julilili42/papers huggingface dataset:
Supplementary material to "Vegetation and climate effects on soil production, chemical weathering, and physical erosion rates"
2021-04-01

Compilation of soil production rates, climate, topographic, vegetation, and other parametersThe formation rate of erodible material can be quantified with in situ-produced cosmogenic nuclide concentrations in regolith material.Depending on the sampled material and the assumptions made, the rate is called a regolith (e.g., Ferrier et al., 2012) or soil production rate (e.g., Heimsath et al., 1997).Even though the terms do not identify exactly the same process, the rates are comparable.Not only do they often describe the same process, but the rates should be equal under steady-state conditions.Regolith or soil production rates, from now on called soil production rates, are determined in different tectonic and lithologic settings.In this study, soil production rates of granitic soil-mantled hillslopes are compiled (Table S6) as well as some in nongranitic lithologies (Table S7).For all the studies at granitic point locations the following parameters were compiled (Table S6) and the linear correlation investigated (Tables S8): = 347134 ?-0.5 A0where MAT (°C) and MAP (mm/yr) are mean annual temperature and precipitation, respectively (Rassmussen and Tabor, 2007).As EEMT is an empirical function of MAT and MAP, biotic controls on EEMT are included in Eqn.S5. Based on Eqns, S5 and S6, soil production rates can be calculated.C) Pelak et al. (2016) Whereas Pelletier and Rassmussen (2009) and Norton et al. (2014) address soil production rate in the light of MAP and MAT, Pelak et al. (2016) approach calculation of soil production rates as influenced by plant biomass density b (kg/m 2 ) and soil depth h (m).The so called soil production rate P(h.b) of Pelak et al. ( 2016) is given by:where P0 (mm/yr) is the abiotic soil production rate in the absence of vegetation and soil, Pv (mm 3 /(yr kg)) the sensitivity of soil production to vegetation, and ks (/m) a rate for the decoupling of soil production from surface weathering processes due to increasing soil depth.Typical suggested model parameters are P0 = 0.05 mm/yr, Pv = 0.4 mm 3 /(yr kg), and ks = 0.8 /m (see Table I in Pelak et al., 2016); note unit adjustments were needed).The plant biomass density b (kg/m 2 ) is a function of soil depth h (m) and is calculated with:
A Highly Selective In Vitro JNK3 Inhibitor, FMU200, Restores Mitochondrial Membrane Potential and Reduces Oxidative Stress and Apoptosis in SH-SY5Y Cells
2021-04-02

Current treatments for neurodegenerative diseases (ND) are symptomatic and do not affect disease progression. Slowing this progression remains a crucial unmet need for patients and their families. c-Jun N-terminal kinase 3 (JNK3) are related to several ND hallmarks including apoptosis, oxidative stress, excitotoxicity, mitochondrial dysfunction, and neuroinflammation. JNK inhibitors can play an important role in addressing neuroprotection. This research aims to evaluate the neuroprotective, anti-inflammatory, and antioxidant effects of a synthetic compound (FMU200) with known JNK3 inhibitory activity in SH-SY5Y and RAW264.7 cell lines. SH-SY5Y cells were pretreated with FMU200 and cell damage was induced by 6-hydroxydopamine (6-OHDA) or hydrogen peroxide (H2O2). Cell viability and neuroprotective effect were assessed with an MTT assay. Flow cytometric analysis was performed to evaluate cell apoptosis. The H2O2-induced reactive oxygen species (ROS) generation and mitochondrial membrane potential (ΔΨm) were evaluated by DCFDA and JC-1 assays, respectively. The anti-inflammatory effect was determined in LPS-induced RAW264.7 cells by ELISA assay. In undifferentiated SH-SY5Y cells, FMU200 decreased neurotoxicity induced by 6-OHDA in approximately 20%. In RA-differentiated cells, FMU200 diminished cell death in approximately 40% and 90% after 24 and 48 h treatment, respectively. FMU200 reduced both early and late apoptotic cells, decreased ROS levels, restored mitochondrial membrane potential, and downregulated JNK phosphorylation after H2O2 exposure. In LPS-stimulated RAW264.7 cells, FMU200 reduced TNF-α levels after a 3 h treatment. FMU200 protects neuroblastoma SH-SY5Y cells against 6-OHDA- and H2O2-induced apoptosis, which may result from suppressing the JNK pathways. Our findings show that FMU200 can be a useful candidate for the treatment of neurodegenerative disorders.
Microscopic Dynamics of Liquid-Liquid Phase Separation and Domain Coarsening in a Protein Solution Revealed by X-Ray Photon Correlation Spectroscopy
2021-04-02

While the interplay between liquid-liquid phase separation (LLPS) and glass formation in biological systems is highly relevant for their structure formation and thus function, the exact underlying mechanisms are not well known. The kinetic arrest originates from the slowdown at the molecular level, but how this propagates to the dynamics of microscopic phase domains is not clear. Since with diffusion, viscoelasticity, and hydrodynamics, distinctly different mechanisms are at play, the dynamics needs to be monitored on the relevant time and length scales and compared to theories of phase separation. Using x-ray photon correlation spectroscopy, we determine the LLPS dynamics of a model protein solution upon low temperature quenches and find distinctly different dynamical regimes. We observe that the early stage LLPS is driven by the curvature of the free energy and speeds up upon increasing quench depth. In contrast, the late stage dynamics slows down with increasing quench depth, fingerprinting a nearby glass transition. The dynamics observed shows a ballistic type of motion, implying that viscoelasticity plays an important role during LLPS. We explore possible explanations based on the Cahn-Hilliard theory with nontrivial mobility parameters and find that these can only partially explain our findings.
Associations Between Physical Activity Enjoyment and Age-Related Decline in Physical Activity in Children—Results From a Longitudinal Within-Person Study
2021-04-02

Physical activity declines from childhood to adolescence. Affective factors may partially account for this decline. The present study investigated whether within-person changes in children’s enjoyment of physical activity are associated with the age-related decline in physical activity. Children ( N = 169, 54% female, 56% Hispanic; 8–12 years old at enrollment) took part in a longitudinal study with six assessment waves across 3 years. At each wave, enjoyment of physical activity was reported, and moderate to vigorous physical activity (MVPA) was measured with an accelerometer across seven consecutive days. MVPA and enjoyment of physical activity both declined across waves. Multilevel analyses revealed that within-person changes in enjoyment moderated the effects of age on within-person changes in MVPA. Enjoyment appeared to be a dynamic factor that buffered against the age-related decline in physical activity in youth. These findings call for health promotion interventions that encourage enjoyable physical activities.
The Socio-Political Roles of Neuroethics and the Case of Klotho
2021-04-02

An increasing amount of very diverse scholarship self-identifies as belonging to the field of neuroethics, illuminating a need to provide some reference points for what that field actually entails. We argue that neuroethics is a single field with distinct perspectives, roles, and subspecialties. We propose that-in addition to the three traditional perspectives delineated by Eric Racine-a fourth, socio-political perspective, must be recognized in neuroethics. The socio-political perspective in neuroethics focuses on the interplay between the behavioral as well as the brain sciences and the socio-political system; this interplay includes social regulation in addition to all other realistic elements of social and political <i>neurodiscourses</i>. Thus, defining what-if any-roles the socio-political perspective in neuroethics might have is a pressing issue. Doing so could provide guidance for defining the criteria for prospective ethical evaluations in neuroethics. A promising approach to doing this could be by describing the roles of neuroethics in terms of the more concrete examples of the roles of political philosophy in general, as in the tradition of John Rawls. We take klotho, the supposed "longevity protein," as a modern neuroethics case to exemplify the obstacles faced in securing neuroethics' legitimacy and how the Rawlsian framework we propose may be applied to handle cases such as this. Ultimately, the socio-political perspective in neuroethics should not be swayed by the media hype and ought to offer useful ethical guidance and articulation of genuine ethical concerns to policy makers and the public alike.
Heteroatom Cycloaddition at the (BN)2Bay Region of Dibenzoperylene
2021-04-02

Abstract Cycloaddition‐dehydration involving a BNBN‐butadiene analogue at the bay region of a dibenzoperylene and a non‐enolizable aldehyde provides a novel strategy for incorporation of the oxadiazadiborinane (B 2 N 2 CO) ring into the scaffold of a polycyclic aromatic hydrocarbon resulting in highly emissive compounds.
The effect of tryptamine on Serratia marcescens, Pseudomonas aeruginosa and Escherichia coli
2021-04-02

Aims:Tryptamine is an amine compound derived from tryptophan by decarboxylation process.This compound can be found in fermented food and beverages, and in human gut and skin as well.This study aims to investigate the effect of tryptamine, on Gram-negative bacteria, namely Escherichia coli, Serratia marcescens and Pseudomonas aeruginosa. Methodology and results:In this study, we used E. coli, S. marcescens and P. aeruginosa due to their relatively observable quorum sensing-regulated phenotype, such as motility, prodigiosin and pyocyanin sequentially.Our results showed that tryptamine started to inhibit the growth and prodigiosin production of S. marcescens at concentration 250 μg/mL, while it inhibits the growth and pyocyanin production of P. aeruginosa at concentration 250 μg/mL and 500 μg/mL, respectively.Tryptamine inhibits both the growth and motility of E. coli at concentration 100 μg/mL.Conclusion, significance and impact of study: These results suggest that tryptamine is able to inhibit the growth of E. coli, S. marcescens and P. aeruginosa at relatively high concentration, thus decreases the quorum sensing-regulated phenotypes.It implies that the growth and quorum sensing of Gram-negative bacteria most likely will not be affected by the low concentration of tryptamine that present in the gut.
Expression of CD146 and Regenerative Cytokines by Human Placenta-Derived Mesenchymal Stromal Cells upon Expansion in Different GMP-Compliant Media
2021-04-02

Mesenchymal stromal cells (MSCs) have been successfully employed in clinical applications. In most studies, autologous MSCs from the bone marrow (bmMSCs) were used, and others employed autologous adipose tissue-derived stromal cells (ADSCs). Recently, clinical feasibility studies provided evidence that MSCs from human term placenta (pMSCs) can be used for homologous therapy facilitating access to regenerative cells in emergency situations, when autologous cells are not available or not suitable. We therefore investigated the expression of MSC stemness marker CD146 and the expression of neuro- and myoregenerative cytokines by human pMSCs after expansion in three different media compliant with good manufacturing protocols (GMP) in comparison to pMSCs expanded in a commercial MSC expansion media. To replace xenobiotic serum in the GMP-compliant media employed in this study, either human serum, human serum plus platelet lysate (PLL), or human plasma plus PLL was used. We report that enrichment of media with PLL accelerates pMSC proliferation but reduces the expression of the stemness marker CD146 significantly, while PLL deprivation enhanced the CD146 expression. In contrast, the reduced expression of CD146 by PLL deprivation was not observed on bmMSCs. The expression of the cytokines investigated was not modulated significantly by PLL. We conclude that accelerated expansion of pMSCs in GMP-compliant media enriched by PLL reduces the expression of stemness marker CD146, but does not influence the expression of neuro- and myoregenerative cytokines.
Increasing Inequality in Long‐Term Earnings: A Tale of Educational Upgrading and Changing Employment Patterns
2021-04-02

This paper provides a detailed decomposition analysis of rising long‐term earnings inequality among West German men born between the years 1955 and 1974 based on high‐quality administrative data. Educational upgrading is identified as a leading factor behind increasing inequality in the upper part of the long‐term earnings distribution. The study also reveals a substantial shift from full‐ to part‐time employment and shows this to be an important factor in explaining rising inequality in the lower part. This effect seems to be quantitatively more important than the increasing incidence of non‐employment for the studied cohorts. Overall, increasing inequality in long‐term earnings can primarily be attributed to an increasing inequality in average yearly earnings during times of employment as opposed to changes in the total years of employment. The analysis also reveals similarities with the development in the US by documenting a stagnation in long‐term earnings among the cohorts studied.
ThreadStates: State-based Visual Analysis of Disease Progression
2021-04-02

A growing number of longitudinal cohort studies are generating data with extensive patient observations across multiple timepoints. Such data offers promising opportunities to better understand the progression of diseases. However, these observations are usually treated as general events in existing visual analysis tools. As a result, their capabilities in modeling disease progression are not fully utilized. To fill this gap, we designed and implemented ThreadStates, an interactive visual analytics tool for the exploration of longitudinal patient cohort data. The focus of ThreadStates is to identify the states of disease progression by learning from observation data in a human-in-the-loop manner. We propose a novel Glyph Matrix design and combine it with a scatter plot to enable seamless identification, observation, and refinement of states. The disease progression patterns are then revealed in terms of state transitions using Sankey-based visualizations. We employ sequence clustering techniques to find patient groups with distinctive progression patterns, and to reveal the association between disease progression and patient-level features. The design and development were driven by a requirement analysis and iteratively refined based on feedback from domain experts over the course of a 10-month design study. Case studies and expert interviews demonstrate that ThreadStates can successively summarize disease states, reveal disease progression, and compare patient groups.
Individual cardiovascular responsiveness to work-matched exercise within the moderate- and severe-intensity domains
2021-04-03

Abstract Purpose We investigated the cardiovascular individual response to 6 weeks (3×/week) of work-matched within the severe-intensity domain (high-intensity interval training, HIIT) or moderate-intensity domain (moderate-intensity continuous training, MICT). In addition, we analyzed the cardiovascular factors at baseline underlying the response variability. Methods 42 healthy sedentary participants were randomly assigned to HIIT or MICT. We applied the region of practical equivalence-method for identifying the levels of responders to the maximal oxygen uptake (V̇O 2max ) response. For investigating the influence of cardiovascular markers, we trained a Bayesian machine learning model on cardiovascular markers. Results Despite that HIIT and MICT induced significant increases in V̇O 2max , HIIT had greater improvements than MICT ( p &lt; 0.001). Greater variability was observed in MICT, with approximately 50% classified as “non-responder” and “undecided”. 20 “responders”, one “undecided” and no “non-responders” were observed in HIIT. The variability in the ∆V̇O 2max was associated with initial cardiorespiratory fitness, arterial stiffness, and left-ventricular (LV) mass and LV end-diastolic diameter in HIIT; whereas, microvascular responsiveness and right-ventricular (RV) excursion velocity showed a significant association in MICT. Conclusion Our findings highlight the critical influence of exercise-intensity domains and biological variability on the individual V̇O 2max response. The incidence of “non-responders” in MICT was one third of the group; whereas, no “non-responders” were observed in HIIT. The incidence of “responders” was 11 out of 21 participants in MICT, and 20 out of 21 participants in HIIT. The response in HIIT showed associations with baseline fitness, arterial stiffness, and LV-morphology; whereas, it was associated with RV systolic function in MICT.
Where Asia meets Europe – recent insights from ancient human genomics
2021-04-03

In recent years, archaeogenetic studies have contributed to the understanding of human genetic diversity through time in regions located at the doorstep of Europe. Further studies focussing on these areas will allow for a better characterisation of genetic shifts and regionally-specific patterns of admixture across western Eurasia.
Reconstruction of the human peopling of Europe: a genetic insight
2021-04-03

Despite the long-lasting and interdisciplinary work carried out by different research fields, such as archaeology, history, linguistics, genetics, palaeoanthropology, molecular anthropology, and more recently, palaeogenomics, the reconstruction of the human peopling of Europe is still a highly debated topic. The present issue– composed of review articles and research papers– is largely devoted to discussing and enlarging our current knowledge on the ancestries that contributed to the European genetic make-up through time.
Focal fMRI signal enhancement with implantable inductively coupled detectors
2021-04-04

ABSTRACT Despite extensive efforts to increase the signal-to-noise ratio (SNR) of fMRI images for brain-wide mapping, technical advances of focal brain signal enhancement are lacking, in particular, for animal brain imaging. Emerging studies have combined fMRI with fiber optic-based optogenetics to decipher circuit-specific neuromodulation from meso to macroscales. Acquiring fMRI signal with high spatiotemporal resolution is needed to bridge cross-scale functional dynamics, but SNR of targeted cortical regions is a limiting factor. We have developed a multi-modal fMRI imaging platform with an implanted inductive coil detector. This detector boosts the tSNR of MRI images, showing a 2-3 fold sensitivity gain over conventional coil configuration. In contrast to the cryoprobe or array coils with limited spaces for implanted brain interface, this setup offers a unique advantage to study brain circuit connectivity with optogenetic stimulation and can be further extended to other multi-modal fMRI mapping schemes.
Molecular epidemiology of Respiratory Syncytial Virus in children in sub‐Saharan Africa
2021-04-04

Objectives This study investigated the molecular epidemiology of respiratory syncytial virus (RSV) among febrile children with acute respiratory tract infection in Ghana, Gabon, Tanzania and Burkina Faso between 2014 and 2017 as well as the evolution and diversification of RSV strains from other sub-Saharan countries. Methods Pharyngeal swabs were collected at four study sites (Agogo, Ghana: n = 490; Lambaréné, Gabon: n = 182; Mbeya, Tanzania: n = 293; Nouna, Burkina Faso: n = 115) and analysed for RSV and other respiratory viruses using rtPCR. For RSV-positive samples, sequence analysis of the second hypervariable region of the G gene was performed. A dataset of RSV strains from sub-Saharan Africa (2011–2017) currently available in GenBank was compiled. Phylogenetic analysis was conducted to identify the diversity of circulating RSV genotypes. Results In total, 46 samples were tested RSV positive (Ghana n = 31 (6.3%), Gabon n = 4 (2.2%), Tanzania n = 9 (3.1%) and Burkina Faso n = 2 (1.7%)). The most common RSV co-infection was with rhinovirus. All RSV A strains clustered with genotype ON1 strains with a 72-nucleotide duplication and all RSV B strains belonged to genotype BAIX. Phylogenetic analysis of amino acid sequences from sub-Saharan Africa revealed the diversification into 11 different ON1 and 22 different BAIX lineages and differentiation of ON1 and BAIX strains into potential new sub-genotypes, provisionally named ON1-NGR, BAIX-KEN1, BAIX-KEN2 and BAIX-KEN3. Conclusion The study contributes to an improved understanding of the molecular epidemiology of RSV infection in sub-Saharan Africa. It provides the first phylogenetic data for RSV from Tanzania, Gabon and Burkina Faso and combines it with RSV strains from all other sub-Saharan countries currently available in GenBank.
Nocathioamides, uncovered by a Tunable Metabologenomic Approach, define a Novel Class of Chimeric Lanthipeptides
2021-04-04

Metabologenomic investigation of <em>Nocardia terpenica </em>IFM 0406 and 0706<sup>T</sup> resulted in the discovery of nocathioamides (A-C), founder of a new class of chimeric lanthipeptides I. Nocathioamide A in d<sub>4, </sub>d<sub>3</sub>-CH<sub>3</sub>OH_400 MHz NMR Datasets Nocathioamide A in d<sub>3</sub>-CH<sub>3</sub>OH_700 MHz NMR Dataset Nocathioamide A in d<sub>6</sub>-DMSO_400 MHz NMR Dataset Nocathioamide B in d<sub>4, </sub>d<sub>3</sub>-CH<sub>3</sub>OH_400 MHz NMR Datasets Nocathioamide B in<sub> </sub>d<sub>3</sub>-CH<sub>3</sub>OH_700 MHz NMR Dataset
Slack K + channels attenuate NMDA‐induced excitotoxic brain damage and neuronal cell death
2021-04-05

Abstract The neuronal Na + ‐activated K + channel Slack ( aka Slo2.2, K Na 1.1, or Kcnt1 ) has been implicated in setting and maintaining the resting membrane potential and defining excitability and firing patterns, as well as in the generation of the slow afterhyperpolarization following bursts of action potentials. Slack activity increases significantly under conditions of high intracellular Na + levels, suggesting this channel may exert important pathophysiological functions. To address these putative roles, we studied whether Slack K + channels contribute to pathological changes and excitotoxic cell death caused by glutamatergic overstimulation of Ca 2+ ‐ and Na + ‐permeable N ‐methyl‐D‐aspartic acid receptors (NMDAR). Slack‐deficient (Slack KO) and wild‐type (WT) mice were subjected to intrastriatal microinjections of the NMDAR agonist NMDA. NMDA‐induced brain lesions were significantly increased in Slack KO vs WT mice, suggesting that the lack of Slack renders neurons particularly susceptible to excitotoxicity. Accordingly, excessive neuronal cell death was seen in Slack‐deficient primary cerebellar granule cell (CGC) cultures exposed to glutamate and NMDA. Differences in neuronal survival between WT and Slack KO CGCs were largely abolished by the NMDAR antagonist MK‐801, but not by NBQX, a potent and highly selective competitive antagonist of α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid (AMPA)‐type ionotropic glutamate receptors. Interestingly, NMDAR‐evoked Ca 2+ signals did not differ with regard to Slack genotype in CGCs. However, real‐time monitoring of K + following NMDAR activation revealed a significant contribution of this channel to the intracellular drop in K + . Finally, TrkB and TrkC neurotrophin receptor transcript levels were elevated in NMDA‐exposed Slack‐proficient CGCs, suggesting a mechanism by which this K + channel contributes to the activation of the extracellular‐signal‐regulated kinase (Erk) pathway and thereby to neuroprotection. Combined, our findings suggest that Slack‐dependent K + signals oppose the NMDAR‐mediated excitotoxic neuronal injury by promoting pro‐survival signaling via the BDNF/TrkB and Erk axis.