bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling peptide self-assembly within a partially disordered tau filament
Authors: Maraba Oguzhan , Bhattacharya Shayon , Conda-Sheridan Martin , Thompson Damien 
Published: February 2023

Abstract
Peptide self-assemblies are a natural template for designing bio-inspired functional materials given the extensive characterisation of neurodegenerative and non-disease biological amyloid protein assemblies and advances in rational, modelling-led materials design. These bioinspired materials employ design rules obtained from known aggregation-prone peptides or de novo screening for sequences most amenable to self-assemble functional nanostructures. Here, we exploit the hybrid nature of a complex peptide with both ordered crystalline and intrinsically disordered regions, namely, the microtubule-binding domain (MBD) of tau protein, to probe the physical driving forces for self-assembly at the molecular level. We model the peptide in its native and mutated states to identify the supramolecular packing driving stabilisation at the prefibrillar level. We use extensive atomic-resolution molecular dynamics computer simulations, contact maps, hydrogen-bond networks and free energy calculations to model the tau MBD and its two known familial mutants, the P301L and K280Δ, along with a control double mutant, P301L + K280Δ as a first step towards understanding their effects on oligomer stability in fibrillar fold. Our results indicate that the mutations destabilise supramolecular packing in the pro-fibrillar hexamer by breaking contacts in the ordered domain of tau MBD, which helps explain mutation-induced toxicity levels as the more stable wild-type peptide assemblies may be less prone to crumbling, producing fewer toxic small oligomeric seeds. Our most important finding is that tau familial mutations causing frontotemporal dementia may show distinct morphologies delineating different stages of self-assembly. The models show that the P301L mutant is more pro-nucleating with low tendency for assembly polymerisation, whereas K280Δ is more pro-elongating with potential for protofibrillar growth. Our data provides a predictive mechanistic model for distinct peptide self-assembly features depending on the location and nature of single missense mutations on the partially disordered pathogenic MBD, which may explain the prevalence of polymorphic filamentous tau strains observed experimentally.
Silver nanoclusters prepared in water-in-oil emulsions
Authors: Oyem Hector H , Houlton Andrew , Horrocks Benjamin R 
Published: February 2023

Abstract
Stable silver clusters can be prepared by a simple electroless reduction reaction taking place in water-in-oil emulsions. An emulsion containing AgNO3 in the water droplets was mixed with a similar emulsion containing aqueous NaBH4 droplets. The droplet diameter, based on Rayleigh scattering, was 41 nm and the mean number of Ag+ ions in each droplet varied from 2.0 to 21.7 as the concentration increased from 90 μM to 1 mM AgNO3. The low number of Ag+ ions in each droplet inhibits the growth of large nanoparticles and these emulsions do not show the large plasmon band observed for Ag nanoparticles obtained by the analogous reaction in bulk solution at the same Ag+ concentrations. Atomic force microscopy provides evidence of small Ag nanoclusters and a much lower number of larger nanoparticles. Electrospray mass spectrometry suggests that the clusters are mainly Ag4 species coordinated to water and BH4
−. The Ag nanocluster-containing emulsions are fluorescent and show an emission band with a peak wavelength of 427 nm and a Stokes shift of 81 nm from the first peak at 346 nm in the excitation spectrum. The intensity of fluorescence decreased as the [Ag(I)] increased and our most fluorescent samples were prepared from 90 μM AgNO3 because at higher concentrations more Ag nanoparticles are formed. DFT calculations on Agn clusters indicated that Ag4 species favour a planar rhombic geometry even in the presence of coordinating water molecules or BH4
−. However calculations of vertical excitation energies for Ag4 species do not match the experimental excitation spectra and this suggests the fluorescence arises from bright AgNCs of different nuclearity present at lower abundance in the mixture of species produced by the emulsion reaction. Calculated excitation energies for Ag6 give the best fit to the available data.
Natural Law Theory, “New” and Old
Authors: Coyle Sean 
Published: February 2023

Abstract
In the second edition of Natural Law and Natural Rights John Finnis observes that, whilst he expected criticism of his theory from positivists, he did not expect it from traditional natural law theorists who felt that the theory was insufficiently grounded in Aquinas’s doctrines. Finnis argued that the divergence was a mirage occasioned by his addressing topics out of the standard orders of treatment. This essay considers what Finnis’s theory would look like if placed back into Aquinas’s orders of treatment, and gauges the extent to which it conforms to Aquinas’s doctrines, and the extent to which it is divergent and “new.” This analysis may hopefully serve as a starting point for further study.
The evolution of the spike protein and hACE2 interface of SARS-CoV-2 omicron variants determined by hydrogen bond formation
Authors: Yang Yu-Yuan , Tseng Yufeng Jane 
Published: February 2023

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in December 2019. As of mid-2021, the delta variant was the primary type; however, in January 2022, the omicron (BA.1) variant rapidly spread and became the dominant type in the United States. In June 2022, its subvariants surpassed previous variants in different temporal and spatial situations. To investigate the high transmissibility of omicron variants, we assessed the complex of spike protein 1 receptor-binding domain (S1RBD) and human angiotensin-converting enzyme 2 (hACE2) from the Protein Data Bank (6m0j, 7a91, 7mjn, 7v80, 7v84, 7v8b, 7wbl and 7xo9) and directly mutated specific amino acids to simulate several variants, including variants of concern (alpha, beta, gamma, delta), variants of interest (delta plus, epsilon, lambda, mu, mu without R346K) and omicron variants (BA.1, BA.2, BA.2.12.1, BA.4, BA.5). Molecular dynamics (MD) simulations for 100 ns under physiological conditions were then performed. We found that the omicron S1RBD–hACE2 complexes become more compact with increases in hydrogen-bond interactions at the interface, which is related to the transmissibility of SARS-CoV-2. Moreover, the relaxation time of hydrogen bonds is relatively short among the omicron variants, which implies that the interface conformation alterations are fast. From the molecular perspective, PHE486 and TYR501 in omicron S1RBDs need to involve hydrogen bonds and hydrophobic interactions on the interface. Our study provides structural features of the dominant variants that explain the evolution trend and their increased contagiousness and could thus also shed light on future variant changes.
Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding
Authors: Chang Christine H , Nelson William C , Jerger Abby , Wright Aaron T , Egbert Robert G , McDermott Jason E 
Published: February 2023

Abstract

Motivation
The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families.

Results
Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes.

Availability and implementation
Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
NIAPU: network-informed adaptive positive-unlabeled learning for disease gene identification
Authors: Stolfi Paola , Mastropietro Andrea , Pasculli Giuseppe , Tieri Paolo , Vergni Davide 
Published: February 2023

AbstractMotivationGene–disease associations are fundamental for understanding disease etiology and developing effective interventions and treatments. Identifying genes not yet associated with a disease due to a lack of studies is a challenging task in which prioritization based on prior knowledge is an important element. The computational search for new candidate disease genes may be eased by positive-unlabeled learning, the machine learning (ML) setting in which only a subset of instances are labeled as positive while the rest of the dataset is unlabeled. In this work, we propose a set of effective network-based features to be used in a novel Markov diffusion-based multi-class labeling strategy for putative disease gene discovery.ResultsThe performances of the new labeling algorithm and the effectiveness of the proposed features have been tested on 10 different disease datasets using three ML algorithms. The new features have been compared against classical topological and functional/ontological features and a set of network- and biological-derived features already used in gene discovery tasks. The predictive power of the integrated methodology in searching for new disease genes has been found to be competitive against state-of-the-art algorithms.Availability and implementationThe source code of NIAPU can be accessed at https://github.com/AndMastro/NIAPU. The source data used in this study are available online on the respective websites.Supplementary informationSupplementary data are available at Bioinformatics online.
Sohlh1loss of function male and female infertility model impacts overall health beyond gonadal dysfunction in mice
Authors: Rodríguez-Escribà Marta , Rodríguez-Alonso Beatriz , Belur Shweta , Rajkovic Aleksandar 
Published: February 2023

AbstractReproductive longevity is associated with health outcomes. Early menopause, loss of ovarian function, and male infertility are linked to shorter lifespan and increased adverse health outcomes. Here we examined the extragonadal effects of whole animal loss of spermatogenesis and oogenesis specific basic helix–loop–helix 1 (Sohlh1) gene in mice, a well-described mouse model of female and male infertility. Sohlh1 encodes a transcription factor that is primarily expressed in the male and female germline and regulates germline differentiation. The Sohlh1 knockout mouse model, just like human individuals with SOHLH1 loss of function, presents with hypergonadotropic hypogonadism and loss of ovarian function in females and impaired spermatogenesis in males, with a seemingly gonad restricted phenotype in both sexes. However, extragonadal phenotyping revealed that Sohlh1 deficiency leads to abnormal immune profiles in the blood and ovarian tissues of female animals, sex-specific alterations of metabolites, and behavior and cognition changes. Altogether, these results show that Sohlh1 deficiency impacts overall health in both male and female mice.
Between Ordinary Harm and Deviance: Evaluating the UK’s Regulatory Regime For Controlling Air Pollution From Wood Burning Stoves
Authors: Heydon James 
Published: February 2023

Abstract
Particulate matter (PM) in air pollution causes illness, injury and premature death by infiltrating essential organs. Wood burning stoves are a primary source of PM in the United Kingdom, where domestic wood burning emissions have tripled over the last decade. This article adopts a constructivist lens to examine the regulatory regime controlling these pollutants. Combining analysis of ‘expert’ interviews, responses to Freedom of Information requests and government records exempting appliances from Smoke Control Area rules, it illustrates how efforts at controlling ‘smoke’ in the past have become instrumental in encouraging the production of PM from stoves in the present. In doing so, this article demonstrates the utility of research sensitive to processes underpinning the (non)construction of environmental issues as deviant and suggests a lens through which ordinary harms can be better understood.
Quality indicators for post-resuscitation care after out-of-hospital cardiac arrest: a joint statement from the Association for Acute Cardiovascular Care of the European Society of Cardiology, the European Resuscitation Council, the European Society of Intensive Care Medicine, and the European Society for Emergency Medicine
Authors: Grand Johannes , Schiele Francois , Hassager Christian , Nolan Jerry P , Khoury Abdo , Sionis Alessandro , Nikolaou Nikolaos , Donadello Katia , Behringer Wilhelm , Böttiger Bernd W , Combes Alain , Quinn Tom , Price Susanna , Jorge-Perez Pablo , Tavazzi Guido , Ristagno Giuseppe , Cariou Alain , Bonnefoy Cudraz Eric 
Published: February 2023

Abstract

Aims
Quality of care (QoC) is a fundamental tenet of modern healthcare and has become an important assessment tool for healthcare authorities, stakeholders and the public. However, QoC is difficult to measure and quantify because it is a multifactorial and multidimensional concept. Comparison of clinical institutions can be challenging when QoC is estimated solely based on clinical outcomes. Thus, measuring quality through quality indicators (QIs) can provide a foundation for quality assessment and has become widely used in this context. QIs for the evaluation of QoC in acute myocardial infarction are now well-established, but no such indicators exist for the process from resuscitation of cardiac arrest and post-resuscitation care in Europe.

Methods and results
The Association of Acute Cardiovascular Care of the European Society Cardiology, the European Resuscitation Council, European Society of Intensive Care Medicine and the European Society for Emergency Medicine, have reflected on the measurement of QoC in cardiac arrest. A set of QIs have been proposed, with the scope to unify and evolve QoC for the management of cardiac arrest across Europe.

Conclusion
We present here the list of QIs (6 primary QIs and 12 secondary Qis), with descriptions of the methodology used, scientific justification and motives for the choice for each measure with the aim that this set of QIs will enable assessment of the quality of postout-of-hospital cardiac arrest management across Europe.
Do the various interceptive treatment modalities improve the position of palatally displaced permanent canines? A meta-analysis
Authors: Habib Ahlam , Athanasiou Athanasios E , Makrygiannakis Miltiadis A , Kaklamanos Eleftherios G 
Published: February 2023

Summary

Background
Removal of maxillary primary canines and other interceptive treatment modalities in the mixed dentition have been suggested as methods used to increase the rate of normal eruption of palatally displaced permanent canines (PDCs). However, the information on the overall effect on PDCs’ position has been inconclusive.

Objective
To assess whether this practice improves the position of PDCs and to investigate the quality of the evidence.

Search methods
Unrestricted searches in 7 databases and manual searching of the reference lists in relevant studies were performed up to June 2022 (Medline via PubMed, CENTRAL, Cochrane Database of Systematic Reviews, Scopus, Web of Science, ClinicalTrials.gov, ProQuest Dissertations, and Theses Global).

Selection criteria
We looked for data on the positional changes of PDCs (mesial inclination, vertical position, canine crown cusp tip to midline) from randomized controlled trials assessing the various interceptive treatment modalities.

Data collection and analysis
Following study retrieval and selection, relevant data were extracted, and the risk of bias was assessed using the Cochrane Risk of Bias 2 Tool. Exploratory synthesis and meta-regression were conducted using the random effects model and the overall quality of the available evidence was assessed with the Grades of Recommendation, Assessment, Development, and Evaluation approach.

Results
Five studies (3 at low risk of bias) were identified, involving 238 individuals, followed for up to 18 months post-intervention with OPG (orthopantomogram) or CBCT (cone-beam computed tomography). Exploratory data synthesis showed that PDCs’ position improved more in the extraction sites compared to non-extraction. Analysis of the studies at low risk confirmed the above observations (6- and 12-month). Improvements were observed in patients using headgear after extraction of primary canines compared to extraction alone, but not in patients with double extraction of primary canines and first molars. The quality of available evidence was rated at best as moderate.

Conclusions
Interceptive treatment modalities in the mixed dentition may improve the position of PDCs. However, more studies are necessary in order to determine the clinical significance of the changes.

Registration
PROSPERO (CRD42015029130).
Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae
Authors: Davis John T , Li Ruijuan , Kim Seungmo , Michelmore Richard , Kim Shinje , Maloof Julin N 
Published: February 2023

Abstract
Brassica napus, a globally important oilseed crop, is an allotetraploid hybrid species with two subgenomes originating from Brassica rapa and Brassica oleracea. The presence of two highly similar subgenomes has made the assembly of a complete draft genome challenging and has also resulted in natural homoeologous exchanges between the genomes, resulting in variations in gene copy number, which further complicates assigning sequences to correct chromosomes. Despite these challenges, high-quality draft genomes of this species have been released. Using third generation sequencing and assembly technologies, we generated a new genome assembly for the synthetic B. napus cultivar Da-Ae. Through the use of long reads, linked-reads, and Hi-C proximity data, we assembled a new draft genome that provides a high-quality reference genome of a synthetic B. napus. In addition, we identified potential hotspots of homoeologous exchange between subgenomes within Da-Ae, based on their presence in other independently derived lines. The occurrence of these hotspots may provide insight into the genetic rearrangements required for B. napus to be viable following the hybridization of B. rapa and B. oleracea.
The New A(I)rt Movement and Its Copyright Protection: Immoral or E-Moral?
Authors: Varytimidou Christina 
Published: February 2023

Abstract
Artificial intelligence (‘AI’) has left few well-established laws and norms unchallenged, and copyright is not an exception. Nowadays art can be created by algorithms and continental Europe’s copyright law ‒ which inter alia includes Greece ‒ no longer seems fit for purpose, persisting as it does in searching for a human behind each creative outcome. This paper aims to analyse the issues algorithmic generated art brings in terms of copyright protection, and to explain why the current legislation and proposed solutions are inadequate to resolve them. Inspired by a theory already applicable in Germany in certain civil law cases, this paper will then propose a new twofold sui generis right that includes a new, partial e-moral right and a sui generis economic right. The paper will then explain how this proposed sui generis right manages to avoid potential pitfalls from granting legal personhood to AI, while letting humans reap the financial benefits.
A D-cysteine desulfhydrase, SlDCD2, participates in tomato fruit ripening by modulating ROS homoeostasis and ethylene biosynthesis
Authors: Zhao Yu-Qi , Hu Kang-Di , Yao Gai-Fang , Wang Si-Yue , Peng Xiang-Jun , Zhang Hua 
Published: February 2023

AbstractHydrogen sulfide (H2S) is involved in multiple processes during plant growth and development. D-cysteine desulfhydrase (DCD) can produce H2S with D-cysteine as the substrate; however, the potential developmental roles of DCD have not been explored during the tomato lifecycle. In the present study, SlDCD2 showed increasing expression during fruit ripening. Compared with the control fruits, the silencing of SlDCD2 by pTRV2-SlDCD2 accelerated fruit ripening. A SlDCD2 gene-edited mutant was constructed by CRISPR/Cas9 transformation, and the mutant exhibited accelerated fruit ripening, decreased H2S release, higher total cysteine and ethylene contents, enhanced chlorophyll degradation and increased carotenoid accumulation. Additionally, the expression of multiple ripening-related genes, including NYC1, PAO, SGR1, PDS, PSY1, ACO1, ACS2, E4, CEL2, and EXP was enhanced during the dcd2 mutant tomato fruit ripening. Compared with the wild-type fruits, SlDCD2 mutation induced H2O2 and malondialdehyde (MDA) accumulation in fruits, which led to an imbalance in reactive oxygen species (ROS) metabolism. A correlation analysis indicated that H2O2 content was strongly positively correlated with carotenoids content, ethylene content and ripening-related gene expression and negatively correlated with the chlorophyll content. Additionally, the dcd2 mutant showed earlier leaf senescence, which may be due to disturbed ROS homeostasis. In short, our findings show that SlDCD2 is involved in H2S generation and that the reduction in endogenous H2S production in the dcd2 mutant causes accelerated fruit ripening and premature leaf senescence. Additionally, decreased H2S in the dcd2 mutant causes excessive H2O2 accumulation and increased ethylene release, suggesting a role of H2S and SlDCD2 in modulating ROS homeostasis and ethylene biosynthesis.