1 MHz into the ice core samples and measure variations in the travel times of these waves for a set of azimuthal angles. In addition, the elasticity tensor is obtained from laboratory-measured COF, and we calculate the associated seismic velocities. We compare these COF-derived velocity profiles with the measured ultrasonic profiles. Especially in the presence of large ice grains, these two methods show significantly different velocities since the ultrasonic measurements examine a limited volume of the ice core, whereas the COF-derived velocities are integrated over larger parts of the core. This discrepancy between the ultrasonic and COF-derived profiles decreases with an increasing number of grains that are available within the sampling volume, and both methods provide consistent results in the presence of a similar amount of grains. We also explore the limitations of ultrasonic measurements and provide suggestions for improving their results. These ultrasonic measurements could be employed continuously along the ice cores. They are suitable to support the COF analyses by bridging the gaps between discrete measurements since these ultrasonic measurements can be acquired within minutes and do not require an extensive preparation of ice samples when using point-contact transducers.
1.5 vs 3 Tesla Magnetic Resonance Imaging
2021-07-28

Abstract Whole-body magnetic resonance imaging (MRI) systems with a field strength of 3 T have been offered by all leading manufacturers for approximately 2 decades and are increasingly used in clinical diagnostics despite higher costs. Technologically, MRI systems operating at 3 T have reached a high standard in recent years, as well as the 1.5-T devices that have been in use for a longer time. For modern MRI systems with 3 T, more complexity is required, especially for the magnet and the radiofrequency (RF) system (with multichannel transmission). Many clinical applications benefit greatly from the higher field strength due to the higher signal yield (eg, imaging of the brain or extremities), but there are also applications where the disadvantages of 3 T might outweigh the advantages (eg, lung imaging or examinations in the presence of implants). This review describes some technical features of modern 1.5-T and 3-T whole-body MRI systems, and reports on the experience of using both types of devices in different clinical settings, with all sections written by specialist radiologists in the respective fields. This first part of the review includes an overview of the general physicotechnical aspects of both field strengths and elaborates the special conditions of diffusion imaging. Many relevant aspects in the application areas of musculoskeletal imaging, abdominal imaging, and prostate diagnostics are discussed.
Taking back control of the welfare state: Brexit, rational-imaginaries and welfare chauvinism
2021-07-28

Brexit is about more than the UK exiting the EU. For the Conservative Party, it is about reacting to the challenge from the radical right, both in terms of the electoral threat from UKIP and a long-term internal struggle between moderate Conservatives and the more radical Eurosceptic faction within the party. We ask to what extent Brexit could also be considered as the mobilisation of specific welfare chauvinist discourses and practices. Through a combination of Qualitative Content Analysis (QCA) and Critical Discourse Analysis (CDA) of key speeches and documents from the official Leave campaign, we demonstrate that, rather than merely reinforcing deservingness along ethno-national lines, Brexit invokes social citizenship to delegitimize EU institutions. The referendum result catalyses a longer-term redrawing of the boundaries of social citizenship, and the ideas of membership that grants access to services and benefits. Brexit is discursively framed to mobilise people to consent to this redrawing of boundaries.
309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar Peninsula
2021-07-28

Abstract Prokaryoplankton genomes from the deep marine sediments are less explored compared to shallow shore sediments. The Gulfs of Kathiawar peninsula experience varied currents and inputs from different on-shore activities. Any perturbations would directly influence the microbiome and their normal homeostasis. Advancements in reconstructing genomes from metagenomes allows us to understand the role of individual unculturable microbes in ecological niches like the Gulf sediments. Here, we report 309 bacterial and archaeal genomes assembled from metagenomics data of deep sediments from sites in the Gulf of Khambhat and Gulf of Kutch as well as a sample from the Arabian Sea. Phylogenomics classified them into 5 archaeal and 18 bacterial phyla. The genomes will facilitate understanding of the physiology, adaptation and impact of on-shore anthropogenic activities on the deep sediment microbes.
Psychological Determinants of Collective Action for Climate Justice: Insights From Semi-Structured Interviews and Content Analysis
2021-07-28

Student initiatives for climate justice are driving forces in the climate change debate, but the psychological determinants of students’ engagement for climate justice have hardly been investigated so far. For this study, we posited student engagement for climate justice to be a form of collective action and analyzed psychological determinants of collective action as well as subjective processes of change in these determinants. For this purpose, semi-structured interviews were conducted with four individuals who were engaged in different student initiatives. The results of a qualitative content analysis showed that student collective action for climate justice as reported by the respondents reinforced some of the psychological conditions of collective action established in the literature, such as collective and participatory self-efficacy expectations and feelings of fear and anger. We also found, however, that (first-time) participation in collective action cannot be fully explained by those known predictors. A sense of responsibility, awareness of problems, and extrinsic motives, such as social contact, were also conducive to participation, whereas politicized collective identities did not play a significant role. Finally, we discuss the results against the background of existing theoretical considerations and outline implications for further psychological study of collective action.
Circadian activity of the fat dormouse Glis glis measured with camera traps at bait stations
2021-07-28

Abstract Monitoring of small nocturnal and arboreal rodents is difficult and often conducted using indirect techniques. Here, we measured the circadian activity of the fat dormouse ( Glis glis ) directly using camera traps. The study took place at the Spitzberg in SW Germany. Data were collected using six Bushnell Natureview cameras with a macro lens at baited feeding stations. At 14 out of 41 active camera locations, edible dormice occurred. We collected 301 events between 8th July and 5th October 2018. There were 21.5 events per camera trap (SD 30.4), ranging from 1 to 82. The edible dormouse showed a nocturnal pattern, with a mean activity around midnight at 24:15 h. The pattern shows a slightly bimodal activity. Feeding activity started around or even slightly before sunset and stopped right before sunrise. The study shows that circadian activity, in this respect feeding activity, can be captured by camera trapping, which is a non-invasive method, and can be applied easily in the field.
Erectile function and connective tissue diseases. Prevalence of erectile dysfunction in German men with systemic sclerosis compared to other connective tissue diseases and healthy subjects
2021-07-28

This is the first study to show increased prevalence of ED, especially severe ED, in men with SSc compared to other CTD and age-matched HC. Physicians should be aware of this influence on sexual health and its correlation to depression and disease severity.
Distinct synaptic transfer functions in same-type photoreceptors
2021-07-28

Many sensory systems use ribbon-type synapses to transmit their signals to downstream circuits. The properties of this synaptic transfer fundamentally dictate which aspects in the original stimulus will be accentuated or suppressed, thereby partially defining the detection limits of the circuit. Accordingly, sensory neurons have evolved a wide variety of ribbon geometries and vesicle pool properties to best support their diverse functional requirements. However, the need for diverse synaptic functions does not only arise across neuron types, but also within. Here we show that UV-cones, a single type of photoreceptor of the larval zebrafish eye, exhibit striking differences in their synaptic ultrastructure and consequent calcium to glutamate transfer function depending on their location in the eye. We arrive at this conclusion by combining serial section electron microscopy and simultaneous ‘dual-colour’ two-photon imaging of calcium and glutamate signals from the same synapse in vivo. We further use the functional dataset to fit a cascade-like model of the ribbon synapse with different vesicle pool sizes, transfer rates, and other synaptic properties. Exploiting recent developments in simulation-based inference, we obtain full posterior estimates for the parameters and compare these across different retinal regions. The model enables us to extrapolate to new stimuli and to systematically investigate different response behaviours of various ribbon configurations. We also provide an interactive, easy-to-use version of this model as an online tool. Overall, we show that already on the synaptic level of single-neuron types there exist highly specialised mechanisms which are advantageous for the encoding of different visual features.
Singlet fission in acene blends
2021-07-28

Singlet fission (SF), the photophysical process converting an excited singlet exciton into two triplet excitons, is a promising approach to boost solar cell efficiencies. It is controlled by various parameters such as intermolecular interactions, energetics, entropy and vibronic coupling and a controlled modification of these parameters is key to a fundamental understanding. Blends of organic semiconductors present an interesting alternative to established methods of chemical functionalization and their potential for the study of SF pathways will be discussed using acene blends as example. Mixed thin films of SF chromophores and weakly interacting, high-bandgap spacer molecules allow one to study the impact of a replacement of nearest neighbors on the SF rates. While the SF rate in pentacene, for which SF is a coherent process, is unaffected by the introduction of spacer molecules into the film, we observe a significant decrease in the SF rate in tetracene, indicating incoherent SF. Mixing the two SF chromophores pentacene and tetracene with low pentacene concentrations leads to heterofission of a singlet on pentacene into two triplets on pentacene and tetracene, respectively, when selectively exciting pentacene. This heterofission process is outcompeted by pentacene homofission if the pentacene concentration exceeds 5%. Photoexcitation above the tetracene band gap additionally allows for energy transfer from tetracene to pentacene and results in complex dynamics.
Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave
2021-07-29

Abstract Denisova Cave, a Pleistocene site in the Altai Mountains of Russian Siberia, has yielded significant fossil and lithic evidence for the Pleistocene in Northern Asia. Abundant animal and human bones have been discovered at the site, however, these tend to be highly fragmented, necessitating new approaches to identifying important hominin and faunal fossils. Here we report the results for 8253 bone fragments using ZooMS. Through the integration of this new ZooMS-based data with the previously published macroscopically-identified fauna we aim to create a holistic picture of the zooarchaeological record of the site. We identify trends associated with climate variability throughout the Middle and Upper Pleistocene as well as patterns explaining the process of bone fragmentation. Where morphological analysis of bones from the site have identified a high proportion of carnivore bones (30.2%), we find that these account for only 7.6% of the ZooMS assemblage, with large mammals between 3 and 5 more abundant overall. Our analysis suggests a cyclical pattern in fragmentation of bones which sees initial fragmentation by hominins using percussive tools and secondary carnivore action, such as gnawing and digestion, likely furthering the initial human-induced fragmentation.
Isotopic Labeling Reveals Microbial Methane Oxidation Coupled to Fe(III) Mineral Reduction in Sediments from an As-Contaminated Aquifer
2021-07-29

Although arsenic (As) groundwater contamination in South and Southeast Asia is a threat to human health, mechanisms of its release from sediment to groundwater are still not fully understood. In many aquifers, Fe(III) minerals are often the main hosting phases for As and their stability is crucial for As mobility. Recently, a new mechanism for As mobilization into groundwater was proposed with methane (CH4) serving as an electron donor for microbially mediated reductive dissolution of As-bearing Fe(III) minerals. To provide unequivocal evidence for the occurrence of Fe(III)-coupled methanotrophy, we incubated sediments from an As-contaminated aquifer in Hanoi (Vietnam) anoxically with isotopically labeled 13CH4. Up to 35% of the available Fe(III) was reduced within 232 days with simultaneous production of 13CO2 demonstrating anaerobic oxidation of 13CH4 with Fe(III) as the electron acceptor. The microbial community at the end of the incubation was dominated by archaea affiliating with Candidatus Methanoperedens, implying its involvement in Fe(III)-dependent CH4 oxidation. These results suggest that methanotrophs can contribute to dissolution of As-bearing Fe(III) minerals, which eventually leads to As-release into groundwater.
An Analysis of Heterogeneity in German Speaking Birdwatchers Reveals Three Distinct Clusters and Gender Differences
2021-07-29

The purpose of this study was to segment birdwatchers into clusters. Members from a wide range of bird related organizations, from highly specialized birders as well as Facebook bird group members were studied to provide a diverse dataset (n = 2766; 50.5% men). Birding specialization was measured with a battery of questionnaires. Birding specialization encompassed the three constructs of skill/competence, behavior, personal and behavioral commitment. Additionally, involvement, measured by centrality to lifestyle, attraction, social bonding, and identity, was used. The NbClust analyses showed that a three-cluster solution was the optimal solution. Then, k-means cluster analysis was applied on three groups: casual/novice, intermediate, and specialist/advanced birdwatchers. More men than women were in the specialist/advanced group and more women than men in the casual/novice group. As a conclusion, this study confirms a three-cluster solution for segmenting German birdwatchers based on a large and diverse sample and a broad conceptualization of the construct birding specialization. These data can be used to address different target audiences (novices, advanced birders) with different programs, e.g., in nature conservation.