julilili42/papers huggingface dataset:
Sediment budgeting of short‐term backfilling processes: The erosional collapse of a Carolingian canal construction
2020-08-14

ABSTRACT Sediment budgeting concepts serve as quantification tools to decipher the erosion and accumulation processes within a catchment and help to understand these relocation processes through time. While sediment budgets are widely used in geomorphological catchment‐based studies, such quantification approaches are rarely applied in geoarchaeological studies. The case of Charlemagne's summit canal (also known as Fossa Carolina) and its erosional collapse provides an example for which we can use this geomorphological concept and understand the abandonment of the Carolingian construction site. The Fossa Carolina is one of the largest hydro‐engineering projects in Medieval Europe. It is situated in Southern Franconia (48.9876°N, 10.9267°E; Bavaria, southern Germany) between the Altmühl and Swabian Rezat rivers. It should have bridged the Central European watershed and connected the Rhine–Main and Danube river systems. According to our dendrochronological analyses and historical sources, the excavation and construction of the Carolingian canal took place in AD 792 and 793. Contemporary written sources describe an intense backfill of excavated sediment in autumn AD 793. This short‐term erosion event has been proposed as the principal reason for the collapse and abandonment of the hydro‐engineering project. We use subsurface data (drillings, archaeological excavations, and direct‐push sensing) and geospatial data (a LiDAR digital terrain model (DTM), a pre‐modern DTM, and a 3D model of the Fossa Carolina] for the identification and sediment budgeting of the backfills. Dendrochronological findings and radiocarbon ages of macro remains within the backfills give clear evidence for the erosional collapse of the canal project during or directly after the construction period. Moreover, our quantification approach allows the detection of the major sedimentary collapse zone. The exceedance of the manpower tipping point may have caused the abandonment of the entire construction site. The spatial distribution of the dendrochronological results indicates a north–south direction of the early medieval construction progress. © 2020 The Authors. Earth Surface Processes and Landforms published by John Wiley &amp; Sons Ltd
Do Open Science Badges increase trust in scientists among undergraduates, scientists, and the public?
2020-08-14

Open science badges are a promising method to signal a study’s adherence to open science practices (OSP). In three experimental studies, we investigated whether badges affect trust in scientists by undergraduates (N = 270), scientists (N = 250), or the public (N = 257). Furthermore, we analyzed the moderating role of epistemic beliefs in this regard. Participants were randomly assigned to two of three conditions: Badges awarded (visible compliance to OSP), badges not awarded (visible noncompliance to OSP), and no badges (control). In all samples, our Bayesian analyses indicated that badges influence trust as expected with one exception in the public sample: an additional positive effect of awarded badges compared to no badges was not supported here. Further, we found evidence for the absence of a moderation by epistemic beliefs. Our results demonstrate that badges are an effective means to foster trust in scientists among target audiences of scientific papers.
Carbenaporphyrins: A Missing Ligand in N-Heterocyclic Carbene Chemistry
2020-08-14

The successful synthesis of a carbenaporphyrin ligand based on carbazole and triazolylidene (CTP) is reported. Instead of a macrocyclic aromatic or antiaromatic character, the aromaticity of each heterocyclic moiety is preserved, which results in optical properties different from porphyrins, e.g. fluorescence. In Li&lt;sup&gt;+&lt;/sup&gt; and Sc&lt;sup&gt;3+&lt;/sup&gt; complexes the ligand reveals striking geometric similarity to porphyrins, but is stronger electron donating.
Carbenaporphyrins: A Missing Ligand in N-Heterocyclic Carbene Chemistry
2020-08-14

The successful synthesis of a carbenaporphyrin ligand based on carbazole and triazolylidene (CTP) is reported. Instead of a macrocyclic aromatic or antiaromatic character, the aromaticity of each heterocyclic moiety is preserved, which results in optical properties different from porphyrins, e.g. fluorescence. In Li + and Sc 3+ complexes the ligand reveals striking geometric similarity to porphyrins, but is stronger electron donating.
LanguageStructure/TuDeT v0.1
2020-08-14

The pre-release v0.1 contains only a dozen sentences in each of the three languages: Akuntsú, Ka'apor, Mundurukú, and Tupinambá. The documentation is being prepared, including a mapping from UPOS (universal POS) to XPOS (language-specific POS).
LanguageStructure/TuDeT v0.1
2020-08-14

&lt;p&gt;The pre-release v0.1 contains only a dozen sentences in each of the three languages: Akunts&uacute;, Ka&#39;apor, Munduruk&uacute;, and Tupinamb&aacute;. The documentation is being prepared, including a mapping from UPOS (universal POS) to XPOS (language-specific POS).&nbsp;&lt;/p&gt;
Pre‐ and postnatal findings in a patient with a recombinant chromosome rec(8)(qter→q21.11::p23.3→qter) due to a paternal pericentric inversion inv(8)(p23.3q21.11) and review of the literature
2020-08-16

Abstract Recombinant chromosome 8 (Rec8) syndrome (San Luis Valley [SLV] syndrome; OMIM #179613) is a rare chromosome disorder associated with intellectual disability, congenital heart defects, variable skeletal and urogenital anomalies, and dysmorphic features. It is characterized by a partial terminal deletion of 8p and a partial terminal duplication of 8q, which is usually due to meiotic recombination of a pericentric inversion of chromosome 8 of a healthy carrier parent. There are only few reports of cases with breakpoints defined at the molecular level by molecular karyotyping. We report on a case of Rec8 syndrome with previously unreported breakpoints in a male fetus with intrauterine growth restriction, hypogenesis of the corpus callosum, bilateral cleft lip/palate, and congenital heart defect. Cytogenetic analysis revealed a recombinant chromosome 8 [46,XY,rec(8)(qter→q21.11::p23.3→qter)] secondary to a paternal pericentric inversion [46,XY,inv(8)(p23.3q21.11)]. Molecular karyotyping correspondingly showed a terminal copy number loss of 1.4 Mb (arr[hg19] 8p23.3(158048_1514749)×1) and a terminal copy number gain of chromosome band 8q21.11q24.3 of 69.8 Mb (arr[hg19] 8q21.11q24.3(76477367_146295771)×3). To our knowledge, this is the fourth reported case diagnosed prenatally. We describe the postnatal clinical course of the male newborn. Furthermore, we review and compare the phenotypic features and breakpoints of 74 reported Rec8/SLV cases.
Opposing Associations of NT-proBNP With Risks of Diabetes and Diabetes-Related Complications
2020-08-17

OBJECTIVE Circulating N-terminal pro B-type natriuretic peptide (NT-proBNP) is a classic diagnostic and prognostic marker for heart failure. However, it is inversely associated with diabetes risk. We aimed to investigate relationships of NT-proBNP with risk of diabetes-related complications in initially healthy individuals. RESEARCH DESIGN AND METHODS We performed a case-cohort study within the European Prospective Investigation Into Cancer and Nutrition (EPIC)-Potsdam cohort including a random subcohort (n = 1,294) and incident cases of type 2 diabetes (n = 649) and cardiovascular diseases (n = 478). Incident cases of type 2 diabetes (n = 545) were followed up for microvascular (n = 133) and macrovascular (n = 50) complications. Plasma NT-proBNP was measured at baseline in initially healthy participants. RESULTS In multivariable models, NT-proBNP was linearly inversely associated with incident type 2 diabetes with a hazard ratio (HR) (95% CI) per doubling in NT-proBNP of 0.91 (0.86, 0.98). The association was only observable in women (0.80 [0.72, 0.90]) compared with men (0.98 [0.91, 1.07]). Among people with incident diabetes, NT-proBNP was positively associated with diabetes complications: overall, 1.31 (1.13, 1.53); microvascular complications, 1.20 (1.01, 1.43); and macrovascular complications, 1.37 (1.03, 1.83). CONCLUSIONS Although higher NT-proBNP levels are associated with lower diabetes risk, NT-proBNP is a biomarker for vascular complications in people who develop diabetes independent of potential confounders. Thus, NT-proBNP might be informative to monitor risk for diabetes-related microvascular and macrovascular complications, which should be further explored in future prospective studies.
Antiviral Activity of Ivermectin Against SARS-CoV-2: An Old-Fashioned Dog with a New Trick—A Literature Review
2020-08-17

The coronavirus disease 2019 (COVID-19) pandemic is a major global threat. With no effective antiviral drugs, the repurposing of many currently available drugs has been considered. One such drug is ivermectin, an FDA-approved antiparasitic agent that has been shown to exhibit antiviral activity against a broad range of viruses. Recent studies have suggested that ivermectin inhibits the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), thus suggesting its potential for use against COVID-19. This review has summarized the evidence derived from docking and modeling analysis, in vitro and in vivo studies, and results from new investigational drug protocols, as well as clinical trials, if available, which will be effective in supporting the prospective use of ivermectin as an alternative treatment for COVID-19.
Uncovering targeting priority to yeast peroxisomes using an in-cell competition assay
2020-08-17

Significance Half of eukaryotic proteins reside in organelles to which they are directed by dedicated targeting pathways, each recognizing unique targeting signals. Multiple proteins compete for any targeting pathway and might have different priority of reaching an organelle. However, the proteins with targeting priority, and the mechanisms underlying it, have not been explored. We developed a systematic tool to study targeting priority. We expressed a competitor protein and examined how it affects the localization of all other proteins targeted by the same pathway. We found several proteins with high targeting priority, dissected the mechanism of priority, and suggest that priority is governed by different parameters. This approach can be modified to study targeting priority in various organelles, cell types, and organisms.
Small benthic fish strike at prey over distances that fall within theoretical predictions for active sensing using light
2020-08-17

Abstract Small, benthic, cryptic fishes represent a species‐rich guild on marine substrates. Most of them are micropredators that feed on crustaceans that are often smaller than 1 mm. Typical examples are seahorses and pipefishes (Syngnathidae), most gobies (Gobiidae), dragonets (Callionymidae) and triplefins (Tripterygiidae). Previous work on the yellow black‐headed triplefin Tripterygion delaisi demonstrated that it actively redirects downwelling sunlight sideways using its iris and can use this to locally illuminate objects of interest. We call this form of active sensing using light “diurnal active photolocation”. Visual modelling predicted that light redirection can be sufficient to induce a perceivable change in luminance in the eyes of one of its prey species, a cryptic gammarid crustacean ( Cheirocratus sp.), over distances of 1–2 cm. Empirical validation, however, was not possible because measurements of predation distances have not been quantified for free‐ranging, small, benthic fishes before. Here, we present interaction distances measured from videos of T. delaisi approaching and striking at prey in the field. Out of 160 recordings, we were able to quantify 78 prey approaching distances and 100 striking distances. Approaching distances ranged from 2.1 to 4.1 cm (interquartile range, IQR) and involved one to five approaching steps before the actual strike occurred. The distance over which the final strike took place varied from 0.7 to 1.6 cm (IQR). Both approaching and striking distances increased with fish body size. We conclude that most approaching sequences started too far away to be explained by prey detection through light redirection. Striking distances, however, fell well with the distances predicted by the model. We conclude that if diurnal active photolocation plays a role in prey detection, it is during the final decision whether to strike or not.
Clinical Protocols for the Evaluation of Rod Function
2020-08-17

This work presents a quick clinical protocol for dark-adapted chromatic (DAC) perimetry as well as a novel clinical tool, scotopic chromatic pupil campimetry (CPC). The goal of the study was to explore the applicability of these methods in a clinical setting, their test-retest repeatability, and the congruence of the results. Local rod sensitivity was assessed at 36 locations within 30° eccentricity of the visual field in 15 healthy subjects (mean age 43 ± 16 years; 7 females and 8 males) with DAC perimetry (red and cyan stimuli) and CPC 2 times in repeated measurements. The duration of individual measurements was 370 ± 5 s for CPC and 366 ± 62 s for DAC perimetry. The intraclass correlation (ICC) coefficient was 0.53 for DAC perimetry cyan stimuli, 0.67 for red stimuli, and 0.93 for CPC. However, the spatial resolution of CPC was substantially smaller than in DAC perimetry. We did not find a correlation of DAC perimetry and CPC measurements on the global or the local level. In comparison to DAC perimetry, CPC shows a superior intervisit repeatability in detecting functional changes in the rod population in an objective way with lower spatial resolution. Our results also indicate that these 2 methods measure the rod function in different ways and could thus constitute complementary scotopic functional diagnostics.
Immediate sensorimotor grounding of novel concepts learned from language alone
2020-08-17

Theories of grounded cognition postulate that concepts are grounded in sensorimotor experience. But how can that be for concepts like Atlantis for which we do not have that experience? We claim that such concepts obtain their sensorimotor grounding indirectly, via already-known concepts used to describe them. Participants learned novel words referring to up or down concepts (mende = enhanced head or mende = bionic foot). In a first experiment, participants then judged the sensibility of sentences implying up or down actions (e.g., "You scratch your bionic foot") by performing up or down hand movements. Reactions were faster when the hand movement matched the direction of the implied movement. In the second experiment, we observed the same congruency effect for sentences like, "You scratch your mende", whose implied direction depended entirely on the learning phase. This offers a perspective on how concepts learned without direct experience can nonetheless be grounded in sensorimotor experience.
Socrates’ First City:Pleonexiaand the Thought Experiment
2020-08-17

Abstract The present study provides an analysis of Socrates’ account of the first polis in Republic 2 as a thought experiment and draws attention to the fact that Socrates combines both explanatory and evaluative aspects in his scenario. The paper further shows how the analysis of the city of pigs as a thought experiment can explain the lack of pleonexia by saving both the letter of the text, according to which there are no “pleonectic” desires in the city of pigs, and the fact that the first polis is nonetheless concerned with human beings. For, in contrast to the account offered by Glaucon earlier in Book 2, Socrates highlights our needs and lack of self-sufficiency as well as our compatibility with an advantageous and happy life in a community.
Binocular disparity-based learning does not generalize to the other visual hemifield
2020-08-17

Abstract Visual perceptual learning refers to long-lasting performance improvements on a visual skill, an ability presumably supported by plastic changes in early visual brain areas. Visual perceptual learning has been shown to be induced by training and to benefit from consolidation during sleep, presumably via the reactivation of learning-associated neuronal firing patterns. However, previous studies have almost exclusively relied on a single paradigm, the texture discrimination task, on which performance improvements may not rely on strictly perceptual skills. Here, we tested whether sleep has beneficial effects on a visual disparity discrimination task. We confirm previous findings in showing that the ability to discriminate different disparities is unaffected by sleep during a 12-hour retention period after training. Importantly, we extend these results by providing evidence against an effect of sleep on the generalization of improved disparity discrimination across the vertical meridian. We further rule out carry-over effects as a possible confound in our earlier within-subject study by relying on a between-subject design. The combined data from both studies argue against sleep as an important factor in the consolidation of a strictly perceptual skill. This sets important constraints on models of the role of sleep and sleep-associated neural reactivation in the consolidation of non-declarative memories.
Retrospective accuracy analysis of MRI based lesion size measurement in neuroblastic tumors: which sequence should we choose?
2020-08-17

Abstract Background: MR imaging of neuroblastic tumors is widely used for assessing the effect of chemotherapy on tumor size. However, there are some concerns that MRI might falsely estimate lesion diameters due to calcification and fibrosis. Therefore, the aim of our study was to compare neuroblastic tumor size based on MRI measurements to histopathology measurements of the resected specimens as standard of reference. Methods: Inclusion criteria were diagnosis of a neuroblastic tumor, MR imaging within 100 days to surgery and gross total resection without fragmentation of the tumor between 2008-2019. Lesion diameters were measured by two radiologists according to RECIST 1.1 in axial plane in T2w turbo spin echo (TSE), diffusion-weighted imaging (DWI), and in T1w pre- and postcontrast sequences. Furthermore, the largest lesion size in three-dimensions was noted. The largest diameter of histopathology measurements of each specimen was used for comparison with MRI. Results: Thirty-seven patients (mean age: 5±4 years) with 38 lesions (neuroblastoma: n=17; ganglioneuroblastoma: n=11; ganglioneuroma: n=10) were included in this retrospective study. There was excellent intra-class correlation coefficient between both readers for all sequences (&gt;0.9) Tumor dimensions of reader 1 based on axial MRI measurements were significantly smaller with the following median differences (cm): T1w precontrast -1.4 (interquartile range (IQR): 1.8 ), T1w postcontrast -1.0 (IQR: 1.9), T2w TSE: -1.0 (IQR: 1.6), and DWI -1.3 (IQR: 2.2) (p&lt;0.001 for all sequences). However, the evaluation revealed no significant differences between the three-dimensional measurements and histopathology measurements of the resected specimens regardless of the applied MRI sequence. Conclusions: Axial MRI based lesion size measurements are significantly smaller than histopathological measurements. However, there was no significant difference between three-dimensional measurements and histopathology measurements of the resected specimens. T2w TSE and T1w postcontrast images provided the lowest deviation and might consequently be preferred for measurements.
Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing
2020-08-18

Infections with multidrug-resistant bacteria represent a major threat to global health. While the spread of multidrug-resistant bacterial clones is frequently studied in the hospital setting, surveillance of the transfer of mobile genetic elements between different bacterial species was difficult until recent advances in sequencing technologies. Nanopore sequencing technology was applied to track antimicrobial gene transfer in a long-term outbreak of multidrug-resistant Pseudomonas aeruginosa , Citrobacter freundii , and Citrobacter cronae in a German hospital over 6 years. We developed a novel computational pipeline, pathoLogic , which enables de novo assembly of genomes and plasmids, antimicrobial resistance gene annotation and visualization, and comparative analysis. Applying this approach, we detected plasmid transfer between different bacterial species as well as plasmid fusion and frequent rearrangements of the antimicrobial resistance gene cassette. This study demonstrated the feasibility of near-real-time tracking of plasmid-based antimicrobial resistance gene transfer in hospitals, enabling countermeasures to contain plasmid-mediated outbreaks.
Transbronchial cryobiopsy increases diagnostic confidence in interstitial lung disease: a prospective multicentre trial
2020-08-18

Introduction The accurate diagnosis of individual interstitial lung diseases (ILD) is often challenging, but is a critical determinant of appropriate management. If a diagnosis cannot be made after multidisciplinary team discussion (MDTD), surgical lung biopsy is the current recommended tissue sampling technique according to the most recent guidelines. Transbronchial lung cryobiopsy (TBLC) has been proposed as an alternative to surgical lung biopsy. Methods This prospective, multicentre, international study analysed the impact of TBLC on the diagnostic assessment of 128 patients with suspected idiopathic interstitial pneumonia by a central MDTD board (two clinicians, two radiologists, two pathologists). The level of confidence for the first-choice diagnoses were evaluated in four steps, as follows: 1) clinicoradiological data alone; 2) addition of bronchoalveolar lavage (BAL) findings; 3) addition of TBLC interpretation; and 4) surgical lung biopsy findings (if available). We evaluated the contribution of TBLC to the formulation of a confident first-choice MDTD diagnosis. Results TBLC led to a significant increase in the percentage of cases with confident diagnoses or provisional diagnoses with high confidence (likelihood ≥70%) from 60.2% to 81.2%. In 32 out of 52 patients nondiagnostic after BAL, TBLC provided a diagnosis with a likelihood ≥70%. The percentage of confident diagnoses (likelihood ≥90%) increased from 22.7% after BAL to 53.9% after TBLC. Pneumothoraces occurred in 16.4% of patients, and moderate or severe bleeding in 15.7% of patients. No deaths were observed within 30 days. Interpretation TBLC increases diagnostic confidence in the majority of ILD patients with an uncertain noninvasive diagnosis, with manageable side-effects. These data support the integration of TBLC into the diagnostic algorithm for ILD.
Small vessel disease more than Alzheimer's disease determines diffusion MRI alterations in memory clinic patients
2020-08-18

Abstract Introduction Microstructural alterations as assessed by diffusion tensor imaging (DTI) are key findings in both Alzheimer's disease (AD) and small vessel disease (SVD). We determined the contribution of each of these conditions to diffusion alterations. Methods We studied six samples (N = 365 participants) covering the spectrum of AD and SVD, including genetically defined samples. We calculated diffusion measures from DTI and free water imaging. Simple linear, multivariable random forest, and voxel‐based regressions were used to evaluate associations between AD biomarkers (amyloid beta, tau), SVD imaging markers, and diffusion measures. Results SVD markers were strongly associated with diffusion measures and showed a higher contribution than AD biomarkers in multivariable analysis across all memory clinic samples. Voxel‐wise analyses between tau and diffusion measures were not significant. Discussion In memory clinic patients, the effect of SVD on diffusion alterations largely exceeds the effect of AD, supporting the value of diffusion measures as markers of SVD.