julilili42/papers huggingface dataset:
Excess postexercise oxygen consumption decreases with swimming duration in a labriform fish: Integrating aerobic and anaerobic metabolism across time
2019-09-27

Abstract Many vertebrate animals employ anaerobic pathways during high‐speed exercise, even if it imposes an energetic cost during postexercise recovery, expressed as excess postexercise oxygen consumption (EPOC). In ectotherms such a fish, the initial anaerobic contribution to exercise is often substantial. Even so, fish may recover from anaerobic pathways as swimming exercise ensues and aerobic metabolism stabilizes, thus total energetic costs of exercise could depend on swimming duration and subsequent physiological recovery. To test this hypothesis, we examined EPOC in striped surfperch ( Embiotoca lateralis ) that swam at high speeds (3.25 L s −1 ) during randomly ordered 2‐, 5‐, 10‐, and 20‐min exercise periods. We found that EPOC was highest after the 2‐min period (20.9 mg O 2 kg −1 ) and lowest after the 20‐min period (13.6 mg O 2 kg −1 ), indicating that recovery from anaerobic pathways improved with exercise duration. Remarkably, EPOC for the 2‐min period accounted for 72% of the total O 2 consumption, whereas EPOC for the 20‐min period only accounted for 14%. Thus, the data revealed a striking decline in the total cost of transport from 0.772 to 0.226 mg O 2 ·kg −1 ·m −1 during 2‐ and 20‐min periods, respectively. Our study is the first to combine anaerobic and aerobic swimming costs to demonstrate an effect of swimming duration on EPOC in fish. Clarifying the dynamic nature of exercise‐related costs is relevant to extrapolating laboratory findings to animals in the wild.
Modelling multi-modal integration -- The case of the McGurk effect
2019-09-27

The McGurk effect is a well known perceptual phenomenon in which listeners perceive [da], when presented with visual instances of [ga] syllables combined with the audio of [ba] syllables. However, the underlying cognitive mechanisms are not yet fully understood. In this study, we investigated the McGurk effect from the perspective of two learning theories – the Exemplar theory and Discriminative Learning. We hypothesized that the McGurk effect arises from distributional differences of the [ba, da, ga] syllables in a lexicon of a given language. We tested this hypothesis using computational implementations of these theories, simulating learning on the basis of lexica in which we varied the distributions of these syllables systematically. These simulations support our hypothesis. For both learning theories, we found that the probability of observing the McGurk effect in our simulations was greater, when lexica contained a larger percentage of [da] and [ba] instances. Crucially, the probability of the McGurk effect was inversely proportional to the percentage of [ga], what ever the percentage of [ba] and [da]. To validate our results, we inspected the distributional properties of [ba, da, ga] in different languages for which the McGurk effect was or was not previously attested. Our results mirror the findings for these languages. Our study shows that the McGurk effect – an instance of multi-modal perceptual integration – arises from distributional properties in different languages and thus depends on language learning.
Next‐generation sequencing for the diagnosis ofMYH9‐RD: Predicting pathogenic variants
2019-09-28

The heterogeneous manifestations of MYH9-related disorder (MYH9-RD), characterized by macrothrombocytopenia, Döhle-like inclusion bodies in leukocytes, bleeding of variable severity with, in some cases, ear, eye, kidney, and liver involvement, make the diagnosis for these patients still challenging in clinical practice. We collected phenotypic data and analyzed the genetic variants in more than 3,000 patients with a bleeding or platelet disorder. Patients were enrolled in the BRIDGE-BPD and ThromboGenomics Projects and their samples processed by high throughput sequencing (HTS). We identified 50 patients with a rare variant in MYH9. All patients had macrothrombocytes and all except two had thrombocytopenia. Some degree of bleeding diathesis was reported in 41 of the 50 patients. Eleven patients presented hearing impairment, three renal failure and two elevated liver enzymes. Among the 28 rare variants identified in MYH9, 12 were novel. HTS was instrumental in diagnosing 23 patients (46%). Our results confirm the clinical heterogeneity of MYH9-RD and show that, in the presence of an unclassified platelet disorder with macrothrombocytes, MYH9-RD should always be considered. A HTS-based strategy is a reliable method to reach a conclusive diagnosis of MYH9-RD in clinical practice.
Formyl-Peptide Receptor Activation Enhances Phagocytosis of Community-Acquired Methicillin-Resistant Staphylococcus aureus
2019-09-28

Abstract Background Formyl-peptide receptors (FPRs) are important pattern recognition receptors that sense specific bacterial peptides. Formyl-peptide receptors are highly expressed on neutrophils and monocytes, and their activation promotes the migration of phagocytes to sites of infection. It is currently unknown whether FPRs may also influence subsequent processes such as bacterial phagocytosis and killing. Staphylococcus aureus, especially highly pathogenic community-acquired methicillin-resistant S aureus strains, release high amounts of FPR2 ligands, the phenol-soluble modulins. Methods We demonstrate that FPR activation leads to upregulation of complement receptors 1 and 3 as well as FCγ receptor I on neutrophils and, consequently, increased opsonic phagocytosis of S aureus and other pathogens. Results Increased phagocytosis promotes killing of S aureus and interleukin-8 release by neutrophils. Conclusions We show here for the first time that FPRs govern opsonic phagocytosis. Manipulation of FPR2 activation could open new therapeutic opportunities against bacterial pathogens.
A tale of scale: Plot but not neighbourhood tree diversity increases leaf litter ant diversity
2019-09-28

Abstract Diversity of producers (e.g. plants) usually increases the diversity of associated organisms, but the scale (i.e. the spatial area of plant diversity considered) at which plant diversity acts on other taxa has rarely been studied. Most evidence for cross‐taxon diversity relations come from above‐ground consumers that directly interact with plants. Experimental tests of plant diversity effects on elusive organisms inhabiting the leaf litter layer, which are important for nutrient cycling and decomposition, are rare. Using a large tree diversity experiment, we tested whether tree diversity at the larger plot (i.e. community) or the smaller neighbourhood scale relates to the abundance, species richness, functional and phylogenetic diversity of leaf litter ants, which are dominant organisms in brown food webs. Contrary to our expectations of scale‐independent positive tree diversity effects, ant diversity increased only with plot but not neighbourhood tree diversity. While the exact causal mechanisms are unclear, nest relocation or small‐scale competition among ants may explain the stronger tree diversity effects at the plot scale. Our results indicate that even for small and less mobile organisms in the leaf litter, effects of tree diversity are stronger at relatively larger scales. The finding emphasizes the importance of diverse forest stands, in which mixing of tree species is not restricted to small patches, for supporting arthropod diversity in the leaf litter.
Inversion effects on mental arithmetic in English- and Polish-speaking adults
2019-09-28

In some languages the order of tens and units in number words is inverted compared with the symbolic digital notation (e.g., German 23 → “ dreiundzwanzig,” literally: “ three-and-twenty”). In other languages only teen-numbers are inverted (e.g., English 17 → “ seventeen”; Polish 17 → “ siedemnaście” literally “ seventeen”). Previous studies have focused on between group comparisons of inverted and non-inverted languages and showed that number word inversion impairs performance on basic numerical tasks and arithmetic. In two independent experiments, we investigated whether number word inversion affects addition performance within otherwise non-inverted languages (Exp. 1: English, Exp. 2: Polish). In particular, we focused on the influence of inverted ( I; English: teen-numbers ⩾ 13, Polish: numbers 11–19) and non-inverted ( N) summands with sums between 13 and 39. Accordingly, three categories of addition problems were created: N + N, N + I, and I + I with problem size matched across categories. Across both language groups, we observed that problems with results in the 20 and 30 number range were responded to faster when only non-inverted summands were part of the problems as opposed to problems with one or two inverted summands. In line with this, the cost of a carry procedure was the largest for two inverted summands. The results support the notion that both language-specific and language-invariant aspects contribute to addition problem-solving. In particular though, regarding language-specific aspects, the results indicate that inverted number word formation of teens influences place-value processing of Arabic digits even in otherwise non-inverted languages.
Long term outcomes of immunomodulatory drugs in SSc-ILD - data from the German SSc-network
2019-09-28

<b>Background:</b> Data from prospective clinical trials support the use of immunomodulatory therapies (IT) for treatment of SSc-ILD. However, outcomes for SSc-ILD in respect to IT use in large real-life cohorts has only sparsely been reported. <b>Methods:</b> The German Network for Systemic Scleroderma (DNSS), which includes SSc pts. prospectively, was analyzed for SSc-ILD. Patients were categorized in IT vs. no-IT users and outcome was assessed. <b>Results:</b> SSc-ILD was reported in 1886 out of 4306 pts. 1109 used IT while 777 did not. Baseline characteristics at ILD diagnosis were similar with regards to gender, FVC (no IT 82% vs. IT 78%, p=0.117) and use of PH drugs. Significant differences in no-IT vs. IT were found for age, time since SSc diagnosis (10 vs. 7 years p&lt;0.001), SSc subtype (p&lt;0.001, diffuse 45% vs. 53%), DLCO (62% vs. 58%, p&lt;0.001), mRSS (10.8 vs. 12.3, p=0.005), specific organ involvements (e.g. esophagus p=0.002, kidneys p=0.002), auto-antibody profile, and steroid use (33% vs. 56%, p&lt;0.001). Disease progression (defined as either death or decline of FVC≥10% or DLCO≥15%) did not differ between groups (27.8% vs. 28.6%, p=0.712). All-cause mortality was similar with 14.6% for no-IT and 13.9% for IT. Also decline of FVC≥10% with 34% in the no-IT and 28% in the IT group (p=0.24) and of DLCO≥15% (35.5% vs. 30%, p=0.088) were comparable. A multinomial logistic regression model revealed an increased risk for the development of SSc-ILD by factor 1.16 if IT was applied (p=0.065). <b>Conclusions:</b> In this large real-life cohort of SSc-patients, the use of immunomodulatory therapies had no significant impact on outcomes in SSc-ILD. Yet, differences in baseline characteristics have to be taken into account.
Articulatory variability is reduced by repetition and predictability
2019-09-28

Repeating the movements involved in activities such as drawing or sports typically leads toimprovement in kinematic behavior: associated movements become faster, smoother, and lessvariable. While practice has also been shown to lead faster and smoother movement trajectoriesin speech articulation, little is known about its effect on articulatory variability. To address this,we investigate the extent to which the repetition and predictability of articulatory gestures affectvariability in the articulation of the frequent German word ‘sie’ [zi]. We find that articulatory variabilityis proportional to the duration of [zi] and speaking rate. By contrast, we find that articulatory variabilityis reduced with repetition during the experiment. In addition, variability becomes smaller when theconditional probability of [zi] increases. The maximum reduction of variability is located during theexecution of the vocalic target of [i]. These results indicate that speakers are capable of fine tuningeven highly practiced articulatory movements.
Generation and activation of myeloid derived suppressor cells using prostaglandin E2 and EP receptor agonists in vitro
2019-09-28

<b>Background:</b> Previously, we showed that adoptively transferred MDSCs were recruited to the lungs of asthmatic animals and reduced lung inflammation. But the signals that drive MDSCs generation and activation in lung inflammatory conditions remained unclear. <b>Methods:</b> To study the role of PGE2 and different EP receptor agonists (EP1-4) on the in vitro generation of MDSCs (both G-MDSCs and M-MDSCs), bone marrow cells from six to eight weeks-old female BALB/c mice were cultured in the presence of different concentrations of PGE2 (1, 10, 100 μM), Sulprostone (EP1/3 agonist), Butaprost (EP2 agonist) and L-902,688 (EP4 agonist) for 72 hours. To study the role of PGE2 and different EP receptor agonists on the in vitro activation of MDSCs, G-MDSCs and M-MDSCs from bone marrow cell culture were isolated and T-cell suppression functionality of MDSCs was measured using MDSC – T cells co-culture suppression assays in the presence of different concentrations of PGE2 and EP receptor agonists by using flow cytometry. <b>Results:</b> Our results show that PGE2 increases the number of M-MDSCs in the bone marrow culture in vitro. Among the EP agonists, only EP4 receptor agonist increases the number of both G-MDSCs and M-MDSCs in the bone marrow culture in vitro. Furthermore, proliferation of CD4+ T cells in the presence of PGE2 and the EP2 and EP4 receptor agonists was reduced in co-culture with both G-MDSC and M-MDSCs. <b>Conclusion:</b> Our results demonstrate that PGE2 and mainly EP4 agonist generate and activate anti-inflammatory MDSCs to suppress the proliferation of T cells in vitro, a phenomenon which needs to be confirmed in our upcoming in vivo studies in a murine model of asthma.
Nintedanib in Progressive Fibrosing Interstitial Lung Diseases
2019-09-29

In patients with progressive fibrosing interstitial lung diseases, the annual rate of decline in the FVC was significantly lower among patients who received nintedanib than among those who received placebo. Diarrhea was a common adverse event. (Funded by Boehringer Ingelheim; INBUILD ClinicalTrials.gov number, NCT02999178.).
The Incomplete Puzzle of the BCL2 Proteins
2019-09-29

The proteins of the BCL2 family are key players in multiple cellular processes, chief amongst them being the regulation of mitochondrial integrity and apoptotic cell death. These proteins establish an intricate interaction network that expands both the cytosol and the surface of organelles to dictate the cell fate. The complexity and unpredictability of the BCL2 interactome resides in the large number of family members and of interaction surfaces, as well as on their different behaviours in solution and in the membrane. Although our current structural knowledge of the BCL2 proteins has been proven therapeutically relevant, the precise structure of membrane-bound complexes and the regulatory effect that membrane lipids exert over these proteins remain key questions in the field. Here, we discuss the complexity of BCL2 interactome, the new insights, and the black matter in the field.
Snails in the sun: Strategies of terrestrial gastropods to cope with hot and dry conditions
2019-09-30

Abstract Terrestrial gastropods do not only inhabit humid and cool environments but also habitat in which hot and dry conditions prevail. Snail species that are able to cope with such climatic conditions are thus expected to having developed multifaceted strategies and mechanisms to ensure their survival and reproduction under heat and desiccation stress. This review paper aims to provide an integrative overview of the numerous adaptation strategies terrestrial snails have evolved to persist in hot and dry environments as well as their mutual interconnections and feedbacks, but also to outline research gaps and questions that remained unanswered. We extracted relevant information from more than 140 publications in order to show how biochemical, cellular, physiological, morphological, ecological, thermodynamic, and evolutionary parameters contribute to provide an overall picture of this classical example in stress ecology. These mechanisms range from behavioral and metabolic adaptations, including estivation, to the induction of chaperones and antioxidant enzymes, mucocyte and digestive gland cell responses and the modification and frequency of morphological features, particularly shell pigmentation. In this context, thermodynamic constraints call for processes of complex adaptation at varying levels of biological organization that are mutually interwoven. We were able to assemble extensive, mostly narrowly focused information from the literature into a web of network parameters, showing that future work on this subject requires multicausal thinking to account for the complexity of relationships involved in snails' adaptation to insolation, heat, and drought.
Recommendations for Improving Methods and Models for Aquatic Hazard Assessment of Ionizable Organic Chemicals
2019-09-30

Abstract Ionizable organic chemicals (IOCs) such as organic acids and bases are an important substance class requiring aquatic hazard evaluation. Although the aquatic toxicity of IOCs is highly dependent on the water pH, many toxicity studies in the literature cannot be interpreted because pH was not reported or not kept constant during the experiment, calling for an adaptation and improvement of testing guidelines. The modulating influence of pH on toxicity is mainly caused by pH-dependent uptake and bioaccumulation of IOCs, which can be described by ion-trapping and toxicokinetic models. The internal effect concentrations of IOCs were found to be independent of the external pH because of organisms’ and cells’ ability to maintain a stable internal pH milieu. If the external pH is close to the internal pH, existing quantitative structure–activity relationships (QSARs) for neutral organics can be adapted by substituting the octanol–water partition coefficient by the ionization-corrected liposome–water distribution ratio as the hydrophobicity descriptor, demonstrated by modification of the target lipid model. Charged, zwitterionic and neutral species of an IOC can all contribute to observed toxicity, either through concentration-additive mixture effects or by interaction of different species, as is the case for uncoupling of mitochondrial respiration. For specifically acting IOCs, we recommend a 2-step screening procedure with ion-trapping/QSAR models used to predict the baseline toxicity, followed by adjustment using the toxic ratio derived from in vitro systems. Receptor- or plasma-binding models also show promise for elucidating IOC toxicity. The present review is intended to help demystify the ecotoxicity of IOCs and provide recommendations for their hazard and risk assessment. Environ Toxicol Chem 2020;39:269–286. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC. Abstract pH-dependence of the toxicity of ionizable organic chemicals (IOCs) is caused by the pH-dependence of the uptake with constant internal effect concentrations that depend on the mode of action of the IOC, for example, baseline toxicity, uncoupling, or receptor activation.
Calcification and latitudinal distribution of extant coccolithophores across the Drake Passage during late austral summer 2016
2019-09-30

Abstract. Coccolithophores are globally distributed microscopic marine algae that exert a major influence on the global carbon cycle through calcification and primary productivity. There is recent interest in coccolithophore polar communities; however field observations regarding their biogeographic distribution are scarce for the Southern Ocean (SO). This study documents the latitudinal, as well as in depth, variability in the coccolithophore assemblage composition and the coccolith mass variation in the ecologically dominant Emiliania huxleyi across the Drake Passage. Ninety-six water samples were taken between 10 and 150 m water depth from 18 stations during POLARSTERN Expedition PS97 (February–April 2016). A minimum of 200 coccospheres per sample were identified in the scanning electron microscope, and coccolith mass was estimated with light microscopy. We find that coccolithophore abundance, diversity and maximum depth habitat decrease southwards, marking different oceanographic fronts as ecological boundaries. We characterize three zones: (1) the Chilean margin, where E. huxleyi type A (normal and overcalcified) and type R are present; (2) the Subantarctic Zone (SAZ), where E. huxleyi reaches maximum values of 212.5×103 cells L−1 and types B/C, C and O are dominant; and (3) the Polar Front Zone (PFZ), where E. huxleyi types B/C and C dominate. We link the decreasing trend in E. huxleyi coccolith mass to the poleward latitudinal succession from the type A to the type B group. Remarkably, we find that coccolith mass is strongly anticorrelated to total alkalinity, total CO2, the bicarbonate ion and pH. We speculate that low temperatures are a greater limiting factor than carbonate chemistry in the Southern Ocean. However, further in situ oceanographic data are needed to verify the proposed relationships. We hypothesize that assemblage composition and calcification modes of E. huxleyi in the Drake Passage will be strongly influenced by the ongoing climate change.
Spatial patterns of erosion and landscape evolution in a bivergent metamorphic core complex revealed by cosmogenic 10Be: The central Menderes Massif (western Turkey)
2019-09-30

Abstract In extensional provinces with low-angle normal faulting (such as the Aegean region), both tectonic processes and erosion induce landscape change, but their interaction during the evolution of topography and relief accompanying continental extension has rarely been addressed. Here we present local and catchment-wide 10Be erosion rates that document the spatial pattern of erosion in the central Menderes Massif, a metamorphic core complex consisting of two asymmetric mountain ranges (Bozdağ and Aydın) bound by detachment faults and active grabens. Catchment-wide erosion rates on the northern flank of the Bozdağ Range are rather low (40–110 mm/k.y.) but reach values of &gt;300 mm/k.y. on the steep southern escarpment—a pattern that reflects both topography and bedrock lithology. In the Aydın Range, erosion rates are generally higher, with mean erosion rates of ∼190 and ∼260 mm/k.y. on the northern and southern flank, respectively, and more variable along strike. In both ranges, erosion rates of ridge crests derived from amalgamated clasts are 30–90 mm/k.y. The difference between local and catchment-wide erosion rates indicates that topographic relief increases in most parts of the massif in response to ongoing fault-related uplift and concomitant river incision. Our findings document that tectonic processes exert a significant control on landscape evolution during active continental extension and are reflected in both the topographic signature and the spatial pattern of erosion. In the Menderes Massif, rock susceptibility to weathering and erosion is a dominant factor that controls the erosional contribution to rock exhumation, which varies spatially between ∼10% and ∼50%.