julilili42/papers huggingface dataset:
Microbial communities living inside plant leaves or on the leaf surface are differently shaped by environmental cues
2024-01-01

Abstract Leaf-associated microbial communities can promote plant health and resistance to biotic and abiotic stresses. However, the importance of environmental cues in the assembly of the leaf endo- and epi-microbiota remains elusive. Here, we aimed to investigate the impact of seasonal environmental variations, on the establishment of the leaf microbiome, focusing on long-term changes (five years) in bacterial, fungal, and nonfungal eukaryotic communities colonizing the surface and endosphere of six wild Arabidopsis thaliana populations. While leaf-microbial communities were found to be highly stochastic, the leaf niche had a predominant importance with endophytic microbial communities consistently exhibiting a lower diversity and variability. Among environmental factors, radiation- and humidity-related factors are the most important drivers of diversity patterns in the leaf, with stronger effects on epiphytic communities. Using linear models, we identified 30 important genera whose relative abundance in leaf compartments could be modeled from environmental variables, suggesting specific niche preferences for these taxa. With the hypothesis that environmental factors could impact interactions within microbial communities, we analyzed the seasonal patterns of microbial interaction networks across leaf compartments. We showed that epiphytic networks are more complex than endophytic and that the complexity and connectivity of these networks are partially correlated with the mentioned environmental cues. Our results indicate that humidity and solar radiation function as major environmental cues shaping the phyllosphere microbiome at both micro (leaf compartment) and macro (site) scales. These findings could have practical implications for predicting and developing field-adapted microbes in the face of global change.
Targeted therapies in retinoblastoma: GD2-directed immunotherapy following autologous stem cell transplantation and evaluation of alternative target B7-H3
2024-01-01

Abstract Background GD2-directed immunotherapy is highly effective in the treatment of high-risk neuroblastoma (NB), and might be an interesting target also in other high-risk tumors. Methods The German-Austrian Retinoblastoma Registry, Essen, was searched for patients, who were treated with anti-GD2 monoclonal antibody (mAb) dinutuximab beta (Db) in order to evaluate toxicity, response and outcome in these patients. Additionally, we evaluated anti-GD2 antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) in retinoblastoma cell lines in vitro. Furthermore, in vitro cytotoxicity assays directed against B7-H3 (CD276), a new identified potential target in RB, were performed. Results We identified four patients with relapsed stage IV retinoblastoma, who were treated with Db following autologous stem cell transplantation (ASCT). Two out of two evaluable patients with detectable tumors responded to immunotherapy. One of these and another patient who received immunotherapy without residual disease relapsed 10 and 12 months after start of Db. The other patients remained in remission until last follow-up 26 and 45 months, respectively. In vitro , significant lysis of RB cell lines by ADCC and CDC with samples from patients and healthy donors and anti-GD2 and anti-CD276-mAbs were demonstrated. Conclusion Anti-GD2-directed immunotherapy represents an additional therapeutic option in high-risk metastasized RB. Moreover, CD276 is another target of interest.
PD-1 checkpoint inhibition enhances the antilymphoma activity of CD19-CAR-iNKT cells that retain their ability to prevent alloreactivity
2024-01-01

Background Relapse and graft-versus-host disease (GVHD) are the main causes of death after allogeneic hematopoietic cell transplantation (HCT). Preclinical murine models and clinical data suggest that invariant natural killer T (iNKT) cells prevent acute and chronic GVHD. In addition, iNKT cells are crucial for efficient immune responses against malignancies and contribute to reduced relapse rates after transplantation. Chimeric antigen receptors (CAR) redirect effector cells to cell surface antigens and enhance killing of target cells. With this study, we aimed to combine enhanced cytotoxicity of CD19-CAR-iNKT cells against lymphoma cells with their tolerogenic properties. Methods iNKT cells were isolated from peripheral blood mononuclear cells and transduced with an anti-CD19-CAR retrovirus. After in vitro expansion, the functionality of CD19-CAR-iNKT cells was assessed by flow cytometry, image stream analysis and multiplex analysis in single-stimulation or repeated-stimulation assays. Moreover, the immunoregulatory properties of CD19-CAR-iNKT cells were analyzed in apoptosis assays and in mixed lymphocyte reactions. The effect of checkpoint inhibition through nivolumab was analyzed in these settings. Results In this study, we could show that the cytotoxicity of CD19-CAR-iNKT cells was mediated either through engagement of their CAR or their invariant T-cell receptor, which may circumvent loss of response through antigen escape. However, encounter of CD19-CAR-iNKT cells with their target induced a phenotype of exhaustion. Consequently, checkpoint inhibition increased cytokine release, cytotoxicity and survival of CD19-CAR-iNKT cells. Additionally, they showed robust suppression of alloreactive immune responses. Conclusion In this work, we demonstrate that CAR-iNKT cells are a powerful cytotherapeutic option to prevent or treat relapse while potentially reducing the risk of GVHD after allogeneic HCT.
Soil Erosion Research and Soil Conservation Policy in South Africa
2024-01-01

Abstract Soil erosion has been identified as an issue in South African farming for more than a century. Erosion of land surfaces by water or wind is a natural process which might be accelerated directly by human impact on land surface properties, e.g., vegetation and soils. An assessment of soil erosion risk indicates average soil loss rates two orders of magnitude larger than long-term soil formation rates. This challenging condition clearly underlines the need for continuous application of established policies and principles as well as emerging modes of conservation agriculture in farming activities in most parts of South Africa. In addition, conservation agriculture has been shown to have positive effects on the cost–value ratio, but diffusion and adoption of this innovative approach still meet resistance often founded in traditional faith and belief systems. However, to cope with challenges from global climate change, e.g., intensified extreme weather conditions (droughts and flooding), strengthened resilience of farming systems is required to i) meet increased domestic and global demand for food and ii) to put into practice sustainable management to diminish on-site and off-site damages from soil erosion on the way to reach sustainable development goals.
Preoperative growth dynamics of untreated glioblastoma: Description of an exponential growth type, correlating factors, and association with postoperative survival
2024-01-01

Abstract Background Little is known about the growth dynamics of untreated glioblastoma and its possible influence on postoperative survival. Our aim was to analyze a possible association of preoperative growth dynamics with postoperative survival. Methods We performed a retrospective analysis of all adult patients surgically treated for newly diagnosed glioblastoma at our center between 2010 and 2020. By volumetric analysis of data of patients with availability of ≥3 preoperative sequential MRI, a growth pattern was aimed to be identified. Main inclusion criterion for further analysis was the availability of two preoperative MRI scans with a slice thickness of 1 mm, at least 7 days apart. Individual growth rates were calculated. Association with overall survival (OS) was examined by multivariable. Results Out of 749 patients screened, 13 had ≥3 preoperative MRI, 70 had 2 MRI and met the inclusion criteria. A curve estimation regression model showed the best fit for exponential tumor growth. Median tumor volume doubling time (VDT) was 31 days, median specific growth rate (SGR) was 2.2% growth per day. SGR showed negative correlation with tumor size (rho = −0.59, P &amp;lt; .001). Growth rates were dichotomized according to the median SGR.OS was significantly longer in the group with slow growth (log-rank: P = .010). Slower preoperative growth was independently associated with longer overall survival in a multivariable Cox regression model for patients after tumor resection. Conclusions Especially small lesions suggestive of glioblastoma showed exponential tumor growth with variable growth rates and a median VDT of 31 days. SGR was significantly associated with OS in patients with tumor resection in our sample.
Impaired glymphatic system in genetic frontotemporal dementia: a GENFI study
2024-01-01

Abstract The glymphatic system is an emerging target in neurodegenerative disorders. Here, we investigated the activity of the glymphatic system in genetic frontotemporal dementia with a diffusion-based technique called diffusion tensor image analysis along the perivascular space. We investigated 291 subjects with symptomatic or presymptomatic frontotemporal dementia (112 with chromosome 9 open reading frame 72 [C9orf72] expansion, 119 with granulin [GRN] mutations and 60 with microtubule-associated protein tau [MAPT] mutations) and 83 non-carriers (including 50 young and 33 old non-carriers). We computed the diffusion tensor image analysis along the perivascular space index by calculating diffusivities in the x-, y- and z-axes of the plane of the lateral ventricle body. Clinical stage and blood-based markers were considered. A subset of 180 participants underwent cognitive follow-ups for a total of 640 evaluations. The diffusion tensor image analysis along the perivascular space index was lower in symptomatic frontotemporal dementia (estimated marginal mean ± standard error, 1.21 ± 0.02) than in old non-carriers (1.29 ± 0.03, P = 0.009) and presymptomatic mutation carriers (1.30 ± 0.01, P &amp;lt; 0.001). In mutation carriers, lower diffusion tensor image analysis along the perivascular space was associated with worse disease severity (β = −1.16, P &amp;lt; 0.001), and a trend towards a significant association between lower diffusion tensor image analysis along the perivascular space and higher plasma neurofilament light chain was reported (β = −0.28, P = 0.063). Analysis of longitudinal data demonstrated that worsening of disease severity was faster in patients with low diffusion tensor image analysis along the perivascular space at baseline than in those with average (P = 0.009) or high (P = 0.006) diffusion tensor image analysis along the perivascular space index. Using a non-invasive imaging approach as a proxy for glymphatic system function, we demonstrated glymphatic system abnormalities in the symptomatic stages of genetic frontotemporal dementia. Such measures of the glymphatic system may elucidate pathophysiological processes in human frontotemporal dementia and facilitate early phase trials of genetic frontotemporal dementia.
An interconnected data infrastructure to support large-scale rare disease research
2024-01-01

Abstract The Solve-RD project brings together clinicians, scientists, and patient representatives from 51 institutes spanning 15 countries to collaborate on genetically diagnosing (“solving”) rare diseases (RDs). The project aims to significantly increase the diagnostic success rate by co-analyzing data from thousands of RD cases, including phenotypes, pedigrees, exome/genome sequencing, and multiomics data. Here we report on the data infrastructure devised and created to support this co-analysis. This infrastructure enables users to store, find, connect, and analyze data and metadata in a collaborative manner. Pseudonymized phenotypic and raw experimental data are submitted to the RD-Connect Genome-Phenome Analysis Platform and processed through standardized pipelines. Resulting files and novel produced omics data are sent to the European Genome-Phenome Archive, which adds unique file identifiers and provides long-term storage and controlled access services. MOLGENIS “RD3” and Café Variome “Discovery Nexus” connect data and metadata and offer discovery services, and secure cloud-based “Sandboxes” support multiparty data analysis. This successfully deployed and useful infrastructure design provides a blueprint for other projects that need to analyze large amounts of heterogeneous data.
Helical interfacial modulation for perovskite photovoltaics
2024-01-01

Helical modulators improve the operational stability of perovskite solar cells without a significant effect on photovoltaic characteristics, challenging the role of chiral interfacial modulators in hybrid perovskite photovoltaics.
Emerging investigator series: preferential adsorption and coprecipitation of permafrost organic matter with poorly crystalline iron minerals
2024-01-01

This study reports the decrease in iron-bound organic carbon quantity and change in its composition in thawing permafrost soils, with implications for the bioavailability of the dissolved organic carbon pool.
Development of slow oscillation–spindle coupling from infancy to toddlerhood
2024-01-01

Abstract Sleep has been demonstrated to support memory formation from early life on. The precise temporal coupling of slow oscillations (SOs) with spindles has been suggested as a mechanism facilitating this consolidation process in thalamocortical networks. Here, we investigated the development of sleep spindles and SOs and their coordinate interplay by comparing frontal, central, and parietal electroencephalogram recordings during a nap between infants aged 2–3 months (n = 31) and toddlers aged 14–17 months (n = 49). Spindles and SOs showed quite different maturational patterns between age groups, as to topography, amplitude, and density. Notably, spindle–SO co-occurrence in the infants did not exceed chance levels and was increased to significant levels only in the toddlers. In the infants, the slow SO upstate over frontocortical regions was even associated with a significant decrease in spindles, contrasting with the adult-like increase in spindles seen in toddlers. These results point to an immature processing in thalamocortical networks during sleep in early infancy, possibly diminishing the efficacy of sleep-dependent memory formation at this age.
Xenogenic Application of Human Placenta-Derived Mesenchymal Stromal Cells in a Porcine Large Animal Model
2024-01-01

In animal models, cell therapies for different diseases or injuries have been very successful. Preclinical studies with cells aiming at a stroke, heart attack, and other emergency situations were promising but sometimes failed translation in clinical situations. We, therefore, investigated if human placenta-derived mesenchymal stromal cells can be injected in pigs without provoking rejection to serve as a xenogenic transplantation model to bridge preclinical animal studies to more promising future preclinical studies. Male human placenta-derived mesenchymal stromal cells were isolated, expanded, and characterized by flow cytometry, in vitro differentiation, and quantitative reverse-transcription polymerase chain reaction to prove their nature. Such cells were injected into the sphincter muscle of the urethrae of female pigs under visual control by cystoscopy employing a Williams needle. The animals were observed over 7 days of follow-up. Reactions of the host to the xenogeneic cells were explored by monitoring body temperature, and inflammatory markers including IL-1ß, CRP, and haptoglobin in blood. After sacrifice on day 7, infiltration of inflammatory cells in the tissue targeted was investigated by histology and immunofluorescence. DNA of injected human cells was detected by PCR. Upon injection in vascularized porcine tissue, human placenta-derived mesenchymal stromal cells were tolerated, and systemic inflammatory parameters were not elevated. DNA of injected cells was detected in situ 7 days after injection, and moderate local infiltration of inflammatory cells was observed. The therapeutic potential of human placenta-derived mesenchymal stromal cells can be explored in porcine large animal models of injury or disease. This seems a promising strategy to explore technologies for cell injections in infarcted hearts or small organs and tissues in therapeutically relevant amounts requiring large animal models to yield meaningful outcomes.
2nd Workshop on Maritime Computer Vision (MaCVi) 2024: Challenge Results
2024-01-01

The 2nd Workshop on Maritime Computer Vision (MaCVi) 2024 addresses maritime computer vision for Unmanned Aerial Vehicles (UAV) and Unmanned Surface Vehicles (USV). Three challenges categories are considered: (i) UAV-based Maritime Object Tracking with Re-ideruification, (ii) USV-based Maritime Obstacle Segmentation and Detection, (iii) USV-based Maritime Boat Tracking. The USV-based Maritime Obstacle Segmentation and Detection features three sub-challenges, including a new embedded challenge addressing efficicent inference on real-world embedded devices. This report offers a comprehensive overview of the findings from the challenges. We provide both statistical and qualitative analyses, evaluating trends from over 195 submissions. All datasets, evaluation code, and the leaderboard are available to the public at https://macvi.org/workshop/macvi24. © 2024 IEEE.
A Versatile Calibration Method for Rotary-Wing UAS as Wind Measurement Systems
2024-01-01

Abstract The use of small uncrewed aircraft systems (UAS) can effectively capture the wind profile in the lower atmospheric boundary layer. This study presents a calibration process to estimate the horizontal wind vector using a rotary-wing UAS in hovering conditions. This procedure does not require wind tunnels or meteorological masts, only the data from the flight control unit and a specific set of calibration flights. A model based on the UAS drag coefficient was proposed and compared to a traditional approach. Validation flights at the German Weather Service MOL-RAO observatory showed that the system can accurately predict wind speed and direction. A modified DJI S900 hexacopter with a Styrofoam sphere casing was used for the study and calibrated for wind speeds between 1 and 14 m s −1 . Power spectral density analysis showed the system’s ability to resolve atmospheric eddies up to 0.1 Hz. The overall root-mean-square error was less than 0.7 m s −1 for wind speed and less than 8° for wind direction.
Generalizability of control across cognitive and emotional conflict.
2024-01-01

People can learn to control their thoughts and emotions. The scientific study of control has been conducted mostly independently for cognitive and emotional conflicts. However, recent theoretical proposals suggest a close link between emotional and cognitive control processes. Indeed, mounting evidence from clinical sciences, social and personality psychology, and developmental neuroscience suggests that the ability to control thoughts and behavior goes hand in hand with the ability to control emotions. Yet, the precise interface between control over cognition and emotions remains controversial. The present study investigates the question whether control is a general-purpose mechanism or rather a set of domain-specific mechanisms. Following previous research, we tested participants' control in a cognitive and an emotional Stroop task and assessed the congruency sequence effect (CSE) which has been taken as a marker of cognitive or (implicit) emotional control, respectively. Going beyond previous research, we asked how control in one domain (e.g., cognitive) interacts with control in the other domain (e.g., emotional) on a trial-by-trial basis. In four experiments (N = 259) presented participants with a task-switching design that intermixed cognitive and emotional conflicts. This procedure produced significant CSEs across cognitive-emotional domains, suggesting that control can interact across domains. However, effect sizes of within-domain CSEs were twice as large, indicating that control is also domain-specific. These results neither support the general-purpose account nor the domain-specificity hypothesis of control. Rather, a hybrid account fits the data best, which also reconciles previous behavioral and neurophysiological findings, suggesting domain-general and specific processes. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
Direct laser induced writing of high precision gold nanosphere SERS patterns
2024-01-01

Introducing a fast, reliable, and flexible “Direct Laser Writing” technology for printing precise and complex SERS-patters on different substrates of any desired structure with nanometer resolution for applications in sensor technology and optoelectronics.
Gender Representation and Policy Implementation: Is it Women or the Left Wing that Increases the Childcare Supply?
2024-01-01

Abstract This study investigates the impact of the accumulation of gender representation during the policy implementation stage on the childcare supply expansion. Previous studies faced two key issues: first, they primarily focused on the impact of gender representation during the policy introduction stage, and second, they often lacked sensitivity in distinguishing whether the outcome was driven by partisanship or gender. Using the city-level dataset from western Germany, this study argues that although the effect of female mayors is model dependent, a 10 percentage point increase in the average share of women city councils leads to an increase in the childcare expansion by about 2.5 percentage points. Notably, regardless of left-wing/right-wing positions, women councilors expanded the childcare supply.
Altering glycopeptide antibiotic biosynthesis through mutasynthesis allows incorporation of fluorinated phenylglycine residues
2024-01-01

Novel, fluorinated glycopeptide antibiotics (GPAs) have been generated using mutasynthesis approaches. This also expands our knowledge of the tolerance of modified phenylglycine amino acid residues by the GPA biosynthetic assembly machinery.
(Mal)adaptive Mentalizing in the Cognitive Hierarchy, and Its Link to Paranoia
2024-01-01

Interacting competitively requires vigilance to avoid deception. However, excessive caution can have adverse effects, stemming from false beliefs of intentional harm. So far there is no formal cognitive account of what may cause this suspiciousness. Here we present an examination of this phenomenon through the lens of Theory of Mind - the cognitive ability to consider the beliefs, intentions, and desires of others. By simulating interacting computer agents we illustrate how well-aligned agents can give rise to successful deception and justified skepticism. Crucially, we also reveal that overly cautious agents develop false beliefs that an ingenuous partner is attempting malicious trickery, leading to tangible losses. As well as formally defining a plausible mechanism for suspiciousness, paranoia, and conspiratorial thinking, our theory indicates that rather than a deficit in Theory of Mind, paranoia may involve an over-application of strategy to genuine behaviour.