Negative Fragment Research Articles

Quantitative evaluation of noncovalent interactions with negative fragmentation approach including basis set superposition error correction

Abstract We propose a negative fragmentation approach (NFA), including counterpoise (CP) correction to basis set superposition error (BSSE) for quantitatively evaluating intra- and intermolecular noncovalent interactions. Noncovalent interactions are widely found in chemistry and biology and are regarded as essential interactions. However, there are few general methods for evaluating these individual intra- and intermolecular interaction energies because of two issues: (i) difficulty in the evaluation of intramolecular interactions due to the interacting sites connected with covalent bonds and (ii) BSSE affecting the quantitative accuracy of interaction analysis. In our scheme, we overcome the issue (i) using the NFA scheme, which can evaluate intra- and intermolecular interactions as a fragment–fragment interaction of interacting sites, and address the issue (ii) using the CP method. Here, NFA including the CP correction was applied to various molecular systems, providing comparable results for intermolecular interactions to supermolecule calculations with the CP correction and also succeeding in the evaluation of intramolecular interactions and its BSSEs. It is notable that our NFA scheme does not require any particular program or a modification of the program codes. These indicate that many researchers can apply our NFA scheme to various molecular systems.

Habitat amount modulates biodiversity responses to fragmentation.

Anthropogenic habitat destruction leads to habitat loss and fragmentation, both of which interact to determine how biodiversity changes at the landscape level. While the detrimental effects of habitat loss are clear, there is a long-standing debate about the role of habitat fragmentation per se. We identify the influence of the total habitat amount lost as a modulator of the relationship between habitat fragmentation and biodiversity. Using a simple metacommunity model characterized by colonization-competition (C-C) trade-offs, we show that the magnitude of habitat loss can induce a unimodal response of biodiversity to habitat fragmentation. When habitat loss is low, habitat fragmentation promotes coexistence by suppressing competitively dominant species, while habitat fragmentation at high levels of habitat loss can shape many smaller isolated patches that drive extinctions of superior competitors. While the C-C trade-off is not the only mechanism for biodiversity maintenance, the modulation of habitat fragmentation effects by habitat loss is probably common. Reanalysis of a globally distributed dataset of fragmented animal and plant metacommunities shows an overall pattern that supports this hypothesis, suggesting a resolution to the debate regarding the relative importance of positive versus negative fragmentation effects.

Time-lag effects of habitat loss, but not fragmentation, on deadwood-dwelling lichens

ContextLandscape habitat amount is known to increase biodiversity, while the effects of habitat fragmentation are still debated. It has been suggested that negative fragmentation effects may occur with a time lag, which could explain inconsistent results. However, there is so far no empirical support for this idea.ObjectivesWe evaluated whether habitat amount and fragmentation at the landscape scale affect the species density of deadwood-dwelling lichens, and whether these effects occur with a time lag.MethodsWe surveyed deadwood-dwelling lichens in woodland key habitats in two regions in northern Sweden, and modelled their species density as a function of past (1960s) and present (2010s) habitat amount (old forest area) and fragmentation (edge density) in the surrounding landscapes.ResultsPresent habitat amount generally had weak positive effects on lichen species density. Positive effects of the past habitat amount were stronger, indicating a time lag in habitat amount effects. Habitat fragmentation effects were generally weak and similar whether fragmentation was measured in the past or the present landscapes, indicating no time lag in fragmentation effects.ConclusionsWe found a time lag effect of habitat amount, but not fragmentation. This result is not consistent with suggestions that time lags explain the mixed observations of fragmentation effects. Time-lag effects of habitat amount suggest that the studied lichen communities face an extinction debt. Conservation should therefore prioritize increasing the amount of old forest, for example by creating forest reserves, to maintain the current lichen diversity. More generally, our results imply that studies examining only the present habitat amount risk under-estimating its importance.

Fragment answers with negative dependencies in Korean: a direct interpretation approach

Abstract Fragment answers are nonsentential utterances quite pervasive in daily-life dialogues. This article focuses on fragment answers involving a negative dependency expression in Korean. The key question for the analysis of such a negative fragment expression is how to resolve sentential meaning from its non-sentential status. This article argues against sentential approaches that postulate clausal sources together with move-and-delete operations to generate negative fragments. Instead, the article supports a discourse-based direct interpretation analysis that allows negative fragment answers to be directly projected as a full utterance and obtain their propositional meaning by referring to the organized discourse structure in question.

<i>Ab initio</i> molecular dynamics study on dissociation process of 2-thiouracil and its tautomers under low-energy electron interactions

When biomolecules interact with high-energy particles and rays, they are directly ionized or dissociated, then a large number of low-energy electrons are formed as secondary particles. These low-energy electrons will attach to biomolecules, and trigger off the secondary dissociation, forming free radicals and ions with high reactivity, which can damage the structure and function of the biomolecule and cause irreversible radiation damage to the biomolecule. It is important to study the low-energy dissociative electron attachment (DEA) process of biomolecules for understanding radiation damage to biological organisms. Currently, the theoretical studies of DEA have mainly focused on the bound states of negative ions and the types of resonances in the dissociation process. The dissociation process is well described by quantum computational method, but the diversity and complexity of dissociation channels present in the dissociation process of 2-thiouracil molecule also pose a great computational challenge to these methods. In addition, the quantum computational methods are not ideal for dealing with the discrete states of chemical bonds and the problem of continuity coupling of electrons. The dissociation dynamics of biomolecules mainly results from ionization and electron attachment. <i>Ab initio</i> molecular dynamics simulation can reasonably describe these processes. In light of these considerations, <i>ab initio</i> molecular dynamics simulation is used in this work to study dynamic variation process in DEA. The low-energy electron dissociative attachment to 2-thiouracil in the gas phase is studied by using the Born-Oppenheimer molecular dynamics model combined with density functional theory. It is found that an important dehydrogenation phenomenon of 2-thiouracil and its tautomers occurs in the DEA process, and that the N—H and C—H bond are broken at specific locations. Due to the loss of hydrogen atoms at the N and C sites, the closed-shell dehydrogenated negative ion (TU-H)<sup>–</sup> forms, which is the most important negative ion fragments in the dissociation process. The potential energy curves, the bond dissociation energy and the electron affinity energy of the broken bond show that the N—H bond is the most likely to break, indicating the formation of the negative ion (TU-H)<sup>–</sup> mainly comes from the breaking of N—H bond. The theoretical calculations in this work are in good agreement with the available experimental results, indicating that the chosen calculation method is fully reliable. ​The BOMD simulations can not only dynamically recover the process of dissociative attachment of low-energy electrons to 2-thiouracil, but also more importantly provide an insight into the mechanisms of dehydrogenation and dissociation channels of 2-thiouracil molecules in DEA process.

Hydrogen Bond Energies in Helical Peptides Investigated by Negative Fragmentation Approach with Density Functional Theory

Hydrogen Bond Energies in Helical Peptides Investigated by Negative Fragmentation Approach with Density Functional Theory

Material dialogues for first-order logic in constructive type theory: extended version

Abstract Dialogues are turn-taking games which model debates about the satisfaction of logical formulas. A novel variant played over first-order structures gives rise to a notion of first-order satisfaction. We study the induced notion of validity for classical and intuitionistic first-order logic in the constructive setting of the calculus of inductive constructions. We prove that such material dialogue semantics for classical first-order logic admits constructive soundness and completeness proofs, setting it apart from standard model-theoretic semantics of first-order logic. Furthermore, we prove that completeness with regard to intuitionistic material dialogues fails in both constructive and classical settings. As an alternative, we propose material dialogues played over Kripke structures. These Kripke material dialogues exhibit constructive completeness when restricting to the negative fragment. The results concerning classical material dialogues have been mechanized using the Coq interactive theorem prover.

Dynamic Asymmetric Causality of Bitcoin’s Price-Volume Relation

Bitcoin has attracted incessant attentions in recent times. Studies have completed models to examine the relationship between Bitcoin and other multiple attendant variables. This paper considers a simple and direct price-volume relation. The paper offers causality evidence according to the dynamic asymmetric causality test. Based on available monthly data spanning 2010:M7-2022:M10, the paper shows that Bitcoin price and volume are integrated, both been I(0)’s. Moreover, the paper discloses the short- and long-term price-volume behaviors of Bitcoin using the cointegration test and vector error correction model (VECM). Taken together, the study first confirms long run relations and presents the estimates of the parsimonious VECM. The results show short run evidence of positive price-volume relations, and in the long run, the disequilibria are as well corrective and mean reversing. The outcomes of the Hatemi-J’s causality testing suggest likely evidence of bidirectional causality between the positive and negative fragments of the shocks of Bitcoin price and volume during the periods.

Aeromicelle—A new form of liquid aerosol for delivering aqueous samples into a single-particle mass spectrometer

For applying highly sensitive mass spectrometry to chemical analysis of aqueous samples, we have developed a novel technique using a new form of liquid droplets, which we call “aeromicelle” (AM), to deliver aqueous sample solutions directly into the vacuum region of a single-particle mass spectrometer in liquid form and conduct immediate mass analysis. AMs are generated by spraying an aqueous solution containing a surfactant at a concentration significantly lower than its critical micelle concentration (CMC). When the solution is sprayed, liquid droplets containing the surfactant are formed, which gradually dry in an air flow. Upon drying, the surfactant concentration in the droplet exceeds its CMC, and consequently, the surfactant molecules begin to cover the droplet surface. Finally, the surface is expected to be fully covered with surfactant molecules such as reverse micelles. The surface coverage helps suppress the evaporation of water, thereby enhancing the residence time of the liquid droplet. Our experimental results show that the AMs retained a liquid form for at least 100 s in air and survived even under vacuum conditions for further mass analysis: each AM delivered in the vacuum region of a single-particle mass spectrometer is ablated with an intense laser pulse and then, mass analyzed. Individual AMs generated from an aqueous solution containing CsCl were analyzed using a single-particle mass spectrometer. The Cs+ ion peak was observed even in AMs generated from the 10 nM solution. The number of Cs atoms in each AM was estimated to be approximately 7 × 103, which corresponds to 1.2 × 10−20 mol (12 zmol). Meanwhile, in the mass analysis of tyrosine, both positive and negative fragmentation ions from tyrosine in AMs were observed in the mass spectrum and 4.6 × 105 (760 zmol) tyrosine molecules were detected.

Algebraic logic for the negation fragment of classical logic

Abstract The general aim of this article is to study the negation fragment of classical logic within the framework of contemporary (Abstract) Algebraic Logic. More precisely, we shall find the three classes of algebras that are canonically associated with a logic in Algebraic Logic, i.e. we find the classes $\textrm{Alg}^*$, $\textrm{Alg}$ and the intrinsic variety of the negation fragment of classical logic. In order to achieve this, firstly, we propose a Hilbert-style axiomatization for this fragment. Then, we characterize the reduced matrix models and the full generalized matrix models of this logic. Also, we classify the negation fragment in the Leibniz and Frege hierarchies.

Strigolactones in Sugarcane Growth and Development

Sugarcane is a complex polyploid aneuploid cash crop, and transgenic varieties are important for molecular genetic and traditional breeding approaches. Herein, the sugarcane variety ROC22 served as the receptor, the Bar gene served as a screening marker, and positive and negative fragments of the ScD27.2 gene, upstream of strigolactones (SLs) biosynthesis genes driven by the 35S promoter, were introduced by Agrobacterium tumefaciens-mediated transformation. Regenerated plants were obtained by co-culture, screening culture, and differentiation induction, and 27 sense and antisense ScD27.2 transgenic seedlings were obtained by herbicide screening. PCR detection and 1% Basta (Glufosinate) application on leaves revealed Bar in all lines, with all testing positive for herbicide application and 23 containing the target gene (positive resistance screening rate = 87.5%). q-PCR and phenotypic analyses showed that ScD27.2 expression, plant height, tiller number, root length, stem diameter, and fresh weight were decreased in transgenic (ScD27.2R-9) compared with non-transgenic (NT and ScD27.2F-2) lines. ScD27.2 expression was downregulated, and growth potential was inhibited. Under 20% PEG treatment, malondialdehyde (MDA) content in ScD27.2R-9 was higher than in NT, while proline content was lower. Under drought stress, ScD27.2 expression, MDA levels, and proline content in ScD27.2F-2 and NT were higher than in non-treated controls, ScD27.2 expression increased with time, and MDA and proline levels also increased. ScD27.2 expression in ScD27.2R-9 decreased under 20% PEG treatment, MDA and proline increased (but not to NT levels), and growth was lower than NT. The 20% PEG treatment also increased the levels of (±)-2′-epi-5-deoxystrigol and (+)-abscisic acid in the rooting culture media of ScD27.2F-2, ScD27.2R-9, and NT lines, but the levels of (+)-abscisic acid content in ScD27.2R-9 was lower than in NT. Thus, interfering with ScD27.2 expression decreased resistance to 20% PEG treatment. ScD27.2 encodes a β-carotene isomerase involved in SLs biosynthesis that might function in sugarcane resistance to drought stress. It explains the role of SLs in sugarcane growth and development and responses to drought stress.

Does negation influence the choice of sentence continuations? Evidence from a four-choice cloze task.

Event plausibility facilitates the processing of affirmative sentences, but little is known about how it affects negative sentences. In six behavioural experiments, we investigated negation's impact on the choice of sentence continuations that differ with respect to event plausibility. In a four-choice cloze task, participants saw affirmative and negative sentence fragments (The child will [not] eat the . . .) in combination with four potential continuations: yoghurt (a plausible word), shellfish (a weak world knowledge violating word), branch (a severe world knowledge violating word), and minivan (a word resulting in a semantic violation). Across all experiments the plausible word was highly preferred in both affirmative and negative sentences. Experiment 2 replicated Experiment 1 while ruling out the possibility that the lack of effect of negation in Experiment 1 stemmed from participants not fully processing the negation. Experiment 3 showed that the observed plausibility effects can be generalised to other aspectual forms (The child has [not] eaten the yoghurt). Experiment 4 ruled out the possibility that the choices were mainly driven by lexical associations and additionally suggested a role for informativity. Experiment 5 replicated Experiment 4 and reinforced the general pattern according to which negative sentences express the denial of plausible positive events. Experiment 6 provided evidence that informativity might be driving patterns of choices in the negative sentences. All in all, these findings suggest that upcoming continuations are chosen to maximise the plausibility of the event in the affirmative sentences and to deny that event in the negative sentences. The observed plausibility effects do not seem to be modulated by the internal representation of events, but they can be modulated by changes to the expected informativity of the sentence.

Gone with the wind: Negative genetic and progeny fitness consequences of habitat fragmentation in the wind pollinated dioecious tree Brosimum alicastrum.

Habitat fragmentation negatively affects population size and mating patterns that directly impact progeny fitness and genetic diversity; however, little is known about the effects of habitat fragmentation on dioecious, wind pollinated trees. We assessed the effects of habitat fragmentation on population sex ratios, genetic diversity, gene flow, mating patterns and early progeny vigor in the tropical dioecious tree, Brosimum alicastrum. We conducted our study in three continuous and three fragmented forest sites in a Mexican tropical dry forest. We used eight microsatellite loci to characterize the genetic diversity, gene flow via pollen distances and mean relatedness of progeny. We compared early progeny vigor parameters of seedlings growing under greenhouse conditions. Sex ratios did not deviate from 1:1 between habitat conditions, except for one population in a fragmented habitat, which was female biased. The genetic diversity of adult trees and their offspring was similar in both habitat conditions. Pollen gene flow distances were similar across habitat types; however, paternity correlations were greater in fragmented than in continuous habitats. Germination rates did not differ between habitat conditions; however, progeny from fragmented habitats produced fewer leaves and had a lower foliar area, total height, and total dry biomass than progeny from continuous habitats. Changes in mating patterns, because of habitat fragmentation, have negative effects on early progeny vigor. We conclude that negative habitat fragmentation effects on mating patterns and early progeny vigor may be a serious threat to the long-term persistence of tropical dioecious trees. This article is protected by copyright. All rights reserved.

Negative fragmentation approach for investigating the depolarization effect of neighboring residues on hydrogen bonds in π-helix

We systematically analyzed hydrogen bond (HB) interaction energies in π-helix with alanine peptide models using the negative fragmentation approach (NFA) combined with the precise density functional theory (DFT) and the molecular mechanics calculation. We conclude that the weaker HB energies in the helical structure as compared with those of the isolated ones originate from the depolarization of both acceptor and donor groups of HB. It was also observed that the longer the helical length, the more stable the HB, suggesting the HB cooperativity.

Plasmonic Hydroxyl Radical-Driven Epoxidation of Fatty Acid Double Bonds in Nanoseconds for On-Tissue Mass-Spectrometric Analysis and Bioimaging.

Lipids represent a large family of compounds with highly diverse structures that are involved in complex biological processes. A photocatalytic technique of on-tissue epoxidation of C=C double bonds has been developed for in situ mass spectrometric identification and spatial imaging of positional isomers of lipids. It is based on the plasmonic hot-electron transfer from irradiated gold nanowires to redox-active organic matrix compounds that undergo bond cleavages and generate hydroxyl radicals in nanoseconds. Intermediate radical anions and negative fragment ions have been unambiguously identified. Under the irradiation of a pulsed laser of the third harmonic of Nd3+:YAG (355 nm), the hydroxyl radical-driven epoxidation of unsaturated lipids with different numbers of C=C bonds can be completed in nanoseconds with high yields of up to 95%. Locations of C=C bonds were recognized with diagnostic fragment ions that were produced by either collision with an inert gas or auto-fragmentation resulting from the impact of energetic hot electrons and vibrational excitation. This technique has been applied to the analysis of breast cancer tissues of mice models without extensive sample processes. It was experimentally demonstrated that C=C bonds may be formed at different positions of not only regular mono- or poly-unsaturated fatty acids but also other odd-numbered long-chain fatty acids.

Transient inhibition of p53 enhances prime editing and cytosine base-editing efficiencies in human pluripotent stem cells

Precise gene editing in human pluripotent stem cells (hPSCs) holds great promise for studying and potentially treating human diseases. Both prime editing and base editing avoid introducing double strand breaks, but low editing efficiencies make those techniques still an arduous process in hPSCs. Here we report that co-delivering of p53DD, a dominant negative fragment of p53, can greatly enhance prime editing and cytosine base editing efficiencies in generating precise mutations in hPSCs. We further apply PE3 in combination with p53DD to efficiently create multiple isogenic hPSC lines, including lines carrying GBA or LRRK2 mutations associated with Parkinson disease and a LMNA mutation linked to Hutchinson-Gilford progeria syndrome. We also correct GBA and LMNA mutations in the patient-specific iPSCs. Our data show that p53DD improves PE3 efficiency without compromising the genome-wide safety, making it feasible for safe and routine generation of isogenic hPSC lines for disease modeling.

Smooth polymers charge negatively: Controlling contact electrification polarity in polymers

Contact electrification is a powerful tool to harvest energy from mechanical motion. However, current models of contact electrification at polymer | polymer interfaces only explain charge transfer for contact between chemically dissimilar polymers. Recently, strong contact electrification between chemically identical polymer surfaces has been observed. Understanding contact electrification between chemically identical polymers is a key issue in developing a wholistic model for polymer triboelectrification. Herein, we present a combined experimental and computational approach to develop a model of the contact electrification between chemically identical polymers. The model developed describes how the relative surface roughness influences surface charge. The chemically identical polymer surfaces show an increase in the surface charge when the difference in surface roughness is increased. Further, the roughest surface was found to present a positive surface charge, and the smoother surface a negative charge. These observations were justified though modelling of a consistently lower strain in rougher surfaces during contact-separation. Molecular dynamics simulations demonstrated the relationship between this strain with bond-scission and charged material transfer. It was found that a negative charged fragment has a higher statistical probability to be transferred due to smaller scission / desorption energies. This comparison of surface roughness can be extended to dissimilar polymer interfaces and will enable engineering of highly efficient triboelectric nanogenerator (TENG) devices in the future.

Logical separability of labeled data examples under ontologies

Finding a logical formula that separates positive and negative examples given in the form of labeled data items is fundamental in applications such as concept learning, reverse engineering of database queries, generating referring expressions, and entity comparison in knowledge graphs. In this paper, we investigate the existence of a separating formula for data in the presence of an ontology. Both for the ontology language and the separation language, we concentrate on first-order logic and the following important fragments thereof: the description logic ALCI, the guarded fragment, the two-variable fragment, and the guarded negation fragment. For separation, we also consider (unions of) conjunctive queries. We consider several forms of separability that differ in the treatment of negative examples and in whether or not they admit the use of additional helper symbols to achieve separation. Our main results are model-theoretic characterizations of (all variants of) separability, the comparison of the separating power of different languages, and the investigation of the computational complexity of deciding separability.

Depolarizing Effects in Hydrogen Bond Energy in 310-Helices Revealed by Quantum Chemical Analysis.

Hydrogen-bond (H-bond) energies in 310-helices of short alanine peptides were systematically examined by precise DFT calculations with the negative fragmentation approach (NFA), a modified method based on the molecular tailoring approach. The contribution of each H-bond was evaluated in detail from the 310-helical conformation of total energies (whole helical model, WH3-10 model), and the results were compared with the property of H-bond in α-helix from our previous study. The H-bond energies of the WH3-10 model exhibited tendencies different from those exhibited by the α-helix in that they depended on the helical position of the relevant H-bond pair. H-bond pairs adjacent to the terminal H-bond pairs were observed to be strongly destabilized. The analysis of electronic structures indicated that structural characteristics cause the destabilization of the H-bond in 310-helices. We also found that the longer the helix length, the more stable the H-bond in the terminal pairs of the WH3-10 model, suggesting the action of H-bond cooperativity.

MiR-1 mediated AMPK pathway on cardiomyocyte apoptosis in hypertensive rats

In recent years, it has been found that miRNA has a very close relationship with cardiovascular system diseases. Heart disease is accompanied by a change of the miRNA expression spectrum. Changing the expression of miRNA in or out of cells can cause heart diseases such as myocardial infarction, hypertrophy or arrhythmia. Mitogen-activated protein kinases (MAPKs) are important transmitters of cell surface signals to the nucleus. The family influences the biological responses of cells (e.g., proliferation, differentiation, transformation and apoptosis) by affecting the transcription and regulation of genes in animal cells. Based on the above background, the purpose of this study was to study the effect of the mir-1-mediated AMPK pathway on cardiomyocyte apoptosis in hypertensive rats. The expression level of miRNA-1 in cultured rat H9c2 cardiomyocytes was detected by real-time PCR to determine the success of the transfection. MTT method was used to detect the cell viability. Flow cytometry was used to detect the cell apoptosis, and real-time PCR and Western blot were used to detect the mRNA and protein expression of bcl-2. The results were compared with those of H9c2 cells (blank control group) and miRNA negative control fragments (negative control group). As an important kinase regulating energy homeostasis, AMPK is one of the central regulators of metabolism in eukaryotic cells and organisms, responsible for regulating cellular capacity input and output and maintaining the smooth functioning of cellular physiological activities. At the same time, AMPK is a key protein involved in a variety of signaling pathways. The results showed that the apoptosis rate of myocardial cells in the miRNA-1 group decreased (0.710 ± 0.009661)% vs (1.066667 ± 0.02603)% compared with that in the spontaneous hypertension control group (P < 0.001). The transfected miRNA-1mimics can up-regulate the expression of miRNA-1 in cells, inhibit the proliferation of cardiomyocytes and promote apoptosis.