julilili42/papers huggingface dataset:
Grassland restoration on former arable land: Fine‐scale grass accumulation and damaged soil conditions limit species establishment
2022-04-01

Abstract Question Which vegetation and soil parameters limit species establishment in restored grasslands? Do these parameters operate predominantly on a fine or a community scale? Location White Carpathian Mountains, SE Czech Republic. Methods We compared 16 grasslands restored on former arable land with 9 well‐preserved reference grasslands. We sampled cover of plant species in plots of 2 m × 2 m (community scale) in which four 20 cm × 20 cm subplots (fine scale) were nested. We quantified fine‐scale heterogeneity as the mean Sørensen dissimilarity index among the species composition of the subplots. To characterize site conditions, we analyzed soil properties, above‐ground plant biomass and its nutrient content. Results Restored grasslands had a lower number of plant species at both the community and fine scales. Species number at the community scale was positively associated with the species number at the fine scale (irrespective of grassland type), but was not associated with fine‐scale heterogeneity. This indicates the importance of fine‐scale biotic interactions for overall species diversity. In support of this, in both grassland types, the species number was negatively associated with the cover of grasses, but only at the fine scale. Total cover (but not the biomass) was lower in restored grasslands, and was positively related with species number, particularly in restored grasslands. This indicates that the lower species number in the restored grasslands mainly resulted from deteriorated abiotic conditions. Such deterioration of the plant environment can be attributed particularly to the soil of the restored, formerly plowed grasslands. They had a lower soil organic matter content and a higher proportion of fine soil particles (silt and clay), indicating reduced soil water availability. The lower soil N content of restored grasslands was also reflected in the nutrient content of plant biomass, where lower N:P and N:K ratios indicated a limitation of plant growth by N‐supply. Conclusion The species number was generally driven by fine‐scale biotic interactions, which operated similarly in both grassland types. The reduced number of plant species in restored grasslands is the result of several factors among which altered soil conditions in the former arable land appears to be highly important.
CBM Performance for Multi-Differential Measurements of Proton and Charged Kaon Directed Flow
2022-04-01

Performance of the Compressed Baryonic Matter (CBM) experiment for the measurement of proton and positively charged kaon directed flow is presented as a function of collision centrality, particle transverse momentum and rapidity. The analysis is based on Au + Au collisions at the top SIS100 beam momentum of 12 GeV/c simulated with the DCM-QGSM-SMM event generator and transported through the CBM material using GEANT4 Monte-Carlo package. The calculations of flow coefficients are performed with respect to projectile spectator symmetry plane. A data-driven procedure is used for event reconstruction, centrality determination, particle identification and symmetry plane reconstruction. Dependence of the results on the details of the spectator symmetry plane estimation and purity of particle identification are studied by comparing the reconstructed signals with the event generator input.
Conviviality, Ecocriticism and the Anthropocene An Approach to Postcolonial Resistance and Ecofeminism in the Latin American Jungle Novel
2022-04-01

In the context of the Anthropocene, ecocriticism is gaining an increasingly important role, foregrounding the inextricability of nature and culture, on the one hand, and the postcolonial cultural representation from the Global South on the other. Against this backdrop, the present working paper will focus on the Latin American context, suggesting that conviviality signifies a crucial contribution to the discourse about the Anthropocene and serves as an ideal theoretical framework for the research project on “Postcolonial Resistance and Ecofeminism in the Latin American Jungle novel”, which is outlined at the end of the paper.
The Greek Fragments of the Works of Māšāʾallāh ibn Aṯarī
2022-04-01

This article provides an overview of the Greek mentions of the Arabic astrologers Māšāʾallāh ibn Aṯarī al-Baṣrī and Abū Maʿšar al-Balḫī, together with the edition of the Greek fragments explicitly attributed to Māšāʾallāh, based on all their witnesses. Moreover, a general introduction to the Greek tradition of the two astrologers and a discussion of their mentions in the manuscript Vatican City, Biblioteca Apostolica Vaticana, Vat. gr. 1056 are supplied.
Total Body PET/CT Biograph Vision Quadra Performance Studies
2022-04-01

Ziel/Aim We aim to gain a better understanding of how to optimize application-specific protocols and analyses for the Biograph Vision Quadra (Siemens Healthineers, Erlangen, Germany) by performing comprehensive phantom measurements, postprocessing and simulations.
ASSESSMENT OF SUBMUCOSAL LAYER QUALITY OF COLORECTAL EMR VERSUS ESD SPECIMENS – A PILOT STUDY
2022-04-01

Aims Analysis of submucosal invasion depth is important to adequately predict lymph node metastasis risk after endoscopic resection of early colorectal cancer. Little is known about the quality of submucosal layer in specimens obtained by standard EMR or ESD. Here, we compare morphometric data on submucosal layer quality in routine histopathology specimens from EMR versus ESD.
Performance Improvements of the CareMiBrain Brain PET Scanner
2022-04-01

Ziel/Aim Our group envisioned in a first step to comprehensively evaluate the performance of the CareMiBrain PET scanner (Oncovision, Valencia, Spain) beyond the NEMA-NU 2-2018 protocol in terms of linearity and homogeneity over the system’s total activity range. In a second step we determined and implemented together with the manufacturer necessary actions to improve the performance.
Tumor prediction using machine leaning trained on dynamic FDG-PET of extra-tumoral organs
2022-04-01

Ziel/Aim Analysis of whole body dynamic FDG acquisitions are still challenging in the clinical setting and its advantages are still not completely elucidated [1]. Glucose metabolism in organs as a result of tumor load may be relevant in order to predict: treatment-response, recurrence or disease stability. We applied machine learning (ML) algorithms to learn this dependency and predict the presence of lung tumors using solely metabolic data from extra tumoral organs.
Keynotes
2022-04-01

Multidimensional visualization is one of the core topics of visualization research.It deals with basic problems of data analysis in visualization and many other disciplines.Despite the long history of work in multidimensional visualization, it is still a striving field with much ongoing progress and many connections to various applications.This talk starts with a brief overview and some theoretical considerations.Then, I illustrate recent advancements, with a focus on presenting results from my own work.In particular, I cover basic visual representations in the form of scatterplots, scatterplot matrices, and parallel coordinates.These are then combined with further analytical support, including dimensionality reduction, local correlation analysis, machine learning, and interactive exploration for visual analytics.I also discuss how multidimensional visualization can serve as a link between information visualization and scientific visualization, and how it can be extended to include uncertainty visualization.The talk closes with an outlook on future research directions.
Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora
2022-04-01

This record contains supplementary information for the article &amp;quot;Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora&amp;quot;. It contains the barcodes (barcodes.txt), the reference contigs (contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the experimental design (design.txt). All data are unfiltered.\\n\\n\\nAll reads are available on SRA (PRJNA798549). Note that the barcode sequences and the control nucleotide were already removed from the demultiplexed files (hence, for each sample, reads are also split into &amp;quot;watson&amp;quot; and &amp;quot;crick&amp;quot; based on the control nucleotide).
Forecasting Intra-individual Changes of Affective States Taking into Account Inter-individual Differences Using Intensive Longitudinal Data from a University Student Dropout Study in Math
2022-04-02

The longitudinal process that leads to university student dropout in STEM subjects can be described by referring to (a) inter-individual differences (e.g., cognitive abilities) as well as (b) intra-individual changes (e.g., affective states), (c) (unobserved) heterogeneity of trajectories, and d) time-dependent variables. Large dynamic latent variable model frameworks for intensive longitudinal data (ILD) have been proposed which are (partially) capable of simultaneously separating the complex data structures (e.g., DLCA; Asparouhov et al. in Struct Equ Model 24:257–269, 2017; DSEM; Asparouhov et al. in Struct Equ Model 25:359–388, 2018; NDLC-SEM, Kelava and Brandt in Struct Equ Model 26:509–528, 2019). From a methodological perspective, forecasting in dynamic frameworks allowing for real-time inferences on latent or observed variables based on ongoing data collection has not been an extensive research topic. From a practical perspective, there has been no empirical study on student dropout in math that integrates ILD, dynamic frameworks, and forecasting of critical states of the individuals allowing for real-time interventions. In this paper, we show how Bayesian forecasting of multivariate intra-individual variables and time-dependent class membership of individuals (affective states) can be performed in these dynamic frameworks using a Forward Filtering Backward Sampling method. To illustrate our approach, we use an empirical example where we apply the proposed forecasting method to ILD from a large university student dropout study in math with multivariate observations collected over 50 measurement occasions from multiple students ( <mml:math xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mnf="http://cambridge.org/core/manifest" xmlns:cup="http://contentservices.cambridge.org" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:m="http://cambridge.org/core/metadata" xmlns:core="http://cambridge.org/core" xmlns:c="http://cambridge.org/core/content"><mml:mrow><mml:mi>N</mml:mi><mml:mo>=</mml:mo><mml:mn>122</mml:mn></mml:mrow></mml:math> \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\end{document} ). More specifically, we forecast emotions and behavior related to dropout. This allows us to predict emerging critical dynamic states (e.g., critical stress levels or pre-decisional states) 8 weeks before the actual dropout occurs.
On Falsifiable Statistical Hypotheses
2022-04-02

Popper argued that a statistical falsification required a prior methodological decision to regard sufficiently improbable events as ruled out. That suggestion has generated a number of fruitful approaches, but also a number of apparent paradoxes and ultimately, no clear consensus. It is still commonly claimed that, since random samples are logically consistent with all the statistical hypotheses on the table, falsification simply does not apply in realistic statistical settings. We claim that the situation is considerably improved if we ask a conceptually prior question: when should a statistical hypothesis be regarded as falsifiable. To that end we propose several different notions of statistical falsifiability and prove that, whichever definition we prefer, the same hypotheses turn out to be falsifiable. That shows that statistical falsifiability enjoys a kind of conceptual robustness. These notions of statistical falsifiability are arrived at by proposing statistical analogues to intuitive properties enjoyed by exemplary falsifiable hypotheses familiar from classical philosophy of science. That demonstrates that, to a large extent, this philosophical tradition was on the right conceptual track. Finally, we demonstrate that, under weak assumptions, the statistically falsifiable hypotheses correspond precisely to the closed sets in a standard topology on probability measures. That means that standard techniques from statistics and measure theory can be used to determine exactly which hypotheses are statistically falsifiable. In other words: the proposed notion of statistical falsifiability both answers to our conceptual demands and submits to standard mathematical techniques.
The final MSA of eastern South Africa: a comparative study between Umbeli Belli and Sibhudu
2022-04-03

The end of the Middle Stone Age in southern Africa, often called the final MSA (∼40–28 ka), represents one of the most understudied technocomplexes in this part of the world. Researchers have often focused on earlier time periods associated with Marine Isotope Stage 4 or have emphasised the transition between the Middle and the Later Stone Age. Thus, the final MSA has been poorly understood and, at least in KwaZulu-Natal, only a few chrono-cultural markers called hollow-based points are known for it. Since 2016, excavations at Umbeli Belli rock shelter have produced new insights into this period. The site provides one of the most accurately dated sequences for the final MSA, spanning four geological horizons, respectively GH7, GH8, GH9 and GH10, that date to between 29.9 ± 2.3 and 40.3 ± 3.5 ka. Significant technological and typological variations are evident between those horizons, raising questions about the mechanisms behind them. A direct comparative analysis with the final MSA layers Coffee – Espresso at Sibhudu, which date to ∼38 ka, places these results in the regional archaeological context. The analysis shows first that the final MSA encompasses diachronic variability within relatively short time frames at Umbeli Belli. Secondly, it reveals several distinct chronological discrepancies between Sibhudu and Umbeli Belli. A detailed review of the environmental setting of the research area helps to explain these changes.
Can involvement induced by guidance foster scientific reasoning and knowledge of participants of a citizen science project?
2022-04-03

Citizen Science projects are continuously growing in popularity as they offer a unique possibility to conduct large-scale research projects as well as allow citizens to broaden their knowledge about the research topic or the process of scientific investigations. However, the benefits for participants vary, depending on the way and the amount of participants' personal involvement in the project. In this study, we investigated whether additional guidance would improve involvement and hence lead to greater knowledge gains, higher commitment and improved scientific reasoning of participants in a Citizen Science project on birdwatching. A group receiving guidance was compared to a group which took part in the same project without receiving additional support. Results showed that both groups enhanced their knowledge about birds and their commitment to birding, while there were no significant changes in scientific reasoning. However, participants receiving additional guidance observed a higher number of different bird species and reported being able to identify significantly more species. Participation in a Citizen Science project either with or without further guidance can be seen as powerful in supporting birders at the beginning of their initial stages. Thus, both versions should be taken into account when designing future Citizen Science projects.
Near-neutral pH increased n-caprylate production in a microbiome with product inhibition of methanogenesis
2022-04-03

Abstract The pH is a critical parameter in chain-elongating bioreactors, affecting: (1) the concentration of inhibitory undissociated carboxylic acids, which in turn affects the efficiency of product extraction; (2) the thermodynamics; and (3) the kinetics. Here, we examined the effect of five different pH levels (5.5 to 7.0) on n -caprylate (C8) production using an anaerobic sequencing batch reactor (ASBR) with continuous membrane-based liquid-liquid extraction (pertraction). We found that the product spectrum was directed by pH: mildly acidic pH (5-6) led to n -caproate (C6) production, while near-neutral and neutral pH (6.75-7) favored n -caprylate production. In particular, the pH of 6.75 led to the maximum values of volumetric n -caprylate production rate (75.6 ± 0.6 mmol C L −1 d −1 ; 0.06 g L −1 d −1 ) and n -caprylate concentration in the fermentation broth (420 mM C; 7.57 g L −1 ). Given that methane production remained low at near-neutral and neutral pH, we theorized that the high concentration of undissociated n -caprylic acid (5.71 mM C) inhibited methanogenesis. We then demonstrated such an inhibitory effect at neutral pH in: (1) microcosm experiments; and (2) the continuous bioreactor by adding methanogenic sludge. Furthermore, 16S rRNA gene sequencing analysis revealed that near-neutral and neutral pH led to more diverse microbial communities than at mildly-acidic pH. For the first time, we report predominant n -caprylate production in a microbiome at near-neutral and neutral pH conditions where methanogenesis was controlled by the inhibitory effects of undissociated n -caprylic acid. At the same time, extraction of this species occurred even at near-neutral and neutral pH.
Effects of caloric restriction on the gut microbiome are linked with immune senescence
2022-04-04

Abstract Background Caloric restriction can delay the development of metabolic diseases ranging from insulin resistance to type 2 diabetes and is linked to both changes in the composition and metabolic function of the gut microbiota and immunological consequences. However, the interaction between dietary intake, the microbiome, and the immune system remains poorly described. Results We transplanted the gut microbiota from an obese female before (AdLib) and after (CalRes) an 8-week very-low-calorie diet (800 kcal/day) into germ-free mice. We used 16S rRNA sequencing to evaluate taxa with differential abundance between the AdLib- and CalRes-microbiota recipients and single-cell multidimensional mass cytometry to define immune signatures in murine colon, liver, and spleen. Recipients of the CalRes sample exhibited overall higher alpha diversity and restructuring of the gut microbiota with decreased abundance of several microbial taxa (e.g., Clostridium ramosum , Hungatella hathewayi , Alistipi obesi ) . Transplantation of CalRes-microbiota into mice decreased their body fat accumulation and improved glucose tolerance compared to AdLib-microbiota recipients. Finally, the CalRes-associated microbiota reduced the levels of intestinal effector memory CD8 + T cells, intestinal memory B cells, and hepatic effector memory CD4 + and CD8 + T cells. Conclusion Caloric restriction shapes the gut microbiome which can improve metabolic health and may induce a shift towards the naïve T and B cell compartment and, thus, delay immune senescence. Understanding the role of the gut microbiome as mediator of beneficial effects of low calorie diets on inflammation and metabolism may enhance the development of new therapeutic treatment options for metabolic diseases. Trial registration NCT01105143 , “Effects of negative energy balance on muscle mass regulation,” registered 16 April 2010.
Biallelic ADAM22 pathogenic variants cause progressive encephalopathy and infantile-onset refractory epilepsy
2022-04-04

Abstract Pathogenic variants in A Disintegrin And Metalloproteinase (ADAM) 22, the postsynaptic cell membrane receptor for the glycoprotein leucine-rich repeat glioma-inactivated protein 1 (LGI1), have been recently associated with recessive developmental and epileptic encephalopathy. However, so far, only two affected individuals have been described and many features of this disorder are unknown. We refine the phenotype and report 19 additional individuals harbouring compound heterozygous or homozygous inactivating ADAM22 variants, of whom 18 had clinical data available. Additionally, we provide follow-up data from two previously reported cases. All affected individuals exhibited infantile-onset, treatment-resistant epilepsy. Additional clinical features included moderate to profound global developmental delay/intellectual disability (20/20), hypotonia (12/20) and delayed motor development (19/20). Brain MRI findings included cerebral atrophy (13/20), supported by post-mortem histological examination in patient-derived brain tissue, cerebellar vermis atrophy (5/20), and callosal hypoplasia (4/20). Functional studies in transfected cell lines confirmed the deleteriousness of all identified variants and indicated at least three distinct pathological mechanisms: (i) defective cell membrane expression; (ii) impaired LGI1-binding; and/or (iii) impaired interaction with the postsynaptic density protein PSD-95. We reveal novel clinical and molecular hallmarks of ADAM22 deficiency and provide knowledge that might inform clinical management and early diagnostics.
Development of a sensitive trial-ready poly(GP) CSF biomarker assay forC9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis
2022-04-04

Objective A GGGGCC repeat expansion in the C9orf72 gene is the most common cause of genetic frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). As potential therapies targeting the repeat expansion are now entering clinical trials, sensitive biomarker assays of target engagement are urgently required. Our objective was to develop such an assay. Methods We used the single molecule array (Simoa) platform to develop an immunoassay for measuring poly(GP) dipeptide repeat proteins (DPRs) generated by the C9orf72 repeat expansion in cerebrospinal fluid (CSF) of people with C9orf72 -associated FTD/ALS. Results and conclusions We show the assay to be highly sensitive and robust, passing extensive qualification criteria including low intraplate and interplate variability, a high precision and accuracy in measuring both calibrators and samples, dilutional parallelism, tolerance to sample and standard freeze–thaw and no haemoglobin interference. We used this assay to measure poly(GP) in CSF samples collected through the Genetic FTD Initiative (N=40 C9orf72 and 15 controls). We found it had 100% specificity and 100% sensitivity and a large window for detecting target engagement, as the C9orf72 CSF sample with the lowest poly(GP) signal had eightfold higher signal than controls and on average values from C9orf72 samples were 38-fold higher than controls, which all fell below the lower limit of quantification of the assay. These data indicate that a Simoa-based poly(GP) DPR assay is suitable for use in clinical trials to determine target engagement of therapeutics aimed at reducing C9orf72 repeat-containing transcripts.