julilili42/papers huggingface dataset:
Geminivirus C5 proteins mediate formation of virus complexes at plasmodesmata for viral intercellular movement
2023-06-12

Abstract Movement proteins (MPs) encoded by plant viruses deliver viral genomes to plasmodesmata (PD) to ensure intracellular and intercellular transport. However, how the MPs encoded by monopartite geminiviruses are targeted to PD is obscure. Here, we demonstrate that the C5 protein of tomato yellow leaf curl virus (TYLCV) anchors to PD during the viral infection following trafficking from the nucleus along microfilaments in Nicotiana benthamiana. C5 could move between cells and partially complement the traffic of a movement-deficient turnip mosaic virus (TuMV) mutant (TuMV-GFP-P3N-PIPO-m1) into adjacent cells. The TYLCV-C5 null mutant (TYLCV-mC5) attenuates viral pathogenicity and decreases viral DNA and protein accumulation, and ectopic overexpression of C5 enhances viral DNA accumulation. Interaction assays between TYLCV-C5 and the other eight viral proteins described in TYLCV reveal that C5 associates with C2 in the nucleus and with V2 in the cytoplasm and at PD. The V2 protein is mainly localized in the nucleus and cytoplasmic granules when expressed alone; in contrast, V2 forms small punctate granules at PD when co-expressed with C5 or in TYLCV-infected cells. The interaction of V2 and C5 also facilitates their nuclear export. Furthermore, C5-mediated PD localization of V2 is conserved in two other geminiviruses. Therefore, this study solves a long-sought-after functional connection between PD and the geminivirus movement and improves our understanding of geminivirus-encoded MPs and their potential cellular and molecular mechanisms.
Mid-Proterozoic day length stalled by tidal resonance
2023-06-12

Abstract We present statistical analysis of a compilation of observational constraints on the Precambrian length of day and find that the day length stalled at about 19 h for about 1 billion years during the mid-Proterozoic. We suggest that the accelerative torque of atmospheric thermal tides from solar energy balanced the decelerative torque of lunar oceanic tides, temporarily stabilizing Earth’s rotation. This stalling coincides with a period of relatively limited biological evolution known as the boring billion.
Early or late initiation of dabigatran versus vitamin-K-antagonists in acute ischemic stroke or TIA: The PRODAST study
2023-06-12

Background: The optimal timing of initiating or resuming anticoagulation after acute ischemic stroke (AIS) or transient ischemic attack (TIA) in patients with atrial fibrillation (AF) is debated. Dabigatran, a non-vitamin K oral anticoagulant (NOAC), has shown superiority against vitamin K antagonists (VKA) regarding hemorrhagic complications. Aims: In this registry study, we investigated the initiation of dabigatran in the early phase after AIS or TIA. Methods: PRODAST (Prospective Record of the Use of Dabigatran in Patients with Acute Stroke or TIA) is a prospective, multicenter, observational, post-authorization safety study. We recruited 10,039 patients at 86 German stroke units between July 2015 and November 2020. A total of 3,312 patients were treated with dabigatran or VKA and were eligible for the analysis that investigates risks for major hemorrhagic events within 3 months after early (⩽ 7 days) or late (&gt; 7 days) initiation of dabigatran or VKA initiated at any time. Further endpoints were recurrent stroke, ischemic stroke, TIA, systemic embolism, myocardial infarction, death, and a composite endpoint of stroke, systemic embolism, life-threatening bleeding and death. Results: Major bleeding event rates per 10,000 treatment days ranged from 1.9 for late administered dabigatran to 4.9 for VKA. Early or late initiation of dabigatran was associated with a lower hazard for major hemorrhages as compared to VKA use. The difference was pronounced for intracranial hemorrhages with an adjusted hazard ratio (HR) of 0.47 (95% confidence interval (CI): 0.10–2.21) for early dabigatran use versus VKA use and an adjusted HR of 0.09 (95% CI: 0.00–13.11) for late dabigatran use versus VKA use. No differences were found between early initiation of dabigatran versus VKA use regarding ischemic endpoints. Conclusions: The early application of dabigatran appears to be safer than VKA administered at any time point with regards to the risk of hemorrhagic complications and in particular for intracranial hemorrhage. This result, however, must be interpreted with caution in view of the low precision of the estimate.
Immunogenicity of COVID‐19 vaccines in adult patients with autoimmune inflammatory rheumatic diseases: A systematic review and meta‐analysis
2023-06-12

Abstract COVID‐19 vaccines approved by the Food and Drug Administration have been studied mainly in healthy individuals and there is limited information on their immunogenicity in patients with autoimmune diseases. Therefore, the current systematic review and meta‐analysis study, aimed to comprehensively investigate the immunogenicity of these vaccines in patients with autoimmune inflammatory rheumatoid diseases (AIRDs). A comprehensive literature search was performed on various databases, including Google Scholar, PubMed, Web of Science, EMBASE, and Cochrane Library, to select cohort and randomized clinical trial (RCT) studies up to January 2022. Also, the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses checklist protocol and the I 2 statistic were used for quality assessment and heterogeneity tests of the selected studies. Fixed and random‐effects models were estimated based on the heterogeneity tests, and pooled data were determined as the ratio of mean (ROM) with a 95% confidence interval (CI). As a result, we found that vaccines can cause favorable immunogenicity and antibody response in vaccinated AIRD patients; however, older age and the concomitant consumption of conventional synthetic disease‐modifying anti‐rheumatic drugs (csDMARDs) and biologic DMARDs (bDMARDs) could significantly reduce the vaccine immunogenicity. Consequently, our findings revealed significant humoral responses (seropositive) in AIRD patients following the administration of COVID‐19 vaccines.
Carotid geometry is independently associated with complicated carotid artery plaques
2023-06-12

Introduction Complicated carotid artery plaques (cCAPs) are associated with an increased risk of rupture and subsequent stroke. The geometry of the carotid bifurcation determines the distribution of local hemodynamics and could thus contribute to the development and composition of these plaques. Therefore, we studied the role of carotid bifurcation geometry in the presence of cCAPs. Methods We investigated the association of individual vessel geometry with carotid artery plaque types in the Carotid Plaque Imaging in Acute Stroke (CAPIAS) study. After excluding arteries without plaque or with insufficient MRI quality, 354 carotid arteries from 182 patients were analyzed. Individual parameters of carotid geometry [i.e., internal carotid artery (ICA)/common carotid artery (CCA) ratio, bifurcation angle, and tortuosity) were derived from time-of-flight MR images. The lesion types of carotid artery plaques were determined according to the American Heart Association classification of lesions by multi-contrast 3T-MRI. The association between carotid geometry and a cCAP was studied using logistic regression after adjusting for age, sex, wall area, and cardiovascular risk factors. Results Low ICA/CCA ratios (OR per SD increase 0.60 [95%CI: 0.42–0.85]; p = 0.004) and low bifurcation angles (OR 0.61 [95%CI: 0.42–0.90]; p = 0.012) were significantly associated with the presence of cCAPs after adjusting for age, sex, cardiovascular risk factors, and wall area. Tortuosity had no significant association with cCAPs. Only ICA/CCA ratio remained significant in a model containing all three geometric parameters (OR per SD increase 0.65 [95%CI: 0.45–0.94]; p = 0.023). Conclusions A steep tapering of the ICA relative to the CCA and, to a lesser extent, a low angle of the carotid bifurcation were associated with the presence of cCAPs. Our findings highlight the contribution of bifurcation geometry to plaque vulnerability. Thus, assessment of carotid geometry could be helpful in identifying patients at risk of cCAPs.
Robustness Implies Fairness in Causal Algorithmic Recourse
2023-06-12

Algorithmic recourse discloses the internal procedures of a black-box decision process where decisions have significant consequences by providing recommendations to empower beneficiaries to achieve a more favorable outcome. To ensure an effective remedy, suggested interventions must not only be cost-effective but also robust and fair. To that end, it is essential to provide similar explanations to similar individuals. This study explores the concept of individual fairness and adversarial robustness in causal algorithmic recourse and addresses the challenge of achieving both. To resolve the challenges, we propose a new framework for defining adversarially robust recourse. That setting observes the protected feature as a pseudometric and demonstrates that individual fairness is a special case of adversarial robustness. Finally, we introduce the fair robust recourse problem and establish solutions to achieve both desirable properties both theoretically and empirically.
On the Richness of Calibration
2023-06-12

Probabilistic predictions can be evaluated through comparisons with observed label frequencies, that is, through the lens of calibration. Recent scholarship on algorithmic fairness has started to look at a growing variety of calibration-based objectives under the name of multi-calibration but has still remained fairly restricted. In this paper, we explore and analyse forms of evaluation through calibration by making explicit the choices involved in designing calibration scores. We organise these into three grouping choices and a choice concerning the agglomeration of group errors. This provides a framework for comparing previously proposed calibration scores and helps to formulate novel ones with desirable mathematical properties. In particular, we explore the possibility of grouping datapoints based on their input features rather than on predictions and formally demonstrate advantages of such approaches. We also characterise the space of suitable agglomeration functions for group errors, generalising previously proposed calibration scores. Complementary to such population-level scores, we explore calibration scores at the individual level and analyse their relationship to choices of grouping. We draw on these insights to introduce and axiomatise fairness deviation measures for population-level scores. We demonstrate that with appropriate choices of grouping, these novel global fairness scores can provide notions of (sub-)group or individual fairness.
Does a white bear help you eat less? The impact of the inhibitory spillover effect on eating behaviour
2023-06-12

Abstract Objective Overweight and obesity are global problems with negative physical, social, and psychological outcomes. Besides other factors, inhibitory control deficits contribute to weight gain and development of overweight. The inhibitory spillover effect (ISE) improves inhibitory control through transfer of inhibitory control capacity from one domain to an unrelated, second domain. For ISE to occur, one inhibitory control task is executed simultaneously with a second, non‐control related task thereby increasing inhibitory control in this task. Method In this preregistered study, we tested the ISE induced through thought suppression in contrast to a neutral task in participants with normal weight and overweight ( N = 92). A simultaneously conducted bogus taste test served as outcome measure for food intake. Results We found neither an interaction effect between group affiliation and condition nor an effect of group affiliation. However, contrary to our expectations, we found higher food intake in participants with active ISE compared to the neutral task. Conclusions This result might indicate rebound effects of applied thought suppression which led to the experience of loss of control and therefore undermined maintenance and function of the ISE. This main result was robust to all moderator variables. We elaborate further factors for the finding, theoretical implications, and future research directions.
Insulin Secretion Capacity as a Crucial Feature to Distinguish Type 1 From Type 2 Diabetes and to Indicate the Need for Insulin Therapy – A Critical Discussion of the ADA/EASD Consensus Statement on the Management of Type 1 Diabetes in Adults
2023-06-12

Abstract In the recently published consensus statement on the treatment and management of type 1 diabetes issued by experts from the American (ADA) and European (EASD) diabetes societies, measurement of endogenous insulin secretion using fasting C-peptide is recommended as a diagnostic criterion. In contrast, our group recently suggested fasting C-peptide/glucose ratio (CGR) for the determination of endogenous insulin secretion. In addition, this ratio may turn out as a potential decision aid for pathophysiologically based differential therapy of diabetes. In this comment, the following points will be discussed: i) CGR as the basis of differential diagnosis of type 1 diabetes, ii) CGR as the basis of treatment decisions for or against insulin in diabetes, and iii) the ease of application of CGR in clinical practice. The use of CGR may complement the ADA/EASD recommendations and should provide a practical application in clinical practice.
Do local expenditures on sports facilities affect sports participation?
2023-06-12

Abstract This paper contributes to the literature evaluating the performance of local governments by analyzing the effect of local public expenditures on sports facilities on sports participation in Germany. To this end, we use a new data base containing public expenditures at the municipality level and link this information with individual level data. We form locally weighted averages of expenditures based on geographic distances and analyze how effects of sports facility expenditures change with different expenditures levels (“dose‐response relationship”). We find no effect of sports facility expenditures on individual sports participation. These findings are robust across age groups and municipality sizes.
The fungal pathogenUstilago maydistargets the maize corepressor TPL2 to modulate host transcription for tumorigenesis
2023-06-12

Summary Ustilago maydis is a biotrophic fungus that causes tumor formation on all aerial parts of maize. U. maydis secretes effector proteins during penetration and colonization to successfully overcome the plant immune response and reprogram host physiology to promote infection. In this study, we functionally characterized the U. maydis effector protein Topless (TPL) interacting protein 6 (Tip6). We found that Tip6 interacts with the N-terminus of ZmTPL2 through its two EAR (Ethylene-responsive element binding factor-associated amphiphilic repression) motifs. We show that the EAR motifs are essential for the virulence function of Tip6 and critical for altering the nuclear distribution pattern of ZmTPL2. We propose that Tip6 mimics the recruitment of ZmTPL2 by plant repressor proteins, thus disrupting host transcriptional regulation. We show that a large group of AP2/ERF B1 subfamily transcription factors are misregulated in the presence of Tip6. Our study suggests a regulatory mechanism where the U. maydis effector Tip6 utilizes repressive domains to recruit the corepressor ZmTPL2 to disrupt the transcriptional networks of the host plant.
Network analysis of scientific advisory committee integration in climate change policy: A comparison of Germany and Japan
2023-06-12

According to the literature on Environmental Policy Integration (EPI), decisionmaking in complex domains of environmental policy—of which climate change is a prime example—tend to fragment and silo into individual dimensions of a problem. Scientific Advisory Committees (SACs) have been widely used to promote more integrated decisionmaking. SACs are intended to integrate the varied, and often fragmented, dimensions of policy problems, and this integration is widely believed to enable more effective use of science in climate change policy. This paper empirically evaluates the degree of integration achieved through SACs in two national climate policy contexts: Germany and Japan. Network analysis is used to examine the myriad scientific advisory committees focused on climate change policy in these nations (N = 218), and quantify the degree of vertical integration (integration among different sectors) and horizontal integration (integration among different governmental bodies). Results show greater vertical integration among German SACs than Japanese SACs, and similar levels of horizontal integration between the two nations despite having very different structures. Such efforts to empirically connect the conceptual discussion of integration in EPI with empirical observations of integration in actual climate policy processes is an important step towards understanding the strategies that may be used to promote more integrated decisionmaking in climate change policy.
Monitoring accuracy suffers when working memory demands increase: Evidence of a dependent relationship.
2023-06-12

Knowing what one knows and accurately monitoring one's own capacities and performance on a moment-to-moment basis are important determinants of task success. Individual differences in such metacognitive monitoring are well documented, but what determines an individual's monitoring accuracy in a particular context is yet to be fully understood. One candidate contributor to monitoring accuracy is working memory. In this study, we investigated whether and how working memory contributes to the accuracy of monitoring processes. Most evidence for a positive relationship between working memory and monitoring accuracy has been provided by correlational studies. Here, an experimental approach was applied in which confidence judgments were collected after each memory recall in three working memory experiments, and the effect of increasing the working memory demands on monitoring accuracy was examined. A visuospatial complex span task, a verbal complex span task, and an updating task served as the working memory tasks, to cover the range of methods used in working memory research. Confirmatory analyses conducted using cumulative link mixed models indicated that in two out of three experiments, monitoring accuracy suffered when working memory demands increased. As such, the weight of evidence supports a dependent relationship between working memory and monitoring processes, whereby monitoring accuracy can fluctuate during a task depending on the available cognitive resources. This indicates that the sensitivity of metacognitive monitoring is at least partly determined by the nature of the cognitive processing taking place in the primary task. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
Ceramic traditions and technological choices revealed by early Iron Age vessels: the case of Vetulonia (southern Tuscany)
2023-06-12

Early Iron Age pottery from central Italian regions has so far largely been studied with a particular emphasis on typological and stylistical features. However, an analytical approach to ancient ceramic technology can reveal a wealth of data on the know-how of early Iron Age central Italian craftspeople and their production choices. With this aim we conducted archaeometric analyses of forty vessels from one of the main protohistoric cemeteries of Vetulonia, coupled with geological surveys of the territory around the settlement and the collection of raw materials. The occurrence of a ceramic fabric marked by fragments of metasedimentary rocks, as opposed to a fabric tempered with flint fragments, indicates the existence of separate traditions, characterised by distinct processes and the addition of specific tempers, probably reflecting different technological practices. The significance of our findings is briefly discussed within the historical and social scenario of early Iron Age Vetulonia, at the dawn of urbanisation.
Engineering of human myotubes toward a mature metabolic and contractile phenotype
2023-06-12

1. Abstract Skeletal muscle mediates the beneficial effects of exercise, thereby improving insulin sensitivity and reducing the risk for type 2 diabetes. Current human skeletal muscle models in vitro are incapable of fully recapitulating its physiological functions especially muscle contractility. By supplementation of insulin-like growth factor 1 (IGF1), a growth factor secreted by myofibers in vivo, we aimed to overcome these limitations. We monitored the differentiation process starting from primary human CD56-positive myoblasts in the presence/absence of IGF1 in serum-free medium in daily collected samples for 10 days. IGF1-supported differentiation formed thicker multinucleated myotubes showing physiological contraction upon electrical pulse stimulation following day 6. Myotubes without IGF1 were almost incapable of contraction. IGF1-treatment shifted the proteome toward skeletal muscle-specific proteins that contribute to myofibril and sarcomere assembly, striated muscle contraction, and ATP production. Elevated PPARGC1A , MYH7 and reduced MYH1/2 suggest a more oxidative phenotype further demonstrated by higher abundance of proteins of the respiratory chain and elevated mitochondrial respiration. IGF1-treatment also upregulated GLUT4 and increased insulin-dependent glucose uptake compared to myotubes differentiated without IGF1. To conclude, utilizing IGF1, we engineered human myotubes that recapitulate the physiological traits of skeletal muscle in vivo superior to established protocols and overcome limitations of previous standards. This novel “easy to use” model enables investigation of exercise on a molecular level. Abstract Figure
Mutual interplay between cognitive offloading and secondary task performance
2023-06-13

Abstract Various modern tools, such as smartphones, allow for cognitive offloading (i.e., the externalization of cognitive processes). In this study, we examined the use and consequences of cognitive offloading in demanding situations in which people perform multiple tasks concurrently—mimicking the requirements of daily life. In a preregistered study, we adapted the dual-task paradigm so that one of the tasks allowed for cognitive offloading. As a primary task, our participants ( N = 172) performed the pattern copy task—a highly demanding working memory task that allows for offloading at various degrees. In this task, we manipulated the temporal costs of offloading. Concurrently, half of the participants responded to a secondary N -back task. As our main research question, we investigated the impact of offloading behavior on secondary task performance. We observed that more pronounced offloading in the condition without temporal costs was accompanied by a more accurate performance in the N -back task. Furthermore, the necessity to respond to the N -back task increased offloading behavior. These results suggest an interplay between offloading and secondary task performance: in demanding situations, individuals increasingly use cognitive offloading, which releases internal resources that can then be devoted to improving performance in other, concurrent tasks.
Virulence-associated type III secretion systems in Gram-negative bacteria
2023-06-13

Virulence-associated bacterial type III secretion systems are multiprotein molecular machines that promote the pathogenicity of bacteria towards eukaryotic host cells. These machines form needle-like structures, named injectisomes, that span both bacterial and host membranes, forming a direct conduit for the delivery of bacterial proteins into host cells. Once within the host, these bacterial effector proteins are capable of manipulating a multitude of host cell functions. In recent years, the knowledge of assembly, structure and function of these machines has grown substantially and is presented and discussed in this review.