julilili42/papers huggingface dataset:
Extensive remodelling of the cell wall during the development of Staphylococcus aureus bacteraemia
2023-07-04

The bloodstream represents a hostile environment that bacteria must overcome to cause bacteraemia. To understand how the major human pathogen Staphylococcus aureus manages this we have utilised a functional genomics approach to identify a number of new loci that affect the ability of the bacteria to survive exposure to serum, the critical first step in the development of bacteraemia. The expression of one of these genes, tcaA, was found to be induced upon exposure to serum, and we show that it is involved in the elaboration of a critical virulence factor, the wall teichoic acids (WTA), within the cell envelope. The activity of the TcaA protein alters the sensitivity of the bacteria to cell wall attacking agents, including antimicrobial peptides, human defence fatty acids, and several antibiotics. This protein also affects the autolytic activity and lysostaphin sensitivity of the bacteria, suggesting that in addition to changing WTA abundance in the cell envelope, it also plays a role in peptidoglycan crosslinking. With TcaA rendering the bacteria more susceptible to serum killing, while simultaneously increasing the abundance of WTA in the cell envelope, it was unclear what effect this protein may have during infection. To explore this, we examined human data and performed murine experimental infections. Collectively, our data suggests that whilst mutations in tcaA are selected for during bacteraemia, this protein positively contributes to the virulence of S. aureus through its involvement in altering the cell wall architecture of the bacteria, a process that appears to play a key role in the development of bacteraemia.
Characterisation of low background CaWO$_4$ crystals for CRESST-III
2023-07-04

The CRESST-III experiment aims at the direct detection of dark matter particles via their elastic scattering off nuclei in a scintillating CaWO _4 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi /><mml:mn>4</mml:mn></mml:msub></mml:math> target crystal. For many years CaWO _4 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi /><mml:mn>4</mml:mn></mml:msub></mml:math> crystals have successfully been produced in-house at Technische Universität München with a focus on high radiopurity. To further improve the CaWO _4 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi /><mml:mn>4</mml:mn></mml:msub></mml:math> crystals, an extensive chemical purification of the raw materials has been performed and the crystal TUM93 was produced from this powder. We present results from an \\alpha <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>α</mml:mi></mml:math> -decay rate analysis performed on 344 days of data collected in the ongoing CRESST-III data-taking campaign. The \\alpha <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>α</mml:mi></mml:math> -decay rate could significantly be reduced.
A fungal pathogen manipulates phytocytokine signaling for plant infection
2023-07-04

Phytocytokines are hormone-like plant peptides that modulate immune homeostasis and development. Phytosulfokine (PSK) mediates plant growth and attenuates activation of plant pattern-triggered immunity (PTI). We show that the small cysteine-containing effector VdSCP8 from Verticillium dahliae (Vd) is a virulence-promoting protein that suppresses PTI in Arabidopsis thaliana and Nicotiana benthamiana. Apoplastic SCP8 suppresses immune activation through leucine-rich repeat ectodomain pattern recognition receptors. SCP8 virulence and immunosuppressive activities require PHYTOSULFOKINE RECEPTOR 1 (PSKR1), which binds PSK and forms a complex with co-receptor BAK1 for PTI suppression. We find that PSK, like SCP8, suppresses PTI, SCP8 stimulates PSKR1-BAK1 complex formation, and that Vd requires PSK signaling for host infection. SCP8 interacts with an apoplastic subtilase, and co-expression of SCP8 and subtilase inhibitors reduces PTI suppression. Our findings suggest that a multi-host plant pathogen manipulates PTI by enhancing immunosuppressive PSK signaling, likely through plant subtilase activity.
The neuroanatomy of multi-target attention: Insights from multivariate and Bayesian lesion analyses in acute stroke
2023-07-04

Multi-target attention, i.e. the ability to attend and respond to multiple visual targets presented simultaneously across both visual fields, is essential for everyday real-world behaviour. Given the close link between the neuropsychological deficit of extinction and attentional limits in healthy subjects, investigating the anatomy that underlies extinction is uniquely capable of providing important insights concerning the anatomy critical for normal multi-target attention. Previous studies into the brain areas critical for multi-target attention and its failure in extinction patients have, however, produced heterogeneous results. In the current study, we used multivariate and Bayesian lesion analysis approaches to investigate the anatomical substrate of visual extinction in a large sample of 108 acute stroke patients. The use of acute stroke patient data and multivariate/Bayesian lesion analysis approaches allowed us to address limitations associated with previous studies and so obtain a more complete picture of the functional network associated with visual extinction. Our results demonstrate that the temporo-parietal junction (TPJ) is critically associated with visual extinction. The Bayesian lesion analysis additionally implicated the intraparietal sulcus (IPS), in line with the results of studies in neurologically healthy participants that highlighted the IPS as the area critical for multi-target attention. Our findings resolve the seemingly conflicting previous findings, and emphasise the urgent need for further research to clarify the precise cognitive role of the TPJ in multi-target attention and its failure in extinction patients.
Teaching characteristics in distance education—associations with teaching quality and students’ learning experiences
2023-07-05

In spring 2020, teaching and learning changed significantly when schools closed in order to contain the COVID-19 pandemic. We investigated the associations between teaching characteristics (teachers' communication, goals, approach to teaching) with ratings of teaching quality and students' learning experiences. Data from students (N = 3.159) in Grades 5–12, their parents (N = 1.688), and teachers (N = 459) collected online in spring/summer 2020 showed that teachers' communication with colleagues, their ability to maintain a good relationship with their students, and the time they spent on lessons were most consistently associated with teaching quality ratings as well as students' learning experiences.
Mean-field dynamics of open quantum systems with collective operator-valued rates: validity and application
2023-07-05

Abstract We consider a class of open quantum many-body Lindblad dynamics characterized by an all-to-all coupling Hamiltonian and by dissipation featuring collective ‘state-dependent’ rates. The latter encodes local incoherent transitions that depend on average properties of the system. This type of open quantum dynamics can be seen as a generalization of classical (mean-field) stochastic Markov dynamics, in which transitions depend on the instantaneous configuration of the system, to the quantum domain. We study the time evolution in the limit of infinitely large systems, and we demonstrate the exactness of the mean-field equations for the dynamics of average operators. We further derive the effective dynamical generator governing the time evolution of (quasi-) local operators. Our results allow for a rigorous and systematic investigation of the impact of quantum effects on paradigmatic classical models, such as quantum generalized Hopfield associative memories or (mean-field) kinetically-constrained models.
Polygenic risk score analysis reveals shared genetic burden between epilepsy and psychiatric comorbidities
2023-07-05

Abstract Background One in three people with epilepsy experiences psychiatric comorbidity, with higher rates in people with drug-resistant epilepsy. Despite their high heritabilities, finding genetic links between epilepsy and psychiatric disorders has proven difficult. We used polygenic risk scoring (PRS) to test whether people with epilepsy have an increased polygenic burden of common genetic variants for depression, anxiety, psychosis, and attention deficit/hyperactivity disorder (ADHD), and examined whether such polygenic burden influences the response to pharmacological treatment of epilepsy. Methods Phenotype data in the UK Biobank were assessed to identify people with 1) epilepsy (n=8 488), 2) depression (n=143 440), 3) psychosis (n=2 357), 4) ADHD (n=89), and 5) anxiety (n=18 222. Using genotype data and restricting to Caucasian-ancestry samples (n=409 634), PRS for each psychiatric trait were calculated and multinomial regression was used to compare 1) population controls, 2) people with epilepsy and no psychiatric illness, 3) people with epilepsy and the psychiatric trait of interest, and 4) people with the psychiatric trait of interest and no epilepsy. Fixed-effect meta-analysis was used to compare psychiatric PRS in drug-resistant and drug-responsive epilepsy samples from the UK Biobank (n=1 640) and the EpiPGX consortium (n=3 449). Results After correction for multiple testing, people with epilepsy showed elevated PRS for depression (p&lt;2 x10 −16 ), psychosis (p=0.04) and ADHD (p&lt;0.001). Patients with drug-resistant epilepsy had an increased PRS for psychosis (p=0.002) and depression (p=0.0004) relative to responsive cases. Conclusion We present evidence that the common genetic basis of epilepsy overlaps with that of psychiatric conditions which are frequently comorbid in people with epilepsy. Common genetic variants that drive psychiatric illness are enriched in people with drug-resistant epilepsy. These results further our understanding of the genetic architecture of epilepsy and suggest a potential future role for polygenic interpretation of common variants in prognostic stratification, both for seizure-treatment outcomes and non-seizure comorbidities.
An imaged 15 MJup companion within a hierarchical quadruple system
2023-07-05

Context. Since 2019, the direct imaging B-star Exoplanet Abundance STudy (BEAST) at SPHERE@VLT has been scanning the surroundings of young B-type stars in order to ascertain the ultimate frontiers of giant planet formation. Recently, the 17 −4 +3 Myr HIP 81208 was found to host a close-in (∼50 au) brown dwarf and a wider (∼230 au) late M star around the central 2.6 M ⊙ primary. Aims. Alongside the continuation of the survey, we are undertaking a complete reanalysis of archival data aimed at improving detection performances so as to uncover additional low-mass companions. Methods. We present here a new reduction of the observations of HIP 81208 using the patch covariance algorithm (PACO), a recent and powerful algorithm dedicated to processing high-contrast imaging datasets, as well as more classical algorithms and a dedicated point spread function subtraction approach. The combination of different techniques allowed for a reliable extraction of astrometric and photometric parameters. Results. A previously undetected source was recovered at a short separation from the C component of the system. Proper motion analysis provided robust evidence for the gravitational bond of the object to HIP 81208 C. Orbiting C at a distance of ∼20 au, this 15 M Jup brown dwarf becomes the fourth object of the hierarchical HIP 81208 system. Conclusions. Among the several BEAST stars which are being found to host substellar companions, HIP 81208 stands out as a particularly striking system. As the first stellar binary system with substellar companions around each component ever found by direct imaging, it yields exquisite opportunities for thorough formation and dynamical follow-up studies.
Functional variations in gamma-secretase activity are critical determinants of the clinical, biomarker, and cognitive progression of autosomal dominant Alzheimer’s disease
2023-07-05

ABSTRACT Background The balance between production, clearance, and toxicity of Aβ peptides is central to Alzheimer’s disease (AD) pathobiology. Though highly variable in terms of age at symptom onset (AAO), hundreds of variants in PSEN1 cause autosomal dominant forms of AD (ADAD) with nearly complete penetrance. PSEN1 forms the catalytic core of the γ-secretase complex and thereby directly mediates the production of longer, aggregation-prone Aβ peptides relative to shorter, non-aggregating peptides. We hypothesized that the broad AAO and biomarker heterogeneity seen across ADAD would be predictable based on mutation-specific differences in the production of Aβ species. Methods Aβ-37, 38, 40, 42, and 43 production was quantified from 161 unique PSEN1 variants expressed in HEK293 cells. Prediction of AAO was carried out in 106 variants with available AAO and then replicated in 55 variants represented across 190 PSEN1 mutation carriers who have detailed cognitive and biomarker data from the Dominantly Inherited Alzheimer’s Network (DIAN). Results Variations in Aβ production across the 161 mutations examined in cell-based models were highly predictive of AAO. In those with corresponding in vivo data from the DIAN study, our cell-based γ-secretase composite was strongly associated with biomarker and cognitive trajectories. Conclusions These findings elucidate the critical link between γ-secretase function, Aβ production, and AD progression and offer mechanistic support for the amyloid hypothesis. The approach used here represents a powerful tool to account for heterogeneity in disease progression in ADAD clinical trials and to assess the pathogenicity of variants of unknown significance or with limited family history.
Increasing Patient Safety and Treatment Quality by Using Intraoperative MRI for Organ-Preserving Tumor Resection and High-Dose Rate Brachytherapy in Children with Bladder/Prostate and Perianal Rhabdomyosarcoma
2023-07-05

In children with bladder/prostate (BP) and perianal rhabdomyosarcoma (RMS), we use a hybrid treatment concept for those suitable, combining organ-preserving tumor resection and high-dose rate brachytherapy (HDR-BT). This treatment concept has been shown to improve outcomes. However, it is associated with specific challenges for the clinicians. The exact position of the tubes for BT is a prerequisite for precise radiotherapy. It can finally be determined only with an MRI or CT scan. We evaluated the use of an intraoperative MRI (iMRI) to control the position of the BT tubes and for radiotherapy planning in all patients with BP and perianal RMS who received the above-mentioned combination therapy in our department since January 2021. iMRI was used in 12 children. All tubes were clearly localized. No adverse events occurred. In all 12 children, radiotherapy could be started on time. In a historical cohort without iMRI, this was not possible in 3 out of 20 children. The use of iMRI in children with BP and perianal RMS improved patient safety and treatment quality. This technology has proven to be successful for the patient population we have defined and has become a standard procedure in our institution.
The role of learning in complex problem solving using MicroDYN
2023-07-05

It is still an open question which cognitive and non-cognitive personality traits are useful for describing and explaining behaviour and performance in complex problems. During complex problem solving (CPS), problem solvers have to interact with the task in a way in which learning ability might be beneficial for successful task completion. By investigating the relationship between learning ability and CPS, while accounting for interactions between complex system characteristics and person characteristics, this paper aims to understand the role of learning processes in CPS more closely. In a sample of N = 241 participants, we performed a preregistered analysis to investigate the relationship between knowledge acquisition performance in a CPS test (MicroDYN) and learning test performance (ADAFI) with a multilevel modeling approach across 10 CPS systems with various characteristics. In line with our expectations, we replicated previous findings on a relationship between learning test and MicroDYN performance and found this relationship to be more pronounced in systems with (vs. without) autonomous changes. Further system and person characteristics also showed effects as expected, with better performance in systems with lower complexity, with more experience with the task, and with more strategic exploration behaviour. Our results provide further evidence for the notion that learning is an important component for the successful completion of CPS tasks.
Influence of Different Bracket Adhesive Systems on Enamel Demineralization—An In Vitro Study
2023-07-05

Background: enamel demineralization is a common side effect of orthodontic therapy with fixed braces. The aim of the present in vitro study was to compare a conventional adhesive system and a modern adhesive system (APC Flash-Free [FF] technology) with regard to the demineralization of enamel by Streptococcus sobrinus (S. sobrinus). Methods: this in vitro study included premolar teeth and compared APC FF adhesive brackets (Group A, n = 15) with conventional adhesive brackets (Group B, n = 15) from the same company. Specimens were incubated with a positive control group (PCG, n = 5) and a negative control group (NCG, n = 5) in an S. sobrinus suspension for three weeks. To evaluate the grade of enamel demineralization, the samples were analyzed using a polarizing microscope. Results: the test specimens of group B with conventionally bonded bracket adhesive showed significantly greater (+10.8 μm) demineralization with regard to the penetration depth of the demineralization than the PCG (p = 0.012). Thus, there was a difference from group A with the new bracket adhesive of the FF brackets (+7.29 μm). Significantly, demineralization was more pronounced cervically than coronally in both groups, and it occurred cervically more frequently than grade 3 demineralization (p = 0.001). Conclusions: it seems plausible that new orthodontic bracket adhesives and the modern FF adhesive system positively contribute to the reduction in enamel demineralization during orthodontic treatment.
Cover Feature: Photolytic Decarbonylation of Oxalyl Diisothiocyanate in Solid Argon Matrices to syn‐anti Carbonyl Diisothiocyanate and Its Isomerization (Eur. J. Inorg. Chem. 22/2023)
2023-07-05

The Cover Feature shows a molecule of oxalyl diisothiocyanate trapped in an argon matrix. After irradiation with UV-light carbon monoxide is cleaved off, leaving carbonyl diisothiocyanate in a rotationally excited state. Subsequent annealing at 30 K leads to a relaxation of the structure into its ground state. Cover art by Cristina Ripoll. More information can be found in the Research Article by J. Pfeiffer, J. P. Wagner, and F. Tambornino.
The developmental trajectory of object recognition robustness: Children are like small adults but unlike big deep neural networks
2023-07-06

In laboratory object recognition tasks based on undistorted photographs, both adult humans and deep neural networks (DNNs) perform close to ceiling. Unlike adults', whose object recognition performance is robust against a wide range of image distortions, DNNs trained on standard ImageNet (1.3M images) perform poorly on distorted images. However, the last 2 years have seen impressive gains in DNN distortion robustness, predominantly achieved through ever-increasing large-scale datasets-orders of magnitude larger than ImageNet. Although this simple brute-force approach is very effective in achieving human-level robustness in DNNs, it raises the question of whether human robustness, too, is simply due to extensive experience with (distorted) visual input during childhood and beyond. Here we investigate this question by comparing the core object recognition performance of 146 children (aged 4-15 years) against adults and against DNNs. We find, first, that already 4- to 6-year-olds show remarkable robustness to image distortions and outperform DNNs trained on ImageNet. Second, we estimated the number of images children had been exposed to during their lifetime. Compared with various DNNs, children's high robustness requires relatively little data. Third, when recognizing objects, children-like adults but unlike DNNs-rely heavily on shape but not on texture cues. Together our results suggest that the remarkable robustness to distortions emerges early in the developmental trajectory of human object recognition and is unlikely the result of a mere accumulation of experience with distorted visual input. Even though current DNNs match human performance regarding robustness, they seem to rely on different and more data-hungry strategies to do so.
Three-Dimensional (3D) Surface-Enhanced Raman Spectroscopy (SERS) Substrates: Fabrication and SERS Applications
2023-07-06

This study introduces a straightforward approach to construct three-dimensional (3D) surface-enhanced Raman spectroscopy (SERS) substrates using chemically modified silica particles as microcarriers and by attaching metal nanoparticles (NPs) onto their surfaces. Tollens’ reagent and sputtering techniques are utilized to prepare the SERS substrates from mercapto-functionalized silica particles. Treatment with Tollens’ reagent generates a variety of silver NPs, ranging from approximately 10 to 400 nm, while sputtering with gold (Au) yields uniformly distributed NPs with an island-like morphology. Both substrates display wide plasmon resonances in the scattering spectra, making them effective for SERS in the visible spectral range, with enhancement factors (ratio of the analyte’s intensity at the hotspot compared to that on the substrate in the absence of metal nanoparticles) of up to 25. These 3D substrates have a significant advantage over traditional SERS substrates because their active surface area is not limited to a 2D surface but offers a much greater active surface due to the 3D arrangement of the NPs. This feature may enable achieving much higher SERS intensity from within streaming liquids or inside cells/tissues.
Advanced Photocatalytic Uranium Extraction Strategies: Progress, Challenges, and Prospects
2023-07-06

Nuclear energy with low carbon emission and high-energy density is considered as one of the most promising future energy sources for human beings. However, the use of nuclear energy will inevitably lead to the discharge of nuclear waste and the consumption of uranium resources. Therefore, the development of simple, efficient, and economical uranium extraction methods is of great significance for the sustainable development of nuclear energy and the restoration of the ecological environment. Photocatalytic U(VI) extraction technology as a simple, highly efficient, and low-cost strategy, received increasing attention from researchers. In this review, the development background of photocatalytic U(VI) extraction and several photocatalytic U(VI) reduction mechanisms are briefly described and the identification methods of uranium species after photocatalytic reduction are addressed. Subsequently, the modification strategies of several catalysts used for U(VI) extraction are summarized and the advantages and disadvantages of photocatalytic U(VI) extraction are compared. Additionally, the research progress of photocatalytic technology for U(VI) extraction in actual uranium-containing wastewater and seawater are evaluated. Finally, the current challenges and the developments of photocatalytic U(VI) extraction technology in the future are prospected.