nils-herrmann/clean_scirepeval huggingface dataset:
Moraine formation in northwestern Ontario: product of subglacial fluvial and glaciolacustrine sedimentation

Long, arcuate, stratified end moraines in northwestern Ontario may represent major and rapid sedimentation events in glacial Lake Agassiz. Rapid lowering of the lake or lift of a marginal ice dam may have triggered widespread outbursts of subglacial meltwater which deposited these end moraines as coalesced or broad subaqueous lacustrine fans. Moraine cores are of undeformed gravel, sand, and silty sand that fine upward. Coarse beds are massive to weakly stratified. Large-scale cross-stratification may be present. Sandy rhythmic beds are laterally transitional to silt–clay rhythmites (varves). Similar facies occur in adjoining eskers.Moraine sediments have the expected characteristics of rapid deposition on subaqueous fans and, therefore, may not represent either prolonged sedimentation or stable ice margins. Rather, they may reflect rapid sedimentation associated with large discharges that induced transient instability in the drainage network and (or) surging prior to marginal sedimentation. This explanat...

Field of study: Environmental science
Distribution of the herbicide atrazine in a microcosm with riparian forest plants

Pesticides applied on sugarcane reach the subsoil of riparian forests and probably contaminate the river water. This work was conducted to learn about the phytoremediation of atrazine and subsoil contamination using the common riparian forest species of Cecropia hololeuca Miq. and Trema micranta (L.) Blum. These plants were grown in soil microcosms where 14C-atrazine at 1/10 of the field-recommended dose was applied at the bottom of the microcosm simulating the movement from contaminated ground water to the upper soil layers and into plants. Residues of 14C-atrazine were detected in all parts of the microcosm including soil, rhizosphere and the roots in different layers of the microcosm, stem and leaves. Atrazine mineralization was higher (10.2%) in the microcosms with plants than the control microcosms without plants (1.2%). The upward movement of this pesticide from deeper to more superficial soil layers occurred in all the microcosms with plants, powered by evapotranspiration process. From the atrazine applied in this study about 45% was taken up by C. hololeuca and 35% by T. micrantha. The highest amount of radioactivity (%) was found in the fine roots and the specific radioactivity (% g−1) showed that thick, fine roots and leaves bioaccumulate atrazine. The enhanced mineralization of atrazine as well the phytostabilization effect of the tree biomass will reduce the bioavailability of these residues and consequently decrease the hazardous effects on the environment.

Field of study: Agricultural and Food sciences
Geographic discrepancies between global and local rarity richness patterns and the implications for conservation

The emerging interest in the biological and conservation significance of locally rare species prompts a number of questions about their correspondence with other categories of biodiversity, especially global rarity. Here we present an analysis of the correspondence between the distributions of globally and locally rare plants. Using biological hotspots of rarity as our framework, we evaluate the extent to which conservation of globally rare plants will act as a surrogate for conservation of locally rare taxa. Subsequently, we aim to identify gaps between rarity hotspots and protected land to guide conservation planning. We compiled distribution data for globally and locally rare plants from botanically diverse Napa County, California into a geographic information system. We then generated richness maps highlighting hotspots of global and local rarity. Following this, we overlaid the distribution of these hotspots with the distribution of protected lands to identify conservation gaps. Based on occupancy of 1 km2 grid cells, we found that over half of Napa County is occupied by at least one globally or locally rare plant. Hotspots of global and local rarity occurred in a substantially smaller portion of the county. Of these hotspots, less than 5% were classified as multi-scale hotspots, i.e. they were hotspots of global and local rarity. Although, several hotspots corresponded with the 483 km2 of protected lands in Napa County, some of the richest areas did not. Thus, our results show that there are important conservation gaps in Napa County. Furthermore, if only hotspots of global rarity are preserved, only a subset of locally rare plants will be protected. Therefore, conservation of global, local, and multi-scale hotspots needs serious consideration if the goals are to protect a larger variety of biological attributes, prevent extinction, and limit extirpation in Napa County.

Field of study: Environmental science
Wave-Base, Marine Profile of Equilibrium, and Wave-Built Terraces: A Critical Appraisal

The concept of wave-base and its corollaries, the marine profile of equilibrium and the wave-built terrace, are largely erroneous. They do not dominantly control the development of the continental shelf and slope. The treatment of these concepts in geologic textbooks and sourcebooks needs revision. Wave-base, although a useful concept if applied generally to the surficial zone of the ocean of high-ambient agitation, does not control shelf deposition as the entire shelf is above any wave-base in this sense. Instead, the shelf is a drowned and relict surface, developed by oscillation of sea level and prograding and regressing paralic sediments—and here surf plays the dominant role. Sedimentation on the continental terrace is not controlled by wave-base but chiefly by topography; the continental slope is undergoing erosion rather than prograding, and ultimate deposition occurs on the continental rise. The wave-cut terrace is not cut at wave-base but at surf-base. Wave-built terraces are nonexistent both on a small scale and on a grand scale as an explanation of the continental slope. A marine profile of equilibrium is developed in the nearshore zone and is associated with a migrating lens of sand, but the outer-shelf profile is not a profile of equilibrium.

Field of study: Geology
Modeling investigation on the viscosity of pure refrigerants and their liquid mixtures by using the Patel–Teja viscosity equation of state

A viscosity model based on the Patel–Teja equation of state has been applied to pure refrigerants and their liquid mixtures. 7490 data points, containing 6481 points for pure refrigerants and 1009 points for binary, ternary and quaternary mixtures, have been used. First, 29 pure refrigerants are selected and the pure-component parameters of the model are then fitted. Subsequently, seven binary mixtures have been used to regress the binary interaction parameters of the model. The resulting binary interaction parameters and pure-component parameters are then used to predict the viscosity of two ternary and one quaternary mixtures. The results show that deviations are generally low for all analyzed compounds and mixtures.

Field of study: Engineering
Reinforcer effectiveness as a function of reinforcer rate and magnitude: a comparison of concurrent performances.

Pigeons' pecks on each of two concurrently available response keys were reinforced under a variable-interval schedule that sometimes allotted food-pellet deliveries to one key and sometimes to the other. The keys differed in the number of reinforcements assigned to each and in the number of pellets delivered during each reinforcement. When the total quantity of food associated with each key during a session was constant, the proportion of responses to a key depended on the particular combinations of reinforcer rate and reinforcer magnitude scheduled on each key. A given quantity of food generated more responding on a key when it was delivered frequently in small amounts than when it was delivered infrequently in large amounts.

Field of study: Biology, Psychology
Resolving independent ion and ion displacement transport mechanisms in ion channels

Univalent metal ion fluxes in gramicidin channels in bilayer membranes produce linear current–voltage plots. Both independent ion models with first-order rate constants or ion–ion displacement models with pseudo-first-order rate constants reproduce the linear current–voltage behavior. To differentiate the mechanisms, the anomalous behavior of the system at low thallous ion mole fractions is studied using a potential ramp protocol. Under these conditions, the current–voltage plots separate into three linear segments with a low conductance segment at lower potentials and parallel outer segments with higher conductance whose voltage axis intercepts are displaced from zero potential. This displaced threshold potential varies with thallous ion mole fraction but has a constant electrochemical potential for all mole fractions. The current–voltage plots and their properties suggest a low conductance mechanism where thallous ion exclusion from the channel obeys Boltzmann statistics in the electrochemical potential. The higher conductance outer segments for electrochemical potentials that exceed the threshold obey a multi-ion displacement.

Field of study: Materials science
Effects of sediment-associated extractable metals, degree of sediment grain sorting, and dissolved organic carbon upon Cryptosporidium parvum removal and transport within riverbank filtration sediments, Sonoma County, California.

Oocysts of the protozoan pathogen Cryptosporidium parvum are of particular concern for riverbank filtration (RBF) operations because of their persistence, ubiquity, and resistance to chlorine disinfection. At the Russian River RBF site (Sonoma County, CA), transport of C. parvum oocysts and oocyst-sized (3 μm) carboxylate-modified microspheres through poorly sorted (sorting indices, σ(1), up to 3.0) and geochemically heterogeneous sediments collected between 2 and 25 m below land surface (bls) were assessed. Removal was highly sensitive to variations in both the quantity of extractable metals (mainly Fe and Al) and degree of grain sorting. In flow-through columns, there was a log-linear relationship (r(2) = 0.82 at p < 0.002) between collision efficiency (α, the probability that colloidal collisions with grain surfaces would result in attachment) and extractable metals, and a linear relationship (r(2) = 0.99 at p < 0.002) between α and σ(1). Collectively, variability in extractable metals and grain sorting accounted for ∼83% of the variability in α (at p < 0.0002) along the depth profiles. Amendments of 2.2 mg L(-1) of Russian River dissolved organic carbon (DOC) reduced α for oocysts by 4-5 fold. The highly reactive hydrophobic organic acid (HPOA) fraction was particularly effective in re-entraining sediment-attached microspheres. However, the transport-enhancing effects of the riverine DOC did not appear to penetrate very deeply into the underlying sediments, judging from high α values (∼1.0) observed for oocysts being advected through unamended sediments collected at ∼2 m bls. This study suggests that in evaluating the efficacy of RBF operations to remove oocysts, it may be necessary to consider not only the geochemical nature and size distribution of the sediment grains, but also the degrees of sediment sorting and the concentration, reactivity, and penetration of the source water DOC.

Field of study: Environmental science
Energy equipartition and fluctuation-dissipation theorems for damped flexible structures

Dynamics and control of flexible mechanical structures has been the topic of much recent research. Here, we examine the energy distribution in finite-dimensional flexible structure models of the type obtained through finite element analysis. Modeling external disturbance forces as zero-mean white noise, we establish that symmetry of the damping matrix is a sufficient condition for the equipartition of potential and kinetic energy in the structure. In addition, we develop upper and lower bounds on the total energy stored in symmetrically damped structures in terms of the strength of the stochastic driving term and the Euclidean norms of the damping matrix and its inverse. In two special cases, explicit solutions for the total energy are obtained and may be viewed as fluctuation-dissipation theorems for the structure models. Convergence conditions for modal expansions of distributed parameter flexible structure models are then developed from these finite-dimensional results. These conditions are interpreted physically as interrelations between assumed damping mechanisms and disturbance force actuator models that must exist in formulating well-posed stochastic distributed-parameter flexible structure models.

Field of study: Mathematics
On the warm absorber in AGN outflow

Warm absorber (WA) is an ionised gas present in the line of sight to the AGN central engine. The effect of the absorber is imprinted in the absorption lines observed in X-ray spectra of AGN. In this work, we model the WA in Seyfert 1 galaxy Mrk 509 using its recently published shape of broad band spectral energy distribution (SED) as a continuum illuminating the absorber. Using the photoionization code {\sc Titan}, recently we have shown that the absorption measure distribution (AMD) found for this object can be successfully modelled as a single slab of gas in total pressure (radiation+gas) equilibrium, contrary to the usual models of constant density multiple slabs. We discuss the transmitted spectrum that would be recorded by an observer after the radiation from the nucleus passes through the WA.

Field of study: Physics
Ni-Al Layered Double Hydroxide Prepared by Liquid Phase Deposition

Al-containing nickel layered double hydroxide was prepared by liquid phase deposition (LPD) using aluminum metal or compounds as the fluorine scavenger in the equilibrium reaction of nickel-fluorine complex ion. The obtained phases depend on the Al content when it is solely used as F- scavenger; α-nickel hydroxide is the predominant phase and a small amount of β-phase is detected. In contrast pure Ni-Al LDH/ C composites, isostructural and isomorphic to α-Ni(OH) 2 are obtained at any range of Al content from 0 to ca. 30 mol % of [Al] / [Al + Ni]. High stability of LDH in 6 M aqueous KOH solution was performed because of low impurity of cation species.

Field of study: Chemistry
Trace fossils and paleoenvironmental control of ichnofacies in a late Quaternary gravel and loess fan delta complex, New Zealand

Remarkably well-preserved trace fossil assemblages of a small, Late Quaternary (> 3000 yr B.P.) fan delta complex are exposed in sea cliffs south of Conway Flat, North Canterbury, New Zealand. Marine trace fossils are common and well-preserved in the bar, embayment and prodelta facies, but deltaic distributary facies contain no trace fossils at all. The preceding paper in this journal ( Lewis and Ekdale, 1991 ) describes the lithofacies and their paleoenvironmental setting in this fan delta complex. Common trace fossils include the ichnogenera Anconichnus, Arenicolites, Asterosoma, Cylindrichnus, Diplocraterion, Gordia, Helminthoida, Ophiomorpha, Piscichnus, Planolites and Skolithos . One new ichnogenus ( Arborichnus ), two new ichnospecies ( Arborichnus sparsus and Diplocraterion asymmetrium ), and three informal varieties of Diplocraterion parallelum (var. lingum, arcum and quadrum ) are introduced. Local ichnofacies include (a) low-divsity Anconichnus horizontalis Ichnofacies of densely packed burrows of deposit-feeding animals in shallow-marine, fine-grained sediment of bar and distal embayment facies, (b) high-diversity Diplocraterion parallelum var. lingum Ichnofacies of burrows of suspension-feeding animals in interbedded mud, clean sand and gravelly sand of the bar facies, (c) moderate-diversity Diplocraterion parallelum var. quadrum Ichnofacies in interbedded mud and sand of distal embayment facies, and (d) low-diversity Planolites montanus Ichnofacies of deformed burrows in bioturbated mud of the prodelta facies. In addition, sparse animal escape structures (fugichnia) occur locally in interbedded sand and gravel of the bar facies. The trace fossil associations of the Conway Flat fan delta complex are unusual in their excellent state of preservation, and many trace fossils are exposed in full-three-dimensional relief. Because of their very young age, they must reflect similar associations of biogenic sedimentary structures in modern deltaic settings that are as yet undescribed. This report appears to be the first documentation of a fully marine trace fossil assemblage in loessial sediments.

Field of study: Environmental science, Geography
Improved Rectangle Attacks on SKINNY and CRAFT

The boomerang and rectangle attacks are adaptions of differential cryptanalysis that regard the target cipher E as a composition of two sub-ciphers, i.e., E = E1 ◦ E0, to construct a distinguisher for E with probability p2q2 by concatenating two short differential trails for E0 and E1 with probability p and q respectively. According to the previous research, the dependency between these two differential characteristics has a great impact on the probability of boomerang and rectangle distinguishers. Dunkelman et al. proposed the sandwich attack to formalise such dependency that regards E as three parts, i.e., E = E1 ◦Em ◦E0, where Em contains the dependency between two differential trails, satisfying some differential propagation with probability r. Accordingly, the entire probability is p2q2r. Recently, Song et al. have proposed a general framework to identify the actual boundaries of Em and systematically evaluate the probability of Em with any number of rounds, and applied their method to accurately evaluate the probabilities of the best SKINNY’s boomerang distinguishers. In this paper, using a more advanced method to search for boomerang distinguishers, we show that the best previous boomerang distinguishers for SKINNY can be significantly improved in terms of probability and number of rounds. More precisely, we propose related-tweakey boomerang distinguishers for up to 19, 21, 23, and 25 rounds of SKINNY-64-128, SKINNY-128-256, SKINNY-64-192 and SKINNY-128-384 respectively, which improve the previous boomerang distinguishers of these variants of SKINNY by 1, 2, 1, and 1 round respectively. Based on the improved boomerang distinguishers for SKINNY, we provide related-tweakey rectangle attacks on 23 rounds of SKINNY-64-128, 24 rounds of SKINNY-128-256, 29 rounds of SKINNY-64-192, and 30 rounds of SKINNY-128-384. It is worth noting that our improved related-tweakey rectangle attacks on SKINNY-64-192, SKINNY-128-256 and SKINNY-128-384 can be directly applied for the same number of rounds of ForkSkinny-64-192, ForkSkinny-128-256 and ForkSkinny-128-384 respectively. CRAFT is another SKINNY-like tweakable block cipher for which we provide the security analysis against rectangle attack for the first time. As a result, we provide a 14-round boomerang distinguisher for CRAFT in the single-tweak model based on which we propose a single-tweak rectangle attack on 18 rounds of this cipher. Moreover, following the previous research regarding the evaluation of switching in multiple rounds of boomerang distinguishers, we also introduce new tools called Double Boomerang Connectivity Table (DBCT), LBCT , and UBCT to evaluate the boomerang switch through the multiple rounds more accurately.

Field of study: Computer science, Mathematics
Algorithm for Constructing Petri Net Based on Language Expression

To create a Petri net that the language it produced is equal to a given language express is an important problem in the Petri nets language theory.The relationships between the language operations of synchronization alternate regular expression and the Petri nets compositions are analyzed.The transformation methods that the regular expression and the α-closure expression is created a Petri net are given.The bounded cover composition operation for Petri net is defined and the language properties about bounded cover composition Petri net is researched.The algorithm for constructing Petri net based on language expression is given.It is realized that to create a Petri net that the language it produced is equal to a given language expression.

Field of study: Computer science
A novel LAMP2 mutation associated with severe cardiac hypertrophy and microvascular remodeling in a female with Danon disease: a case report and literature review.

Danon disease (DD) is a rare disorder characterized by cardiomyopathy, intellectual disability, and proximal myopathy. It is caused by mutations in the LAMP2 gene on X chromosome. Female patients most often present with late-onset cardiomyopathy and slow disease progression, but early-onset cases with unfavorable prognosis have been reported.



We describe the clinical, pathological, and molecular features of a novel LAMP2 c.453delT mutation in a female patient with severe hypertrophic cardiomyopathy, Wolff Parkinson White (WPW) syndrome and rapid progression to heart failure, requiring heart transplant. Immunohistochemical analysis of LAMP2 in the explanted heart revealed a mosaic pattern of distribution, with discrete clusters of either stained or unstained cardiac myocytes, the latter being more frequent in the septum. These findings paralleled X chromosome inactivation within the myocardium. Interestingly, multiple foci of microscarring were found on histology in the Left Ventricle (LV) free wall and septum, in a close spatial relationship with remodeling and severe stenosis of intramural coronary arterioles.



Our findings suggest that several features may contribute to the early and severe cardiac phenotype in female DD patients. The type of mutation may account for the early disease onset, while both the inhomogeneous distribution of LAMP2 loss and the presence of microvascular remodeling may be determinant in the rapid progression to heart failure.

Field of study: Biology, Medicine
The Akoya pearl oyster shell as an archival monitor of lead exposure.

The Akoya pearl oyster (Pinctada imbricata) was experimentally exposed to (a) constant levels of lead (Pb) at 180 microg L(-1) for nine weeks, or (b) two short term (pulse) exposures of Pb at 180 microg L(-1) (three weeks each) with an intervening depuration period (three weeks), to assess its utility as an (i) accumulative monitor of Pb contamination and an (ii) archival monitor for discriminating constant versus pulsed Pb exposure events. P. imbricata showed similar reductions in growth (based on shell morphology and wet weight) and Pb accumulation patterns for whole tissue and shell in response to both Pb exposure regimes. Thus the whole oyster was deemed an inappropriate accumulative monitor for assessing short-term temporal variation of Pb exposure and effect. However, using secondary ion mass spectrometry, Pb was shown to accumulate in the successively deposited nacreous layers of the shell of P. imbricata, documenting the exposure history of constant versus pulsed Pb events. Patterns of Pb deposition not only reflected the frequency of Pb exposure events but also their relative durations. Thus, the shell of P. imbricata may be employed as a suitable biological archive of Pb exposure.

Field of study: Environmental science