julilili42/papers huggingface dataset:
Subspace partitioning in human prefrontal cortex resolves cognitive interference
2022-11-16

Abstract Human prefrontal cortex (PFC) constitutes the structural basis underlying flexible cognitive control, where mixed-selective neural populations encode multiple task-features to guide subsequent behavior. The mechanisms by which the brain simultaneously encodes multiple task-relevant variables while minimizing interference from task-irrelevant features remain unknown. Leveraging intracranial recordings from the human PFC, we first demonstrate that competition between co-existing representations of past and present task variables incurs a behavioral switch cost. Our results reveal that this interference between past and present states in the PFC is resolved through coding partitioning into distinct low-dimensional neural states; thereby strongly attenuating behavioral switch costs. In sum, these findings uncover a fundamental coding mechanism that constitutes a central building block of flexible cognitive control.
SWATH Mass Spectrometry-Based CSF Proteome Profile of GBA-Linked Parkinson’s Disease Patients
2022-11-16

β-glucocerebrosidase (GBA)-associated mutations are a significant risk factor for Parkinson’s disease (PD) that aggravate the disease pathology by upregulating the deposition of α-Synuclein (α-Syn). The resultant clinical profile varies for PD patients without GBA mutations. The current study aimed to identify the proteomic targets involved in the pathogenic pathways leading to the differential clinical presentation of GBA-associated PD. CSF samples (n = 32) were obtained from PD patients with GBA mutations (n = 22), PD patients without GBA mutations (n = 7), and healthy controls that were carriers of GBA mutations (n = 3). All samples were subjected to in-gel tryptic digestion followed by the construction of the spectral library and quantitative SWATH-based analysis. CSF α-Syn levels were reduced in both PDIdiopathic and PDGBA cases. Our SWATH-based mass spectrometric analysis detected 363 proteins involved in immune response, stress response, and cell signaling in various groups. Intergroup analysis showed that 52 proteins were significantly up- or downregulated in various groups. Of these 52 targets, 20 proteins were significantly altered in PDGBA cases only while 2 showed different levels in PDIdiopathic patients. Our results show that the levels of several pathologically relevant proteins, including Contactin-1, Selenium-binding protein 1, Adhesion G Protein-Coupled Receptor, and Apolipoprotein E are significantly different among the sporadic and genetic variants of PD and hint at aggravated synaptic damage, oxidative stress, neuronal loss, and aggregation of α-Syn in PDGBA cases.
Understanding the interplay between targeted motivation interventions and motivational teaching practices in mathematics classrooms
2022-11-16

Abstract Prior research has shown that brief motivation interventions, such as interventions targeting students’ perceptions concerning relevance of the learning material, can have long-lasting effects on students’ motivation and performance. However, the educational contexts in which these interventions have been implemented have their own motivational affordances, such as the extent to which teachers support students’ perceptions of relevance in regular classes. According to the seed-and-soil hypothesis for the effectiveness of psychological interventions, such interventions can be seen like a “seed” that needs to be implemented in a supportive educational context (i.e., the “soil”) in order to work. Therefore, in this study we examined the interplay between a one-time relevance intervention implemented in mathematics classrooms and the mathematics teacher’s relevance support as perceived by the students before and after the intervention. Data stemmed from a cluster-randomized controlled trial with 79 ninth-grade mathematics classes ( N = 1744 students) in which the intervention was implemented by the mathematics teacher or a master’s student, both trained for this purpose. Multilevel moderation models showed that both intervention conditions had larger effects when students perceived higher relevance support before or after the intervention, thus providing support for the seed-and-soil hypothesis. Furthermore, multilevel mediation models indicated a positive effect of the teacher condition on perceived relevance support at posttest compared with the control condition, which partly explained the positive effect of this intervention condition on utility value at follow-up. The results shed light on the contexts in which these interventions are most effective and the mechanisms through which they work.
Predicting the steady-state isochronal stratigraphy of ice shelves using observations and modeling (model data)
2022-11-16

Modeling setup and results for the age field and stratigraphy of the Roi Baudouin ice shelf in Antarctica using Elmer/Ice presented in the publication Predicting the steady-state isochronal stratigraphy of ice shelves using observations and modeling in The Cryosphere.
Altruism during extra-corporeal detoxification in insects
2022-11-16

Altruism is common in eusocial insects. Here, we report on a yet unexplored altruistic extra-corporeal detoxification of insecticides in the non-eusocial Drosophila melanogaster. Wild-type flies incubated with DDT, a contact insecticide, in a closed environment die as expected. However, incubation of a second cohort in the same environment after removal of the dead flies was not lethal. Consistent to the kin selection theory, the effect is significantly lower if un-related wild-type flies are used in the assay. This indicates kin selection. Incubation assays with Chlorpyrifos, another contact insecticide, yielded identical results, while incubation assays with Chlorantraniliprole, again a contact insecticide, was toxic for the second cohort of flies. Consequently, following individuals might be saved from intoxication and therefore, this phenomenon may serve as an example of non-eusocial insect altruism. This novel program is, however, not omnipotent as it targets certain xenobiotics while others remain active. The molecular and genetic mechanisms await identification and characterization.
Sleep electroencephalogram (EEG) oscillations and associated memory processing during childhood and early adolescence.
2022-11-17

The architecture of sleep undergoes distinct changes during childhood and early adolescence. Slow wave sleep is involved in memory processing and may support active consolidation of newly encoded representations to support the formation of abstracted "gist" memories. Here, we examined sleep and overnight memory formation in German school children (<i>n</i> = 33) between 7 and 15 years of age, after the encoding phase of a verbal Deese-Roediger-McDermott (DRM) task. Effects of age were analyzed on sleep electroencephalogram (EEG) signatures of memory processing during nonrapid eye movement (NonREM) sleep, and the overnight formation of veridical and gist-based memories. Increasing age decreases time spent in slow wave sleep, and slow wave activity, whereas density and amplitude of fast sleep spindles in NonREM sleep were increased. Moreover, fast spindles were more consistently and more closely coupled to the upstate of the slow oscillation in the older children. Also, veridical and gist-based recall of words after sleep increased with age. Notably, a closer slow oscillation upstate-fast spindle coupling predicted veridical recall of words, and this relationship was found independent of age. Memory performance in the sleeping children did not differ from that of an age-matched control group (<i>n</i> = 32) tested over a daytime wake retention interval, with adolescents even showing superior veridical recall after wake. Our findings suggest that slow oscillation-spindle coupling as a mechanism of sleep-dependent memory formation becomes increasingly relevant during childhood and early adolescence. However, wake-associated mechanisms similarly effective in forming medium-term memory exist in this age as well. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
Research campaign: Macroscopic quantum resonators (MAQRO)
2022-11-17

Abstract The objective of the proposed macroscopic quantum resonators (MAQRO) mission is to harness space for achieving long free-fall times, extreme vacuum, nano-gravity, and cryogenic temperatures to test the foundations of physics in macroscopic quantum experiments at the interface with gravity. Developing the necessary technologies, achieving the required sensitivities and providing the necessary isolation of macroscopic quantum systems from their environment will lay the path for developing novel quantum sensors. Earlier studies showed that the proposal is feasible but that several critical challenges remain, and key technologies need to be developed. Recent scientific and technological developments since the original proposal of MAQRO promise the potential for achieving additional science objectives. The proposed research campaign aims to advance the state of the art and to perform the first macroscopic quantum experiments in space. Experiments on the ground, in micro-gravity, and in space will drive the proposed research campaign during the current decade to enable the implementation of MAQRO within the subsequent decade.
Novel Approach to Pharmaceutical 3D-Printing Omitting the Need for Filament—Investigation of Materials, Process, and Product Characteristics
2022-11-17

The utilized 3D printhead employs an innovative hot-melt extrusion (HME) design approach being fed by drug-loaded polymer granules and making filament strands obsolete. Oscillatory rheology is a key tool for understanding the behavior of a polymer melt in extrusion processes. In this study, small amplitude shear oscillatory (SAOS) rheology was applied to investigate formulations of model antihypertensive drug Metoprolol Succinate (MSN) in two carrier polymers for pharmaceutical three-dimensional printing (3DP). For a standardized printing process, the feeding polymers viscosity results were correlated to their printability and a better understanding of the 3DP extrudability of a pharmaceutical formulation was developed. It was found that the printing temperature is of fundamental importance, although it is limited by process parameters and the decomposition of the active pharmaceutical ingredients (API). Material characterization including differential scanning calorimetry (DSC) and thermogravimetric analyses (TGA) of the formulations were performed to evaluate component miscibility and ensure thermal durability. To assure the development of a printing process eligible for approval, all print runs were investigated for uniformity of mass and uniformity of dosage in accordance with the European Pharmacopoeia (Ph. Eur.).
Epigenetic variation in the Lombardy poplar along climatic gradients is independent of genetic structure and persists across clonal reproduction
2022-11-17

Summary - Environmental changes can trigger phenotypic variation in plants through epigenetic mechanisms, but strong genetic influences make it difficult to isolate and study epigenetic effects. Clonal trees with low genetic variation, such as the Lombardy poplar (Populus nigra cv. ‘Italica’ Duroi), offer a unique system to study epigenetic variation associated with the environment. - We collected cuttings (ramets) of Lombardy poplar along a wide geographical range in Europe. We performed whole-genome-bisulfite sequencing of 164 ramets grown in a common garden and of a subset of 35 of the original parental individuals. Using historical bioclimatic data, we tested the relationship between DNA methylation and climatic gradients. - We found that average methylation levels in TEs and promoter regions correlate with biologically relevant climatic variables. Furthermore, we observed that DNA methylation was transmitted to the next clonal generation, but a fraction of the methylome changed relatively fast when comparing the parental individuals with the clonal offspring. - Our results suggest that the poplar methylome is a dynamic layer of information that can be transmitted to the clonal offspring and potentially affect how poplars acclimate to new environmental conditions.
Producing Open Data
2022-11-17

Open data offer the opportunity to economically combine data into large-scale datasets, fostering collaboration and re-use in the interest of treating researchers’ resources as well as study participants with care. Whereas advantages of utilising open data might be self-evident, the production of open datasets also challenges individual researchers. This is especially true for open data that include personal data, for which higher requirements have been legislated. Mainly building on our own experience as scholars from different research traditions (life sciences, social sciences and humanities), we describe best-practice approaches for opening up research data. We reflect on common barriers and strategies to overcome them, condensed into a step-by-step guide focused on actionable advice in order to mitigate the costs and promote the benefit of open data on three levels at once: society, the disciplines and individual researchers. Our contribution may prevent researchers and research units from re-inventing the wheel when opening data and enable them to learn from our experience.
Biallelic PRMT7 pathogenic variants are associated with a recognizable syndromic neurodevelopmental disorder with short stature, obesity, and craniofacial and digital abnormalities
2022-11-17

This study further delineates and expands the molecular, phenotypic spectrum and natural history of PRMT7-related syndrome characterized by a neurodevelopmental disorder with skeletal, growth, and endocrine abnormalities.
Transcription Properties of Beta-HPV8 and HPV38 Genomes in Human Keratinocytes
2022-11-17

High-risk HPV, from the genus alpha, can cause anogenital or oropharyngeal malignancies. The oncogenic properties of high-risk HPV are important for their differentiation-dependent replication in human keratinocytes, the natural target cell for HPV.
Halogens in serpentinised-troctolites from the Atlantis Massif: implications for alteration and global volatile cycling
2022-11-17

Abstract The concentrations of halogens in serpentinised olivine-rich lithologies in the lower oceanic crust (e.g. troctolites and wehrlites) and altered-gabbros, recovered from IODP Hole U1309D on the Atlantis Massif of the Mid-Atlantic Ridge, are contrasted. The aims were to evaluate if serpentinisation of lower crustal lithologies could significantly contribute to the volatile budget of oceanic lithosphere and test if serpentinites formed from seawater preserve seawater-like halogen signatures. The olivine-rich lithologies are variably serpentinised by lizardite with minor chrysotile. The maximum concentrations of halogens in the most strongly serpentinised samples are 70 μg/g F, 2,100 μg/g Cl, 9,800 ng/g Br and 8 ng/g I. In comparison, the maxima in interlayered gabbros are 200 μg/g F, 130 μg/g Cl, 400 ng/g Br and 9 ng/g I. The Br/Cl ratios of the altered gabbros are strongly influenced by the presence of amphibole, which preferentially incorporates the smaller halides. The serpentinised lithologies have low F/Cl ratios, due to their strong enrichment in seawater-derived Cl, and they have Br/Cl and I/Cl ratios intermediate of unaltered oceanic crust and seawater-derived fluids. Br/Cl and I/Cl ratios similar to seawater are best preserved in the most Cl-rich samples consistent with these ratios fingerprinting the fluid responsible for serpentinisation. Serpentinites formed from seawater in the lower ocean crust and lithosphere are likely to have low I/Cl ratios. Serpentinsed lithologies in the lower crust (and mantle lithosphere) could, therefore, significantly contribute to halogen subduction helping to explain the range of I/Cl ratios in arc lavas and a proposed decrease of mantle I/Cl over time.
Transcriptional adaptation of staphylococci during colonization of the authentic human environment: An overview of transcriptomic changes and their relationship to physiological conditions
2022-11-17

Staphylococci are commensals of human skin and mucous membranes, but some species can also cause serious infections. Host niches during both colonization and infection differ greatly and are characterized by specific environmental conditions (pH, temperature, oxygen, nutrient availability, and microbiota) that can affect gene expression and virulence of microbes. To successfully occupy extremely different habitats at different anatomical sites, Staphylococci are equipped with a variety of regulatory elements that allow specific adaptation to the changing environments. Not surprisingly, gene expression in vivo can be significantly different from the expression pattern observed in vitro . Niche specific stimuli that influence the bacterial ability to either cause infection or maintain colonization are only partially understood. Here, we describe habitat specific conditions and discuss the available literature analyzing staphylococcal gene expression, focusing on Staphylococcus aureus and S. epidermidis during colonization of the nose and skin.
Pre-registered Replication of the Gateway Belief Model – Results from a Representative German Sample
2022-11-17

Consensus messaging aims to increase climate change awareness by communicating the scientific consensus on anthropogenic climate change. According to the gateway belief model, consensus messages improve the estimation of scientific consensus, which then causes subsequent changes in personal attitudes about climate change. Most studies investigating this communication strategy refer to US-American samples. Therefore, the present study replicated existing research on consensus messaging using a national representative German sample (N = 1,110), which represents a high-consensus context. We further tested confidence in perceived scientific consensus as moderator variable in the gateway belief model. The consensus message improved the participants’ estimates of scientific consensus on anthropogenic climate change but had no effect on the climate change attitudes (belief in climate change, belief in human causation of climate change, worry about climate change, support for action on climate change). Regarding the moderation analysis, confidence in perceived scientific consensus did not moderate the consensus messaging process. However, we found a significant main effect of confidence in perceived scientific consensus on worry about climate change. This finding adds to existing literature arguing that metacognition might influence political and societal beliefs.
Resemblance of the Recurrence Patterns in Primary Systemic, Primary Surgery and Secondary Oncoplastic Surgery
2022-11-17

Purpose: Surgical interventions tend to have an effect on the generation of recurrences in tumor patients due to the anesthesia involved as well as tissue damage and subsequent inflammation. This can also be found in patients with breast cancer. Methods: In this multicenter study, we investigated data of 632 patients with breast cancer and the subsequent diagnosis of a recurrence. The patient data were acquired from 1 January 2006 to 31 December 2019 in eight different centers in Germany. The data sets were separated into those with primary surgery, primary systemic therapy with subsequent surgery, and reconstructive surgery. Three different starting points for observation were defined: the date of diagnosis, the date of first surgery, and the date of reconstructive surgery, if applicable. The observational period was divided into steps of six months and maxima of recurrences were compared. Furthermore, the variance was calculated using the difference of the distribution in percent. Results: The descriptive analysis showed no resemblance between the groups. The variance of the difference of the recurrence rates analysis using the surgical date as the starting point showed similarities in the age subgroup. Conclusion: Our clinical analysis shows different metastatic behavior in different analysis and treatment regimes. These findings justify further investigations on a larger database. These results may possibly identify an improved follow-up setting depending on tumor stage, biology, treatment, and patient factors (i.e., age, ...).
Straight roads into nowhere – obvious and not-so-obvious biological models for ferrophobic surfaces
2022-11-17

There are currently efforts to improve strategies for biomimetic approaches, to identify pitfalls and to provide recommendations for a successful biomimetic work flow. In this contribution, a case study of a concrete biomimetic project is described that started with a posed technical problem for which seemingly obvious biological models exist. The technical problem was to devise a ferrophobic surface that prevents the contact between the copper surface of a tuyère (a water cooled aeration pipe within a blast furnace) and liquid iron. Therefore, biological external surfaces that strongly repel liquids appeared to be suitable, particularly the hair cover of the water fern Salvinia molesta and the surface of Collembola (an arthropod group). It turned out, however, that it was not feasible to realise the functional structures of both biological models for the tuyère problem. Instead, a seemingly not obvious biological model was identified, namely micropores within the cell walls of water-transporting conduits of plants that connect the conduits to a three-dimensional flow network. These specially shaped pores are assumed to be able to create stable air bodies, which support the refilling of embolised conduits. By adopting the shape of these micropores, a successful prototype for a ferrophobic copper surface repelling liquid iron could be devised. This case study illustrates that straight road maps from technical problems to obvious biological models are no guarantee for success, and that it is difficult to arrive at a formalised biomimetic working scheme. Rather, a broad understanding of biological function and its complexity is beneficial.
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
2022-11-18

Abstract With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.