bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14)
Authors: Schaeffer R. Dustin , Kinch Lisa , Kryshtafovych Andriy , Grishin Nick V. 
Published: August 2021

AbstractThe high accuracy of some CASP14 models at the domain level prompted a more detailed evaluation of structure predictions on whole targets. For the first time in critical assessment of structure prediction (CASP), we evaluated accuracy of difficult domain assembly in models submitted for multidomain targets where the community predicted individual evaluation units (EUs) with greater accuracy than full‐length targets. Ten proteins with domain interactions that did not show evidence of conformational change and were not involved in significant oligomeric contacts were chosen as targets for the domain interaction assessment. Groups were ranked using complementary interaction scores (F1, QS score, and Jaccard coefficient), and their predictions were evaluated for their ability to correctly model inter‐domain interfaces and overall protein folds. Target performance was broadly grouped into two clusters. The first consisted primarily of targets containing two EUs wherein predictors more broadly predicted domain positioning and interfacial contacts correctly. The other consisted of complex two‐EU and three‐EU targets where few predictors performed well. The highest ranked predictor, AlphaFold2, produced high‐accuracy models on eight out of 10 targets. Their interdomain scores on three of these targets were significantly higher than all other groups and were responsible for their overall outperformance in the category. We further highlight the performance of AlphaFold2 and the next best group, BAKER‐experimental on several interesting targets.
A multiscale approach to predict the binding mode of metallo beta‐lactamase inhibitors
Authors: Gervasoni Silvia , Spencer James , Hinchliffe Philip , Pedretti Alessandro , Vairoletti Franco , Mahler Graciela , Mulholland Adrian J. 
Published: August 2021

AbstractAntibiotic resistance is a major threat to global public health. β‐lactamases, which catalyze breakdown of β‐lactam antibiotics, are a principal cause. Metallo β‐lactamases (MBLs) represent a particular challenge because they hydrolyze almost all β‐lactams and to date no MBL inhibitor has been approved for clinical use. Molecular simulations can aid drug discovery, for example, predicting inhibitor complexes, but empirical molecular mechanics (MM) methods often perform poorly for metalloproteins. Here we present a multiscale approach to model thiol inhibitor binding to IMP‐1, a clinically important MBL containing two catalytic zinc ions, and predict the binding mode of a 2‐mercaptomethyl thiazolidine (MMTZ) inhibitor. Inhibitors were first docked into the IMP‐1 active site, testing different docking programs and scoring functions on multiple crystal structures. Complexes were then subjected to molecular dynamics (MD) simulations and subsequently refined through QM/MM optimization with a density functional theory (DFT) method, B3LYP/6‐31G(d), increasing the accuracy of the method with successive steps. This workflow was tested on two IMP‐1:MMTZ complexes, for which it reproduced crystallographically observed binding, and applied to predict the binding mode of a third MMTZ inhibitor for which a complex structure was crystallographically intractable. We also tested a 12‐6‐4 nonbonded interaction model in MD simulations and optimization with a SCC‐DFTB QM/MM approach. The results show the limitations of empirical models for treating these systems and indicate the need for higher level calculations, for example, DFT/MM, for reliable structural predictions. This study demonstrates a reliable computational pipeline that can be applied to inhibitor design for MBLs and other zinc‐metalloenzyme systems.
Simultaneous voltammetric determination of tramadol and paracetamol exploiting glassy carbon electrode modified with FeNi3 nanoalloy in biological and pharmaceutical media
Authors: Hajmalek Saeed , Jahani Shohreh , Foroughi Mohammad Mehdi 
Published: September 2021

AbstractThe present study aimed to develop FeNi3 nanoalloy‐modified glassy carbon electrode (FeNi3/GCE) to detect paracetamol and tramadol drugs individually and simultaneously. Differential pulse voltammetry (DPV), chronoamperometry (CA) and cyclic voltammetry (CV) were applied to analyze the electrochemical properties of these drugs. The obtained results indicated the facilitation of paracetamol and tramadol oxidation on the FeNi3/GCE surface. The DPV findings confirmed the co‐detection of paracetamol and tramadol within a linear working range between 0.1 and 900.0 μM, with a limit of detection (S/N=3) of 10.0 and 8.2 nM, respectively. Multiple strengths were found for the synthesized electrode, including simplicity, high stability, potent reproducibility and excellent regeneration via simple polishing. The practical application of FeNi3/GCE in serum and urine specimens and pharmaceutical preparations confirmed high selectivity and sensitivity of this electrode to detect both paracetamol and tramadol.
From Glycals to Nitrogen Heterocycles and Carbocycles via “Cleavage‐Intramolecular Recombination Strategy”
Authors: Ramesh Namakkal G. 
Published: September 2021

AbstractGlycals (carbohydrate enol‐ethers) have enjoyed profound applications in organic synthesis for more than a century. They not only serve as versatile glycosyl donors or as substrates for Ferrier rearrangement, but also find extensive synthetic applications especially as a “chiral pool” for accomplishing the synthesis of a variety of natural and biologically important compounds. As cyclic enol ethers, they demonstrate high reactivity and are among the most and variously transformable monosaccharide derivatives. The uniqueness of the reactivity of glycals is that they can be synthetically tuned to get a library of derivatives through stereo‐ and regioselective introduction of a variety of functional groups at C1, C2, C3 as well as C4 carbons of the sugar. We have developed a practical approach for stereoselective mono‐ and diamination of glycals and over the years utilized these scaffolds for the synthesis of a variety of biologically important nitrogen heterocycles and carbocycles through a “Diversity Oriented Approach”. Our synthetic strategy in this direction mainly relied on the cleavage of ring O−C bond of the sugar followed by an “intramolecular recombination” reaction. Utilizing this strategy, we have accomplished the synthesis of several biologically important natural products, their analogues and related unnatural derivatives. Examples of such compounds reported from our group include polyhydroxypyrrolidines, DMDP, anisomycin, steviamine, pochonicine, conduramines, bulgecinine, aminocyclitols, azepanes, 4‐hydroxy‐D‐proline, azanucleosides and their analogues. A personal account highlighting these syntheses is presented here.
Cane toad (Rhinella marina) vitamin A, vitamin E, and carotenoid kinetics
Authors: Freel Tarra , Koutsos Elizabeth , Minter Larry J. , Tollefson Troy , Ridgley Frank , Smith Dustin , Scott Heather , Ange‐van Heugten Kimberly 
Published: August 2021

AbstractMany amphibian species are threatened with extinction. Understanding their vitamin A (retinol), E (alpha‐tocopherol), and carotenoid requirements is vital, as normal levels of these nutrients have a known connection to breeding success with abnormal levels leading to disease. This research examined vitamins A, E, and carotenoids (apocarotenoid, beta‐carotene; beta‐cryptoxanthin, lutein, zeaxanthin, and esters) concentration kinetics in the liver and plasma of 65 (57.8) cane toads (Rhinella marina) over 4 months supplemented with commercially available invertebrates in human care. Cane toads were opportunistically collected as part of a population control program for use as an amphibian model species. Toads were randomly assigned to one of two diets: treatment 1 was brown house crickets (Acheta domesticus) consuming Mazuri® Hi Calcium Gut Loading Diet without vitamin A or E supplement, plus fresh raw vegetables (carrot/sweet potato); Treatment 2 was the same diet except no vegetables. Ten toads were euthanized on Day 0 to analyze baseline free‐ranging liver and plasma metabolites. Six toads consuming each treatment were euthanized on Days 22, 50, and 81, and n = 7 on Day 119 for analysis. Regardless of dietary treatment, most liver and blood metabolites were substantially higher at time 0 than all time points thereafter (p < .05); Ex: liver vitamin A at time 0 was 87.7 ± 16.12 µg/g while Day 119 for treatments 1 and 2 were 11.6 ± 1.19 and 8.2 ± 0.74, respectively. Few statistically significant differences between diets at the same time point were noted (p < .05). The results from this study indicate that additional or alternative diet supplementation may be needed for cane toads (and potentially other amphibians) to mimic their free‐ranging diets.
Mortality trends for five species of macropods from a single institution from 1995 to 2016
Authors: Anderson Kadie , Dennis Patricia M. 
Published: August 2021

AbstractMacropods are commonly kept and exhibited species worldwide. Mortality records were reviewed for five species of macropods housed at Cleveland Metroparks Zoo from 1995 to 2016. One hundred sixty‐seven deaths occurred including Western grey kangaroo (Macropus fuliginosus) (n = 22), Bennett's wallaby (M. rufogriseus) (n = 64), red kangaroo (M. rufus) (n = 56), wallaroo (M. robustus) (n = 9), and Tammar wallaby (M. eugenii) (n = 16). The leading cause of death was trauma, followed by bronchopneumonia for all species. Gastric dilatation was identified as a concern for red kangaroo. Females lived longer than males across species and were overrepresented by the data set. Oral necrobacillosis and osteomyelitis were health concerns for macropods in this review. Mortality reviews are important as they identifying collection trends and influencing long‐term care.
(Non)-escape of mass and equidistribution for horospherical actions on trees
Authors: Ciobotaru Corina , Finkelshtein Vladimir , Sert Cagri 
Published: August 2021

AbstractLetGbe a large group acting on a biregular treeTand$$\Gamma \le G$$Γ≤Ga geometrically finite lattice. In an earlier work, the authors classified orbit closures of the action of the horospherical subgroups on$$G/\Gamma $$G/Γ. In this article we show that there is no escape of mass and use this to prove that, in fact, dense orbits equidistribute to the Haar measure on$$G/\Gamma $$G/Γ. On the other hand, we show that new dynamical phenomena for horospherical actions appear on quotients by non-geometrically finite lattices: we give examples of non-geometrically finite lattices where an escape of mass phenomenon occurs and where the orbital averages along a Følner sequence do not converge. In the last part, as a by-product of our methods, we show that projections to$$\Gamma \backslash T$$Γ\Tof the uniform distributions on large spheres in the treeTconverge to a natural probability measure on$$\Gamma \backslash T$$Γ\T. Finally, we apply this equidistribution result to a lattice point counting problem to obtain counting asymptotics with exponential error term.
Additional lateral extra-articular tenodesis in revision ACL reconstruction does not influence the outcome of patients with low-grade anterior knee laxity
Authors: Eggeling Lena , Drenck T. C. , Frings J. , Krause M. , Korthaus Alexander , Krukenberg Anna , Frosch Karl-Heinz , Akoto Ralph 
Published: August 2021

Abstract
Introduction
There is limited evidence on the indications of lateral extra-articular tenodesis (LET) in revision ACLR. The aim of this study was to evaluate the influence of the LET in patients with revision ACLR with preoperative low-grade anterior knee laxity.

Methods
Between 2013 and 2018, 78 patients who underwent revision ACLR with preoperative low-grade anterior knee laxity [≤ 5 mm side-to-side difference (SSD)] were included in the retrospective cohort study. An additional modified Lemaire tenodesis was performed in 23 patients during revision ACLR and patients were clinically examined with a minimum of 2 years after revision surgery. Postoperative failure of the revision ACLR was defined as SSD in Rolimeter® testing ≥ 5 mm or pivot-shift grade 2/3.

Results
In total, failure of the revision ACLR occurred in 11.5% (n = 9) of the cases at a mean follow-up of 28.7 ± 8.8 (24–67) months. Patients with an additional LET and revision ACLR did not show a significantly reduced failure rate (13% vs. 11%) or an improved clinical outcome according to the postoperative functional scores or pain in regards to patients with an isolated revision ACLR (Tegner 5.7 ± 1.3 vs. 5.9 ± 1.5, n.s.; IKDC 77.5 ± 16.2 vs. 80.1 ± 14.9, n.s., Lysholm 81.9 ± 14.2 vs. 83.8 ± 14.5, n.s.; VAS 1.9 ± 2.2 vs. 1.2 ± 1.7, n.s.).

Conclusions
An additional LET in patients with revision ACLR with low-grade anterior knee laxity does not influence patient-related outcomes or failure rates. Subjects with preoperative low-grade anterior knee laxity may not benefit from a LET in revision ACLR.

Level of evidence
III
The role of objective and subjective effort costs in voluntary task choice
Authors: Dreisbach Gesine , Jurczyk Vanessa 
Published: August 2021

AbstractHuman beings tend to avoid effort, if a less effortful option is equally rewarding. However, and in sharp contrast to this claim, we repeatedly found that (a subset of) participants deliberately choose the more difficult of two tasks in a voluntary task switching (VTS) paradigm even though avoidance of the difficult task was allowed (Jurczyk et al., Motivation Science 5:295–313, 2019). In this study, we investigate to what extent the deliberate switch to the difficult task is determined by the actual objective or the subjective effort costs for the difficult task. In two experiments, participants (N = 100, each) first went through several blocks of voluntary task choices between an easy and a difficult task. After that, they worked through an effort discounting paradigm, EDT, (Westbrook et al., PLoS One 8(7):e68210, 2013) that required participants to make a series of iterative choices between re-doing a difficult task block for a fixed amount or an easy task block for a variable (lower) amount of money until the individual indifference point was reached. In Experiment 1, the EDT comprised the same tasks from the VTS, in Experiment 2, EDT used another set of easy vs. difficult tasks. Results showed that the voluntary switch to the difficult task was mostly predicted by the objective performance costs and only marginally be the subjective effort cost. The switch to the difficult task may thus be less irrational than originally thought and at its avoidance at least partially driven by economic considerations.
Computing the effective crack energy of heterogeneous and anisotropic microstructures via anisotropic minimal surfaces
Authors: Ernesti Felix , Schneider Matti 
Published: August 2021

AbstractA variety of materials, such as polycrystalline ceramics or carbon fiber reinforced polymers, show a pronounced anisotropy in their local crack resistance. We introduce an FFT-based method to compute the effective crack energy of heterogeneous, locally anisotropic materials. Recent theoretical works ensure the existence of representative volume elements for fracture mechanics described by the Francfort–Marigo model. Based on these formulae, FFT-based algorithms for computing the effective crack energy of random heterogeneous media were proposed, and subsequently improved in terms of discretization and solution methods. In this work, we propose a maximum-flow solver for computing the effective crack energy of heterogeneous materials with local anisotropy in the material parameters. We apply this method to polycrystalline ceramics with an intergranular weak plane and fiber structures with transversely isotropic crack resistance.
Effect of different thawing methods on the quality of mackerel (Pneumatophorus japonicus)
Authors: Zhou Peng-cheng , Xie Jing 
Published: August 2021

AbstractFive thawing methods such as flow water thawing, ultrasonic flowing water thawing, air thawing, microwave thawing and low temperature thawing were used, and the physical, chemical properties and structure of mackerels after thawing were assessed. The results showed that the low temperature thawing had the best water retention, lower protein and fat oxidation. The microwave thawing had the shortest thawing time, but uneven heating leads to partial maturation. Air thawing prolonged exposure to air leads to high levels of protein and fat oxidation. The flow water thawing had better water retention than that of the ultrasonic flowing water thawing, only the thawing time was slightly longer than that of the ultrasonic flowing water thawing. In general, the low temperature thawing performed well after thawing. The flow water thawing used only 1/43 of the low temperature thawing's elapsed time after sacrificing some acceptable qualities. Thus, flow water thawing is more suitable for thawing frozen mackerel.
Synergistic effects of habitat configuration and land-use intensity shape the structure of bird assemblages in human-modified landscapes across three major neotropical biomes
Authors: Nogueira Olinda Maira Alves , Palmeirim Ana Filipa , Peres Carlos A. , dos Santos-Filho Manoel 
Published: August 2021

AbstractMaximizing biodiversity persistence in heterogeneous human-modified landscapes is hindered by the complex interactions between habitat quality and configuration of native and non-native habitats. Here we examined these complex interactions considering avian diversity across 26 sampling sites, each of which comprised of three sampling points located across a gradient of disturbance: core native habitat fragment, fragment edge, and non-native adjacent matrix. The 78 sampling points were further nested within three neotropical biomes—Amazonia, Cerrado and Pantanal—in central-western Brazil. Matrix type consisted of cattle pastures in the Amazon and teak plantations in the Pantanal and Cerrado. We considered the interactive effects of (1) disturbance-context: fragment core, edge and adjacent matrix, (2) matrix type: tree plantation or cattle pastures, both subject to varying land-use intensity, and (3) native habitat configuration (fragment size, shape and isolation) on bird species richness, abundance and composition. Based on point-count surveys, we recorded 210 bird species. Bird species richness and abundance declined across the disturbance gradient, while genus composition only differed within the adjacent matrix, particularly cattle-pastures. The effect of native habitat area was positive but only detected at fragment edges. Overall bird diversity increased at sites characterized by higher availability of either relict trees within pasture landscapes or old-growth trees within teak plantation landscapes. The core of native fragments played a primary role in ensuring the persistence of bird diversity, regardless of fragment size. In contrast to pastures, tree plantations likely harbour a higher proportion of forest-dependent species while bird diversity can be further enhanced by reduced management intensity in both matrix types. Strategies to maximize avian persistence should not only include retaining native habitats, but also maximizing the size of core native habitats. Likewise, more structurally complex matrix types should be encouraged while maintaining low levels of land-use intensity.
Tourism governance during the COVID-19 pandemic crisis: A proposal for a sustainable model to restore the tourism industry
Authors: Robina-Ramírez Rafael , Sánchez Marcelo Sánchez-Oro , Jiménez-Naranjo Héctor Valentín , Castro-Serrano José 
Published: August 2021

AbstractUnsustainable models of governance belonging to a widespread neoliberal mindset in developed countries have commonly been applied in the tourism industry. The management of the COVID-19 pandemic crisis has provided exemplary lessons regarding the application of sustainable models of governance. Through a participatory research, guidances are provided to tackle the COVID-19 effects in the tourist sector, namely in the Spanish southwestern region of Sierra de Gata. Seventeen indicators are proposed to enhance the safety measures, commitment of tourist authorities, communities empowered and protection of common resources among tourism industry, tourist authority and communities to spread cooperative awareness, mutual trust and shared objectives. Using a sample of 161 tourism companies, we tested a model of tourism governance with two focus groups during May and October 2020. Structural equation modelling (SEM) was utilized. Based on the data attained from a questionnaire and interviews, a sustainable tourism model to recover the threatened tourism sector is proposed. Indeed, our results can be used to draw theoretical and practical conclusions such as 1.) connecting private and public interactions to tackle the spread of the virus and strategies to recover the damaged tourist sector, 2.) to develop corporative values among the tourist industry and communities, 3.) to enhance governance models (trusts, consortia, tourist boards, clusters) to promote cooperation, 4.) to improve the local participation of companies, communities and associations in decision-making, and 5.) to prioritize qualitative development goals over quantitative ones, in the touristic territory. These conclusions are applicable to other regions suffering from the damaging consequences of the pandemic.
Data-driven remote governance of sparsely populated areas: measurement and commensuration of wildcat gold mining in French Guiana
Authors: Noucher Matthieu , Le Tourneau François-Michel , Gautreau Pierre 
Published: August 2021

AbstractThe increase in the price of gold, due to a shift to safe investments during the global economic crisis, has led to a rapid expansion of gold production. Alongside legal gold mines, wildcat gold mining has developed in French Guiana since the early 2000s. This phenomenon, with its social, environmental and economic consequences, is at the heart of the environmental governance of this territory. However, its difficult quantification is the subject of multiple controversies. Environmental governance is increasingly dependent on metrological regimes aimed at quantifying political action in order to objectify it. This article examines the role of metrology in implementing environmental policies in sparsely populated regions via the example of wildcat gold mining in French Guiana. Based on the study of two observatories, one managed by public authorities, the other by an NGO, we deconstruct their maps and counter-maps of wildcat gold mining. To do so, we make a distinction between measurement, commensuration and its diffusion. This focus on “measurement-commensuration-diffusion” allows us to identify three key phases in the production of nature statistics. We argue that the critical analysis of metrological processes through this three-step framework reveals methodological controversies that reflect different and even divergent political visions. The article also shows that metrological systems for environmental protection are the focus of targeted political disputes. It reports on the current disagreements—not only between the State and NGOs but also within the State itself—on the proposed solutions for fighting the impacts of wildcat gold mining in French Guiana and the broader issues of data production in Amazonia.