julilili42/papers huggingface dataset:
Estimating the SARS-CoV-2 infection fatality rate by data combination: the case of Germany’s first wave
2022-01-29

Summary Assessing the infection fatality rate (IFR) of SARS-CoV-2 in a population is a controversial issue. Due to asymptomatic courses of COVID-19, many infections remain undetected. Reported case fatality rates are therefore poor estimates of the IFR. We propose a strategy to estimate the IFR that combines official data on cases and fatalities with data from seroepidemiological studies in infection hotspots. The application of the method yields an estimate of the IFR of wild-type SARS-CoV-2 in Germany during the first wave of the pandemic of 0.83% (95% CI: [0.69%; 0.98%]), notably higher than the estimate reported in the prominent study by Streeck et al. (2020) (0.36% [0.17%; 0.77%]) and closer to that obtained from a world-wide meta analysis (0.68% [0.53%; 0.82%]), where the difference can be explained by Germany’s disadvantageous age structure. Provided that suitable data are available, the proposed method can be applied to estimate the IFR of virus variants and other regions.
Effect of Probiotics on Psychiatric Symptoms and Central Nervous System Functions in Human Health and Disease: A Systematic Review and Meta-Analysis
2022-01-30

Background: The gut microbiota impacts on central nervous system (CNS) function via the microbiota–gut–brain axis. Thus, therapeutics targeting the gut microbiota such as probiotics have the potential for improving mental health. This meta-analysis synthesizes the evidence regarding the impacts of probiotics on psychological well-being, psychiatric symptoms and CNS functioning. Methods: The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were applied for executing this review using the databases PubMed, Web of Science and Cochrane Library. The data were summarized at qualitative and quantitative level. Results: Fifty-four randomized placebo-controlled studies were included, of which 30 were eligible for meta-analysis. If investigated, the probiotics mostly exerted effects on CNS function. Most probiotics did not affect mood, stress, anxiety, depression and psychiatric distress when compared to placebo at the qualitative level. At quantitative level, depression and psychiatric distress improved slightly in the probiotic condition (depression: mean difference −0.37 (95% CI: −0.55, −0.20); p ≤ 0.0001; psychiatric distress: mean difference −0.33 (95% CI: −0.53, −0.13); p = 0.001). Conclusions: To date it is unclear to which extent and in which specific areas next generation probiotics selected and developed for their ability to improve psychiatric condition and potentially other CNS functions are promising.
Roadmap for edge AI
2022-01-30

Based on the collective input of Dagstuhl Seminar (21342), this paper presents a comprehensive discussion on AI methods and capabilities in the context of edge computing, referred as Edge AI. In a nutshell, we envision Edge AI to provide adaptation for data-driven applications, enhance network and radio access, and allow the creation, optimisation, and deployment of distributed AI/ML pipelines with given quality of experience, trust, security and privacy targets. The Edge AI community investigates novel ML methods for the edge computing environment, spanning multiple sub-fields of computer science, engineering and ICT. The goal is to share an envisioned roadmap that can bring together key actors and enablers to further advance the domain of Edge AI.
Data of the Shared Task on the Disambiguation of German Verbal Idioms at KONVENS 2021
2022-01-30

This dataset was used in the Shared Task on the Disambiguation of German Verbal Idioms (VID) at KONVENS 2021. For further details, please refer to the description paper of the shared task: Ehren, Rafael, Timm Lichte, Jakub Waszczuk &amp; Laura Kallmeyer. 2021. Shared Task on the Disambiguation of German Verbal Idioms at KONVENS 2021. In Proceedings of the Shared Task on the Disambiguation of German Verbal Idioms at KONVENS 2021. https://doi.org/10.5281/zenodo.5730322. https://konvens.org/proceedings/2021/index.html. <strong>Please cite this paper when using the dataset.</strong> The content of the zip file is identical to that of the data directory in the Github repository of the shared task. The dataset consists of 9901 instances of a German VID type or its literal counterpart in context. The set of VID types was pre-selected, thus it constitutes a lexical sample data set. It is a merger of two datasets: COLF-VID (instances with T*) German SemEval-2013 task 5b (instances with S*) The data comes in tsv files and every line has the following format: <pre><code>Instance_ID \\t VID_type \\t label \\t text</code></pre> Consider this example: <pre><code>T890202.28.4077 in wasser fallen figuratively Der Streit ums Hormonfleisch zwischen USA und EG provozierte den Polizeieinsatz . Aber nicht nur der Steakverkauf , auch die Aktionen gegen den Hormonstand , auf die sich Gruppen der Bauernopposition schon vorbereitet hatten , &lt;b&gt;fielen&lt;/b&gt; &lt;b&gt;ins&lt;/b&gt; &lt;b&gt;Wasser&lt;/b&gt; . Die Fleischexporteure der USA wollten ihrerseits die " Grüne Woche " zur " Aufklärung " nutzen .</code></pre> So the first column contains the ID (T890202.28.4077 in the example), the second the VID type (in wasser fallen), the third the label (figuratively) and the fourth the sentence with either the instance of the VID type or its literal counterpart (and two additional context sentences). The parts of the target expression are marked with the &lt;b&gt; tag (&lt;b&gt;fielen&lt;/b&gt; &lt;b&gt;ins&lt;/b&gt; &lt;b&gt;Wasser&lt;/b&gt;). There are four possible labels: figuratively literally undecidable both The first two should be self-explanatory. The label undecidable was used by the annotators if it was not possible to disambiguate an instance given the context. The label both was applied when both the literal and the idiomatic readings were active.
Social media use, stress, and coping
2022-01-31

In this review, we systematize work on the relationship between social media use and stress by providing a functional perspective that distinguishes between three functions that social media can have in the stages of the stress-coping process: as stressors, as resources, and as coping tools. Current research provides evidence that social media can cause stress, serve as resources, and can be used as a tool for various coping strategies, but it remains unclear when social media can successfully mitigate stress. Future research should use more fine-grained research designs that consider the timing of social media use, the situational context, and the encountered content to determine when social media serves which function and when social media reduces or increases stress.
Summary-statistics-based power analysis: A new and practical method to determine sample size for mixed-effects modeling.
2022-01-31

This article proposes a summary-statistics-based power analysis-a practical method for conducting power analysis for mixed-effects modeling with two-level nested data (for both binary and continuous predictors), complementing the existing formula-based and simulation-based methods. The proposed method bases its logic on conditional equivalence of the summary-statistics approach and mixed-effects modeling, paring back the power analysis for mixed-effects modeling to that for a simpler statistical analysis (e.g., one-sample t test). Accordingly, the proposed method allows us to conduct power analysis for mixed-effects modeling using popular software such as <i>G*Power</i> or the pwr package in R and, with minimum input from relevant prior work (e.g., <i>t</i> value). We provide analytic proof and a series of statistical simulations to show the validity and robustness of the summary-statistics-based power analysis and show illustrative examples with real published work. We also developed a web app (https://koumurayama.shinyapps.io/summary_statistics_based_power/) to facilitate the utility of the proposed method. While the proposed method has limited flexibilities compared with the existing methods in terms of the models and designs that can be appropriately handled, it provides a convenient alternative for applied researchers when there is limited information to conduct power analysis. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
Distinguishing the molecular diversity, nutrient content, and energetic potential of exometabolomes produced by macroalgae and reef-building corals
2022-01-31

Significance Marine dissolved organic matter (DOM) is one of the most complex and abundant chemical mixtures on earth, comprising thousands of different molecules. The molecular structure of these compounds is one factor structuring the community of microorganisms that metabolize them; in turn, this microbial metabolism mediates the composition of DOM. Decades of coral reef research has established the fundamental importance of microbial biogeochemistry in ecosystem function. This study unveils coral reef DOM by identifying a myriad of specific metabolite classes released into the surrounding waters by reef-building corals and algae, further characterizing their energetic and nutrient content and providing a foundation for linking benthic ecology with microbial processes that influence both the livelihood and demise of coral reefs.
Acetate Facilitated Nickel Catalyzed Coupling of Aryl Chlorides and Alkyl Thiols
2022-01-31

We report a mild, fast, and convenient catalytic system for the coupling of aryl chlorides with primary, secondary, as well as previously challenging tertiary alkyl thiols using an air-stable nickel(II) precatayst in combination with the low-cost base potassium acetate at room temperature. This catalytic system tolerates a variety of functional groups and enables the generation of thioethers for a wide range of substrates, including pharmaceutical compounds in excellent yields. Chemoselective functionalization of disubstituted substrates was demonstrated. Kinetic and NMR studies, as well as DFT computations support a Ni(0)/Ni(II) catalytic cycle and identify the oxidative addition product as the resting state. Acetate coordination and subsequent acetate facilitated formation of a thiolate complex via internal deprotonation play a key role in the catalytic cycle.
Challenges for Clinical Drug Development in Pulmonary Fibrosis
2022-01-31

Pulmonary fibrosis is a pathologic process associated with scarring of the lung interstitium. Interstitial lung diseases (ILDs) encompass a large and heterogenous group of disorders, a number of which are characterized by progressive pulmonary fibrosis that leads to respiratory failure and death. Idiopathic pulmonary fibrosis (IPF) has been described as an archetype of progressive fibrosing ILD, and the development of pirfenidone and nintedanib has been a major breakthrough in the treatment of patients with this deadly disease. Both drugs principally target scar-forming fibroblasts and have been shown to significantly slow down the accelerated decline of lung function by approximately 50%. In addition, nintedanib has been approved for patients with other progressive fibrosing ILDs and systemic sclerosis-associated ILD. However, there is still no cure for pulmonary fibrosis and no meaningful improvement of symptoms or quality of life has been shown. Advancement in research, such as the advent of single cell sequencing technology, has identified additional pathologic cell populations beyond the fibroblast which could be targeted for therapeutic purposes. The preclinical and clinical development of novel drug candidates is hampered by profound challenges such as a lack of sensitive clinical outcomes or suitable biomarkers that would provide an early indication of patient benefit. With the availability of these anti-fibrotic treatments, it has become even more difficult to demonstrate added efficacy, in particular in short-term clinical studies. Patient heterogeneity and the paucity of biomarkers of disease activity further complicate clinical development. It is conceivable that future treatment of pulmonary fibrosis will need to embrace more precision in treating the right patient at the right time, explore novel measures of efficacy, and likely combine treatment options.
S1‐guideline atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS)
2022-01-31

Summary Atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS) are rare cutaneous neoplasms representing histomorphological, genetic as well as epigenetic variants of a disease spectrum. Both tumors typically manifest as nonspecific, often ulcerated, skin‐ to flesh‐colored nodules in chronically sun‐damaged skin of elderly male patients. AFX is a rather well demarcated, often rapidly growing tumor. PDS tumors are poorly circumscribed and are characterized by aggressive infiltrative growth. Fast as well as slow growth behavior has been reported for both tumors. Histologically, both are composed of spindle‐shaped and epithelioid tumor cells with pleomorphic nuclei as well as atypical multinucleated giant cells. Atypical mitoses are common. In contrast to AFX, PDS involves relevant parts of the subcutis and shows areas of tumor necrosis and/or perineural infiltration. Due to the poorly differentiated nature of AFX/PDS (Grade 3), histopathologically similar cutaneous sarcomas, undifferentiated carcinomas, melanomas and other diseases have to be excluded by immunohistochemical analysis. The treatment of choice is micrographically controlled surgery. In cases of AFX, a cure can be assumed after complete excision. Local recurrence rates are low as long as PDS tumors are surgically removed with a safety margin of 2 cm. Metastasis is rare and mostly associated with very thick or incompletely excised tumors; it mainly affects the skin and lymph nodes. Distant metastasis is even more rare. No approved and effective systemic therapy has been established.
Association ofBDNFVal66Met With Tau Hyperphosphorylation and Cognition in Dominantly Inherited Alzheimer Disease
2022-01-31

In DIAD, clinical disease stage and BDNF Met66 were associated with cognitive impairment and levels of site-specific tau phosphorylation. This suggests that pharmacological strategies designed to increase neurotrophic support in the presymptomatic stages of AD may be beneficial.
Criticality enhances the multilevel reliability of stimulus responses in cortical neural networks
2022-01-31

Cortical neural networks exhibit high internal variability in spontaneous dynamic activities and they can robustly and reliably respond to external stimuli with multilevel features–from microscopic irregular spiking of neurons to macroscopic oscillatory local field potential. A comprehensive study integrating these multilevel features in spontaneous and stimulus–evoked dynamics with seemingly distinct mechanisms is still lacking. Here, we study the stimulus–response dynamics of biologically plausible excitation–inhibition (E–I) balanced networks. We confirm that networks around critical synchronous transition states can maintain strong internal variability but are sensitive to external stimuli. In this dynamical region, applying a stimulus to the network can reduce the trial-to-trial variability and shift the network oscillatory frequency while preserving the dynamical criticality. These multilevel features widely observed in different experiments cannot simultaneously occur in non-critical dynamical states. Furthermore, the dynamical mechanisms underlying these multilevel features are revealed using a semi-analytical mean-field theory that derives the macroscopic network field equations from the microscopic neuronal networks, enabling the analysis by nonlinear dynamics theory and linear noise approximation. The generic dynamical principle revealed here contributes to a more integrative understanding of neural systems and brain functions and incorporates multimodal and multilevel experimental observations. The E–I balanced neural network in combination with the effective mean-field theory can serve as a mechanistic modeling framework to study the multilevel neural dynamics underlying neural information and cognitive processes.
Multiple phases of human occupation in Southeast Arabia between 210,000 and 120,000 years ago
2022-01-31

Abstract Changing climatic conditions are thought to be a major control of human presence in Arabia during the Paleolithic. Whilst the Pleistocene archaeological record shows that periods of increased monsoon rainfall attracted human occupation and led to increased population densities, the impact of arid conditions on human populations in Arabia remains largely speculative. Here, we present data from Jebel Faya in Southeast (SE) Arabia, which document four periods of human occupation between c. 210,000 and 120,000 years ago. The Jebel Faya record indicates that human occupation of SE Arabia was more regular and not exclusively linked to major humid periods. Our data show that brief phases of increased rainfall additionally enabled human settlement in the Faya region. These results imply that the mosaic environments in SE Arabia have likely formed a population refugia at the end of the Middle and the beginning of the Late Pleistocene.
Andrographolide Derivatives Target the KEAP1/NRF2 Axis and Possess Potent Anti‐SARS‐CoV‐2 Activity
2022-01-31

Abstract Naturally occurring compounds represent a vast pool of pharmacologically active entities. One of such compounds is andrographolide, which is endowed with many beneficial properties, including the activity against severe acute respiratory syndrome coronavirus type 2 (SARS‐CoV‐2). To initiate a drug repurposing or hit optimization campaign, it is imperative to unravel the primary mechanism(s) of the antiviral action of andrographolide. Here, we showed by means of a reporter gene assay that andrographolide exerts its anti‐SARS‐CoV‐2 effects by inhibiting the interaction between Kelch‐like ECH‐associated protein 1 (KEAP1) and nuclear factor erythroid 2‐related factor 2 (NRF2) causing NRF2 upregulation. Moreover, we demonstrated that subtle structural modifications of andrographolide could lead to derivatives with stronger on‐target activities and improved physicochemical properties. Our results indicate that further optimization of this structural class is warranted to develop novel COVID‐19 therapies.
Association Between Objectively Assessed Sleep and Depressive Symptoms During Pregnancy and Post-partum
2022-01-31

Introduction Sleep problems are common in pregnancy but many studies have relied only on self-reported sleep measures. We studied the association between objectively measured sleep and peripartum depressive symptoms in pregnant women. Material and Methods Sleep was assessed using Actiwatch accelerometers in a sample of 163 pregnant women in the late first (weeks 11–15) or early second trimester (weeks 16–19). Depressive symptoms were assessed in gestational weeks 17, 32 and at 6 weeks post-partum using the Edinburgh Postnatal Depression Scale (EPDS). Multiple linear regression and logistic regression analyses, adjusting for age, BMI, pre-pregnancy smoking, ongoing mental health problems, trimester and season of sleep assessment were carried out to test the association between sleep and depression. Sleep was measured by total sleep time and sleep efficiency, whereas depression was indicated by depressive symptoms and depression caseness. Results are presented as unstandardized beta (B) coefficients or adjusted odds ratios (AOR) and 95% confidence intervals (CI). Results Total sleep time ranged from 3 to 9 h (mean 7.1, SD 0.9) and average sleep efficiency was 83% (SD 6.0). Women with the shortest total sleep time, i.e., in the lowest quartile (&amp;lt;6.66 h), reported higher depressive symptoms during pregnancy (week 17, B = 2.13, 95% CI 0.30–3.96; week 32, B = 1.70, 95% CI 0.03–3.37) but not post-partum. Their probability to screen positive for depression in gestational week 17 was increased more than 3-fold (AOR = 3.46, 95% CI 1.07–11.51) but unchanged with regards to gestational week 32 or 6 weeks post-partum. Sleep efficiency was not associated with depressive symptoms at any stage of pregnancy or post-partum. Discussion In one of the few studies to use objective sleep measures to date, mental health of pregnant women appeared to be affected by shortened sleep, with total sleep time being negatively associated with depressive symptoms in the early second and third trimester. This finding highlights the relevance of identifying and treating sleep impairments in pregnant women early during antenatal care to reduce the risk of concomitant depression.
A snapshot into the Oligocene vegetation of the Tethyan southern shores: new fossil pollen evidence from North Africa (Egypt)
2022-01-31

A palynological investigation was carried out on 24 samples from the Oligocene Dabaa Formation, which cuts across the Amana-1X well, located in the Abu El Gharadig Basin, north Western Desert, Egypt. Palynological evidence presented here suggests an early Oligocene age for the studied Dabaa Formation. In addition, the palynological assemblages provide supplementary evidence for depositional environments. They are generally indicative of outer-shelf to upper slope environment under oxic to anoxic conditions for the lower part of the studied Dabaa Formation, but infrequent occurrences of more diverse assemblages suggest an inner neritic marine environment for strata at some levels in the upper part of the studied section. It was during the Oligocene that marked floral changes leading to the development of modern plant associations began such as temperate deciduous forests (with e.g., Acer and Betulaceae) which expanded greatly in the mid latitudes. A distinctive vegetational pattern could be outlined within the deposition of the Dabaa Formation. This pattern includes mangroves represented by taxa such as Zonocostites ramonae, Psilatricolporites crassus and Verrucatosporites usmensis. Another considerably different association with plenty of the freshwater algae Botryococcus and Pediastrum spp. at this level or tropical forests at slightly elevated altitudes (ever wet climate) are dominated by a variety of tropical forest taxa including Malvaceae and Striatricolpites, together with Retitricolporites irregularis, Psilatricolporites operculatus, Retibrevitricolporites ibadanensis, Retitricolporites spp. and Psilamonocolpites spp. in addition to ferns and tree ferns where tropical floras dominate. Also recognized are elements of savanna or open woodland (less humid climate) taxa like Poaceae pollen (grass) such as Monoporopollenites annulatus associated with Amaranthaceae (e.g., Chenopodipollis multiplex), Cyperaceae spp., Echiperiporites estelae, Proteacidites cooksonii, Cicatricosisporites dorogensis and Pteris. Finally, the montane ecosystems may have occurred at the slopes of mountains including rare pollen assigned to Sapotaceae (Psilastephanocolporites spp.) and Anacardiaceae (Retitricolpites simplex) which are probably part of the palynoflora due to long-distance transport.