julilili42/papers huggingface dataset:
Motivation resides only in our language, not in our mental processes.
2021-01-13

“Motivation” is one of the most popular and important concepts in psychology. But what is motivation actually? To answer the question, in this essay, I argue that motivation does not exist in our mental processes --- rather, motivation is a naïve linguistic expression that loosely represents emergent properties of underlying mental processes. Therefore, there are no definitive features of motivation, and there is no such entity in our mental processes. As an example, I showed that a reward-learning framework of knowledge acquisition can sufficiently describe autonomous behaviors often attributed to “need for competence”, without assuming the existence of such motivation. I further argue that the term motivation is so useful to explain behavior that it could often even stop us from thinking deeply about our mental processes, potentially preventing the mechanistic understanding of human mind.
The Wisdom of Solomon
2021-01-13

Abstract The Wisdom of Solomon combines Greek philosophical traditions with biblical exegesis to portray the eschatological fate of humans. To develop his argument, the author draws upon earlier texts in both a creative and a critical way, and integrates them, inconsistently, with Platonic philosophical themes. Imagery of and associations with the figure of Solomon from 1 Kings and Proverbs unite the sections of the book, but the biblical figure remains unnamed since the characteristics of all biblical figures are universalized. The author of Wisdom clearly used the Greek versions of such Hebrew works as Proverbs, 1 Kings, and Sirach, but also shows apparent familiarity with terms and themes from Hebrew works among the Dead Sea Scrolls, especially 4QInstruction. This would suggest some intermediary Greek version or a ready transfer of ideas between Hebrew and Greek Jewish writings. The philosophical material and social context place the work in late first century bce.
Predicting lifestyle and host from positive selection data and genome properties in oomycetes
2021-01-13

Abstract Background Host and niche shifts are a source of genomic and phenotypic diversification as evidenced in parasitism. Exemplary is core metabolism reduction as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone lifestyle or host change have not been fully investigated. Results Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a broad range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyle. Besides, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaption in oomycetes. Discussion Given the high correlation between lifestyle and genome properties in our oomycete dataset and the convergent evolution of fungal and oomycete genomes, we have developed a model that predicts plant pathogen lifestyles with high accuracy based on functional annotations. Understanding how genomes and selective pressures correlate with lifestyle may be crucial to identify new emerging diseases and pandemic threats.
Nanoscale Phase Segregation in Supramolecular π‑Templating for Hybrid Perovskite Photovoltaics from NMR Crystallography
2021-01-13

Raw and processed NMR data, molecular dynamics data, structure files, photovoltaic data, and additional characterisation data for Nanoscale Phase Segregation in Supramolecular π‐Templating for Hybrid Perovskite Photovoltaics from NMR Crystallography, DOI: 10.1021/jacs.0c11563. For more details see README file. NMR_data.zip: Raw and processed NMR data in the file structure of the TopSpin software, which is available from Bruker. NMR_calculations.zip: The input and output Quantum Espresso files are given for both the single point (*.scf.in and *.scf.out) and NMR calculations (*.nmr.in and *.nmr.out). cif_files_all_structures.zip: All structures in cif format. MD_*.zip: MD trajectories of (PEA)2PbI4, (FEA)2PbI4 and configuration 1 of (PF)2PbI4. The full trajectories are given in dcd format which can be opened using the VMD software. The trajectories are also shown as movies. PV+characterisation.zip: The data for the photovoltaic analysis, XPS spectra and XRD patterns in Excel format.
Nanoscale Phase Segregation in Supramolecular π-Templating for Hybrid Perovskite Photovoltaics from NMR Crystallography
2021-01-14

The use of layered perovskites is an important strategy to improve the stability of hybrid perovskite materials and their optoelectronic devices. However, tailoring their properties requires accurate structure determination at the atomic scale, which is a challenge for conventional diffraction-based techniques. We demonstrate the use of nuclear magnetic resonance (NMR) crystallography in determining the structure of layered hybrid perovskites for a mixed-spacer model composed of 2-phenylethylammonium (PEA<sup>+</sup>) and 2-(perfluorophenyl)ethylammonium (FEA<sup>+</sup>) moieties, revealing nanoscale phase segregation. Moreover, we illustrate the application of this structure in perovskite solar cells with power conversion efficiencies that exceed 21%, accompanied by enhanced operational stability.
The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria
2021-01-14

Bulk production of medium-chain carboxylates (MCCs) with 6–12 carbon atoms is of great interest to biotechnology. Open cultures (e.g., reactor microbiomes) have been utilized to generate MCCs in bioreactors. When in-line MCC extraction and prevention of product inhibition is required, the bioreactors have been operated at mildly acidic pH (5.0–5.5). However, model chain-elongating bacteria grow optimally at neutral pH values. Here, we isolated a chain-elongating bacterium (strain 7D4C2) that grows at mildly acidic pH. We studied its metabolism and compared its whole genome and the reverse β-oxidation (rBOX) genes to other bacteria. Strain 7D4C2 produces lactate, acetate, n -butyrate, n -caproate, biomass, and H 2 /CO 2 from hexoses. With only fructose as substrate (pH 5.5), the maximum n -caproate specificity (i.e., products per other carboxylates produced) was 60.9 ± 1.5%. However, this was considerably higher at 83.1 ± 0.44% when both fructose and n -butyrate (electron acceptor) were combined as a substrate. A comparison of 7D4C2 cultures with fructose and n -butyrate with an increasing pH value from 4.5 to 9.0 showed a decreasing n -caproate specificity from ∼92% at mildly acidic pH (pH 4.5-5.0) to ∼24% at alkaline pH (pH 9.0). Moreover, when carboxylates were extracted from the broth (undissociated n -caproic acid was ∼0.3 mM), the n -caproate selectivity (i.e., product per substrate fed) was 42.6 ± 19.0% higher compared to 7D4C2 cultures without extraction. Based on the 16S rRNA gene sequence, strain 7D4C2 is most closely related to the isolates Caproicibacter fermentans (99.5%) and Caproiciproducens galactitolivorans (94.7%), which are chain-elongating bacteria that are also capable of lactate production. Whole-genome analyses indicate that strain 7D4C2, C. fermentans , and C. galactitolivorans belong to the same genus of Caproiciproducens . Their rBOX genes are conserved and located next to each other, forming a gene cluster, which is different than for other chain-elongating bacteria such as Megasphaera spp. In conclusion, Caproiciproducens spp., comprising strain 7D4C2, C. fermentans , C. galactitolivorans , and several unclassified strains, are chain-elongating bacteria that encode a highly conserved rBOX gene cluster. Caproiciproducens sp. 7D4C2 (DSM 110548) was studied here to understand n -caproate production better at mildly acidic pH within microbiomes and has the additional potential as a pure-culture production strain to convert sugars into n -caproate.
A Review of the Microstructural Location of Impurities in Polar Ice and Their Impacts on Deformation
2021-01-14

Insoluble and soluble impurities, enclosed in polar ice sheets, have a major impact on the deformation behaviour of the ice. Macro- and Micro-scale deformation observed in ice sheets and ice cores has been retraced to chemical loads in the ice, even though the absolute concentration is negligible. And therefore the exact location of the impurities matters: Allocating impurities to specific locations inside the ice microstructure inherently determines the physical explanation of the observed interaction between chemical load and the deformational behaviour. Both, soluble and non-soluble impurities were located in grain boundaries, triple junctions or in the grain interior, using different methods, samples and theoretical approaches. While each of the observations is adding to the growing understanding of the effect of impurities in polar ice, the growing number of ambiguous results calls for a dedicated and holistic approach in assessing the findings. Thus, we here aim to give a state of the art overview of the development in microstructural impurity research over the last 20 years. We evaluate the used methods, discuss proposed deformation mechanisms and identify two main reasons for the observed ambiguity: 1) limitations and biases of measurement techniques and 2) the physical state of the analysed impurity. To overcome these obstacles we suggest possible approaches, such as the continuous analysis of impurities in deep ice cores with complementary methods, the implementation of these analyses into established in-situ ice core processing routines, a more holistic analysis of the microstructural location of impurities, and an enhanced knowledge-transfer via an open access data base.
Comparison of path-based centrality measures in protein-protein interaction networks revealed proteins with phenotypic relevance during adaptation to changing nitrogen environments
2021-01-14

Plants must rapidly adapt to changes in nutrient conditions. Especially adaptations to changing nitrogen environments are very complex involving also major adjustments on the protein level. Here, we used a size-exclusion chromatography-coupled to mass spectrometry approach to study the dynamics of protein-protein interactions induced by transition from full nutrition to nitrogen starvation. Comparison of interaction networks established for each nutrient condition revealed a large overlap of proteins which were part of the protein-protein interaction network, but that same set of proteins underwent different interactions at each treatment. Network topology parameter betweenness centrality (BC) was found to best reflect the relevance of individual proteins in the information flow within each network. Changes in BC for individual proteins may therefore indicate their involvement in the cellular adjustments to the new condition. Based on this analysis, a set of proteins was identified showing high nitrogen-dependent changes in their BC values: The receptor kinase AT5G49770, co-receptor QSK1, and proton-ATPase AHA2. Mutants of those proteins showed a nitrate-dependent root growth phenotype. Individual interactions within the reconstructed network were tested using FRET-FLIM technology. Taken together, we present a systematic strategy comparing dynamic changes in protein-protein interaction networks based on their network parameters to identify regulatory nodes. SIGNIFICANCE: Protein-protein interactions are known to be important in cellular signaling events, but the dynamic changes in interaction networks induced by external stimuli are still rarely studied. We systematically analyzed how changes in the nutrient environment induced a rewiring of protein-protein interactions in roots. We observed small changes in overall protein abundances, but instead a rewiring of pairwise protein-protein interactions. Betweenness centrality was found to be the optimal network topology parameter to identify protein candidates with high relevance to the information flow in the (dynamic) network. Predicted interactions of those relevant nodes were confirmed in FLIM/FRET experiments and in phenotypic analysis. The network approach described here may be a useful application in dynamic network analysis more generally.
The European Reference Network for Rare Neurological Diseases
2021-01-14

While rare diseases (RDs) are by definition of low prevalence, the total number of patients suffering from an RD is high, and the majority of them have neurologic manifestations, involving central, peripheral nerve, and muscle. In 2017, 24 European Reference Networks (ERNs), each focusing on a specific group of rare or low-prevalence complex diseases, were formed to improve the care for patients with an RD. One major aim is to have “the knowledge travel instead of the patient,” which has been put into practice by the implementation of the Clinical Patient Management System (CPMS) that enables clinicians to perform pan-European virtual consultations. The European Reference Network for Rare Neurological Diseases (ERN-RND) provides an infrastructure for knowledge sharing and care coordination for patients affected by a rare neurological disease (RND) involving the most common central nervous system pathological conditions. It covers the following disease groups: (i) Cerebellar Ataxias and Hereditary Spastic Paraplegias; (ii) Huntington's disease and Other Choreas; (iii) Frontotemporal dementia; (iv) Dystonia, (non-epileptic) paroxysmal disorders, and Neurodegeneration with Brain Iron Accumulation; (v) Leukoencephalopathies; and (vi) Atypical Parkinsonian Syndromes. At the moment, it unites 32 expert centers and 10 affiliated partners in 21 European countries, as well as patient representatives, but will soon cover nearly all countries of the European Union as a result of the ongoing expansion process. Disease expert groups developed and consented on diagnostic flowcharts and disease scales to assess the different aspects of RNDs. ERN-RND has started to discuss diagnostically unclear patients in the CPMS, is one of four ERNs that serve as foundation of Solve-RD, and has established an RND training and education program. The network will facilitate trial readiness through the establishment of an ERN-RND registry with a minimal data of all patients seen at the ERN-RND centers, thus providing a unique overview of existing genotype-based cohorts. The overall aim of the ERNs is to improve access for patients with RDs to quality diagnosis, care, and treatment. Based on this objective, ERNs are monitored by the European Commission on a regular basis to provide transparency and reassurance to the RD community and the general public.
p53 and p16 expression profiles in vulvar cancer: a translational analysis by the Arbeitsgemeinschaft Gynäkologische Onkologie Chemo and Radiotherapy in Epithelial Vulvar Cancer study group
2021-01-14

p16 overexpression is associated with an improved prognosis whereas p53 positivity is linked to an adverse outcome. Our data support the hypothesis of a clinically relevant third subgroup of vulvar squamous cell carcinoma with a p53-/p16- phenotype showing an intermediate prognosis that needs to be further characterized.
Experimental simulation of environmental warming selects against pigmented morphs of land snails
2021-01-14

Abstract In terrestrial snails, thermal selection acts on shell coloration. However, the biological relevance of small differences in the intensity of shell pigmentation and the associated thermodynamic, physiological, and evolutionary consequences for snail diversity within the course of environmental warming are still insufficiently understood. To relate temperature‐driven internal heating, protein and membrane integrity impairment, escape behavior, place of residence selection, water loss, and mortality, we used experimentally warmed open‐top chambers and field observations with a total of &gt;11,000 naturally or experimentally colored individuals of the highly polymorphic species Theba pisana (O.F. M ÜLLER , 1774). We show that solar radiation in their natural Mediterranean habitat in Southern France poses intensifying thermal stress on increasingly pigmented snails that cannot be compensated for by behavioral responses. Individuals of all morphs acted neither jointly nor actively competed in climbing behavior, but acted similarly regardless of neighbor pigmentation intensity. Consequently, dark morphs progressively suffered from high internal temperatures, oxidative stress, and a breakdown of the chaperone system. Concomitant with increasing water loss, mortality increased with more intense pigmentation under simulated global warming conditions. In parallel with an increase in mean ambient temperature of 1.34°C over the past 30 years, the mortality rate of pigmented individuals in the field is, currently, about 50% higher than that of white morphs. A further increase of 1.12°C, as experimentally simulated in our study, would elevate this rate by another 26%. For 34 T. pisana populations from locations that are up to 2.7°C warmer than our experimental site, we show that both the frequency of pigmented morphs and overall pigmentation intensity decrease with an increase in average summer temperatures. We therefore predict a continuing strong decline in the frequency of pigmented morphs and a decrease in overall pigmentation intensity with ongoing global change in areas with strong solar radiation.
Human invariant natural killer T cells promote tolerance by preferential apoptosis induction of conventional dendritic cells
2021-01-14

Graft-versus-host disease (GvHD) is a major cause of morbidity and mortality after allogeneic hematopoietic cell transplantation. We recently showed in murine studies and in vitro human models that adoptively transferred invariant natural killer T (iNKT) cells protect from GvHD and promote graft-versus-leukemia effects. The cellular mechanisms underlying GvHD prevention by iNKT cells in humans, however, remain unknown. In order to study relevant cellular interactions, dendritic cells (DC) were either generated from monocytes or isolated directly from blood of healthy donors or GvHD patients and co-cultured in a mixed lymphocyte reaction (MLR) with T cells obtained from healthy donors or transplantation bags. Addition of culture-expanded iNKT cells to the MLR-induced DC apoptosis in a cell contact-dependent manner, thereby preventing T-cell activation and proliferation. Annexin V/propidium iodide staining and image stream assays showed that CD4+CD8–, CD4–CD8+ and double negative iNKT cells are similarly able to induce DC apoptosis. Further MLR assays revealed that conventional DC (cDC) but not plasmacytoid DC (pDC) could induce alloreactive T-cell activation and proliferation. Interestingly, cDC were also more susceptible to apoptosis induced by iNKT cells, which correlates with their higher CD1d expression, leading to a bias in favor of pDC. Remarkably, these results could also be observed in GvHD patients. We propose a new mechanism how ex vivo expanded human iNKT cells prevent alloreactivity of T cells. iNKT cells modulate T-cell responses by selective apoptosis of DC subsets, resulting in suppression of T-cell activation and proliferation while enabling beneficial immune responses through pDC.
Specific Point-of-Care Testing of Coagulation in Patients Treated with Dabigatran
2021-01-14

Abstract Background and Purpose Accurate and rapid assessment of coagulation status is necessary to guide thrombolysis or reversal of anticoagulation in stroke patients, but commercially available point-of-care (POC) assays are not suited for coagulation testing in patients treated with direct oral anticoagulants (DOACs). We aimed to evaluate the direct thrombin monitoring (DTM) test card by Helena Laboratories (Texas, United States) for anti-IIa-specific POC coagulation testing, hypothesizing that its POC-ecarin clotting time (POC-ECT) accurately reflects dabigatran plasma concentrations. Methods A prospective single-center diagnostic study (ClinicalTrials.gov-identifier: NCT02825394) was conducted enrolling patients receiving a first dose of dabigatran and patients already on dabigatran treatment. Blood samples were collected before drug intake and 0.5, 1, 2, 8, and 12 hours after intake. POC-ECT was performed using whole blood (WB), citrated blood (CB), and citrated plasma (CP). Dabigatran plasma concentrations were determined by mass spectrometry. Results In total, 240 blood samples from 40 patients contained 0 to 275 ng/mL of dabigatran. POC-ECT with WB/CB/CP ranged from 20 to 186/184/316 seconds. Pearson's correlation coefficient showed a strong correlation between dabigatran concentrations and POC-ECT with WB/CB/CP (R2 = 0.78/0.90/0.92). Dabigatran concentrations &gt;30 and &gt;50 ng/mL (thresholds for thrombolysis, surgery, and reversal therapy according to clinical guidelines) were detected by POC-ECT with WB/CB/CP (&gt;36/35/45 and &gt;43/45/59 seconds) with 95/97/97 and 96/98/97% sensitivity, and 81/87/94 and 74/60/91% specificity. Conclusion This first study evaluating DOAC-specific POC coagulation testing revealed an excellent correlation of POC-ECT with actual dabigatran concentrations. Detecting clinically relevant dabigatran levels with high sensitivity/specificity, the DTM assay represents a suitable diagnostic tool in acute stroke, hemorrhage, and urgent surgery.
Variation in regrowth ability in relation to land-use intensity in three common grassland herbs
2021-01-14

Abstract Aims Plant populations in managed grasslands are subject to strong selection exerted by grazing, mowing and fertilization. Many previous studies showed that this can cause evolutionary changes in mean trait values, but little is known about the evolution of phenotypic plasticity in response to land use. In this study, we aimed to elucidate the relationships between phenotypic plasticity—specifically, regrowth ability after biomass removal—and the intensity of grassland management and levels of temporal variation therein. Methods We conducted an outdoor common garden experiment to test if plants from more intensively mown and grazed sites showed an increased ability to regrow after biomass removal. We used three common plant species from temperate European grasslands, with seed material from 58 to 68 populations along gradients of land-use intensity, ranging from extensive (only light grazing) to very intensive management (up to four cuts per year). Important Findings In two out of three species, we found significant population differentiation in regrowth ability after clipping. While variation in regrowth ability was unrelated to the mean land-use intensity of populations of origin, we found a relationship with its temporal variation in Plantago lanceolata, where plants experiencing less variable environmental conditions over the last 11 years showed stronger regrowth in reproductive biomass after clipping. Therefore, while mean grazing and mowing intensity may not select for regrowth ability, the temporal stability of the environmental heterogeneity created by land use may have caused its evolution in some species.