julilili42/papers huggingface dataset:
A Portable low-cost Device to Quantify Advective Gas Fluxes from Mofettes into the Lower Atmosphere: First Application to Starzach Mofettes (Germany)
2023-10-27

In this study, we introduce a portable low-cost device for in situ gas emission measurement from focused point sources of CO2, such as mofettes. We assess the individual sensors' precision with calibration experiments and perform an independent verification of the system's ability to measure gas flow rates in the range of liters per second. The results from one week of continuous CO2 flow observation from a wet mofette at the Starzach site is presented and correlated with the ambient meteorological dynamics. In the observed period, the gas flow rate of the examined mofette exhibits a dominant cycle of around four seconds that is linked to the gas rising upwards through a water column. We find the examined mofette to have a daily emission of 465kg±16%. Furthermore, two events were observed that increased the flow rate abruptly by around 25% within only a few minutes and a decaying period of 24 hours. These types of events were previously observed by others at the same site but dismissed as measurement errors. We discuss these events as a hydrogeological phenomenon similar to cold-water geyser eruptions. For meteorological events like the passages of high pressure fronts with steep changes in atmospheric pressure, we do not see a significant correlation between atmospheric parameters and the rate of gas exhalation in our one-week time frame, suggesting that on short timescales the atmospheric pumping effect plays a minor role for wet mofettes at the Starzach site.
Divergent age-dependent conformational rearrangement within Aβ amyloid deposits in APP23, APPPS1, and AppNL-Fmice
2023-10-27

Abstract Amyloid plaques composed of fibrils of misfolded Aβ peptides are pathological hallmarks of Alzheimer’s disease (AD). Aβ fibrils are polymorphic in their tertiary and quaternary molecular structures. This structural polymorphism may carry different pathologic potency and can putatively contribute to clinical phenotypes of AD. Therefore, mapping of structural polymorphism of Aβ fibrils is valuable to understand disease mechanisms. Here, we investigated how Aβ fibril morphology in situ differs in Aβ plaque of different mouse models expressing familial mutations in the AβPP gene. We used a combination of conformation-sensitive luminescent conjugated oligothiophene (LCO) ligands, Aβ-specific antibodies, and different fluorescence microscopy techniques. LCO fluorescence mapping revealed that mouse models APP23, APPPS1, and App NL-F have different fibril structures depending on AβPP-processing genotype. Co-staining of Aβ-specific antibodies showed that individual plaques from APP23 mice, expressing Swedish mutations (NL) have two distinct fibril polymorph regions of core and corona. The plaque core is predominantly composed of compact Aβ40 fibrils and the corona region is dominated by diffusely packed Aβ40 fibrils. On the other hand, the APP knock-in mouse App NL-F , expressing Iberian mutation (F) along with Swedish mutation has tiny, cored plaques consisting mainly of compact Aβ42 fibrils, vastly different from APP23 even at elevated age up to 21 months. Age dependent polymorph maturation of plaque cores observed for APP23 and APPPS1 mice &gt;12 months, was minuscule in App NL-F . These structural studies of amyloid plaques in situ can map disease-relevant fibril polymorph distributions to guide the design of diagnostic and therapeutic molecules. Significance Alzheimer’s disease (AD) is associated with the formation of deposits in the brain known as Aβ-amyloid plaques. AD can emerge as a sporadic disease or due to familial mutations in genes encoding for Aβ precursor and processing proteins. The Aβ-amyloid found in plaques displays different structures in sporadic AD and in various types of familial AD. We hypothesize that understanding plaque morphology and development is crucial for understanding the initiation and progression of AD. We here compared amyloid structures in three of the most used mouse models of human Aβ-plaque formation. Our findings suggest significant differences in plaque morphologies and structural maturation processes during aging. Our results emphasize that strain-like differences of Aβ-amyloids develop as a function of Aβ precursor protein-processing genetics and age.
Visuo-haptic processing of unfamiliar shapes: Comparing children and adults
2023-10-27

The question of how our sensory perception abilities develop has been an active area of research, establishing trajectories of development from infancy that last well into late childhood and even adolescence. In this context, several studies have established changes in sensory processing of vision and touch around the age of 8 to 9 years. In this experiment, we explored the visual and haptic perceptual development of elementary school children of ages 6–11 in similarity-rating tasks of unfamiliar objects and compared their performance to adults. The participants were presented with parametrically-defined objects to be explored haptically and visually in separate groups for both children and adults. Our results showed that the raw similarity ratings of the children had more variability compared to adults. A detailed multidimensional scaling analysis revealed that the reconstructed perceptual space of the adult haptic group was significantly closer to the parameter space compared to the children group, whereas both groups’ visual perceptual space was similarly well reconstructed. Beyond this, however, we found no clear evidence for an age effect in either modality within the children group. These results suggest that haptic processing of unfamiliar, abstract shapes may continue to develop beyond the age of 11 years later into adolescence.
Mott transition and pseudogap of the square-lattice Hubbard model: results from center-focused cellular dynamical mean-field theory
2023-10-27

The recently proposed center-focused post-processing procedure [Phys. Rev. Research 2, 033476 (2020)] of cellular dynamical mean-field theory suggests that central sites of large impurity clusters are closer to the exact solution of the Hubbard model than the edge sites. In this paper, we systematically investigate results in the spirit of this center-focused scheme for several cluster sizes up to in and out of particle-hole symmetry. First we analyze the metal-insulator crossovers and transitions of the half-filled Hubbard model on a simple square lattice. We find that the critical interaction of the crossover is reduced with increasing cluster sizes and the critical temperature abruptly drops for the cluster. Second, for this cluster size, we apply the center-focused scheme to a system with more realistic tight-binding parameters, investigating its pseudogap regime as a function of temperature and doping, where we find doping dependent metal-insulator crossovers, Lifshitz transitions and a strongly renormalized Fermi-liquid regime. Additionally to diagnosing the real space origin of the suppressed antinodal spectral weight in the pseudogap regime, we can infer hints towards underlying charge ordering tendencies.
Belowground niche partitioning is maintained under extreme drought
2023-10-28

Abstract Belowground niche partitioning presents a key mechanism for maintaining species coexistence and diversity. Its importance is currently reinforced by climate change that alters soil hydrological conditions. However, experimental tests examining the magnitude of its change under climate change are scarce. We combined measurements of oxygen stable isotopes to infer plant water‐uptake depths and extreme drought manipulation in grasslands. Belowground niche partitioning was evidenced by different water‐uptake depths of co‐occurring species under ambient and extreme drought conditions despite an increased overlap among species due to a shift to shallower soil layers under drought. A co‐occurrence of contrasting strategies related to the change of species water‐uptake depth distribution was likely to be key for species to maintain some extent of belowground niche partitioning and could contribute to stabilizing coexistence under drought. Our results suggest that belowground niche partitioning could mitigate negative effects on diversity imposed by extreme drought under future climate.
Differential survival of Staphylococcal species in macrophages
2023-10-28

Abstract Staphylococcus aureus is considered an extracellular pathogen, yet the bacterium is able to survive within and escape from host cells. An agr / sae mutant of strain USA300 is unable to escape from macrophages but can replicate and survive within. We questioned whether such “non‐toxic” S. aureus resembles the less pathogenic coagulase‐negative Staphylococcal (CoNS) species like S. epidermidis , S. carnosus , S. lugdunensis , S. capitis , S. warneri , or S. pettenkoferi. We show that the CoNS are more efficiently killed in macrophage‐like THP‐1 cells or in human primary macrophages. Mutations in katA , copL , the regulatory system graRS , or sigB did not impact bacterial survival in THP‐1 cells. Deletion of the superoxide dismutases impaired S. aureus survival in primary macrophages but not in THP‐1 cells. However, expression of the S. aureus ‐specific sodM in S. epidermidis was not sufficient to protect this species from being killed. Thus, at least in those cells, better bacterial survival of S. aureus could not be linked to higher protection from ROS. However, “non‐toxic” S. aureus was found to be insensitive to pH, whereas most CoNS were protected when phagosomal acidification was inhibited. Thus, species differences are at least partially linked to differences in sensitivity to acidification.
Neural entrainment induced by periodic audiovisual stimulation: A large-sample EEG study
2023-10-28

Stroboscopic or “flicker” stimulation is a form of periodic visual stimulation that induces geometric hallucinations through closed eyelids. While the visual effects of this form of sensory stimulation have received considerable attention, few studies have investigated the neural entrainment effects of periodic visual stimulation. Here, we introduce two variants of the classic flicker paradigm while recording EEG to study neural entrainment effects in a large sample (over 80 participants per condition). In the first condition, we used multimodal stimulation composed of two simultaneous visual strobe frequencies paired with binaural beats which provided auditory stimulation at roughly the same frequency as the slower strobe. We compared this condition to sham stimulation, in which both strobes were set to very low frequencies and in which the binaural beats were absent. Additionally, we compared both conditions to a control group in which participants focused on their breathing during eyes-closed meditation (no stimulation). Our results demonstrate powerful evidence of neural entrainment at the frequency of the slower strobe in the experimental condition. Moreover, our findings resemble effects reported in prior literature using conventional non-invasive techniques for electromagnetic brain stimulation. We argue that stroboscopic stimulation should be further developed along these lines, e.g., as a potential therapeutic technique in psychiatric disorders.
GGC expansion inZFHX3causes SCA4 and impairs autophagy
2023-10-28

Abstract Despite linkage to 16q in 1996, the mutation for spinocerebellar ataxia type 4 (SCA4), a late-onset sensory and cerebellar ataxia, escaped detection for 25 years. Using long- read PacBio-HiFi and ONT-Nanopre sequencing and bioinformatic analysis, we identified expansion of a GGC DNA repeat in a &gt;85% GC-rich region in exon 10 of the ZFHX3 gene coding for poly-glycine (polyG). In a total of 15 nuclear families from Utah and 9 from Europe, the repeat was expanded to &gt;40 repeats in SCA4 patients accompanied by significant phenotypic variation independent of repeat size compared to the most common normal repeat size of 21 repeats. The RE event likely occurred in a frequent Swedish haplotype shared by cases from Utah and Germany. Six characteristic ultra-rare SNVs in the vicinity of the RE in cases from Utah and Lübeck (Germany) indicate a common founder event for some of the patients. In fibroblast and iPS cells, the GGC expansion leads to increased ZFHX3 protein levels, polyG aggregates, and abnormal autophagy, which normalized with ZFHX3 siRNA. Increasing autophagic flux may provide a therapeutic avenue for this novel polyG disease.
Quantitative analysis of the glutathione pathway cellular metabolites by targeted liquid chromatography‐tandem mass spectrometry
2023-10-29

Glutathione, its biosynthesis intermediates, and other thiol metabolites are of central relevance for the redox homeostasis of cells. Their analysis is critical due to the facile interconversion of redox pairs during sampling, sample preparation, and data acquisition, in particular in the electrospray ionization interface. In this work, we propose a fast‐targeted liquid chromatography‐tandem mass spectrometry method to accurately analyze 14 metabolites from the glutathione pathway. N ‐Ethylmaleimide reagent is added with the extraction solvent and instantly stabilizes the thiol‐redox state by derivatization. Liquid chromatographic separation of the analytes was performed on a sub‐2 μm superficially porous hydrophilic interaction liquid chromatography column with sulfobetaine chemistry. Tandem mass spectrometry with triple‐quadrupole mass spectrometry in multiple‐reaction monitoring acquisition mode allowed sensitive detection of the targeted metabolites with limits of quantification in the range of 5–25 nM. Run times of 3 min enable a high throughput analysis of cellular samples. For calibration, a 13 C‐labelled cell extract was used as an internal standard. The method was validated and the concentrations of glutathione and its biosynthesis intermediates were determined in HeLa cells.
Microhymenoptera in roadside verges and the potential of arthropod‐friendly mowing for their preservation
2023-10-29

Abstract The worldwide decline of insects is one of the major challenges for humankind. One of its main drivers is intensive farming, which reduces habitats and food resources for insect populations and causes direct mortality by pesticides. In addition, mowing of grassland poses another threat to insects, especially when it is done frequently, such as in roadside verges. Roadside verges comprise large areas worldwide and can serve as habitats for animals and plants and as corridors to connect populations when they are maintained ecologically, for example when mowing is done arthropod‐friendly and with low frequency. Microhymenoptera are highly diverse, mostly show a parasitoid lifestyle and occur in large numbers in meadows and grasslands. Although they have an important ecological function in regulating their arthropod host populations, they were mostly neglected in studies on the influence of mowing on insects. Therefore, we assessed which families of microhymenoptera occur in roadside verges and meadows, examined if they are affected by the mowing process with a conventional mulching mower, and studied which groups benefit from arthropod‐friendly mowing, using the mowing head Eco 1200 plus from MULAG, and a flushing bar made of track tarpaulin. In our experimental grassland plots, we found specimens of 18 families from the six microhymenoptera superfamilies Chalcidoidea, Ceraphronoidea, Diaprioidea, Ichneumonoidea, Platygastroidea and Proctotrupoidea. Mowing with a conventional mulching mower caused a significant loss of up to 64% for parasitoid Hymenoptera. The Eco 1200 plus showed an arthropod‐friendly effect only on the number of individuals of Chalcidoidea, saving 38% of individuals compared with the conventional mower. The flushing bar showed a significant effect on total number of individuals with a reduction only on Chalcidoidea and a tendency for Ichneumonoidea with 30% and 47%, respectively. Our study demonstrates the detrimental effect of mowing with a conventional mulching mower on microhymenoptera and shows that this effect can be partly reversed for Chalcidoidea and Ichneumonoidea through the arthropod‐friendly mower and a flushing bar. Our study highlights the importance to consider microhymenoptera in the context of insect decline.
Structural variant calling and clinical interpretation in 6224 unsolved rare disease exomes
2023-10-29

Abstract Structural variants (SVs), including large deletions, duplications, inversions, translocations, and complex SVs have the potential to disrupt gene function resulting in rare disease. Nevertheless, current pipelines and clinical decision support systems for exome sequencing (ES) tend to focus on small alterations such as single nucleotide variants (SNVs) and insertions-deletions shorter than 50 base pairs (indels). Additionally, detection and interpretation of large copy-number variants (CNVs) are frequently performed. However, detection of other types of SVs in ES data is hampered by the difficulty of identifying breakpoints in off-target (intergenic or intronic) regions, which makes robust identification of SVs challenging. In this paper, we demonstrate the utility of SV calling in ES resulting in a diagnostic yield of 0.4% (23 out of 5,825 probands) for a large cohort of unsolved patients collected by the Solve-RD consortium. Remarkably, 8 out of 23 pathogenic SV were not found by comprehensive read-depth-based CNV analysis, resulting in a 0.13% increased diagnostic value.
Comparing digital identification guides with traditional guidebooks in a bird field trip
2023-10-29

Field trips provide real-world learning opportunities in biology education as they promote knowledge about nature among other things. As biodiversity is declining knowledge of species is important for understanding and appreciating the natural world and its implications. Many field guides are digitally available, but differences from traditional book-based guides are understudied. This case study compares the effectiveness of a traditional book field guide with a mobile species identification app during a bird field trip on cognitive, motivational, and affective outcomes for college students (N = 133). Linear mixed models indicate no differences in bird species knowledge between the groups before and after the field trip. However, participants in the book group felt more competent and reported a higher interest after the field trip. This suggests that books could probably still add value to learning in the field. They should not be dismissed as they can be useful tools for students by enhancing confidence and contribute to the learning experience in a different way to mobile apps.
Statistical Analysis of Feature-based Molecular Networking Results from Non-Targeted Metabolomics Data
2023-10-29

&amp;lt;p&amp;gt;This folder contains the following used for the publication:&amp;lt;/p&amp;gt;&amp;lt;ul&amp;gt;&amp;lt;li&amp;gt;MASSIVE Repositories: MSV000082312 and MSV000085786. This contains the original data in both .raw and .mzxml formats.&amp;lt;/li&amp;gt;&amp;lt;li&amp;gt;MZmine 3 files: The feature table (SD_BeachSurvey_GapFilled_quant.csv), the associated mgf file, the batch file (.xml) used for MZmine 3 to obtain the feature table, the mgf file for SIRIUS annotations (SD_BeachSurvey_SIRIUS_fixed.mgf)&amp;lt;/li&amp;gt;&amp;lt;li&amp;gt;SIRIUS and CANOPUS summary files (.tsv files)&amp;lt;/li&amp;gt;&amp;lt;li&amp;gt;FBMN Result files&amp;lt;/li&amp;gt;&amp;lt;/ul&amp;gt;
Statistical Analysis of Feature-based Molecular Networking Results from Non-Targeted Metabolomics Data
2023-10-29

This folder contains the following used for the publication: MASSIVE Repositories: MSV000082312 and MSV000085786. This contains the original data in both .raw and .mzxml formats. MZmine 3 files: The feature table (SD_BeachSurvey_GapFilled_quant.csv), the associated mgf file, the batch file (.xml) used for MZmine 3 to obtain the feature table, the mgf file for SIRIUS annotations (SD_BeachSurvey_SIRIUS_fixed.mgf) SIRIUS and CANOPUS summary files (.tsv files) FBMN Result files
Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs
2023-10-30

Immunomodulatory imide drugs (IMiDs) such as thalidomide, pomalidomide, and lenalidomide are the most common cereblon (CRBN) recruiters in proteolysis-targeting chimera (PROTAC) design. However, these CRBN ligands induce the degradation of IMiD neosubstrates and are inherently unstable, degrading hydrolytically under moderate conditions. In this work, we simultaneously optimized physiochemical properties, stability, on-target affinity, and off-target neosubstrate modulation features to develop novel nonphthalimide CRBN binders. These efforts led to the discovery of conformationally locked benzamide-type derivatives that replicate the interactions of the natural CRBN degron, exhibit enhanced chemical stability, and display a favorable selectivity profile in terms of neosubstrate recruitment. The utility of the most potent ligands was demonstrated by their transformation into potent degraders of BRD4 and HDAC6 that outperform previously described reference PROTACs. Together with their significantly decreased neomorphic ligase activity on IKZF1/3 and SALL4, these ligands provide opportunities for the design of highly selective and potent chemically inert proximity-inducing compounds.
Association neurons in the crow telencephalon link visual signs to numerical values
2023-10-30

Many animals can associate signs with numerical values and use these signs in a goal-directed way during task performance. However, the neuronal basis of this semantic association has only rarely been investigated, and so far only in primates. How mechanisms of number associations are implemented in the distinctly evolved brains of other animal taxa such as birds is currently unknown. Here, we explored this semantic number-sign mapping by recording single-neuron activity in the crows’ nidopallium caudolaterale (NCL), a brain structure critically involved in avian numerical cognition. Crows were trained to associate visual shapes with varying numbers of items in a number production task. The responses of many NCL neurons during stimulus presentation reflected the numerical values associated with visual shapes in a behaviorally relevant way. Consistent with the crow’s better behavioral performance with signs, neuronal representations of numerical values extracted from shapes were more selective compared to those from dot arrays. The existence of number association neurons in crows points to a phylogenetic preadaptation of the brains of cognitively advanced vertebrates to link visual shapes with numerical meaning.
Between prudence and paranoia: Theory of Mind gone right, and wrong
2023-10-30

Agents need to be on their toes when interacting with competitive others in order to avoid being duped. Too much vigilance out of context can, however, be detrimental and produce paranoia. Here, we offer a formal account of this phenomenon through the lens of theory of mind. We simulate agents of different depths of mentalization and show how, if aligned well, deep recursive mentalization gives rise to both successful deception as well as reasonable skepticism. However, we also show how, if theory of mind is too sophisticated, agents become paranoid, losing trust and reward in the process. We discuss our findings in light of computational psychiatry and AI safety.