julilili42/papers huggingface dataset:
How many grains are needed for quantifying catchment erosion from tracer thermochronology?
2022-03-31

Abstract. Detrital tracer thermochronology utilizes the relationship between bedrock thermochronometric age–elevation profiles and a distribution of detrital grain ages collected from riverine, glacial, or other sediment to study spatial variations in the distribution of catchment erosion. If bedrock ages increase linearly with elevation, spatially uniform erosion is expected to yield a detrital age distribution that mimics the shape of a catchment's hypsometric curve. Alternatively, a mismatch between detrital and hypsometric distributions may indicate spatial variability of sediment production within the source area. For studies seeking to identify the pattern of sediment production, detrital samples rarely exceed 100 grains due to the time and costs related to individual measurements. With sample sizes of this order, detecting the dissimilarity between two detrital age distributions produced by different catchment erosion scenarios can be difficult at a high statistical confidence level. However, there are no established software tools to quantify the uncertainty inherent to detrital tracer thermochronology as a function of sample size and spatial pattern of sediment production. As a result, practitioners are often left wondering “how many grains is enough to detect a certain signal?”. Here, we investigate how sample size affects the uncertainty of detrital age distributions and how such uncertainty affects the ability to infer a pattern of sediment production of the upstream area. We do this using the Kolmogorov–Smirnov statistic as a metric of dissimilarity among distributions. From this, we perform statistical hypothesis testing by means of Monte Carlo sampling. These techniques are implemented in a new tool (ESD_thermotrace) to (i) consistently report the confidence level allowed by the sample size as a function of application-specific variables and given a set of user-defined hypothetical erosion scenarios, (ii) analyze the statistical power to discern each scenario from the uniform erosion hypothesis, and (iii) identify the erosion scenario that is least dissimilar to the observed detrital sample (if available). ESD_thermotrace is made available as a new open-source Python-based script alongside the test data. Testing between different hypothesized erosion scenarios with this tool provides thermochronologists with the minimum sample size (i.e., number of bedrock and detrital grain ages) required to answer their specific scientific question at their desired level of statistical confidence.
A novel proxy for tracking the provenance of dust based on paired E1’-peroxy paramagnetic defect centres in fine-grained quartz
2022-03-31

Earth and Space Science Open Archive This work has been accepted for publication in Geophysical Research Letters. Version of RecordESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary. Learn more about preprints. preprintOpen AccessYou are viewing the latest version by default [v1]A novel proxy for tracking the provenance of dust based on paired E1’-peroxy paramagnetic defect centres in fine-grained quartzAuthorsAditi KrishnaDaveiDAlidaTimar-GaborZuzannaKabacińskaGiancarloScardiaiDNosirSafaralievSaidaNigmatovaKathryn EFitzsimmonsiDSee all authors Aditi Krishna DaveiDCorresponding Author• Submitting AuthorUniversity of Tübingen, GermanyiDhttps://orcid.org/0000-0002-2836-9155view email addressThe email was not providedcopy email addressAlida Timar-GaborBabes Bolyai University, Romaniaview email addressThe email was not providedcopy email addressZuzanna KabacińskaBabes Bolyai University, Romaniaview email addressThe email was not providedcopy email addressGiancarlo ScardiaiDUniversidade Estadual Paulista, BraziliDhttps://orcid.org/0000-0003-3710-7197view email addressThe email was not providedcopy email addressNosir SafaralievTajik National University, Tajikistanview email addressThe email was not providedcopy email addressSaida NigmatovaInstitute of Geological Sciences K. Satpaeva, Kazakhstanview email addressThe email was not providedcopy email addressKathryn E FitzsimmonsiDUniversity of Tübingen, GermanyiDhttps://orcid.org/0000-0002-9337-0793view email addressThe email was not providedcopy email address
Applicability of open science practices to completed research projects from different disciplines and research paradigms
2022-03-31

&lt;p&gt;This is the &lt;strong&gt;data &lt;/strong&gt;and &lt;strong&gt;codebook repository &lt;/strong&gt;for the project &quot;Applicability of open science practices to completed research projects from different disciplines and research paradigms&quot;.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;The purpose of this data collection was to uncover the extent to which communities have emerged that cultivate a shared understanding of Open Science. In a cross sectional survey we assessed the applicability of thirteen open science practices over different disciplines and research paradigms. Focusing on completed research projects, participants were able to draw informed evaluations concerning the applicability of open science practices. Participants were collected approximately evenly distributed over six broad disciplines (42 to 52 participants each) with a sample size of N=295. The survey included an attention check.&lt;/p&gt;
Applicability of open science practices to completed research projects from different disciplines and research paradigms
2022-03-31

&amp;lt;p&amp;gt;This is the &amp;lt;strong&amp;gt;data &amp;lt;/strong&amp;gt;and &amp;lt;strong&amp;gt;codebook repository &amp;lt;/strong&amp;gt;for the project &amp;quot;Applicability of open science practices to completed research projects from different disciplines and research paradigms&amp;quot;.&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Abstract&amp;lt;/strong&amp;gt;&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;The purpose of this data collection was to uncover the extent to which communities have emerged that cultivate a shared understanding of Open Science. In a cross sectional survey we assessed the applicability of thirteen open science practices over different disciplines and research paradigms. Focusing on completed research projects, participants were able to draw informed evaluations concerning the applicability of open science practices. Participants were collected approximately evenly distributed over six broad disciplines (42 to 52 participants each) with a sample size of N=295. The survey included an attention check.&amp;lt;/p&amp;gt;
Hypercaloric diet triggers transient molecular rearrangements of astrocytes selectively in the arcuate nucleus
2022-03-31

SUMMARY Hypothalamic astrocytes are particularly affected by energy-dense food consumption. How the anatomical location of these glial cells and their spatial molecular distribution in the arcuate nucleus of the hypothalamus (ARC) determine the cellular response to a high caloric diet remains unclear. In this study, we investigated their distinctive molecular responses following the exposure to a high-fat high-sugar (HFHS) diet, specifically in the ARC. Using RNA sequencing and proteomics, we showed that astrocytes have a distinct transcriptomic and proteomic profile dependent on their anatomical location, with a major proteomic reprogramming in hypothalamic astrocytes. By ARC single-cell sequencing, we observed that a HFHS diet dictates time- and cell-specific transcriptomic responses, revealing that astrocytes have the most distinct regulatory pattern compared to other cell types. Lastly, we topographically and molecularly characterized astrocytes expressing glial fibrillary acidic protein and/or aldehyde dehydrogenase 1 family member L1 in the ARC, of which the abundance was significantly increased, as well as the alteration in their spatial and molecular profiles, with a HFHS diet. Together, our results provide a detailed multi-omics view on the spatial and temporal changes of astrocytes particularly in the ARC during different time points of adaptation to a high caloric diet.
Fear memory in humans is consolidated over time independent of sleep
2022-03-31

Abstract Fear memories can be altered after acquisition by processes such as fear memory consolidation or fear extinction, even without further exposure to the fear-eliciting stimuli, but factors contributing to these processes are not well understood. Sleep is known to consolidate, strengthen and change newly acquired declarative and procedural memories. However, evidence on the role of time and sleep in the consolidation of fear memories is inconclusive. Here, we used highly sensitive electrophysiological measures to examine the development of fear-conditioned responses over time and sleep in humans. We assessed event-related brain potentials (ERP) in 18 healthy young individuals during fear conditioning before and after a 2-hour afternoon nap or a corresponding wake interval in a counterbalanced within-subject design. The procedure involved pairing a neutral tone (CS+) with a highly unpleasant sound (US). As a control, another neutral tone (CS-) was paired with a neutral sound. Fear responses were examined before the interval during a habituation phase and an acquisition phase as well as after the interval during an extinction phase and a re-acquisition phase. Differential fear conditioning during acquisition was evidenced by a more negative slow ERP component (stimulus-preceding negativity) developing before the unconditioned stimulus (loud noise). This differential fear response was even stronger after the interval during re-acquisition compared to initial acquisition, but this effect was similarly pronounced after sleep and wakefulness. These findings suggest that fear memories are consolidated over time, with this effect being independent of intervening sleep.
Liver enzyme evaluation and NAT2 polymorphism in patients on anti-tuberculosis and antiretroviral drugs at Jamot Hospital in Yaound-Cameroon
2022-03-31

Hepatotoxicity is reported frequently as an adverse reaction during tuberculosis (TB) and HIV treatment. This study aimed to investigate the incidence of antiretroviral and anti-tuberculosis drug-induced liver enzymes activities variation in TB and TB-HIV co-infected patients at Jamot Hospital in Yaound&eacute;-Cameroon. From April 2018 to May 2019, 336 treatment-na&iuml;ve TB patients were enrolled. Liver enzymes (AST, ALT, ALP) and total bilirubin were evaluated at baseline and 12 weeks after treatment initiation. Blood was spotted on filter paper for DNA extraction by the chelex method. Standard nested PCR followed by restriction enzyme analysis with KpnI, TaqI, and BamHI to detect NAT2 polymorphisms was performed. TB-HIV co-infection prevalence was 29.46%. There was a significant rise of transaminases (p &lt; 0.05) at baseline in TB-HIV co-infected patients. At 12 weeks, there was a substantial rise of transaminases in TB patients, and total bilirubin in TB-HIV co-infected patients (p &lt; 0.05). The prevalence of slow and fast acetylators was 85.71 and 14.29%, respectively. NAT2*5/5 and NAT2*5/6 genotypes were most represented. Slow acetylating NAT2 phenotype was significantly associated with drug hepatotoxicity (p &lt; 0.05). The prevalence of TB-HIV co-infections remains high, and the rise in transaminases is linked to the slow acetylating NAT2 phenotype. &nbsp; Key words: TB/HIV co-infection, hepatotoxicity, NAT2, Jamot Hospital, Cameroon.&nbsp
Applicability of open science practices to completed research projects from different disciplines and research paradigms
2022-03-31

This is the <strong>data </strong>and <strong>codebook repository </strong>for the project "Applicability of open science practices to completed research projects from different disciplines and research paradigms". <strong>Abstract</strong> The purpose of this data collection was to uncover the extent to which communities have emerged that cultivate a shared understanding of Open Science. In a cross sectional survey we assessed the applicability of thirteen open science practices over different disciplines and research paradigms. Focusing on completed research projects, participants were able to draw informed evaluations concerning the applicability of open science practices. Participants were collected approximately evenly distributed over six broad disciplines (42 to 52 participants each) with a sample size of N=295. The survey included an attention check.
Applicability of open science practices to completed research projects from different disciplines and research paradigms
2022-03-31

&lt;p&gt;This is the &lt;strong&gt;data &lt;/strong&gt;and &lt;strong&gt;codebook repository &lt;/strong&gt;for the project "Applicability of open science practices to completed research projects from different disciplines and research paradigms".&lt;/p&gt; &lt;h2&gt;&lt;strong&gt;Check and run the analyses in your browser by opening the binder!&lt;/strong&gt;&lt;/h2&gt; &lt;ol&gt; &lt;li&gt;Open the GitHub Repo &lt;a title="Open Github repo" href="https://github.com/j-5chneider/subcommunitiesOS"&gt;https://github.com/j-5chneider/subcommunitiesOS&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Scroll down and click on the "launch binder" button in the Readme&lt;/li&gt; &lt;li&gt;Wait until RStudio instance is loaded in your browser (this may take some time)&lt;/li&gt; &lt;/ol&gt; &lt;h2&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&lt;/h2&gt; &lt;p&gt;The purpose of this data collection was to uncover the extent to which communities have emerged that cultivate a shared understanding of Open Science. In a cross sectional survey we assessed the applicability of thirteen open science practices over different disciplines and research paradigms. Focusing on completed research projects, participants were able to draw informed evaluations concerning the applicability of open science practices. Participants were collected approximately evenly distributed over six broad disciplines (42 to 52 participants each) with a sample size of N=295. The survey included an attention check.&lt;/p&gt;
Microbial iron cycling during palsa hillslope collapse promotes greenhouse gas emissions before complete permafrost thaw
2022-04-01

Abstract Reductive dissolution during permafrost thaw releases iron-bound organic carbon to porewaters, rendering previously stable carbon vulnerable to microbial decomposition and subsequent release to the atmosphere. How mineral iron stability and the microbial processes influencing mineral dissolution vary during transitional permafrost thaw are poorly understood, yet have important implications for carbon cycling and emissions. Here we determine the reactive mineral iron and associated organic carbon content of core extracts and porewaters along thaw gradients in a permafrost peatland in Abisko, Sweden. We find that iron mineral dissolution by fermentative and dissimilatory iron(III) reduction releases aqueous Fe 2+ and aliphatic organic compounds along collapsing palsa hillslopes. Microbial community analysis and carbon emission measurements indicate that this release is accompanied by an increase in hydrogenotrophic methanogen abundance and methane emissions at the collapsing front. Our findings suggest that dissolution of reactive iron minerals contributes to carbon dioxide and methane production and emission, even before complete permafrost thaw.
Inputs of disinfection by-products to the marine environment from various industrial activities: Comparison to natural production
2022-04-01

Oxidative treatment of seawater in coastal and shipboard installations is applied to control biofouling and/or minimize the input of noxious or invasive species into the marine environment. This treatment allows a safe and efficient operation of industrial installations and helps to protect human health from infectious diseases and to maintain the biodiversity in the marine environment. On the downside, the application of chemical oxidants generates undesired organic compounds, so-called disinfection by-products (DBPs), which are discharged into the marine environment. This article provides an overview on sources and quantities of DBP inputs, which could serve as basis for hazard analysis for the marine environment, human health and the atmosphere. During oxidation of marine water, mainly brominated DBPs are generated with bromoform (CHBr<sub>3</sub>) being the major DBP. CHBr<sub>3</sub> has been used as an indicator to compare inputs from different sources. Total global annual volumes of treated seawater inputs resulting from cooling processes of coastal power stations, from desalination plants and from ballast water treatment in ships are estimated to be 470-800 × 10<sup>9</sup> m<sup>3</sup>, 46 × 10<sup>9</sup> m<sup>3</sup> and 3.5 × 10<sup>9</sup> m<sup>3</sup>, respectively. Overall, the total estimated anthropogenic bromoform production and discharge adds up to 13.5-21.8 × 10<sup>6</sup> kg/a (kg per year) with contributions of 11.8-20.1 × 10<sup>6</sup> kg/a from cooling water treatment, 0.89 × 10<sup>6</sup> kg/a from desalination and 0.86 × 10<sup>6</sup> kg/a from ballast water treatment. This equals approximately 2-6% of the natural bromoform emissions from marine water, which is estimated to be 385-870 × 10<sup>6</sup> kg/a.
The CCAS-scale in hereditary ataxias: helpful on the group level, particularly in SCA3, but limited in individual patients
2022-04-01

Abstract Background A brief bedside test has recently been introduced by Hoche et al. (Brain, 2018) to screen for the Cerebellar Cognitive Affective Syndrome (CCAS) in patients with cerebellar disease. Objective This multicenter study tested the ability of the CCAS-Scale to diagnose CCAS in individual patients with common forms of hereditary ataxia. Methods A German version of the CCAS-Scale was applied in 30 SCA3, 14 SCA6 and 20 FRDA patients, and 64 healthy participants matched for age, sex, and level of education. Based on original cut-off values, the number of failed test items was assessed, and CCAS was considered possible (one failed item), probable (two failed items) or definite (three failed items). In addition a total sum raw score was calculated. Results On a group level, failed items were significantly higher and total sum scores were significantly lower in SCA3 patients compared to matched controls. SCA6 and FRDA patients performed numerically below controls, but respective group differences failed to reach significance. The ability of the CCAS-Scale to diagnose CCAS in individual patients was limited to severe cases failing three or more items. Milder cases failing one or two items showed a great overlap with the performance of controls exhibiting a substantial number of false-positive test results. The word fluency test items differentiated best between patients and controls. Conclusions As a group, SCA3 patients performed below the level of SCA6 and FRDA patients, possibly reflecting additional cerebral involvement. Moreover, the application of the CCAS-Scale in its present form results in a high number of false-positive test results, that is identifying controls as patients, reducing its usefulness as a screening tool for CCAS in individual patients.
Fight INflammation to Improve outcome after aneurysmal Subarachnoid HEmorRhage (FINISHER) trial: Study protocol for a randomized controlled trial
2022-04-01

Rationale: Aneurysmal subarachnoid hemorrhage (SAH) has high morbidity and mortality. While the primary injury results from the initial bleeding cannot currently be influenced, secondary injury through vasospasm and delayed cerebral ischemia worsens outcome and might be a target for interventions to improve outcome. To date, beside the aneurysm treatment to prevent re-bleeding and the administration of oral nimodipine, there is no therapy available, so novel treatment concepts are needed. Evidence suggests that inflammation contributes to delayed cerebral ischemia and poor outcome in SAH. Some studies suggest a beneficial effect of anti-inflammatory glucocorticoids, but there are no data from randomized controlled trials examining the efficacy of glucocorticoids. Therefore, current guidelines do not recommend the use of glucocorticoids in SAH. Aim: The Fight INflammation to Improve outcome after aneurysmal Subarachnoid HEmorRhage (FINISHER) trial aims to determine whether dexamethasone improves outcome in a clinically relevant endpoint in SAH patients. Methods and design: FINISHER is a multicenter, prospective, randomized, double-blinded, placebo-controlled clinical phase III trial which is testing the outcome and safety of anti-inflammatory treatment with dexamethasone in SAH patients. Sample size estimates: In all, 334 patients will be randomized to either dexamethasone or placebo within 48 h after SAH. The dexamethasone dose is 8 mg tds for days 1–7 and then 8 mg od for days 8–21. Study outcome: The primary outcome is the modified Rankin Scale (mRS) at 6 months, which is dichotomized to favorable (mRS 0–3) versus unfavorable (mRS 4–6). Discussion: The results of this study will provide the first phase III evidence as to whether dexamethasone improves outcome in SAH.
Preclinical Efficacy and Toxicity Analysis of the Pan-Histone Deacetylase Inhibitor Gossypol for the Therapy of Colorectal Cancer or Hepatocellular Carcinoma
2022-04-01

Gossypol, a sesquiterpenoid found in cotton seeds, exerts anticancer effects on several tumor entities due to inhibition of DNA synthesis and other mechanisms. In clinical oncology, histone deacetylase inhibitors (HDACi) are applied as anticancer compounds. In this study, we examined whether gossypol harbors HDAC inhibiting activity. In vitro analyses showed that gossypol inhibited class I, II, and IV HDAC, displaying the capability to laterally interact with the respective catalytic center and is, therefore, classified as a pan-HDAC inhibitor. Next, we studied the effects of gossypol on human-derived hepatoma (HepG2) and colon carcinoma (HCT-116) cell lines and found that gossypol induced hyperacetylation of histone protein H3 and/or tubulin within 6 h. Furthermore, incubation with different concentrations of gossypol (5–50 μM) over a time period of 96 h led to a prominent reduction in cellular viability and proliferation of hepatoma (HepG2, Hep3B) and colon carcinoma (HCT-116, HT-29) cells. In-depth analysis of underlying mechanisms showed that gossypol induced apoptosis via caspase activation. For pre-clinical evaluation, toxicity analyses showed toxic effects of gossypol in vitro toward non-malignant primary hepatocytes (PHH), the colon-derived fibroblast cell line CCD-18Co, and the intestinal epithelial cell line CCD 841 CoN at concentrations of ≥5 μM, and embryotoxicity in chicken embryos at ≥2.5 μM. In conclusion, the pronounced inhibitory capacity of gossypol on cancer cells was characterized, and pan-HDACi activity was detected in silico, in vitro, by inhibiting individual HDAC isoenzymes, and on protein level by determining histone acetylation. However, for clinical application, further chemical optimization is required to decrease cellular toxicity.