julilili42/papers huggingface dataset:
Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies
2021-11-09

Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.
Denitrification-driven transcription and enzyme production at the river–groundwater interface: Insights from reactive-transport modeling
2021-11-09

Earth and Space Science Open Archive This work has been accepted for publication in Water Resources Research. Version of RecordESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary. Learn more about preprints. preprintOpen AccessYou are viewing the latest version by default [v2]Denitrification-driven transcription and enzyme production at the river–groundwater interface: Insights from reactive-transport modelingAuthorsAnnaStörikoiDHolgerPageliDAdrianMellageiDPhilippeVan CappelleniDOlaf A.CirpkaiDSee all authors Anna StörikoiDCorresponding Author• Submitting AuthorUniversity of TübingeniDhttps://orcid.org/0000-0002-9281-0881view email addressThe email was not providedcopy email addressHolger PageliDUniversity of HohenheimiDhttps://orcid.org/0000-0003-2424-351Xview email addressThe email was not providedcopy email addressAdrian MellageiDUniversity of TübingeniDhttps://orcid.org/0000-0003-2708-4518view email addressThe email was not providedcopy email addressPhilippe Van CappelleniDUniversity of WaterlooiDhttps://orcid.org/0000-0001-5476-0820view email addressThe email was not providedcopy email addressOlaf A. CirpkaiDUniversity of TübingeniDhttps://orcid.org/0000-0003-3509-4118view email addressThe email was not providedcopy email address
The Undivided Self: Aristotle and the ‘Mind-Body Problem’, by David Charles
2021-11-09

This important and challenging book is the fruit of many years of engagement with Aristotle’s thinking about the soul-body relation by one of the most distinguished experts in the field. David Charles does what many have tried to do during the past fifty years, but he does it with more radicalism and ingenuity than, as far as I can see, anyone has done before. He applies Aristotle’s psychological hylomorphism to the modern mind-body problem arguing that it is both distinctive and philosophically preferable to all other positions in the post-Cartesian theoretical landscape, including recent so-called neo-Aristotelian theories of the mind. The book conveys a very clear philosophical message. According to Charles, contemporary analytic philosophy of mind is still very much in the grip of a profoundly Cartesian way of distinguishing mind and body. This, he argues, besets it with a problem which is both superfluous and prevents it from an adequate understanding of the phenomena of the mental: modern analytic philosophers of mind continue to conceive of mind and body as definitionally separate, that is, in such a way that their definitions do not contain reference to each other. Charles’ point is that definitional separability is the common conceptual core shared by all post-Cartesian treatments of the mind-body problem, that it is a residue of Descartes’ substance-dualism, and that it suffices by itself to create the host of problems characteristic of the post-Cartesian predicament. How can definitionally separate entities interact with each other? How do they come to form unified psychophysical selves in the first place? Charles argues that this way of carving up reality makes truly gapless accounts of the relation between mind and body impossible from the outset. The underlying conceptions of the purely physical (res extensa) and the purely mental (res cogitans), that is, the conceptions that gave rise to the mind-body problem in the first place, are false abstractions, and the very cause of the need to somehow bridge or otherwise overcome the gap they produce.
Data for "The use of principal component analysis to measure fundamental cognitive processes in neuropsychological data"
2021-11-09

Simulation scripts for "The use of principal component analysis to measure fundamental cognitive processes in neuropsychological data". All scripts were written in Matlab 2021a. See the Readme and comments in the scripts for further information. The archive can be unzipped for example with 7zip freeware.
Tooth Loss During Supportive Periodontal Care in a Strict Non-surgically Treated Cohort – a Retrospective Data Analysis
2021-11-09

Abstract Background: This retrospective study aimed to evaluate tooth loss (TL) within a strict non-surgically treated patient cohort after supportive periodontal care (SPC) of 2.5-10.7 years. Methods: Data for non-surgically treated patients were checked for: complete periodontal examination data at baseline ( T 0), after active periodontal therapy ( T 1), and after ≥2.5 years of SPC ( T 2); Smoking, diabetes mellitus, age (at least 18 years), plaque and gingival indices, bleeding on probing (BOP), percentage of residual pockets, SPC adherence, and number of SPCs were assessed as risk factors for TL. Results: 132 patients were included (76 female, mean age 56.7±10.3 years), mean T 1– T 2: 4.5±1.6 years. 26.5% of all patients lost 118 teeth (0.5 teeth/patient, 0.12 teeth/patient/year). Plaque and bleeding parameters: mean plaque control record (PCR): 59.77±28.07%, mean papilla bleeding index (PBI): 47.46±34.12%, mean BOP: 33.46±21.52%. SPC duration ( p=0.013 ) and T2 BOP ( p=0.048 ) were identified as patient-related risk factors for TL. Conclusion: The strictly non-surgical approach within the reported cohort was characterized by elevated BOP, PBI, and PCR scores, possibly highlighting the lack of surgical intervention and regular SPC as negative effect. An apparently low TL rate could be observed. Duration of SPC and BOP (T2) were identified as risk factors for TL.
Reference data and analysis software for "Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane"
2021-11-09

&amp;lt;p&amp;gt;Reference data set for the single molecule co-tracking analysis presented in&amp;nbsp;&amp;quot;Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane&amp;quot;. Corresponding author for further inquiries:&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;Prof. Dr. Jacob Piehler&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;University of Osnabr&amp;uuml;ck, Department of Biology/Chemistry, Division of Biophysics, Barbarastr. 11, 49076 Osnabr&amp;uuml;ck, Germany&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;https://www.biophysik.uni-osnabrueck.de/&amp;lt;/p&amp;gt;
Potentials of the Three Spaces Theory for Understandings of Cartography, Virtual Realities, and Augmented Spaces
2021-11-10

Abstract For about three decades, cartography has been (critically) studied from a theoretical perspective. This perspective has contributed to the recognition of the social preconditions and effects of cartographic representations, but little to their further development. From the theory of three worlds, a theory of three spaces or its special case of landscapes is derived, whose modes of construction are presented as well as the derivations from the different modes. The categories of material, virtual and their combination of augmented spaces as well as the media (such as painting, texts or models) of the construction of space/landscape are added. The formulas derived from this illustrate the different aspects and relations of the constructions of space on the different levels and against the background of the different categories. Thus developed, the theory of three spaces or landscapes provides a framework for neopragmatic exploration, here, of maps, virtual and augmented spaces.
Extended Peer Communities: Appraising the contributions of tacit knowledges in climate change decision-making
2021-11-10

&lt;p&gt;This paper explores the implications of assessing tacit knowledges of climatic change in extended peer communities, as applied in two European research projects on climate action. Post-normal science (PNS) proposes the extension of the peer community to co-produce better quality knowledge for decision-making on issues like climate change, where facts are uncertain, values in dispute, stakes high and decisions urgent. The paper has two aims. The first, more practical, is to explore methods for critically appraising tacit knowledges for climate action, using the example of two ongoing research projects. The second, more conceptual, is to improve practices and discourses surrounding tacit knowledge in current PNS praxis, with close consideration to the implications and challenges involved in including these forms of knowledge in decision making processes. By exploring theoretical perspectives on the topic of tacit knowledge, four challenges facing extended peer communities in engaging with tacit forms of knowledge have been identified: communication, representation, appropriation, and assessment.&lt;/p&gt;
Simulating Personal Carbon Trading (PCT) with an Agent-Based Model (ABM): Investigating Adaptive Reduction Rates and Path Dependence
2021-11-10

A decade after the publication of seminal papers on personal carbon trading (PCT), few empirical studies on its implementation exist. Investigating how to design, set up and implement a PCT scheme for a community or country raises several difficulties. For instance, it is unclear how to introduce a reduction rate of CO2 allowances to ensure a steady decrease in CO2 emissions from households. Computational approaches have been introduced to address these challenges of PCT by providing an opportunity to test counterfactual scenarios. Among the benefits of an agent-based modeling approach (ABM) is the potential to directly address dynamic developments and introduce counterfactual situations. In this paper, we review existing modeling approaches and present an ABM for PCT. With simulations of an artificial population of 1000 and 30,000 agents, we address questions on the price and reduction rate of allowances. A key contribution of our model is the inclusion of an adaptive reduction rate, which reduces the yearly allocated amount of allowances depending on a set CO2 abatement target. The results confirm that increased emissions targets are related to higher allowance prices and a higher proportion of buying households. Our analysis also suggests a significant path dependence in the dynamics of allowance prices and availability, but that adaptive reduction rates have little impact on outcomes other than the price. We discuss data availability and computational challenges to modeling a PCT scheme with an ABM. Ideal data to populate an ABM on PCT are not available due to the lack of real-world implementations of a PCT. Nonetheless, meaningful insights about the dynamics and the focal variables in a PCT scheme can be generated by the exploratory use of an ABM.
Habitability Is Binary, But It Is Used by Astrobiologists to Encompass Continuous Ecological Questions
2021-11-10

The term "habitability" is pervasive throughout the space sciences and astrobiology literature and is broadly used to describe an environment's ability to support life. Here, we argue that, while it is fundamentally a binary matter whether an organism can persist in an environment or not, these binary assessments lead to continuous ecological measurements that are often collected under the umbrella term "habitability" by astrobiologists. Although the use of habitability in this way has provided a framework for those studying the potential of environments to support life, including comparative analyses between terrestrial and extraterrestrial environments, it can also generate confusion and limit interdisciplinary understanding. Namely, differing ecological metrics used as proxies for habitability can yield differing conclusions depending upon the metrics chosen. Therefore, we suggest that in this continuous sense, the terms habitable and habitability lose meaning unless the specific scientific question and biological metric chosen to address it are defined. As a corollary, the search for universal single metrics to make habitability assessments is not to be encouraged, and as we argue, attempting to do so would oversimply analyses of the ability of environments to support life.
Fibroblast-expressed LRRC15 suppresses SARS-CoV-2 infection and controls antiviral and antifibrotic transcriptional programs
2021-11-10

Abstract Although ACE2 is the primary receptor for SARS-CoV-2 infection, a systematic assessment of host factors that regulate binding to SARS-CoV-2 spike protein has not been described. Here we use whole genome CRISPR activation to identify host factors controlling cellular interactions with SARS-CoV-2. Our top hit was a TLR -related cell surface receptor called leucine-rich repeat-containing protein 15 ( LRRC15 ). LRRC15 expression was sufficient to promote SARS-CoV-2 Spike binding where they form a cell surface complex. LRRC15 mRNA is expressed in human collagen-producing lung myofibroblasts and LRRC15 protein is induced in severe COVID-19 infection where it can be found lining the airways. Mechanistically, LRRC15 does not itself support SARS-CoV-2 infection, but fibroblasts expressing LRRC15 can suppress both pseudotyped and authentic SARS-CoV-2 infection in trans . Moreover, LRRC15 expression in fibroblasts suppresses collagen production and promotes expression of IFIT, OAS, and MX-family antiviral factors. Overall, LRRC15 is a novel SARS-CoV-2 spike-binding receptor that can help control viral load and regulate antiviral and antifibrotic transcriptional programs in the context of COVID-19 infection.
Social structure and the imagined mobility of youth football athletes in Dakar
2021-11-10

Across Dakar are many small football training centres where youth prospects start what could grow into professional careers. At these centres, imaginations of career and social mobility develop. In this paper, I explore the mobility imaginations of the youth athletes. I argue that the imaginations are shaped by existing social and class structures, and that the imaginations among the athletes from poor and working-class backgrounds are predominantly unidimensional. Such imaginations that construct mobility exclusively along a career in football produce barriers to the social mobility that the athletes strive for, thereby, reinforcing the structures of social immobility.
French type-noun constructions based on genre
2021-11-10

Abstract Colloquial French genre is highly polysemous with a variety of functions such as comparison, approximation and the fully pragmaticalized functions as a mitigator, a quotative marker, an exemplifier, a marker of narrative progression, explanation and focussing. So far, the focus has been on the various discourse functions, however, several studies also point out possible paths of pragmaticalization. The aim of this paper is to analyse in greater detail the construction at the root of all these functions, i.e. “X of the same type as Y”, a construction originally used for construing ad hoc categories. This rather learned construction became established in the 19th century for French and transformed into a backgrounded instruction for sloppy categorization and the other derived colloquial functions listed above.
A platform of patient-derived microtumors identifies therapeutic vulnerabilities in ovarian cancer
2021-11-10

Abstract Background In light of the frequent development of therapeutic resistance in cancer treatment, there is a strong need for personalized model systems representing patient tumor heterogeneity, while enabling parallel drug testing and identification of appropriate treatment responses in individual patients. Using ovarian cancer as a prime example of a heterogeneous tumor disease with complex microenvironment and high recurrence rates, we developed a 3D preclinical ovarian cancer model comprised of patient-derived microtumors (PDM) and autologous tumor-infiltrating lymphocytes (TILs) for identification of treatment vulnerabilities and validation of anti-cancer drug efficacy using immunohistochemistry, immune cell phenotyping, functional assays and protein profiling analyses. Methods PDM and TILs were isolated from fresh primary ovarian cancer tissue specimen using mechanical disruption and limited enzymatic digestion and were subsequently cultured in suspension in defined media in the absence of serum. The heterogeneous cellular composition of isolated PDM as well as autologous TILs was analyzed by FFPE immunohistochemistry and multi-color flow cytometry, respectively. For in-depth protein profiling of PDM we established Reverse Phase Protein Array (RPPA) analyses of &gt;110 total and phospho-proteins. Treatment efficacy in response to chemotherapeutics as well as immunotherapeutic compounds was assessed in PDM and PDM-TIL co-cultures using a functional viability assay in microplate format. Results The enzymatic digestion of primary ovarian cancer tissue and suspension culture in defined serum-free media allowed fast and efficient recovery of patient-derived microtumors (PDM). Immunohistochemical analyses demonstrated histopathological comparability of ovarian cancer PDM with corresponding patient tumor tissue. Reverse Phase Protein Array (RPPA)-based analyses of &gt;110 total and phospho-proteins enabled the identification of patient-specific sensitivities to standard, platinum-based therapy and thereby the prediction of potential treatment-responders. Finally, combining PDM and autologous TILs for individual efficacy testing of immune checkpoint inhibitor treatment demonstrated the potential for patient-specific enhancement of cytotoxic TIL activity by this therapeutic approach. Conclusion 3D patient-derived ovarian cancer microtumors represent a preclinical, ex vivo tumor model that reflects intertumoral heterogeneity and represent the cellular complexity of individual patient tumors. Combining protein pathway analysis and anti-cancer drug efficacy testing of PDM enables drug mode-of-action analyses and therapeutic sensitivity prediction within a clinically relevant time frame after surgery. Follow-up studies in larger cohorts are currently under way to further evaluate the applicability of this platform to support clinical decision-making and personalizing cancer treatment.
Reduced platelet forces underlie impaired hemostasis in mouse models of MYH9-related disease
2021-11-10

Abstract MYH9-related disease patients with mutations in the contractile protein non-muscle myosin heavy chain IIA display, among others, macrothrombocytopenia and a mild to moderate bleeding tendency. In this study, we used three mouse lines, each with one point mutation in the Myh9 gene at positions 702, 1424, or 1841, to investigate mechanisms underlying the increased bleeding risk. Agonist-induced activation of Myh9 mutant platelets was comparable to controls. However, myosin light chain phosphorylation after activation was reduced in mutant platelets, which displayed altered biophysical characteristics and generated lower adhesion, interaction, and traction forces. Treatment with tranexamic acid restored clot retraction and reduced bleeding. We verified our findings from the mutant mice with platelets from patients with the respective mutation. These data suggest that reduced platelet forces lead to an increased bleeding tendency in MYH9 -related disease patients, and treatment with tranexamic acid can improve the hemostatic function. Teaser Impaired hemostasis in Myh9 mutant mice due to reduced platelet forces can be improved by tranexamic acid.
Boy et al.: Gradient Studies Reveal the True Drivers of Extreme Life in the Atacama Desert.
2021-11-10

The file contains supplementary data on correlation matrices, spatial visualizations of soil pH, clay content, electric conductivity, and soluble salts as well as tables for salt concentrations in different soil depths across four large-scale soil transects in the Atacama Desert, Chile, from the Earth Shape Project. The excel file provides the values for the measured properties. Corresponding author: Diana Boy (diana.boy@ifmb.uni-hannover.de)
Boy et al.: Gradient Studies Reveal the True Drivers of Extreme Life in the Atacama Desert.
2021-11-10

&lt;p&gt;The file contains supplementary data on correlation matrices, spatial visualizations of soil pH, clay content, electric conductivity, and soluble salts as well as tables for salt concentrations in different soil depths across four large-scale soil transects in the Atacama Desert, Chile, from the Earth Shape Project. The excel file provides the values for the measured properties. &nbsp;&nbsp;&lt;/p&gt; &lt;p&gt;Corresponding author: Diana Boy (&lt;a href="mailto:diana.boy@ifmb.uni-hannover.de)"&gt;diana.boy@ifmb.uni-hannover.de)&lt;/a&gt;&lt;/p&gt; &lt;p&gt;&nbsp;&lt;/p&gt;
Reference data and analysis software for "Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane"
2021-11-10

Reference data set for the single molecule co-tracking analysis presented in "Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane". Corresponding author for further inquiries: Prof. Dr. Jacob Piehler University of Osnabrück, Department of Biology/Chemistry, Division of Biophysics, Barbarastr. 11, 49076 Osnabrück, Germany https://www.biophysik.uni-osnabrueck.de/