julilili42/papers huggingface dataset:
Hip Position Acutely Affects Oxygenation and Perfusion of Kidney Grafts as Measured by Functional Magnetic Resonance Imaging Methods—The Bent Knee Study
2021-08-10

Background: Kidney perfusion and oxygenation are two important determinants of kidney graft function. In kidney transplantation, repeated graft hypoperfusion may occur during hip flexion, for example in the sitting position, due to the progressive development of fibrotic tissue around iliac arteries. The aim of this study was to assess the changes in oxygenation and perfusion of kidney grafts during hip flexion and extension using a new functional magnetic resonance imaging (fMRI) protocol. Methods: Nineteen kidney graft recipients prospectively underwent MRI on a 3T scanner including diffusion-weighted, blood oxygenation level dependent (BOLD), and arterial spin labeling sequences in hip positions 0° and &amp;gt;90° before and after intravenous administration of 20 mg furosemide. Results: Unexpectedly, graft perfusion values were significantly higher in flexed compared to neutral hip position. Main diffusion-derived parameters were not affected by hip position. BOLD-derived cortico-medullary R2 * ratio was significantly modified during hip flexion suggesting an intrarenal redistribution of the oxygenation in favor of the medulla and to the detriment of the cortex. Furthermore, the increase in medullary oxygenation induced by furosemide was significantly blunted during hip flexion ( p &amp;lt; 0.001). Conclusion: Hip flexion has an acute impact on perfusion and tissue oxygenation in kidney grafts. Whether these position-dependent changes affect the long-term function and outcome of kidney transplants needs further investigation.
The association of the 5-HTTLPR polymorphism and the response to different stressors in healthy males
2021-08-10

Abstract The experience of stress is related to individual wellbeing and vulnerability to psychopathology. Therefore, understanding the determinants of individual differences in stress reactivity is of great concern from a clinical perspective. The functional promotor polymorphism of the serotonin transporter gene (5-HTTLPR/rs25531) is such a factor, which has been linked to the acute stress response as well as the adverse effect of life stressors. In the present study, we compared the impact of two different stress induction protocols (Maastricht Acute Stress Test and ScanSTRESS) and the respective control conditions on affective ratings, salivary cortisol levels and cognitive performance. To this end, 156 healthy young males were tested and genotyped for the 5-HTTLPR/rs25531 polymorphism. While combined physiological and psychological stress in the MAST led to a greater cortisol increase compared to control conditions as well as the psychosocial ScanSTRESS, subjective stress ratings were highest in the ScanSTRESS condition. Stress induction in general affected working memory capacity but not response inhibition. Subjective stress was also influenced by 5-HTTLPR/rs25531 genotype with the high expression group showing lower stress ratings than lower expression groups. In line with previous research, we identified the low expression variant of the serotonin transporter gene as a risk factor for increased stress reactivity. While some dimensions of the human stress response may be stressor specific, cognitive outcomes such as working memory performance are influenced by stress in general. Different pathways of stress processing and possible underlying mechanisms are discussed.
The Impact of Action Effects on Infants’ Predictive Gaze Shifts for a Non-Human Grasping Action at 7, 11, and 18 Months
2021-08-10

During the observation of goal-directed actions, infants usually predict the goal at an earlier age when the agent is familiar (e.g., human hand) compared to unfamiliar (e.g., mechanical claw). These findings implicate a crucial role of the developing agentive self for infants’ processing of others’ action goals. Recent theoretical accounts suggest that predictive gaze behavior relies on an interplay between infants’ agentive experience (top-down processes) and perceptual information about the agent and the action-event (bottom-up information; e.g., agency cues). The present study examined 7-, 11-, and 18-month-old infants’ predictive gaze behavior for a grasping action performed by an unfamiliar tool, depending on infants’ age-related action knowledge about tool-use and the display of the agency cue of producing a salient action effect. The results are in line with the notion of a systematic interplay between experience-based top-down processes and cue-based bottom-up information: Regardless of the salient action effect, predictive gaze shifts did not occur in the 7-month-olds (least experienced age group), but did occur in the 18-month-olds (most experienced age group). In the 11-month-olds, however, predictive gaze shifts occurred only when a salient action effect was presented. This sheds new light on how the developing agentive self, in interplay with available agency cues, supports infants’ action-goal prediction also for observed tool-use actions.
Negation Processing in Children with ADHD: The Generic Problem of Using Negation in Instructions
2021-08-10

Abstract Recent studies have suggested that negation comprehension falls back onto inhibitory brain systems that are also crucial for impulse control and other non-linguistic control domains (Beltran et al., 2018, 2019; de Vega et al., 2016; Liu et al., 2020). Against this backdrop, the present pilot study investigated the use of negation within directional instructions (i.e., “not left”, “now left”, “not right”, “now right”) in children with ADHD and a control group. The results indicate that children in general have a long response delay following negative compared to affirmative instructions. Additionally, there was a tendency for this effect to be more pronounced in the ADHD group. Together, these results suggest that negation processing might indeed demand inhibitory control processes, which are differently available across different subgroups. Thus, the current study provides evidence that using negation in imperatives or instructions is generally rather critical and should be avoided if possible, but that negation use is probably even more problematic in specific clinical populations. Potential implications of these results will be discussed.
Spectral inference reveals principal cone-integration rules of the zebrafish inner retina
2021-08-10

ABSTRACT In the vertebrate retina, bipolar cells integrate the signals from different cone types at two main sites: directly, via dendritic inputs in the outer retina, and indirectly, via axonal inputs in the inner retina. Of these, the functional wiring of the indirect route, involving diverse amacrine cell circuits, remains largely uncharted. However, because cone-photoreceptor types differ in their spectral sensitivities, insights into the total functional cone-integration logic of bipolar cell might be gained by linking spectral responses across these two populations of neurons. To explore the feasibility of such a “spectral-circuit-mapping” approach, we here recorded in vivo responses of bipolar cell presynaptic terminals in larval zebrafish to widefield but spectrally resolved flashes of light. We then mapped the results onto the previously established spectral sensitivity functions of the four cones. We find that this approach could explain ∼95% of the spectral and temporal variance of bipolar cell responses by way of a simple linear model that combined weighted inputs from the cones with four stereotyped temporal components. This in turn revealed several notable integration rules of the inner retina. Overall, bipolar cells were dominated by red-cone inputs, often alongside equal sign inputs from blue- and green-cones. In contrast, UV-cone inputs were uncorrelated with those of the remaining cones. This led to a new axis of spectral opponency which was mainly set-up by red-/green-/blue-cone “Off” circuits connecting to “natively-On” UV-cone circuits in the outermost fraction of the inner plexiform layer – much as how key colour opponent circuits are established in mammals. Beyond this, and despite substantial temporal diversity that was not present in the cones, bipolar cell spectral tunings were surprisingly simple. They either approximately resembled both opponent and non-opponent spectral motifs already present in the cones or exhibited a stereotyped non-opponent broadband response. In this way, bipolar cells not only preserved the efficient spectral representations in the cones, but also diversified them to set up a total of six dominant spectral motifs which included three axes of spectral opponency. More generally, our results contribute to an emerging understanding of how retinal circuits for colour vision in ancestral cone-tetrachromats such as zebrafish may be linked to those found in mammals.
Microbial iron(III) reduction during palsa collapse promotes greenhouse gas emissions before complete permafrost thaw
2021-08-10

<title>Abstract</title> Reactive iron (Fe) minerals can preserve organic carbon (OC) in soils overlying intact permafrost. With permafrost thaw, reductive dissolution of iron minerals releases Fe and OC into the porewater, potentially increasing the bioavailability of OC for microbial decomposition. However, the stability of this so-called rusty carbon sink, the microbial community driving mineral dissolution, the identity of the iron-associated carbon and the resulting impact on greenhouse gas emissions are unknown. We examined palsa hillslopes, gradients from intact permafrost-supported palsa to semi-wet partially-thawed bog in a permafrost peatland in Abisko (Sweden). Using high-resolution mass spectrometry, we found that Fe-bound OC in intact palsa is comprised of loosely bound more aliphatic and strongly-bound more aromatic species. Iron mineral dissolution by both fermentative and dissimilatory Fe(III) reduction releases Fe-bound OC along the palsa hillslopes, before complete permafrost thaw. The increasing bioavailability of dissolved OC (DOC) leads to its further decomposition, demonstrated by an increasing nominal oxidation state of carbon (NOSC) and a peak in bioavailable acetate (61.7±42.6 mg C/L) at the collapsing palsa front. The aqueous Fe2+ released is partially re-oxidized by Fe(II)-oxidizing bacteria but cannot prevent the overall loss of the rusty carbon sink with palsa collapse. The increasing relative abundance and activity of Fe(III)-reducers is accompanied by an increasing abundance of methanogens and a peak in methane (CH4) emissions at the collapsing front. Our data suggest that the loss of the rusty carbon sink directly contributes to carbon dioxide (CO2) production by Fe(III) reduction coupled to OC oxidation and indirectly to CH4 emission by promoting methanogenesis even before complete permafrost thaw.
Systemic inflammation induced the delayed reduction of excitatory synapses in the CA3 during ageing
2021-08-11

Abstract Sepsis‐associated encephalopathy (SAE) represents diverse cerebral dysfunctions in response to pathogen‐induced systemic inflammation. Peripheral exposure to lipopolysaccharide (LPS), a component of the gram‐negative bacterial cell wall, has been extensively used to model systemic inflammation. Our previous studies suggested that LPS led to hippocampal neuron death and synaptic destruction in vivo . However, the underlying roles of activated microglia in these neuronal changes remained unclear. Here, LPS from two different bacterial strains ( Salmonella enterica or E . coli ) were compared and injected in 14‐ to 16‐month‐old mice and evaluated for neuroinflammation and neuronal integrity in the hippocampus at 7 or 63 days post‐injection (dpi). LPS injection resulted in persistent neuroinflammation lasting for seven days and a subsequent normalisation by 63 dpi. Of note, increases in proinflammatory cytokines, microglial morphology and microglial mean lysosome volume were more pronounced after E . coli LPS injection than Salmonella LPS at 7 dpi. While inhibitory synaptic puncta density remained normal, excitatory synaptic puncta were locally reduced in the CA3 region of the hippocampus at 63 dpi. Finally, we provide evidence that excitatory synapses coated with complement factor 3 (C3) decreased between 7 dpi and 63 dpi. Although we did not find an increase of synaptic pruning by microglia, it is plausible that microglia recognised and eliminated these C3‐tagged synapses between the two time points of investigation. Since a region‐specific decline of CA3 synapses has previously been reported during normal ageing, we postulate that systemic inflammation may have accelerated or worsened the CA3 synaptic changes in the ageing brain. image
Competing sexual-asexual generic names in Agaricomycotina (Basidiomycota) with recommendations for use
2021-08-11

Abstract With the change to one scientific name for fungal taxa, generic names typified by species with sexual or asexual morph types are being evaluated to determine which names represent the same genus and thus compete for use. In this paper generic names of the Agaricomycotina ( Basidiomycota ) were evaluated to determine synonymy based on their type. Forty-seven sets of sexually and asexually typified names were determined to be congeneric and recommendations are made for which generic name to use. In most cases the principle of priority is followed. However, 16 generic names are recommended for use that do not have priority and thus need to be protected: Aleurocystis over Matula; Armillaria over Acurtis and Rhizomorpha; Asterophora over Ugola; Botryobasidium over Acladium , Allescheriella, Alysidium, Haplotrichum , Physospora, and Sporocephalium; Coprinellus over Ozonium; Coprinopsis over Rhacophyllus; Dendrocollybia over Sclerostilbum and Tilachlidiopsis; Diacanthodes over Bornetina; Echinoporia over Echinodia; Neolentinus over Digitellus; Postia over Ptychogaster; Riopa over Sporotrichum; Scytinostroma over Artocreas, Michenera , and Stereofomes; Tulasnella over Hormomyces; Typhula over Sclerotium; and Wolfiporia over Gemmularia and Pachyma. Nine species names are proposed for protection: Botryobasidium aureum, B. conspersum , B. croceum , B. simile, Pellicularia lembosporum (syn. B. lembosporum ), Phanerochaete chrysosporium , Polyporus metamorphosus (syn. Riopa metamorphosa ), Polyporus mylittae (syn. Laccocephalum mylittae ), and Polyporus ptychogaster (syn . Postia ptychogaster ). Two families are proposed for protection: Psathyrellaceae and Typhulaceae . Three new species names and 30 new combinations are established, and one lectotype is designated.
Why has personality psychology played an outsized role in the credibility revolution?
2021-08-11

Personality is not the most popular subfield of psychology. But, in one way or another, personality psychologists have played an outsized role in the ongoing “credibility revolution” in psychology. Not only have individual personality psychologists taken on visible roles in the movement, but our field’s practices and norms have now become models for other fields to emulate (or, for those who share Baumeister’s (2016, https://doi.org/10.1016/j.jesp.2016.02.003) skeptical view of the consequences of increasing rigor, a model for what to avoid). In this article we discuss some unique features of our field that may have placed us in an ideal position to be leaders in this movement. We do so from a subjective perspective, describing our impressions and opinions about possible explanations for personality psychology’s disproportionate role in the credibility revolution. We also discuss some ways in which personality psychology remains less-than-optimal, and how we can address these flaws.
Perinatal Remains of Livestock: An Under-utilised Line of Evidence for Animal Penning in the Neolithic of Southwest Asia
2021-08-11

Archaeological evidence for penned animals is increasingly used to indicate managed livestock. Advances in techniques allowing the identification of dung and urine-derived components in sediments have enabled the expansion of this line of enquiry. Corralling animals into settlements protected them from predators at night and provided more control over their breeding. Deposits associated with livestock management at Neolithic settlements across Southwest Asia sometimes contain bones of perinatal animals. Reviewing the literature, it is evident that these faunal remains are not systematically reported or preserved in all burial environments. However, their distribution may reflect different patterns of livestock integration into human settlements. The presence of perinatal remains at sites where early livestock herding took place has important implications. Not only are they compelling evidence for herd management, particularly if there is also evidence for penning deposits, but also death of livestock during the perinatal phase of life informs us about the health of animals in early herds. This in turn, provides information about the skills needed by early pastoralists as they developed animal management strategies and the possible effect of transmissible diseases as animals were kept together in closer proximity.
Naïve orangutans (Pongo abelii and Pongo pygmaeus) individually acquire nut‐cracking using hammer tools
2021-08-11

Abstract Nut‐cracking with hammer tools (henceforth: nut‐cracking) has been argued to be one of the most complex tool‐use behaviors observed in nonhuman animals. So far, only chimpanzees, capuchins, and macaques have been observed using tools to crack nuts in the wild (Boesch and Boesch, 1990; Gumert et al., 2009; Mannu and Ottoni, 2009). However, the learning mechanisms behind this behavior, and the extent of nut‐cracking in other primate species are still unknown. The aim of this study was two‐fold. First, we investigated whether another great ape species would develop nut‐cracking when provided with all the tools and appropriate conditions to do so. Second, we examined the mechanisms behind the emergence of nut‐cracking by testing a naïve sample. Orangutans ( Pongo abelii and Pongo pygmaeus ) have the second most extensive tool‐use repertoire among the great apes (after chimpanzees) and show flexible problem‐solving capacities. Orangutans have not been observed cracking nuts in the wild, however, perhaps because their arboreal habits provide limited opportunities for nut‐cracking. Therefore, orangutans are a valid candidate species for the investigation of the development of this behavior. Four nut‐cracking‐naïve orangutans at Leipzig zoo ( P. abelii; M age = 16; age range = 10–19; 4F; at the time of testing) were provided with nuts and hammers but were not demonstrated the nut‐cracking behavioral form. Additionally, we report data from a previously unpublished study by one of the authors (Martina Funk) with eight orangutans housed at Zürich zoo (six P. abelii and two P. pygmaeus; M age = 14; age range = 2–30; 5F; at the time of testing) that followed a similar testing paradigm. Out of the twelve orangutans tested, at least four individuals, one from Leipzig ( P. abelii ) and three from Zürich ( P. abelii and P. pygmaeus ), spontaneously expressed nut‐cracking using wooden hammers. These results demonstrate that nut‐cracking can emerge in orangutans through individual learning and certain types of non‐copying social learning.
AI models and the future of genomic research and medicine: True sons of knowledge?
2021-08-11

Abstract The increasing availability of large‐scale, complex data has made research into how human genomes determine physiology in health and disease, as well as its application to drug development and medicine, an attractive field for artificial intelligence (AI) approaches. Looking at recent developments, we explore how such approaches interconnect and may conflict with needs for and notions of causal knowledge in molecular genetics and genomic medicine. We provide reasons to suggest that—while capable of generating predictive knowledge at unprecedented pace and scale—if and how these approaches will be integrated with prevailing causal concepts will not only determine the future of scientific understanding and self‐conceptions in these fields. But these questions will also be key to develop differentiated policies, such as for education and regulation, in order to harness societal benefits of AI for genomic research and medicine.
Compendium of secondary metabolite biosynthetic diversity encoded in bacterial genomes
2021-08-11

Bacterial specialized metabolites are a proven source of antibiotics and cancer therapies, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~ 170,000 bacterial genomes and ~ 47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We found that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation of secondary metabolite biosynthetic diversity drops significantly at the genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on Relative Evolutionary Distance revealed that Streptomyces bacteria encode the largest biosynthetic diversity by far, with Amycolatopsis, Kutzneria and Micromonospora also encoding substantial diversity. Finally we find that several less-well-studied taxa, such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), Pleurocapsa and Nostocaceae (Cyanobacteria), have potential to produce highly diverse sets of secondary metabolites that warrant further investigation.
Multiple Events and ‘N Preposition N’
2021-08-11

Abstract This chapter discusses structures like ‘Sandy wrote book after book’, in which a central preposition is combined with two identical nouns. The interpretation is a plurality of events, in the example a plurality of writing books. The semantic properties of the construction are discussed. An analysis is offered in terms of event pluralization, with ‘N-Preposition-N’ a pluractional modifier. This is embedded in a general theory of plural predication.
Emotion-modulated recall: Congruency effects of nonverbal facial and vocal cues on semantic recall
2021-08-11

The current study had two main goals: First, to replicate the ‘bimodal integration’ effect (i.e. the automatic integration of crossmodal stimuli, namely facial emotions and emotional prosody); and second, to investigate whether this phenomenon facilitates or impairs the intake and retention of unattended verbal content. The study borrowed from previous bimodal integration designs and included a two-alternative forced-choice (2AFC) task, where subjects were instructed to identify the emotion of a face (as either ‘angry’ or ‘happy’) while ignoring a concurrently presented sentence (spoken in an angry, happy, or neutral prosody), after which a surprise recall was administered to investigate effects on semantic content retention. While bimodal integration effects were replicated (i.e. faster and more accurate emotion identification under congruent conditions), congruency effects were not found for semantic recall. Overall, semantic recall was better for trials with emotional (vs. neutral) faces, and worse in trials with happy (vs. angry or neutral) prosody. Taken together, our findings suggest that when individuals focus their attention on evaluation of facial expressions, they implicitly integrate nonverbal emotional vocal cues (i.e. hedonic valence or emotional tone of accompanying sentences), and devote less attention to their semantic content. While the impairing effect of happy prosody on recall may indicate an emotional interference effect, more research is required to uncover potential prosody-specific effects. All supplemental online materials can be found on OSF (https://osf.io/am9p2/).