julilili42/papers huggingface dataset:
Distinct identities of leaf phloem cells revealed by single cell transcriptomics
2021-01-01

Abstract The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about leaf vascular cells, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading, yet PP has been characterized only microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified at least 19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. We provide evidence that PP development occurs independently from ALTERED PHLOEM DEVELOPMENT, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CCs), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our single-cell RNA-sequencing analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.
Intranasal Insulin for Alzheimer’s Disease
2021-01-01

Brain insulin signaling contributes to memory function and might be a viable target in the prevention and treatment of memory impairments including Alzheimer's disease. This short narrative review explores the potential of central nervous system (CNS) insulin administration via the intranasal pathway to improve memory performance in health and disease, with a focus on the most recent results. Proof-of-concept studies and (pilot) clinical trials in individuals with mild cognitive impairment or Alzheimer's disease indicate that acute and prolonged intranasal insulin administration enhances memory performance, and suggest that brain insulin resistance is a pathophysiological factor in Alzheimer's disease with or without concomitant metabolic dysfunction. Intranasally administered insulin is assumed to trigger improvements in synaptic plasticity and regional glucose uptake as well as alleviations of Alzheimer's disease neuropathology; additional contributions of changes in hypothalamus-pituitary-adrenocortical axis activity and sleep-related mechanisms are discussed. While intranasal insulin delivery has been conclusively demonstrated to be effective and safe, the recent outcomes of large-scale clinical studies underline the need for further investigations, which might also yield new insights into sex differences in the response to intranasal insulin and contribute to the optimization of delivery devices to grasp the full potential of intranasal insulin for Alzheimer's disease.
Retrieval of digital elevation models from Sentinel-1 radar data – open applications, techniques, and limitations
2021-01-01

Abstract With the launch of Sentinel-1 in 2014, a new era of openly accessible spaceborne radar imagery was begun, and its potential has been demonstrated throughout all fields of applications. However, while interferometric approaches to detect surface deformations are continuously being published, only a few studies address the derivation of digital elevation models (DEMs) from Sentinel-1 data. This is mainly because of the narrow orbital tube, which was primarily designed for subsidence measurements using differential interferometry. Nonetheless, the technical conditions are provided for successful applications involving DEM generation. These are outlined in the first part of this article with a focus on potential error sources and the impact of the most important constraints, namely, temporal and perpendicular baselines. The second part evaluates 21 studies on this topic, their aims, and how they dealt with error sources and the necessity of validation. These studies are then discussed based on the main challenges and potentials including how these can be tackled in the future to lay a solid foundation for scientific discourse.
SMD-Nets: Stereo Mixture Density Networks
2021-01-01

Despite stereo matching accuracy has greatly improved by deep learning in the last few years, recovering sharp boundaries and high-resolution outputs efficiently remains challenging. In this paper, we propose Stereo Mixture Density Networks (SMD-Nets), a simple yet effective learning framework compatible with a wide class of 2D and 3D architectures which ameliorates both issues. Specifically, we exploit bimodal mixture densities as output representation and show that this allows for sharp and precise disparity estimates near discontinuities while explicitly modeling the aleatoric uncertainty inherent in the observations. Moreover, we formulate disparity estimation as a continuous problem in the image domain, allowing our model to query disparities at arbitrary spatial precision. We carry out comprehensive experiments on a new high-resolution and highly realistic synthetic stereo dataset, consisting of stereo pairs at 8Mpx resolution, as well as on real-world stereo datasets. Our experiments demonstrate increased depth accuracy near object boundaries and prediction of ultra high-resolution disparity maps on standard GPUs. We demonstrate the flexibility of our technique by improving the performance of a variety of stereo backbones.
Physical and chemical structure of high-mass star-forming regions: unraveling chemical complexity with CORE: the NOEMA large program
2021-01-01

We use sub-arcsecond resolution ( 0.4 ) observations with NOEMA at 1.37 mm to study the dust emission and molecular gas of 18 high-mass star-forming regions. We combine the derived physical and chemical properties of individual cores in these regions to estimate their ages. The temperature structure of these regions are determined by fitting H2CO and CH3CN line emission. The density profiles are inferred from the 1.37 mm continuum visibilities. The column densities of 11 different species are determined by fitting the emission lines with XCLASS. Within the 18 observed regions, we identify 22 individual cores with associated 1.37 mm continuum emission and with a radially decreasing temperature profile. We find an average temperature power-law index of q = 0.4 0.1 and an average density power-law index of p = 2.0 0.2 on scales on the order of several 1 000 au. Comparing these results with values of p derived in the literature suggest that the density profiles remain unchanged from clump to core scales. The column densities relative to N(C18O) between pairs of dense gas tracers show tight correlations. We apply the physical-chemical model MUSCLE to the derived column densities of each core and find a mean chemical age of 60 000 yrs and an age spread of 20 000-100 000 yrs. With this paper we release all data products of the CORE project available at https://www.mpia.de/core. The CORE sample reveals well constrained density and temperature power-law distributions. Furthermore, we characterize a large variety in molecular richness that can be explained by an age spread confirmed by our physical-chemical modeling. The hot molecular cores show the most emission lines, but we also find evolved cores at an evolutionary stage, in which most molecules are destroyed and thus the spectra appear line-poor again.
Membrane integration into PDMS-free microfluidic platforms for organ-on-chip and analytical chemistry applications
2021-01-01

This review provides an introduction into membrane-based microfluidic systems and their application for analytical and organ-on-chip systems as well as a comprehensive overview of approaches for the integration of membranes into PDMS-free systems.
Navigating trade-offs between dams and river conservation
2021-01-01

Non-technical summary There has been a long history of conflicts, studies, and debate over how to both protect rivers and develop them sustainably. With a pause in new developments caused by the global pandemic, anticipated further implementation of the Paris Agreement and high-level global climate and biodiversity meetings in 2021, now is an opportune moment to consider the current trajectory of development and policy options for reconciling dams with freshwater system health. Technical summary We calculate potential loss of free-flowing rivers (FFRs) if proposed hydropower projects are built globally. Over 260,000 km of rivers, including Amazon, Congo, Irrawaddy, and Salween mainstem rivers, would lose free-flowing status if all dams were built. We propose a set of tested and proven solutions to navigate trade-offs associated with river conservation and dam development. These solution pathways are framed within the mitigation hierarchy and include (1) avoidance through either formal river protection or through exploration of alternative development options; (2) minimization of impacts through strategic or system-scale planning or re-regulation of downstream flows; (3) restoration of rivers through dam removal; and (4) mitigation of dam impacts through biodiversity offsets that include restoration and protection of FFRs. A series of examples illustrate how avoiding or reducing impacts on rivers is possible – particularly when implemented at a system scale – and can be achieved while maintaining or expanding benefits for climate resilience, water, food, and energy security. Social media summary Policy solutions and development pathways exist to navigate trade-offs to meet climate resilience, water, food, and energy security goals while safeguarding FFRs.
The Role of hlb-Converting Bacteriophages in <b><i>Staphylococcus aureus</i></b> Host Adaption
2021-01-01

As an opportunistic pathogen of humans and animals, &lt;i&gt;Staphylococcus aureus&lt;/i&gt; asymptomatically colonizes the nasal cavity but is also a leading cause of life-threatening acute and chronic infections. The evolution of &lt;i&gt;S. aureus&lt;/i&gt; resulting from short- and long-term adaptation to diverse hosts is tightly associated with mobile genetic elements&lt;i&gt;. S. aureus&lt;/i&gt; strains can carry up to four temperate phages, many of which possess accessory genes encoding staphylococcal virulence factors. More than 90% of human nasal isolates of &lt;i&gt;S. aureus&lt;/i&gt; have been shown to carry Sa3int phages, whereas invasive &lt;i&gt;S. aureus&lt;/i&gt; isolates tend to lose these phages. Sa3int phages integrate as prophages into the bacterial &lt;i&gt;hlb&lt;/i&gt; gene, disrupting the expression of the sphingomyelinase Hlb, an important virulence factor under specific infection conditions. Virulence factors encoded by genes carried by Sa3int phages include staphylokinase, enterotoxins, chemotaxis-inhibitory protein, and staphylococcal complement inhibitor, all of which are highly human specific and probably essential for bacterial survival in the human host. The transmission of &lt;i&gt;S. aureus&lt;/i&gt; from humans to animals is strongly correlated with the loss of Sa3int phages, whereas phages are regained once a strain is transmitted from animals to humans. Thus, both the insertion and excision of prophages may confer a fitness advantage to this bacterium&lt;i&gt;.&lt;/i&gt; There is also growing evidence that Sa3int phages may perform “active lysogeny,” a process during which prophages are temporally excised from the chromosome without forming intact phage particles. The molecular mechanisms controlling the peculiar life cycle of Sa3int phages remain largely unclear. Nevertheless, their regulation is likely fine-tuned to ensure bacterial survival within different hosts.
Cholón and the linguistic prehistory of Northern Peru: triangulating toponymy, substrate lexis, and areal typology
2021-01-01

At the eve of Spanish conquest, Northern Peru is thought to have been home to a multitude of languages of relatively modest geographical extension, especially when compared with the widespread Quechuan and Aymaran languages. In this contribution, I suggest the possibility that a language or several languages relatively closely related to Cholón were spoken in a much wider part of Northern Peru than that in which Cholón is historically attested. A prior “Cholonoid” area might have covered not only the western part of today’s San Martín department, but also almost the entire department of Cajamarca as well as parts of La Libertad and Amazonas. This interpretation results from a triangulation of three independent lines of evidence, namely the toponymic record, substrate lexis in the local variety of Quechua at Chachapoyas, and typological properties of the extinct northern Peruvian languages.
Local tumor microbial signatures and response to checkpoint blockade in non-small cell lung cancer
2021-01-01

In cancer patients, the clinical response to checkpoint-based immunotherapy is associated with the composition and functional quality of the host microbiome. While the relevance of the gut microbiome for checkpoint immunotherapy outcome has been addressed intensively, data on the role of the local tumor microbiome are missing. Here, we set out to molecularly characterize the local non-small cell lung cancer microbiome using 16S rRNA gene amplicon sequencing of bronchoscopic tumor biopsies from patients treated with PD-1/PD-L1-targeted checkpoint inhibitors. Our analyses showed significant diversity of the tumor microbiome with high proportions of Firmicutes, Bacteroidetes and Proteobacteria. Correlations with clinical data revealed that high microbial diversity was associated with improved patient survival irrespective of radiology-based treatment response. Moreover, we found that the presence of Gammaproteobacteria correlated with low PD-L1 expression and poor response to checkpoint-based immunotherapy, translating into poor survival. Our study suggests novel microbiome-specific/derived biomarkers for checkpoint immunotherapy response prediction and prognosis in lung cancer. In a broader sense, our data draw attention to the local tumor microbial habitat as an important addition to the spatially separated microbiome of the gut compartment.
Polyhydroxybutyrate: A Useful Product of Chlorotic Cyanobacteria
2021-01-01

Polyhydroxybutyrate (PHB) is a carbon polymer with diverse functions, varying greatly on the organism producing it. This microreview describes the current knowledge about PHB metabolism, structure, and different physiological roles with a special focus on cyanobacteria. Despite the physiological function of PHB in the cyanobacterial phylum still being unknown, these organisms provide the unique opportunity to directly convert atmospheric CO&lt;sub&gt;2&lt;/sub&gt; into bioplastic using a solar-based process. Recent research on PHB metabolism in the cyanobacterial model organism &lt;i&gt;Synechocystis&lt;/i&gt; revealed a sophisticated control of PHB granule formation. Novel insights about the metabolic background of PHB synthesis resulted in the engineering of the first cyanobacterial superproducer strain.
Peristaltic on-chip pump for tunable media circulation and whole blood perfusion in PDMS-free organ-on-chip and Organ-Disc systems
2021-01-01

We present an Organ-Disc with integrated peristaltic pump for the closed-loop perfusion of microphysiological systems with tunable flow rates, enabling time-resolved monitoring of cell states and media properties, and the perfusion of whole blood.
Practices and experiences of distant education during the COVID-19 pandemic: The perspectives of six- to sixteen-year-olds from three high-income countries
2021-01-01

The paper explores children's perspectives of distance education, their learning experiences and school satisfaction in Luxembourg, Germany and Switzerland during the first wave of the COVID-19 pandemic. The data stem from an online questionnaire completed by 1773 primary and secondary school children aged 6-16. While the paper uses quantitative and qualitative data, it aligns with the qualitative research tradition and predominantly uses an inductive approach. The findings show that teachers offered varied types of distance education and that parents supported children. The children's contact time with teachers and their time spent on schoolwork varied within and between countries. Their school satisfaction dropped in the three countries. The paper calls for training and development on distant education.
Kinetic Analysis of a Protein-protein Complex to Determine its Dissociation Constant (KD) and the Effective Concentration (EC50) of an Interplaying Effector Molecule Using Bio-layer Interferometry
2021-01-01

Biolayer interferometry (BLI) is an emerging analytical tool that allows the study of protein complexes in real time to determine protein complex kinetic parameters. This article describes a protocol to determine the K<sub>D</sub> of a protein complex using a 6×His tagged fusion protein as bait immobilized on the NTA sensor chip of the FortéBio<sup>®</sup> Octet K2 System (Sartorius). We also describe how to determine the half maximal effective concentration (EC<sub>50</sub>, also known as IC<sub>50</sub> for inhibiting effectors) of a metabolite. The complete protocol allows the determination of protein complex K<sub>D</sub> and small molecular effector EC<sub>50</sub> within 8 h, measured in triplicates. Graphic abstract: <b>Principle of the Biolayer interferometry measurement.</b> (Middle, top) Exemplary result of the BLI measurement using Octet<sup>®</sup> (Raw Data). Wavelength shift (Δλ) against time. (A) Baseline 1. Baseline measurement. When the sensor is equilibrated in the kinetics buffer. The light is reflected with no difference. (B) Load. The his-tagged proteins (ligand) are loaded onto the sensor surface. The light is reflected with a shift of the wavelength. (C) Baseline 2. The loaded sensor is equilibrated in the kinetics buffer. No further wavelength shift appears. (D) Association. The loaded sensor is dipped into the analyte solution. The analyte binds to the immobilized ligand along with an increased wavelength shift. (E) Dissociation. Afterward, the sensor is dipped again into the kinetics buffer without the analyte. Some analyte molecules dissociate. The wavelength shift decreases. (Subfigures A-E) The left side shows the position of the sensor during the measurement seen in the representative BLI measurement, marked with the figure label. The right side shows the light path in the sensor. Black waves represent the light emitted to the sensor surface. The red waves show the light reflected from the sensor surface back to the detector.
Our Mythical Hope. The Ancient Myths as Medicine for the Hardships of Life in Children’s and Young Adults’ Culture
2021-01-01

Classical Antiquity is a particularly important field in terms of “Hope studies” [...]. For centuries, the ancient tradition, and classical mythology in particular, has been a common reference point for whole hosts of creators of culture, across many parts of the world, and with the new media and globalization only increasing its impact. Thus, in our research at this stage, we have decided to study how the authors of literary and audiovisual texts for youth make use of the ancient myths to support their young protagonists (and readers or viewers) in crucial moments of their existence, on their road into adulthood, and in those dark hours when it seems that life is about to shatter and fade away. However, if Hope is summoned in time, the crisis can be overcome and the protagonist grows stronger, with a powerful uplifting message for the public. [...] Owing to this, we get a chance to remain true to our ideas, to keep faith in our dreams, and, when the decisive moment comes, to choose not hatred but love, not darkness but light. Katarzyna Marciniak, University of Warsaw, From the introductory chapter
LC‐HRMS Profiling and Antidiabetic, Antioxidant, and Antibacterial Activities of Acacia catechu (L.f.) Willd
2021-01-01

Acacia catechu (L.f.) Willd is a profoundly used traditional medicinal plant in Asia. Previous studies conducted in this plant are more confined to extract level. Even though bioassay‐based studies indicated the true therapeutic potential of this plant, compound annotation was not performed extensively. This research is aimed at assessing the bioactivity of different solvent extracts of the plant followed by annotation of its phytoconstituents. Liquid chromatography equipped with high resolution mass spectrometry (LC‐HRMS) is deployed for the identification of secondary metabolites in various crude extracts. On activity level, its ethanolic extract showed the highest inhibition towards α- amylase and α ‐glucosidase with an IC 50 of 67.8 ± 1 μ g/mL and 10.3 ± 0.1 μ g/mL respectively, inspected through the substrate‐based method. On the other hand, the plant extract showed an antioxidant activity of 23.76 ± 1.57 μ g/mL, measured through radical scavenging activity. Similarly, ethyl acetate and aqueous extracts of A. catechu showed significant inhibition against Staphylococcus aureus with a zone of inhibition (ZoI) of 13 and 14 mm, respectively. With the LC‐HRMS‐based dereplication strategy, we have identified 28 secondary metabolites belonging to flavonoid and phenolic categories. Identification of these metabolites from A. catechu and its biological implication also support the community‐based usage of this plant and its medicinal value.
Contribution of the Clp Protease to Bacterial Survival and Mitochondrial Homoeostasis
2021-01-01

Fast adaptation to environmental changes ensures bacterial survival, and proteolysis represents a key cellular process in adaptation. The Clp protease system is a multi-component machinery responsible for protein homoeostasis, protein quality control, and targeted proteolysis of transcriptional regulators in prokaryotic cells and prokaryote-derived organelles of eukaryotic cells. A functional Clp protease complex consists of the tetradecameric proteolytic core ClpP and a hexameric ATP-consuming Clp-ATPase, several of which can associate with the same proteolytic core. Clp-ATPases confer substrate specificity by recognising specific degradation tags, and further selectivity is conferred by adaptor proteins, together allowing for a fine-tuned degradation process embedded in elaborate regulatory networks. This review focuses on the contribution of the Clp protease system to prokaryotic survival and summarises the current state of knowledge for exemplary bacteria in an increasing degree of interaction with eukaryotic cells. Starting from free-living bacteria as exemplified by a non-pathogenic and a pathogenic member of the Firmicutes, i.e., &lt;i&gt;Bacillus subtilis&lt;/i&gt; and &lt;i&gt;Staphylococcus aureus&lt;/i&gt;, respectively, we turn our attention to facultative and obligate intracellular bacterial pathogens, i.e., &lt;i&gt;Mycobacterium tuberculosis, Listeria monocytogenes,&lt;/i&gt; and &lt;i&gt;Chlamydia trachomatis&lt;/i&gt;, and conclude with mitochondria. Under stress conditions, the Clp protease system exerts its pivotal role in the degradation of damaged proteins and controls the timing and extent of the heat-shock response by regulatory proteolysis. Key regulators of developmental programmes like natural competence, motility, and sporulation are also under Clp proteolytic control. In many pathogenic species, the Clp system is required for the expression of virulence factors and essential for colonising the host. In accordance with its evolutionary origin, the human mitochondrial Clp protease strongly resembles its bacterial counterparts, taking a central role in protein quality control and homoeostasis, energy metabolism, and apoptosis in eukaryotic cells, and several cancer cell types depend on it for proliferation.