julilili42/papers huggingface dataset:
Nest sites, breeding cycle and possible cleptoparasites of Monoeca catarina Aguiar (Hymenoptera, Apidae, Tapinotaspidini) from Santa Catarina Island, southern Brazil
2019-10-24

The recently described solitary bee Monoeca catarina Aguiar (Apidae, Tapinotaspidini) is only known from two nest aggregations on Santa Catarina Island, state of Santa Catarina, southern Brazil. Nests are excavated in sandy soils along trails near dunes and beaches. Up to 287 nests were counted in one aggregation. Bees were active for about seven weeks from late November to mid-January suggesting a univoltine life cycle. Males perform patrolling flights over the nest area and mate with females sitting on low vegetation. Males and females visited Stachytarpheta cayennensis (Verbenaceae) for nectar, and females were observed foraging on Tetrapterys sp. or Heteropterys sp. flowers (Malpighiaceae). Pollen loads consisted almost exclusively of Malpighiaceae pollen. Potential natural enemies are the cleptoparasitic bee Protosiris Roig-Alsina sp. (Apidae, Osirini) recorded within the aggregations, and the mutillid wasp Hoplocrates specularis (Gerstaecker) (Mutillidae, Sphaeropthalmini) seen entering the Monoeca nests and mating within the aggregations. Except for the soil characteristics, our observations on nesting and foraging behavior and associated potential enemies fit well into the facts reported from other Monoeca species.
The BIR2/BIR3-interacting Phospholipase D gamma 1 negatively regulates immunity in Arabidopsis
2019-10-24

ABSTRACT Plants have evolved effective strategies to defend themselves against pathogen invasion. Starting from the plasma membrane with the recognition of microbe-associated molecular patterns (MAMPs) via pattern recognition receptors, internal cellular signaling pathways are induced to ultimately fend off the attack. Phospholipase D (PLD) hydrolyzes membrane phospholipids to produce phosphatidic acid (PA), which has been proposed to play a second messenger role in immunity. The Arabidopsis PLD family consists of 12 members and for some a specific function in resistance towards a subset of pathogens has been shown. We demonstrate here that Arabidopsis PLDγ1, but not its close homologs PLDγ2 and PLDγ3, is specifically involved in plant immunity. Genetic inactivation of PLDγ1 resulted in increased resistance towards the virulent bacterium Pseudomonas syringae pv. tomato DC3000 and the necrotrophic fungus Botrytis cinerea . As pldγ1 mutant plants responded with elevated levels of reactive oxygen species to MAMP-treatment, a negative regulatory function for this PLD isoform is proposed. Importantly, PA levels in pldγ1 mutants were not affected compared to stressed wild-type plants, suggesting that alterations in PA levels are unlikely the cause for the enhanced immunity in the pldγ1 line. Instead, the plasma-membrane-attached PLDγ1 protein colocalized and associated with the receptor-like kinases BIR2 and BIR3, which are known negative regulators of pattern-triggered immunity. Moreover, complex formation of PLDγ1 and BIR2 was further promoted upon MAMP-treatment. Hence, we propose that PLDγ1 acts as a negative regulator of plant immune responses in complex with immunity-related proteins BIR2 and BIR3. One-sentence summary A phospholipase D is a novel negative regulator of plant immunity and forms complexes with regulatory receptor-like kinases.
Multi-proxy analyses of a mid-15th century ‘Middle Iron Age’ Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome
2019-10-24

ABSTRACT The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. Our results indicate that the distal IM of the Neolithic ‘Middle Iron Age’ ( c. AD 1485) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians, reveals that this IM precedes recent adaptation to ‘Western’ diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c . 12,000 years ago.
Commentary: Selective Intensive Care Unit Admission After Adult Supratentorial Tumor Craniotomy: Complications, Length of Stay, and Costs
2019-10-24

Department of Neurosurgery, University Hospital Tuebingen, Eberhard-Karls-University, Tuebingen, Germany Center for CNS Tumors, Comprehensive Cancer Center Tuebingen Stuttgart, University Hospital Tuebingen, Eberhard-Karls University Tuebingen, Tuebingen, Germany Correspondence: Felix Behling, MD, Department of Neurosurgery, University Hospital Tuebingen, Eberhard-Karls-University, Hoppe-Seyler Street 3, Tuebingen, Germany. Email: [email protected]
Theory of Mind, emotion recognition, delusions and the quality of the therapeutic relationship in patients with psychosis – a secondary analysis of a randomized-controlled therapy trial.
2019-10-24

<title>Abstract</title> Background: Cognitive models of psychosis postulate an important role of Theory of mind (ToM) in the formation and maintenance of delusions, but research on this plausible conjecture has gathered conflicting findings. In addition, it is still an open question whether problems in emotion recognition (ER) - an important precondition to ToM - are associated with delusions. We examined the association of problems in ToM and ER with different aspects of delusions in a large sample of patients with psychosis enrolled in a therapy trial. This also enabled us to explore the possible impact of ToM and ER on one part of patients’ social life: the quality of their therapeutic relationship.Methods: Patients with psychotic disorders and delusions and/or hallucinations (n=185) and healthy controls (n=48) completed a ToM picture sequencing task and an ER task. Subsequently, patients were enrolled in a randomized-controlled Cognitive Behavior Therapy (CBT) trial (ISRCTN29242879). Patients and therapists rated the quality of the therapeutic relationship during the first five sessions of therapy.Results: In comparison to controls, patients were impaired in both ToM and ER. Patients with deficits in ER experienced more severe delusional distress, whereas ToM problems were not related to delusions. In addition, deficits in ER predicted a less favorable therapeutic relationship and interactional problems viewed by the therapist. Impaired ER also moderated (increased) the negative influence of delusions on the therapeutic relationship and interactional difficulties viewed by the therapist. Conclusions: Cognitive models on the formation and maintenance of delusions should consider ER as a potential candidate that might be related to the formation and maintenance of delusional distress, whereas problems in ToM might not be directly related to delusions and secondary dimensions of delusions. In addition, problems in ER in patients with psychosis might have an impact on the quality of the therapeutic relationship and patients with problems in ER are more likely to be viewed as problematic by their therapists. Nevertheless, training ER might be a way to improve the quality of the therapeutic relationship and potentially the effectiveness of CBT or other interventions for patients with psychosis.
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
2019-10-25

Abstract The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detail new content and features in the repository, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites. We describe the addition of 31 new models that expand the portion of the phylogenetic tree covered by BiGG Models. We also describe new functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. Finally, the models in the knowledge base have been benchmarked using Memote, a new community-developed validator for genome-scale models to demonstrate the improving quality and transparency of model content in BiGG Models.
Chikungunya
2019-10-25

Chikungunya, a zoonotic disease caused by the Chikungunya virus (CHIKV), is transmitted by infected Aedes spp mosquitoes. CHIKV has now spread to more than 100 countries and is listed on the WHO Blueprint priority pathogens. After an incubation period of 1 to 12 days, symptoms similar to other febrile infections appear, with a sudden onset of high fever, nausea, polyarthralgia, myalgia, widespread skin rash, and conjunctivitis. Serious complications include myocarditis, uveitis, retinitis, hepatitis, acute renal disease, severe bullous lesions, meningoencephalitis, Guillain-Barré syndrome, myelitis, and cranial nerve palsies. Treatment is supportive; there is no specific antiviral treatment and no effective vaccine.
The impact of planet wakes on the location and shape of the water ice line in a protoplanetary disk
2019-10-25

Context. Planets in accretion disks can excite spiral shocks and if these planets are massive enough, they can even open gaps in their vicinity. Both of these effects can influence the overall thermal structure of the disk. Aims. We model planets of different masses and semimajor axes in disks of various viscosities and accretion rates to examine their impact on disk thermodynamics and to highlight the mutable, non-axisymmetric nature of ice lines in systems with massive planets. Methods. We conducted a parameter study using numerical hydrodynamics simulations where we treated viscous heating, thermal cooling, and stellar irradiation as additional source terms in the energy equation, with some runs including radiative diffusion. Our parameter space consists of a grid containing different combinations of planet and disk parameters. Results. Both gap opening and shock heating can displace the ice line, with the effects amplified for massive planets in optically thick disks. The gap region can split an initially hot ( T &gt; 170 K) disk into a hot inner disk and a hot ring just outside of the planet’s location, while shock heating can reshape the originally axisymmetric ice line into water-poor islands along spirals. We also find that radiative diffusion does not alter the picture significantly in this context. Conclusions. Shock heating and gap opening by a planet can effectively heat up optically thick disks and, in general, they can move or reshape the water ice line. This can affect the gap structure and migration torques. It can also produce azimuthal features that follow the trajectory of spiral arms, creating hot zones which lead to “islands” of vapor and ice around spirals that could affect the accretion or growth of icy aggregates.
Spectral Lines of Quantized, Spinning Black Holes and their Astrophysical Relevance
2019-10-25

In this Letter, we study black hole area quantization in the context of gravitational wave physics. It was recently argued that black hole area quantization could be a mechanism to produce so-called echoes as well as characteristic absorption lines in gravitational wave observations of merging black holes. One can match the spontaneous decay of these quantum black holes to Hawking radiation calculations. Using some assumptions, one can then estimate the natural widths of these states. As can be seen from a classical paper by Bekenstein and Mukhanov, the ratio between width and spacing of nonspinning black hole states approaches a small constant, which seems to confirm the claim. However, we find that, including the effect of black hole spin, the natural widths increase. To properly address any claim about astrophysical black holes, one should examine the spinning case, as real black holes spin. Thus, the word spinning is key to the question of whether or not black holes should have an observable spectrum in nature. Our results suggest that it should be possible to distinguish between any scenarios for which the answer to this question is yes. However, for all of the commonly discussed scenarios, our answer is almost certainly no.
Following Protein Dynamics in Real Time during Crystallization
2019-10-25

The process of protein crystallization from aqueous protein solutions is still insufficiently understood. During macroscopic crystal formation, occurring often on time scales from a few hours to several days, protein dynamics evolves on the molecular level. Here, we present a proof of concept and a framework to observe this evolving diffusive dynamics on the pico- to nanosecond time scale, associated with cluster or precursor formation that ultimately results in emerging crystals. We investigated the model system of the protein β-lactoglobulin in D2O in the presence of ZnCl2, which induces crystallization by electrostatic bridges. First, the structural changes occurring during crystallization were followed by small-angle neutron scattering. Furthermore, we employed neutron backscattering and spin-echo spectroscopy to measure the ensemble-averaged self- and collective diffusion on nanosecond time scales of protein solutions with a kinetic time resolution on the order of 15 min. The experiments provide information on the increasing number fraction of immobilized proteins as well as on the diffusive motion of unbound proteins in an increasingly depleted phase. Simultaneously, information on the internal dynamics of the proteins is obtained.
Homogeneous Nickel‐Catalyzed Hydrogenations
2019-10-25

Homogeneous nickel-catalyzed hydrogenation constitutes an emerging field. Several efficient catalysts, which include defined complexes and in situ precursor/ligand systems, were introduced for the reduction of alkenes, alkynes, and carbonyl groups.
Reflection spectra of thick accretion discs
2019-10-26

ABSTRACT Relativistic reflection features are commonly observed in the X-ray spectra of stellar-mass and supermassive black holes and originate from illumination of the inner part of the accretion disc by a hot corona. All the available relativistic reflection models assume that the disc is infinitesimally thin and the inner edge is at the innermost stable circular orbit or at a larger radius. However, we know that several sources, especially among supermassive black holes, have quite high-mass accretion rates. In such a case, the accretion disc becomes geometrically thick and the inner edge of the disc is expected to be inside the innermost stable circular orbit. In this work, we employ the Polish donut model to describe geometrically thick discs and we study the iron-line shapes from similar systems. We also simulate full reflection spectra and we analyse the simulated observations with a thin disc relativistic reflection model to determine the impact of the disc structure on the estimation of the model parameters, in particular in the case of tests of the Kerr hypothesis.
Experimental infections in humans—historical and ethical reflections
2019-10-26

Abstract Vaccine efficacy and prophylactic treatment of infections are tested best when the vaccinated or treated individual is challenged through deliberate infection with the respective pathogen. However, this trial design calls for particular ethical caution. Awareness of the history of challenge trials is indispensable, including trials that were problematic or even connected to abuse. We briefly introduce historical aspects of experimental infections in humans and the ethical debate around them and give estimates of the numbers of volunteers participating in human experimental infection models. Challenge models can offer a great chance and benefit for the development of medical interventions to fight infectious diseases, but only when they are appropriately controlled and regulated.
Relation between gamma oscillations and neuronal plasticity in the visual cortex
2019-10-28

Significance Learning is thought to be mediated by activity-dependent modification of neuronal interactions. To avoid maladaptive modifications of synaptic transmission by spurious activity, synaptic plasticity has to be gated. In the case of supervised learning, these gating functions are accomplished by reinforcement through value-assigning systems. Here we show that the dynamic state of local circuits correlates with the occurrence of activity-dependent long-term changes in neuronal response properties. We find that repeated visual stimuli induce long-term changes of orientation preference of neuronal populations in visual cortex if stimuli induce synchronized population responses oscillating at ɣ-frequencies. This suggests that neuronal plasticity is controlled by a hierarchy of gating systems and assigns critical gating functions to resonance properties of local circuits.
Development of an AAV-Based MicroRNA Gene Therapy to Treat Machado-Joseph Disease
2019-10-28

Spinocerebellar ataxia type 3 (SCA3), or Machado-Joseph disease (MJD), is a progressive neurodegenerative disorder caused by a CAG expansion in the <i>ATXN3</i> gene. The expanded CAG repeat is translated into a prolonged polyglutamine repeat in the ataxin-3 protein and accumulates within inclusions, acquiring toxic properties, which results in degeneration of the cerebellum and brain stem. In the current study, a non-allele-specific <i>ATXN3</i> silencing approach was investigated using artificial microRNAs engineered to target various regions of the <i>ATXN3</i> gene (miATXN3). The mi<i>ATXN3</i> candidates were screened <i>in vitro</i> based on their silencing efficacy on a luciferase (Luc) reporter co-expressing <i>ATXN3</i>. The three best miATXN3 candidates were further tested for target engagement and potential off-target activity in induced pluripotent stem cells (iPSCs) differentiated into frontal brain-like neurons and in a SCA3 knockin mouse model. Besides a strong reduction of <i>ATXN3</i> mRNA and protein, small RNA sequencing revealed efficient guide strand processing without passenger strands being produced. We used different methods to predict alteration of off-target genes upon AAV5-mi<i>ATXN3</i> treatment and found no evidence for unwanted effects. Furthermore, we demonstrated in a large animal model, the minipig, that intrathecal delivery of AAV5 can transduce the main areas affected in SCA3 patients. These results proved a strong basis to move forward to investigate distribution, efficacy, and safety of AAV5-mi<i>ATXN3</i> in large animals.
Advanced cutaneous squamous cell carcinoma: real world data of patient profiles and treatment patterns
2019-10-28

Abstract Background Cutaneous squamous cell carcinoma ( cSCC ) is one of the most common types of cancer in the Caucasian population, with an increasing incidence. cSCC is mostly a local invasive disease that can be treated surgically in the majority of the cases. However, in the case of advanced cSCC (ac SCC ), a multimodality approach also involving systemic therapies needs to be considered. Methods One hundred and ninety‐five patients diagnosed with ac SCC (stages III and IV ) treated in our centre between 2011 and 2018 were included. Patient and tumour characteristics along with treatment patterns were documented and analyzed. Descriptive analysis was performed and survival rates were estimated according to Kaplan‐Meier and compared with the Log‐rank test. Follow‐up was defined as the time between diagnosis of advanced disease and last contact or death. All causes of death were considered as events. Results The median follow‐up was 21 months [ IQR = (10.0; 21.0)]. The median age at time of advanced disease diagnosis was 78 years [ IQR = (72; 84)], with 40.5% of the patients in stage III and 59.5% in stage IV . One hundred and forty‐five patients had resectable tumours. In this group the median overall survival ( mOS ) was 59 months (95% CI : 28.2–89.8), significantly higher than the mOS in patients with inoperable tumour [ n = 50; mOS: 19 months (96% CI : 7–31, P &lt;0.0001)]. Patients receiving immunotherapy ( n = 20) showed a statistically significant better survival compared to those treated with other systemic therapies ( n = 37; mOS not reached vs. mOS : 22 months (95% CI : 6.5–43.5), P = 0.034). For patients without systemic therapy, a combination of surgery and radiotherapy provided better outcomes compared to radiotherapy alone or best supportive care ( P &lt;0.001). Conclusion Surgical complete resection should be the first therapeutic option for patients with ac SCC . For patients with inoperable tumour, first‐line immunotherapy should be preferably considered.
Clinical Characteristics of Inpatients with Childhood vs. Adolescent Anorexia Nervosa
2019-10-28

We aimed to compare the clinical data at first presentation to inpatient treatment of children (&lt;14 years) vs. adolescents (≥14 years) with anorexia nervosa (AN), focusing on duration of illness before hospital admission and body mass index (BMI) at admission and discharge, proven predictors of the outcomes of adolescent AN. Clinical data at first admission and at discharge in 289 inpatients with AN (children: n = 72; adolescents: n = 217) from a German multicenter, web-based registry for consecutively enrolled patients with childhood and adolescent AN were analyzed. Inclusion criteria were a maximum age of 18 years, first inpatient treatment due to AN, and a BMI &lt;10th BMI percentile at admission. Compared to adolescents, children with AN had a shorter duration of illness before admission (median: 6.0 months vs. 8.0 months, p = 0.004) and higher BMI percentiles at admission (median: 0.7 vs. 0.2, p = 0.004) as well as at discharge (median: 19.3 vs. 15.1, p = 0.011). Thus, in our study, children with AN exhibited clinical characteristics that have been associated with better outcomes, including higher admission and discharge BMI percentile. Future studies should examine whether these factors are actually associated with positive long-term outcomes in children.
Isoindoline‐Based Nitroxides as Bioresistant Spin Labels for Protein Labeling through Cysteines and Alkyne‐Bearing Noncanonical Amino Acids
2019-10-28

Abstract Electron paramagnetic resonance (EPR) spectroscopy in combination with site‐directed spin labeling (SDSL) is a powerful tool in protein structural research. Nitroxides are highly suitable spin labeling reagents, but suffer from limited stability, particularly in the cellular environment. Herein we present the synthesis of a maleimide‐ and an azide‐modified tetraethyl‐shielded isoindoline‐based nitroxide (M‐ and Az‐TEIO) for labeling of cysteines or the noncanonical amino acid para ‐ethynyl‐ l ‐phenylalanine ( p ENF). We demonstrate the high stability of TEIO site‐specifically attached to the protein thioredoxin (TRX) against reduction in prokaryotic and eukaryotic environments, and conduct double electron–electron resonance (DEER) measurements. We further generate a rotamer library for the new residue p ENF‐Az‐TEIO that affords a distance distribution that is in agreement with the measured distribution.