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Stimulus data and experimental design for a self-paced reading study on emoji-word substitutions
(2022)
This data paper presents the experimental design and stimuli from an online self-paced reading study on the processing of emojis substituting lexically ambiguous nouns. We recorded reading times for the target ambiguous nouns and for emojis depicting either the intended target referent or a contextually inappropriate homophonous noun. Furthermore, we recorded comprehension accuracy, demographics and a self-assessment of the participants' emoji usage frequency. The data includes all stimuli used, the raw data, the full JavaScript code for the online experiment, as well as Python and R code for the data analysis. We believe that our dataset may give important insights related to the comprehension mechanisms involved in the cognitive processing of emojis. For interpretation and discussion of the experiment, please see the original article entitled "The processing of emoji-word substitutions: A self-paced-reading study".
Large-Scale interseismic strain mapping of the NE Tibetan Plateau from Sentinel-1 Interferometry
(2022)
The launches of the Sentinel-1 synthetic aperture radar satellites in 2014 and 2016 started a new era of high-resolution velocity and strain rate mapping for the continents. However, multiple challenges exist in tying independently processed velocity data sets to a common reference frame and producing high-resolution strain rate fields. We analyze Sentinel-1 data acquired between 2014 and 2019 over the northeast Tibetan Plateau, and develop new methods to derive east and vertical velocities with similar to 100 m resolution and similar to 1 mm/yr accuracy across an area of 440,000 km(2). By implementing a new method of combining horizontal gradients of filtered east and interpolated north velocities, we derive the first similar to 1 km resolution strain rate field for this tectonically active region. The strain rate fields show concentrated shear strain along the Haiyuan and East Kunlun Faults, and local contractional strain on fault junctions, within the Qilianshan thrusts, and around the Longyangxia Reservoir. The Laohushan-Jingtai creeping section of the Haiyuan Fault is highlighted in our data set by extremely rapid strain rates. Strain across unknown portions of the Haiyuan Fault system, including shear on the eastern extension of the Dabanshan Fault and contraction at the western flank of the Quwushan, highlight unmapped tectonic structures. In addition to the uplift across most of the lowlands, the vertical velocities also contain climatic, hydrological or anthropogenic-related deformation signals. We demonstrate the enhanced view of large-scale active tectonic processes provided by high-resolution velocities and strain rates derived from Sentinel-1 data and highlight associated wide-ranging research applications.
Manganese (Mn), although important for multiple cellular processes, has posed environmental health concerns due to its neurotoxic effects. In recent years, there have been extensive studies on the mechanism of Mn-induced neuropathology, as well as the sex-dependent vulnerability to its neurotoxic effects. Nonetheless, cellular mechanisms influenced by sex differences in susceptibility to Mn have yet to be adequately characterized. Since oxidative stress is a key mechanism of Mn neurotoxicity, here, we have probed Hsp70 and Nrf2 proteins to investigate the sex-dependent changes following exposure to Mn. Male and female rats were administered intraperitoneal injections of MnCl2 (10 mg/kg and 25 mg/kg) 48 hourly for a total of eight injections (15 days). We evaluated changes in body weight, as well as Mn accumulation, Nrf2 and Hsp70 expression across four brain regions; striatum, cortex, hippocampus and cerebellum in both sexes. Our results showed sex-specific changes in body-weight, specifically in males but not in females. Additionally, we noted sex-dependent accumulation of Mn in the brain, as well as in expression levels of Nrf2 and Hsp70 proteins. These findings revealed sex-dependent susceptibility to Mn-induced neurotoxicity corresponding to differential Mn accumulation, and expression of Hsp70 and Nrf2 across several brain regions.
Numerous phosphorus-rich metal phosphides containing both P-P bonds and metal-P bonds are known from the solid-state chemistry literature. A method to grow these materials in thin-film form would be desirable, as thin films are required in many applications and they are an ideal platform for high-throughput studies. In addition, the high density and smooth surfaces achievable in thin films are a significant advantage for characterization of transport and optical properties. Despite these benefits, there is hardly any published work on even the simplest binary phosphorus-rich phosphide films. Here, we demonstrate growth of single-phase CuP2 films by a two-step process involving reactive sputtering of amorphous CuP2+x and rapid annealing in an inert atmosphere. At the crystallization temperature, CuP2 is thermodynamically unstable with respect to Cu3P and P-4. However, CuP2 can be stabilized if the amorphous precursors are mixed on the atomic scale and are sufficiently close to the desired composition (neither too P poor nor too P rich). Fast formation of polycrystalline CuP2, combined with a short annealing time, makes it possible to bypass the diffusion processes responsible for decomposition. We find that thin-film CuP2 is a 1.5 eV band gap semiconductor with interesting properties, such as a high optical absorption coefficient (above 10(5) cm(-1)), low thermal conductivity (1.1 W/(K m)), and composition-insensitive electrical conductivity (around 1 S/cm). We anticipate that our processing route can be extended to other phosphorus-rich phosphides that are still awaiting thin-film synthesis and will lead to a more complete understanding of these materials and of their potential applications.
We investigate a class of diffusion-controlled reactions that are initiated at the time instance when a prescribed number K among N particles independently diffusing in a solvent are simultaneously bound to a target region.
In the irreversible target-binding setting, the particles that bind to the target stay there forever, and the reaction time is the Kth fastest first-passage time to the target, whose distribution is well-known. In turn, reversible binding, which is common for most applications, renders theoretical analysis much more challenging and drastically changes the distribution of reaction times.
We develop a renewal-based approach to derive an approximate solution for the probability density of the reaction time.
This approximation turns out to be remarkably accurate for a broad range of parameters.
We also analyze the dependence of the mean reaction time or, equivalently, the inverse reaction rate, on the main parameters such as K, N, and binding/unbinding constants. Some biophysical applications and further perspectives are briefly discussed.
The James Ross archipelago houses numerous lakes and ponds. In this region, a vast diatom and cyanobacterial variety has been reported; however, the prokaryotic diversity in microbial mats from these lakes remains poorly explored.
Here, a high-throughput sequencing of 16S rRNA gene in microbial mats from Lake Bart-Roja in James Ross Island and lakes Pan Negro and North Pan Negro located in Vega Island was performed. Combined with mineralogical and environmental characteristics, we analyzed the diversity and structure of the microbial communities. Sequences assigned to Archaea were extremely low, while Bacteria domain prevailed with the abundance of Proteobacteria (mostly Betaproteobacteriales) followed by Bacteroidetes, Verrucomicrobia, Firmicutes, and Cyanobacteria.
Local environmental conditions, such as conductivity and Eh, provided differential microbial assemblages that might have implications in the oligotrophic status of the lakes. Consequently, a clear segregation at the family level was observed.
In this sense, the assigned diversity was related to taxa recognized as denitrifiers and sulfur oxidizers. Particularly, in Lake Pan Negro sulfur-reducing and methanogenic representatives were also found and positively correlate with alkalinity and water depth.
Moreover, Deinococcus-Thermus was observed in Lake Bart-Roja, while Melainabacteria (Cyanobacteria)-poorly reported in Antarctic mats-was detected in Lake Pan Negro. Epsilonbacteraeota was exclusively found in this lake, suggesting new potential phylotypes. This study contributes to the understanding of the diversity, composition, and structure of Antarctic benthic microbial ecosystems and provides highly valuable information, which can be used as a proxy to evaluate environmental changes affecting Antarctic microbiota.
Landslides in deglaciated and deglaciating mountains represent a major hazard, but their distribution at the spatial scale of entire mountain belts has rarely been studied. Traditional models of landslide distribution assume that landslides are concentrated in the steepest, wettest, and most tectonically active parts of the orogens, where glaciers reached their greatest thickness.
However, based on mapping large landslides (>0.9 km(2)) over an unprecedentedly large area of Southern Patagonia (similar to 305,000 km(2)), we show that the distribution of landslides can have the opposite trend.
We show that the largest landslides within the limits of the former Patagonian Ice Sheet (PIS) cluster along its eastern margins occupying lower, tectonically less active, and arid part of the Patagonian Andes. In contrast to the heavily glaciated, highest elevations of the mountain range, the peripheral regions have been glaciated only episodically, leaving a larger volume of unstable sedimentary and volcanic rocks that are subject to ongoing slope instability.
Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein's coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyr(CUA) were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs).
Law smells
(2022)
Building on the computer science concept of code smells, we initiate the study of law smells, i.e., patterns in legal texts that pose threats to the comprehensibility and maintainability of the law. With five intuitive law smells as running examples-namely, duplicated phrase, long element, large reference tree, ambiguous syntax, and natural language obsession-, we develop a comprehensive law smell taxonomy. This taxonomy classifies law smells by when they can be detected, which aspects of law they relate to, and how they can be discovered. We introduce text-based and graph-based methods to identify instances of law smells, confirming their utility in practice using the United States Code as a test case. Our work demonstrates how ideas from software engineering can be leveraged to assess and improve the quality of legal code, thus drawing attention to an understudied area in the intersection of law and computer science and highlighting the potential of computational legal drafting.
Deep lipidomics in human plasma: cardiometabolic disease risk and effect of dietary fat modulation
(2022)
Background: In blood and tissues, dietary and endogenously generated fatty acids (FAs) occur in free form or as part of complex lipid molecules that collectively represent the lipidome of the respective tissue. We assessed associations of plasma lipids derived from high-resolution lipidomics with incident cardiometabolic diseases and subsequently tested if the identified risk-associated lipids were sensitive to dietary fat modification. Methods: The EPIC Potsdam cohort study (European Prospective Investigation into Cancer and Nutrition) comprises 27 548 participants recruited within an age range of 35 to 65 years from the general population around Potsdam, Germany. We generated 2 disease-specific case cohorts on the basis of a fixed random subsample (n=1262) and all respective cohort-wide identified incident primary cardiovascular disease (composite of fatal and nonfatal myocardial infarction and stroke; n=551) and type 2 diabetes (n=775) cases. We estimated the associations of baseline plasma concentrations of 282 class-specific FA abundances (calculated from 940 distinct molecular species across 15 lipid classes) with the outcomes in multivariable-adjusted Cox models. We tested the effect of an isoenergetic dietary fat modification on risk-associated lipids in the DIVAS randomized controlled trial (Dietary Intervention and Vascular Function; n=113). Participants consumed either a diet rich in saturated FAs (control), monounsaturated FAs, or a mixture of monounsaturated and n-6 polyunsaturated FAs for 16 weeks. Results: Sixty-nine lipids associated (false discovery rate<0.05) with at least 1 outcome (both, 8; only cardiovascular disease, 49; only type 2 diabetes, 12). In brief, several monoacylglycerols and FA16:0 and FA18:0 in diacylglycerols were associated with both outcomes; cholesteryl esters, free fatty acids, and sphingolipids were largely cardiovascular disease specific; and several (glycero)phospholipids were type 2 diabetes specific. In addition, 19 risk-associated lipids were affected (false discovery rate<0.05) by the diets rich in unsaturated dietary FAs compared with the saturated fat diet (17 in a direction consistent with a potential beneficial effect on long-term cardiometabolic risk). For example, the monounsaturated FA-rich diet decreased diacylglycerol(FA16:0) by 0.4 (95% CI, 0.5-0.3) SD units and increased triacylglycerol(FA22:1) by 0.5 (95% CI, 0.4-0.7) SD units. Conclusions: We identified several lipids associated with cardiometabolic disease risk. A subset was beneficially altered by a dietary fat intervention that supports the substitution of dietary saturated FAs with unsaturated FAs as a potential tool for primary disease prevention.