julilili42/papers huggingface dataset:
The impact of emotional stimuli on response inhibition in an inpatient and day-hospital patient psychosomatic cohort
2023-06-30

Objectives To correctly recognize and respond to your counterpart's emotion is essential for a successful get-together. To ensure this, emotional processes and inhibitory control are linked and interact with each other. However, this interaction can be altered in several mental disorders. In a group of psychosomatic patients, we investigated possible differences in the response inhibition between neutral and emotional stimuli and whether a psychosomatic inpatient and day-hospital patient treatment influences response inhibition profiles. Methods One hundred and one patients, diagnosed with different psychiatric diagnoses (77 women, 41.43 ± 13.13 years), completed an emotional stop-signal task (ESST) and an impulsive behavior scale upon admission in an inpatient and day-hospital patient treatment on a psychosomatic ward (T0) and at discharge (T1). Patients with depressive disorders completed the test again after 1 year (follow-up measurement T2, n = 22). Emotional stimuli were angry and neutral faces. Stop-signal reaction time (SSRT) and stop-signal delay (SSD) were calculated as the main behavioral parameters. Results We found a significantly higher SSRT for neutral than angry faces at both admission (8.538 ms, p &amp;lt; 0.001) and discharge (11.142 ms, p &amp;lt; 0.001), with a matching higher SSD for angry than neutral faces at both timepoints (T0: 8.360 ms, p &amp;lt; 0.001, T1: (6.950 ms, p &amp;lt; 0.001). The SSRT for angry faces significantly decreased after treatment (-8.485 ms, p = 0.0110). For neutral faces, the decrease failed to reach significance (−5.881 ms, p = 0.250). A significant decrease in SSRT for neutral faces in patients with depressive disorders was found 1 year after discharge compared with admission (−19.040 ms, p = 0.0380). Conclusion Our data demonstrate a decreased response inhibition for neutral compared with emotional stimuli and an improved response inhibition for angry faces after discharge in a psychosomatic inpatient and day-hospital patient cohort. Additionally, patients with depressive disorders displayed a significantly better response inhibition for neutral faces 1 year after discharge compared with the baseline measurement. With this study, we provide more evidence for altered emotional response inhibition in different mental disorders and a hint that psychosomatic inpatient and day-hospital patient treatment may help to normalize it, even if the effects remained small and it needs further research to prove causality.
History as a visual concept: editing Peter of Poitiers' "Compendium historiae in genealogia Christi"
2023-06-30

&amp;lt;p&amp;gt;The poster will report on a new edition of Peter of Poitiers&amp;#39; &amp;quot;Compendium historiae&amp;quot;. The highly visual chracter of the work makes editing a challenging task and the project team will report on preliminary work during the first year and present an outlook on future work and the project goals.&amp;lt;/p&amp;gt;
Dental Metric on The Late Holocene to Current Era Population from The Lowland Part of Indonesian-Papua
2023-06-30

In an attempt to understand human history in this world, the researchers have applied several methods to identify the group of populations based on the teeth trait characteristic. However, the lack of knowledge about human diversity from several regions in this world derived from the osteological study from archaeological context has limited the understanding of human history in many societies including the populations that occupied the lowland part of Indonesian-Papua. For this, the aim of this study is to reconstruct the population history by employing the dental metric measurement on the 304 samples from the archaeological sites in the lowland parts of Indonesian- Papua which are classified into two different groups, Late Holocene and Current Era. The multivariate statistics analysis was applied to compare the results from the Lowland Indonesian- Papua samples with 17 groups of the population included in this study. The results from the statistics measurement were further used to reconstruct and visualize the phylogenic tree by employing The Neighbor-Joining method and UPGMA algorithm. The result from this clustering group presents the data about East Asian affinities for the Late Holocene and Australo Melanesian for the. Current Era group.
Multidimensional Signals and Analytic Flexibility: Estimating Degrees of Freedom in Human-Speech Analyses
2023-07-01

Recent empirical studies have highlighted the large degree of analytic flexibility in data analysis that can lead to substantially different conclusions based on the same data set. Thus, researchers have expressed their concerns that these researcher degrees of freedom might facilitate bias and can lead to claims that do not stand the test of time. Even greater flexibility is to be expected in fields in which the primary data lend themselves to a variety of possible operationalizations. The multidimensional, temporally extended nature of speech constitutes an ideal testing ground for assessing the variability in analytic approaches, which derives not only from aspects of statistical modeling but also from decisions regarding the quantification of the measured behavior. In this study, we gave the same speech-production data set to 46 teams of researchers and asked them to answer the same research question, resulting in substantial variability in reported effect sizes and their interpretation. Using Bayesian meta-analytic tools, we further found little to no evidence that the observed variability can be explained by analysts’ prior beliefs, expertise, or the perceived quality of their analyses. In light of this idiosyncratic variability, we recommend that researchers more transparently share details of their analysis, strengthen the link between theoretical construct and quantitative system, and calibrate their (un)certainty in their conclusions.
The new frontier of microstructural impurity research in polar ice
2023-07-01

Abstract Deciphering the localisation of solid and dissolved impurities on the micron-scale in glacial ice remains a challenge, but is critical to understand the integrity of ice core records and internal deformation. Here we report on the state-of-the-art in microstructural impurity research by highlighting recent progress in bringing together cryo-Raman spectroscopy and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). We show the potential of both methods and discuss possibilities to improve inter-method approaches aiming for a more holistic understanding of the evolution of impurity localisation throughout the ice column, including post-depositional processes. In this framework, we elaborate on future research priorities such as LA-ICP-MS imaging on firn samples and integrating a large cryo-cell with imaging capabilities.
Statistical Analysis in Clinical and Experimental Medical Research: Simplified Guidance for Authors and Reviewers
2023-07-01

There has been a growing emphasis in recent years on the importance of statistical analysis in medical research.Accurate statistical analysis is essential for ensuring the validity and reliability of research findings, as well as experiment reproducibility.However, many researchers may not have a strong background in statistics, which can lead to problems with study design, data analysis, and result interpretation.The main takeaway from our extensive editorial experience is that basic statistical rules are not routinely followed by the authors, including extremely small group size, data distribution assessment, inappropriate use of parametric tests and pseudoreplication, and this is missed during the peer review process.To address this issue we are, hereby, providing guidance for authors and peer reviewers on medical statistics.These guidelines provide a helpful framework for the researchers to follow when designing studies and analysing data, and for the reviewers to use when assessing the quality and accuracy of the manuscripts.Our authors are kindly requested to provide a detailed data and statistical analysis paragraph within the Methods section to facilitate the implementation of these guidelines.
Recent evolution of flowering time across multiple European plant species correlates with changes in aridity
2023-07-01

Abstract Ongoing global warming and increasing drought frequencies impact plant populations and potentially drive rapid evolutionary adaptations. Historical comparisons, where plants grown from seeds collected in the past are compared to plants grown from freshly collected seeds from populations of the same sites, are a powerful method to investigate recent evolutionary changes across many taxa. We used 21–38 years old seeds of 13 European plant species, stored in seed banks and originating from Mediterranean and temperate regions, together with recently collected seeds from the same sites for a greenhouse experiment to investigate shifts in flowering phenology as a potential result of adaptive evolution to changes in drought intensities over the last decades. We further used single nucleotide polymorphism (SNP) markers to quantify relatedness and levels of genetic variation. We found that, across species, current populations grew faster and advanced their flowering. These shifts were correlated with changes in aridity at the population origins, suggesting that increased drought induced evolution of earlier flowering, whereas decreased drought lead to weak or inverse shifts in flowering phenology. In five out of the 13 species, however, the SNP markers detected strong differences in genetic variation and relatedness between the past and current populations collected, indicating that other evolutionary processes may have contributed to changes in phenotypes. Our results suggest that changes in aridity may have influenced the evolutionary trajectories of many plant species in different regions of Europe, and that flowering phenology may be one of the key traits that is rapidly evolving.
Inferring human neutral genetic variation from craniodental phenotypes
2023-07-01

Abstract There is a growing consensus that global patterns of modern human cranial and dental variation are shaped largely by neutral evolutionary processes, suggesting that craniodental features can be used as reliable proxies for inferring population structure and history in bioarchaeological, forensic, and paleoanthropological contexts. However, there is disagreement on whether certain types of data preserve a neutral signature to a greater degree than others. Here, we address this unresolved question and systematically test the relative neutrality of four standard metric and nonmetric craniodental data types employing an extensive computational genotype–phenotype comparison across modern populations from around the world. Our computation draws on the largest existing data sets currently available, while accounting for geographically structured environmental variation, population sampling uncertainty, disparate numbers of phenotypic variables, and stochastic variation inherent to a neutral model of evolution. Our results reveal that the four data types differentially capture neutral genomic variation, with highest signals preserved in dental nonmetric and cranial metric data, followed by cranial nonmetric and dental metric data. Importantly, we demonstrate that combining all four data types together maximizes the neutral genetic signal compared with using them separately, even with a limited number of phenotypic variables. We hypothesize that this reflects a lower level of genetic integration through pleiotropy between, compared to within, the four data types, effectively forming four different modules associated with relatively independent sets of loci. Therefore, we recommend that future craniodental investigations adopt holistic combined data approaches, allowing for more robust inferences about underlying neutral genetic variation.
Radiation and Dose-densification of R-CHOP in Aggressive B-cell Lymphoma With Intermediate Prognosis: The UNFOLDER Study
2023-07-01

UNFOLDER (Unfavorable Young Low-Risk Densification of R-Chemo Regimens) is an international phase-3 trial in patients 18–60 years with aggressive B-cell lymphoma and intermediate prognosis defined by age-adjusted International Prognostic Index (aaIPI) of 0 and bulky disease (≥7.5 cm) or aaIPI of 1. In a 2 × 2 factorial design patients were randomized to 6× R-CHOP-14 or 6× R-CHOP-21 (rituximab, cyclophosphamide, doxorubicin, vincristine, and prediso[lo]ne) and to consolidation radiotherapy to extralymphatic and bulky disease or observation. Response was assessed according to the standardized response criteria published in 1999, not including F-18 fluordesoxyglucose positron emission tomography/computed tomography (FDG-PET). Primary endpoint was event-free survival (EFS). A total of 695 of 700 patients were eligible for the intention-to-treat analysis. Totally 467 patients qualified for radiotherapy of whom 305 patients were randomized to receive radiotherapy (R-CHOP-21: 155; R-CHOP-14: 150) and 162 to observation (R-CHOP-21: 81, R-CHOP-14: 81). Two hundred twenty-eight patients not qualifying for radiotherapy were randomized for R-CHOP-14 versus R-CHOP-21. After a median observation of 66 months 3-year EFS was superior in the radiotherapy-arm versus observation-arm (84% versus 68%; P = 0.0012), due to a lower rate of partial responses (PR) (2% versus 11%). PR often triggered additional treatment, mostly radiotherapy. No significant difference was observed in progression-free survival (PFS) (89% versus 81%; P = 0.22) and overall survival (OS) (93% versus 93%; P = 0.51). Comparing R-CHOP-14 and R-CHOP-21 EFS, PFS and OS were not different. Patients randomized to radiotherapy had a superior EFS, largely due to a lower PR rate requiring less additional treatment (NCT00278408, EUDRACT 2005-005218-19).
A metabologenomics approach to unlock the metabolome of the novel Antarctic deep-sea isolate Lacinutrix shetlandiensis sp. nov. WUR7
2023-07-01

Abstract The South Shetland Trough, Antarctica, is an underexplored region for microbiological and biotechnological exploitation. Herein, we describe the isolation and characterization of the novel bacterium Lacinutrix shetlandiensis sp. nov. WUR7 from a deep-sea environment. We explored its chemical diversity via a metabologenomics approach, wherein the OSMAC strategy was strategically employed to upregulate cryptic genes for secondary metabolite production. Based on hybrid de novo whole genome sequencing and digital DNA–DNA hybridization, isolate WUR7 was identified as a novel species from the Gram-negative genus Lacinutrix. Its genome was mined for the presence of biosynthetic gene clusters with limited results. However, extensive investigation of its metabolism uncovered an unusual tryptophan decarboxylase with high sequence homology and conserved structure of the active site as compared to ZP_02040762, a highly specific tryptophan decarboxylase from Ruminococcus gnavus. Therefore, WUR7's metabolism was directed toward indole-based alkaloid biosynthesis by feeding it with L-tryptophan. As expected, its metabolome profile changed dramatically, by triggering the extracellular accumulation of a massive array of metabolites unexpressed in the absence of tryptophan. Untargeted LC-MS/MS coupled with molecular networking, followed along with chemoinformatic dereplication, allowed for the annotation of 10 indole alkaloids, belonging to β-carboline, bisindole, and monoindole classes, alongside several unknown alkaloids. These findings guided us to the isolation of a new natural bisindole alkaloid 8,9-dihydrocoscinamide B (1), as the first alkaloid from the genus Lacinutrix, whose structure was elucidated on the basis of extensive 1D and 2D NMR and HR-ESIMS experiments. This comprehensive strategy allowed us to unlock the previously unexploited metabolome of L. shetlandiensis sp. nov. WUR7.
SBOannotator: a Python tool for the automated assignment of systems biology ontology terms
2023-07-01

Abstract Motivation The number and size of computational models in biology have drastically increased over the past years and continue to grow. Modeled networks are becoming more complex, and reconstructing them from the beginning in an exchangeable and reproducible manner is challenging. Using precisely defined ontologies enables the encoding of field-specific knowledge and the association of disparate data types. In computational modeling, the medium for representing domain knowledge is the set of orthogonal structured controlled vocabularies named Systems Biology Ontology (SBO). The SBO terms enable modelers to explicitly define and describe model entities, including their roles and characteristics. Results Here, we present the first standalone tool that automatically assigns SBO terms to multiple entities of a given SBML model, named the SBOannotator. The main focus lies on the reactions, as the correct assignment of precise SBO annotations requires their extensive classification. Our implementation does not consider only top-level terms but examines the functionality of the underlying enzymes to allocate precise and highly specific ontology terms to biochemical reactions. Transport reactions are examined separately and are classified based on the mechanism of molecule transport. Pseudo-reactions that serve modeling purposes are given reasonable terms to distinguish between biomass production and the import or export of metabolites. Finally, other model entities, such as metabolites and genes, are annotated with appropriate terms. Including SBO annotations in the models will enhance the reproducibility, usability, and analysis of biochemical networks. Availability and implementation SBOannotator is freely available from https://github.com/draeger-lab/SBOannotator/.
Theory Matters
2023-07-01

Abstract: Following an extended perspective of evidence-centered design, this study provides a methodological exemplar of the theory-based construction of process indicators from log data. We investigated decision-making processes in web search as the target construct, assuming that individuals follow a heuristic search (focusing on search results vs. websites as a primary information source) and stopping rule (following a satisficing vs. sampling strategy). Drawing on these assumptions, we describe our reasoning for identifying the empirical evidence needed and selecting an assessment to obtain this evidence to derive process indicators that represent groups differentiated by search and stopping rule combinations. To evaluate our approach, we reanalyzed the processing behavior of 150 university students who were requested in four tasks to select a specific website from a list of five search results. We determined the process indicators per item and conducted multiple cluster analyses to investigate group recovery. For each item, we found three clusters, two of which matched our assumptions. Additionally, we explored the consistency of students’ cluster membership across items and investigated their relationship with students’ skills in evaluating online information. Based on the results, we discuss the tradeoff between construct breadth and process elaboration for deriving meaningful process indicators.
Mutant SPART causes defects in mitochondrial protein import and bioenergetics reversed by Coenzyme Q
2023-07-01

Pathogenic variants in SPART cause Troyer syndrome, characterized by lower extremity spasticity and weakness, short stature and cognitive impairment, and a severe mitochondrial impairment. Herein, we report the identification of a role of Spartin in nuclear-encoded mitochondrial proteins. SPART biallelic missense variants were detected in a 5-year-old boy with short stature, developmental delay and muscle weakness with impaired walking distance. Patient-derived fibroblasts showed an altered mitochondrial network, decreased mitochondrial respiration, increased mitochondrial reactive oxygen species and altered Ca 2+ versus control cells. We investigated the mitochondrial import of nuclear-encoded proteins in these fibroblasts and in another cell model carrying a SPART loss-of-function mutation. In both cell models the mitochondrial import was impaired, leading to a significant decrease in different proteins, including two key enzymes involved in CoQ10 (CoQ) synthesis, COQ7 and COQ9, with a severe reduction in CoQ content, versus control cells. CoQ supplementation restored cellular ATP levels to the same extent shown by the re-expression of wild-type SPART, suggesting CoQ treatment as a promising therapeutic approach for patients carrying mutations in SPART .
Process Data in Computer-Based Assessment
2023-07-01

Abstract: This editorial provides a comprehensive framework and overview of potential uses and next steps in research on process data in computer-based assessments, expanding toward broad perspectives on the field and an exploration of future directions and emerging trends. After briefly reflecting on the evolution of process data use in research and assessment practice, we discuss three key challenges, namely (1) the theoretical grounding and validation of process data indicators, (2) assessment design for process data, and (3) ethical standards. By considering best practice approaches in all three areas and current discussions in the literature, we conclude that a focus is needed on the following three areas: (1) strong, holistic theoretical frameworks for validating process data, (2) reliable, standardized data collections, preferably with a top-down approach to developing test items and preregistered hypotheses, and (3) ethical norms for data collection, data use, and guidelines for responsible inference, including restraints in decisions based on process data.
Volumetric measurements of weak current–induced magnetic fields in the human brain at high resolution
2023-07-01

Abstract Purpose Clinical use of transcranial electrical stimulation (TES) requires accurate knowledge of the injected current distribution in the brain. MR current density imaging (MRCDI) uses measurements of the TES‐induced magnetic fields to provide this information. However, sufficient sensitivity and image quality in humans in vivo has only been documented for single‐slice imaging. Methods A recently developed, optimally spoiled, acquisition‐weighted, gradient echo–based 2D‐MRCDI method has now been advanced for volume coverage with densely or sparsely distributed slices: The 3D rectilinear sampling (3D‐DENSE) and simultaneous multislice acquisition (SMS‐SPARSE) were optimized and verified by cable‐loop experiments and tested with 1‐mA TES experiments for two common electrode montages. Results Comparisons between the volumetric methods against the 2D‐MRCDI showed that relatively long acquisition times of 3D‐DENSE using a single slab with six slices hindered the expected sensitivity improvement in the current‐induced field measurements but improved sensitivity by 61% in the Laplacian of the field, on which some MRCDI reconstruction methods rely. Also, SMS‐SPARSE acquisition of three slices, with a factor 2 CAIPIRINHA (controlled aliasing in parallel imaging results in higher acceleration) acceleration, performed best against the 2D‐MRCDI with sensitivity improvements for the and Laplacian noise floors of 56% and 78% (baseline without current flow) as well as 43% and 55% (current injection into head). SMS‐SPARSE reached a sensitivity of 67 pT for three distant slices at 2 × 2 × 3 mm 3 resolution in 10 min of total scan time, and consistently improved image quality. Conclusion Volumetric MRCDI measurements with high sensitivity and image quality are well suited to characterize the TES field distribution in the human brain.