bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time step algorithm
Authors: Procacci Piero , Marchi Massimo 
Published: July 2002

Long range electrostatic forces are involved at a fundamental level in many biological phenomena. Their prohibitive computational costs often prevents their correct calculation in molecular dynamics (MD) simulations of biological molecules. In this paper we present a method to handle efficiently and exactly electrostatic interactions in MD simulations with periodic boundary conditions. Our scheme employs a multiple time step r-RESPA integration algorithm in combination with the Ewald summation technique, and is specifically targeted to simulation of large size complex molecular systems such as solvated proteins. In this approach, the force associated with each particle of the system is partitioned into four components which evolve in time with distinct and increasingly longer time scales. We found that a suitable time scale separation is achieved by subdividing the direct space nonbonded interactions, inclusive of Coulombic and van der Waals contributions, in a short, medium and long range shells.
The fastest bonded forces are associated to the component with the shortest timescale, while the reciprocal space nonbonded interaction is included with the medium range direct space forces. Our method is general. It can be straightforwardly implemented for any biomolecular force fields used in condensed phase simulations and can be applied to other complex molecular systems such as molecular liquids and heterogeneous solutions (e.g., micelles, membranes, etc.). We carried out tests on solvated proteins samples containing 7 040 and 20 627 atoms. Due to the nonlinear scaling of the Ewald computational cost with system size, the performance of our r-RESPA algorithm with respect to single time step algorithms with bond constraints grows with the number of particles. We reach a relative speed-up of 4.2 for a system composed of a solvated photosynthetic reaction center.
Drinking and university students: from celebration to inebriation
Authors: ROCHE ANN M. , WATT KERRIANNE 
Published: July 2002

AbstractThere is extensive anecdotal information and considerable interest in the levels and patterns of drinking among university students in Australia. However, few empirical data exist. As a result, a survey was undertaken of students attending the three major universities in the southeast corner of Queensland. Two hundred and nine male and 191 female students, aged 17–25 years, completed a 30‐item survey designed to assess prevalence and patterns of alcohol consumption, associated harms and students' alcohol‐related attitudes. Nearly all (94%) students drank and many drank very heavily. Approximately half the male students and one‐fifth of female students reported drinking to intoxication once or more per week. Consumption of five or more standard drinks on a typical drinking occasion was reported by 54% of students. Overall, more than two‐thirds (69%) of the sample reported drinking at hazardous or harmful levels. About one‐third of the sample reported experiencing an alcohol‐related accident or injury within the last 12 months. Despite this, 62% of students did not believe that a reduction in student drinking was necessary. In addition to examining information on alcohol‐related attitudes and behaviour, this survey identified several groups particularly at risk. [Roche A, Watt K. Drinking and university students: from celebration to inebriation. Drug Alcohol Rev 1999; 18: 389–399]
Anglophilia in crisis: Italian liberals, the ‘English model’ and democracy in the Giolittian era
Authors: Cerasi Laura 
Published: July 2002

SummaryThe image of England was very important to the political culture of Italian liberals during the Risorgimento and the post-unification period. Even if it was viewed as unreachable, it still constituted an example of progress that Italy could strive towards. This article reconstructs the stages of the process that saw a section of Italian political culture become alienated from this image, just at a time when a more complete form of industrial democracy was becoming eswtablished in Britain. This alienation is interpreted here as having its roots in attitudes to the issues raised by the workers’ movement: Italian liberals were reluctant to give it full legitimacy and engage it on the open terrain of social and political competition. The first two sections of the article go over the traits of Italian Anglophilia up to the end of the nineteenth century and single out the earliest reasons for alienation. The third section identifies the Boer War, the figure of Chamberlain and the cluster of issues linking democracy, imperialism and protectionism as key factors in the change of direction. The fourth section shows that the constitutional conflict in Britain and the Parliament Act were a further, decisive, step in Italian liberals’ disaffection with the ‘English model'.
InterPro—an integrated documentation resource for protein

families, domains and functional sites
Authors: Apweiler R. , Attwood T. K. , Bairoch A. , Bateman A. , Birney E. , Biswas M. , Bucher P. , Cerutti L. , Corpet F. , Croning M. D. R. , Durbin R. , Falquet L. , Fleischmann W. , Gouzy J. , Hermjakob H. , Hulo N. , Jonassen I. , Kahn D. , Kanapin A. , Karavidopoulou Y. , Lopez R. , Marx B. , Mulder N. J. , Oinn T. M. , Pagni M. , Servant F. , Sigrist C. J. A. , Zdobnov E. M. 
Published: July 2002

Abstract
Motivation: InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects.
Results: Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc. Merged and individual entries (i.e. those that have no counterpart in the companion resources) are assigned unique accession numbers. Release 1.2 of InterPro (June 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 6581 different regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1000000 hits from 264333 different proteins out of 384572 in SWISS-PROT and TrEMBL).
Availability: The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/.
Contact: Interhelp@ebi.ac.uk
* To whom correspondence should be addressed.
A homolog of mammalian antizyme is present in fission yeast
Schizosaccharomyces pombe but not detected in budding yeast
Saccharomyces cerevisiae
Authors: Zhu Chang , Karplus Kevin , Grate Leslie , Coffino Philip 
Published: July 2002

Abstract
* To whom correspondence should be addressed.
Motivation: The antizymes (AZ) are proteins that regulate cellular polyamine pools in metazoa. To search for remote homologs in single-celled eukaryotes, we used computer software based on hidden Markov models. The most divergent homolog detected was that of the fission yeast Schizosaccharomyces pombe. Sequence identities between S.pombe AZ and known AZs are as low as 18–22% in the most conserved C-terminal regions. The authenticity of the S.pombe AZ is validated by the presence of a conserved nucleotide sequence that, in metazoa, promotes a +1 programmed ribosomal frameshift required for AZ expression. However, no homolog was detected in the completed genome of the budding yeast Saccharomyces cerevisiae. Procedural details and supplementary information can be found at http://itsa.ucsf.edu/~czhu/AZ.
Contact: pcoffin@itsa.ucsf.edu
Transcription-associated protein families are primarily

taxon-specific
Authors: Coulson Richard M.R. , Enright Anton J. , Ouzounis Christos A. 
Published: July 2002

Abstract
The mechanisms controlling gene regulation appear to be fundamentally different in eukaryotes and prokaryotes (Struhl (1999) Cell , 98, 1–4). To investigate this diversity further, we have analysed the distribution of all known transcription-associated proteins (TAPs), as reflected by sequence database annotations. Our results for the primary phylogenetic domains (Archaea, Bacteria and Eukaryota) show that TAP families are mostly taxon-specific and very few transcriptional regulators are common across these domains.
Contact: ouzounis@ebi.ac.uk
Concepts to automate the theoretical design of effective antisense oligonucleotides
Authors: Kretschmer-Kazemi Far Rosel , Nedbal Wolfgang , Sczakiel Georg 
Published: July 2002

Abstract
Among the large number of possible antisense species against a given target RNA, only a small number shows effective suppression of the target gene in living cells. In the case of short-chain antisense oligonucleotides (asON) which usually comprise less than approximately 25 nucleotides, local structures of the target RNA seem to be of particular importance for the extent of gene suppression. Experimental approaches to identify promising local target sequences and, hence, complementary asON sequences, have provided tools to define asON that are biologically active at higher than statistical probability. However, experimental protocols are expensive, time consuming, and are associated with intrinsic basic and technical limitations. As insights into the structure–function relationship of asON as well as the role of sequence motifs increase, it becomes feasible to consider computer-based theoretical approaches for the design of effective asON. In the following we describe how individual steps of the theoretical design of asON may be automated by establishing and implementing suitable algorithms.
Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes
Authors: Sugimoto Naoki , Nakano Shu-ich , Yoneyama Mari , Honda Kei-ich 
Published: July 2002

Abstract
To improve the previous DNA/DNA nearest-neighbor parameters, thermodynamic parameters (Δ H °, Δ S ° and Δ G °) of 50 DNA/DNA duplexes were measured. Enthalpy change of a helix initiation factor is also considered though the parameters reported recently did not contain the factor. A helix initiation factor for DNA/DNA duplex determined here was the same as that of RNA/RNA duplex (ΔG° 37 = 3.4 kcal/mol). The improved nearest-neighbor parameters reproduced not only these 50 experimental values used here but also 15 other experimental values obtained in different studies. Comparing Δ G ° 37 values of DNA/DNA nearest-neighbor parameters obtained here with those of RNA/RNA and RNA/DNA, RNA/RNA duplex was generally the most stable of the three kinds of duplexes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA duplexes is sequence dependent.
Endocannabinoids control spasticity in a multiple sclerosis model
Authors: Baker David , Pryce Gareth , Croxford J. Ludovic , Brown Peter , Pertwee Roger G. , Makriyannis Alexandros , Khanolkar Atmaram , Layward Lorna , Fezza Filomena , Bisogno Tiziana , Marzo Vincenzo Di 
Published: July 2002

ABSTRACTSpasticity is a complicating sign in multiple sclerosis that also develops in a model of chronic relapsing experimental autoimmune encephalomyelitis (CREAE) in mice. In areas associated with nerve damage, increased levels of the endocannabinoids, anandamide (arachidonoylethanolamide, AEA) and 2‐arachidonoyl glycerol (2‐AG), and of the AEA congener, palmitoylethanolamide (PEA), were detected here, whereas comparable levels of these compounds were found in normal and non‐spastic CREAE mice. While exogenously administered endocannabinoids and PEA ameliorate spasticity, selective inhibitors of endocannabinoid re‐uptake and hydrolysis—probably through the enhancement of endogenous levels of AEA, and, possibly, 2‐arachidonoyl glycerol—significantly ameliorated spasticity to an extent comparable with that observed previously with potent cannabinoid receptor agonists. These studies provide definitive evidence for the tonic control of spasticity by the endocannabinoid system and open new horizons to therapy of multiple sclerosis, and other neuromuscular diseases, based on agents modulating endocannabinoid levels and action, which exhibit little psychotropic activity.
Computational analysis of binding of P1 variants to trypsin
Authors: Brandsdal Bjørn O. , Åqvist Johan , Smalås Arne O. 
Published: July 2002

AbstractThe binding of P1 variants of bovine pancreatic trypsin inhibitor (BPTI) to trypsin has been investigated by means of molecular dynamics simulations. The specific interaction formed between the amino acid at the primary binding (P1) position of the binding loop of BPTI and the specificity pocket of trypsin was estimated by use of the linear interaction energy (LIE) method. Calculations for 13 of the naturally occurring amino acids at the P1 position were carried out, and the results obtained were found to correlate well with the experimental binding free energies. The LIE calculations rank the majority of the 13 variants correctly according to the experimental association energies and the mean error between calculated and experimental binding free energies is only 0.38 kcal/mole, excluding the Glu and Asp variants, which are associated with some uncertainties regarding protonation and the possible presence of counter‐ions. The three‐dimensional structures of the complex with three of the P1 variants (Asn, Tyr, and Ser) included in this study have not at present been solved by any experimental techniques and, therefore, were modeled on the basis of experimental data from P1 variants of similar size. Average structures were calculated from the MD simulations, from which specific interactions explaining the broad variation in association energies were identified. The present study also shows that explicit treatment of the complex water‐mediated hydrogen bonding network at the protein–protein interface is of crucial importance for obtaining reliable binding free energies. The successful reproduction of relative binding energies shows that this type of methodology can be very useful as an aid in rational design and redesign of biologically active macromolecules.
Prevalence and Odds of Depressive and Anxiety Disorders and Symptoms in Children and Adults With Alopecia Areata
Authors: Lauron Sophie , Plasse Camille , Vaysset Marion , Pereira Bruno , D’Incan Michel , Rondepierre Fabien , Jalenques Isabelle 
Published: January 2023

ImportanceTwo recent meta-analyses reported a high prevalence of both anxiety and depression in patients with alopecia areata (AA), as well as a positive association of AA with anxiety and depression, without distinguishing between disorders and symptoms. Yet, depression and anxiety can manifest either as symptoms identified in questionnaires or as specific diagnoses defined by Diagnostic and Statistical Manual of Mental Disorders (Fifth Edition) or International Statistical Classification of Diseases and Related Health Problems, Tenth Revision criteria.ObjectiveTo perform a large meta-analysis separating the prevalence of depressive and anxiety disorders from that of depressive and anxiety symptoms in patients with AA.Data SourcesPubMed, ScienceDirect, the Cochrane Library, Embase, and PsycINFO databases were searched from inception through August 1, 2020.Study SelectionStudies that contained data on the prevalence of depressive or anxiety disorders or symptoms were included.Data Extraction and SynthesisThe Meta-analysis of Observational Studies in Epidemiology (MOOSE) reporting guidelines were used. Pooled prevalence was calculated with a random effects model meta-analysis that took into account between- and within-study variability. Meta-regressions were used to study the association between variations in prevalence and study characteristics.Main Outcomes and MeasuresThe prevalence of depressive and anxiety disorders and symptoms in patients with AA.ResultsThirty-seven articles (29 on depression and 26 on anxiety) that met the inclusion criteria were identified. By distinguishing between disorders and symptoms, the prevalence of both depressive disorders (9%) and unspecified anxiety disorders (13%) in patients with AA was shown to be greater than that in the general population. The prevalence and odds ratio (OR) of depressive disorders (prevalence, 9%; OR, 1.38) and anxiety disorders of which each category had been specifically studied (prevalence, 7%-17%; OR, 1.51-1.69) were markedly lower than that of depressive symptoms (prevalence, 37%; OR, 2.70) and anxiety symptoms (prevalence, 34%; OR, 3.07). Meta-regressions showed that variations in prevalence were mainly associated with methodological differences between studies.Conclusions and RelevanceIn this systematic review and meta-analysis, the separate analyses showed that 7% to 17% of patients with AA had depressive or anxiety disorders that require psychiatric care, including specific medication. Additionally, more than one-third of patients had symptoms that are warning signs and that need monitoring because they can develop into disorders.
Highly Sensitive and Durable, Triboelectric Based Self‐Powered Nanosensor for Boundary Detection in Sports Event
Authors: Liu Haisheng , Cao Jie , Feng Shuai , Cheng Guanggui , Zhang Zhongqiang , Ding Jianning 
Published: January 2023

AbstractAssisted adjudication of sports activities and events is becoming more intelligent with the rapid development of the Internet of Things (IoTs). Sensors such as pressure sensors and image sensors have been widely used in sports events, but their durability and energy supply are still challenge. Herein, a novel boundary detection sensor based on hyperelastic triboelectric nanogenerator (H‐TENG) for intelligent boundary detection is proposed. The stress–strain of a tennis ball colliding with H‐TENG at high speed and the sensing stability are investigated by simulation analysis and experimental validation. The pressure sensitivity of 2.96 V kPa−1 is achieved with excellent linearity (R2 = 0.957082) at the pressure of 2.8–13 kPa. And at the velocity of 2–4.47 m s−1, the velocity sensitivity reaches ‐10.76 V (m s−1)−1 with excellent linearity (R2 = 0.948758). Furthermore, a four‐channels signal acquisition system is constructed for enhancing the detection accuracy, and the response times of signal feedback are less than 45 ms. This work not only provides a novel approach for intelligent boundary detection in sporting events, but also demonstrates its promising applications in multiple challenges and quick penalties in sports competitions, as well as in intelligent and digital training of athletes.
Simultaneous Detection of L‐Lactate and D‐Glucose Using DNA Aptamers in Human Blood Serum**
Authors: Huang Po‐Jung Jimmy , Liu Juewen 
Published: January 2023

AbstractL‐lactate is a key metabolite indicative of physiological states, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need additional oxidants. In this work, DNA aptamers for L‐lactate were obtained using a library‐immobilization selection method and the highest affinity aptamer reached a Kd of 0.43 mM as determined using isothermal titration calorimetry. The aptamers showed up to 50‐fold selectivity for L‐lactate over D‐lactate and had little responses to other closely related analogs such as pyruvate or 3‐hydroxybutyrate. A fluorescent biosensor based on the strand displacement method showed a limit of detection of 0.55 mM L‐lactate, and the sensor worked in 90 % serum. Simultaneous detection of L‐lactate and D‐glucose in the same solution was achieved. This work has broadened the scope of aptamers to simple metabolites and provided a useful probe for continuous and multiplexed monitoring.
Towards Axially Chiral Pyrazole‐Based Phosphorus Scaffolds by Dipeptide‐Phosphonium Salt Catalysis
Authors: Wu Jia‐Hong , Tan Jian‐Ping , Zheng Jia‐Yan , He Jiajia , Song Zhenlei , Su Zhishan , Wang Tianli 
Published: January 2023

AbstractGiven the comparatively lower rotational barriers, the catalytic asymmetric construction of axially chiral biaryl structures, especially those containing a five‐membered heterocycle, still remains a challenge. Herein, we described a general and modular protocol to access atropisomeric arylpyrazole scaffolds containing a phosphorus unit by a dipeptide phosphonium salt catalyzed reaction involving an oxidative central‐to‐axial chirality conversion. This reaction features excellent yields and enantioselectivities, broad substrate scope, and a low catalyst loading, delivering axially chiral phosphine compounds.
Solvent‐Controlled Quadruple Catenation of Giant Chiral [8+12] Salicylimine Cubes Driven by Weak Hydrogen Bonding
Authors: Wagner Philippe , Rominger Frank , Gross Jürgen H. , Mastalerz Michael 
Published: January 2023

AbstractMechanically interlocked structures are fascinating synthetic targets and the topological complexity achieved through catenation offers numerous possibilities for the construction of new molecules with exciting properties. In the structural space of catenated organic cage molecules, only few examples have been realized so far, and control over the catenation process in solution is still barely achieved. Herein, we describe the formation of a quadruply interlocked catenane of giant chiral [8+12] salicylimine cubes. The formation could be controlled by the choice of solvent used in the reaction. The interlocked structure was unambiguously characterized by single crystal X‐ray diffraction and weak hydrogen bonding was identified as a central driving force for the catenation. Furthermore, scrambling experiments using partially deuterated cages were performed, revealing that the catenane formation occurs through mechanical interlocking of preformed single cages.
Proton‐Conductive Supramolecular Hydrogen‐Bonded Organic Superstructures for High‐Performance Zinc‐Organic Batteries
Authors: Song Ziyang , Miao Ling , Ruhlmann Laurent , Lv Yaokang , Li Liangchun , Gan Lihua , Liu Mingxian 
Published: January 2023

AbstractWith fast (de)coordination kinetics, the smallest and the lightest proton stands out as the most ideal charge carrier for aqueous Zn‐organic batteries (ZOBs). Hydrogen‐bonding networks with rapid Grotthuss proton conduction is particularly suitable for organic cathodes, yet not reported. We report the supramolecular self‐assembly of cyanuric acid and 1,3,5‐triazine‐2,4,6‐triamine into organic superstructures through in‐plane H‐bonds and out‐of‐plane π‐π interaction. The supramolecular superstructures exhibit highly stable lock‐and‐key H‐bonding networks with an ultralow activation energy for protonation (0.09 eV vs. 0.25 eV of zincification). Then, high‐kinetics H+coordination is prior to Zn2+into protophilic C=O sites via a two‐step nine‐electron reaction. The assembled ZOBs show high‐rate capability (135 mAh g−1at 150 A g−1), high energy density (267 Wh kg−1cathode) and ultra‐long life (50 000 cycles at 10 A g−1), becoming the state‐of‐the‐art ZOBs in comprehensive performances.