bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
Authors: Huggins David J. , Biggin Philip C. , Dämgen Marc A. , Essex Jonathan W. , Harris Sarah A. , Henchman Richard H. , Khalid Syma , Kuzmanic Antonija , Laughton Charles A. , Michel Julien , Mulholland Adrian J. , Rosta Edina , Sansom Mark S. P. , van der Kamp Marc W. 
Published: September 2018

Biomolecular simulation is increasingly central to understanding and designing biological molecules and their interactions. Detailed, physics‐based simulation methods are demonstrating rapidly growing impact in areas as diverse as biocatalysis, drug delivery, biomaterials, biotechnology, and drug design. Simulations offer the potential of uniquely detailed, atomic‐level insight into mechanisms, dynamics, and processes, as well as increasingly accurate predictions of molecular properties. Simulations can now be used as computational assays of biological activity, for example, in predictions of drug resistance. Methodological and algorithmic developments, combined with advances in computational hardware, are transforming the scope and range of calculations. Different types of methods are required for different types of problem. Accurate methods and extensive simulations promise quantitative comparison with experiments across biochemistry. Atomistic simulations can now access experimentally relevant timescales for large systems, leading to a fertile interplay of experiment and theory and offering unprecedented opportunities for validating and developing models. Coarse‐grained methods allow studies on larger length‐ and timescales, and theoretical developments are bringing electronic structure calculations into new regimes. Multiscale methods are another key focus for development, combining different levels of theory to increase accuracy, aiming to connect chemical and molecular changes to macroscopic observables. In this review, we outline biomolecular simulation methods and highlight examples of its application to investigate questions in biology.This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods
Structure and Mechanism > Computational Biochemistry and Biophysics
Molecular and Statistical Mechanics > Free Energy Methods
M3: a new muon missing momentum experiment to probe (g − 2)μ and dark matter at Fermilab
Authors: Kahn Yonatan , Krnjaic Gordan , Tran Nhan , Whitbeck Andrew 
Published: September 2018

AbstractNew light, weakly-coupled particles are commonly invoked to address the persistent ∼ 4σanomaly in (g−2)μand serve as mediators between dark and visible matter. If such particles couple predominantly to heavier generations and decay invisibly, much of their best-motivated parameter space is inaccessible with existing experimental techniques. In this paper, we present a new fixed-target, missing-momentum search strategy to probe invisibly decaying particles that couple preferentially to muons. In our setup, a relativistic muon beam impinges on a thick active target. The signal consists of events in which a muon loses a large fraction of its incident momentum inside the target without initiating any detectable electromagnetic or hadronic activity in downstream veto systems. We propose a two-phase experiment, M3(Muon Missing Momentum), based at Fermilab. Phase 1 with ∼ 1010muons on target can test the remaining parameter space for which light invisibly-decaying particles can resolve the (g− 2)μanomaly, while Phase 2 with ∼ 1013muons on target can test much of the predictive parameter space over which sub-GeV dark matter achieves freeze-out via muon-philic forces, including gaugedU(1)Lμ−Lτ.
Single‐Port Thoracoscopic Minimally Invasive Esophagectomy for Esophageal Cancer
Authors: Hu Weipeng , Yuan Yong , Chen Longqi 
Published: September 2018

AbstractBackgroundThis study was to explore the safety and feasibility of single‐port thoracoscopic esophagectomy for esophageal cancer.MethodsThe patients were placed in left lateral prone position, and a 4‐cm incision through the 4th–5th intercostal space was taken on the post‐axillary line. Except for a surgical wound protector, no other special instruments were used for single‐port technique. The 10‐mm camera and two or three thoracoscopic instruments were used for the thoracic phase. Mobilization of stomach with celiac lymph node dissection was performed via multiple‐port laparoscopic approach. Cervical double‐layered anastomosis was completed by hand‐sewn technique.ResultsA total of twenty‐eight patients with esophageal squamous cell carcinoma underwent the single‐port thoracoscopic surgery. All of the patients underwent R0 resection. The median time taken for thoracic phase and total operation time were 126 min (range, 121–153) and the 253 min (range, 197–309), respectively. The median number of resected thoracic lymph nodes was 16 (range, 12–24). There were no deaths or severe postoperative complications in this study, with no conversion of minimally invasive surgery to open procedure.ConclusionsOur preliminary results demonstrate that this technique is safe and feasible for treating esophageal cancer within an acceptable length of operation time, which does not compromise the surgical radicality.
Realization of Low-Cost Multichannel Surface Plasmon Resonance Based Optical Transducer
Authors: Somarapalli Manjunath , Jolivot Romuald , Mohammed Waleed 
Published: September 2018

Abstract
This paper demonstrates a low-cost and portable multichannel surface plasmon resonance (SPR) based optical transducer. The system’s portability is achieved through the development of compact web-cam based spectrometer, and edge coupling to the SPR chip. Here, two configurations are presented: single-channel integrated system and two-channel system where the SPR chip and the spectrometer are coupled by a pair of plastic optical fibers. For the two-channel configuration, two different approaches are utilized to extract the optical spectrum: manual region cropping and automatic regions detection. For both approaches, image distortion and the size of the fiber tip affect the measured spectrum. For all configurations, mechanical alignment and mounting are made by 3D printing. The developed systems are tested with water and glycerol solution of different concentrations. The measured sensitivity is in the order of 10‒4 RIU (refractive index unit) for all systems under the ambient condition.
Getting the Best Out of Advanced Rehabilitation Technology for the Lower Limbs: Minding Motor Learning Principles
Authors: Spiess Martina Rebekka , Steenbrink Frans , Esquenazi Alberto 
Published: September 2018

AbstractAdvanced technology, including gait‐training devices, is increasingly being integrated into neurorehabilitation. However, to use gait‐training devices to their optimal potential, it is important that they are applied in accordance with motor learning and locomotor training principles. In this article, we outline the most important principles and explain how advanced gait‐training devices are best used to improve therapy outcome.
A ‘fownde patrone and second father’ of the Marian Church: Antonio Buonvisi, religious exile and mid-Tudor Catholicism
Authors: Smith Frederick E. 
Published: September 2018

AbstractDespite receiving particular praise from a range of early modern commentators, from Nicholas Sander to Pedro de Ribadeneyra, most historians have seen the Italian merchant Antonio Buonvisi playing a fairly negligible role in the history of mid-Tudor Catholicism. This article challenges this interpretation. After reassessing some rather simplistic assessments of Buonvisi’s religious beliefs, this article explores his actions and activities following his self-imposed exile from England in 1549. Using research conducted in both the State Archives of Lucca and the Vatican City, it suggests that Buonvisi played a far more significant role in ensuring the survival of English Catholicism over the first decades of the Reformation than is usually acknowledged. Indeed, it argues that Buonvisi may have helped lay core foundations for the Catholic restoration of Mary I’s reign, the success of which has recently been highlighted by historians such as Eamon Duffy.
Whose Atlantic? – Historiographies of South Africa, Namibia, OPSAAAL, and Central America
Authors: Houser Myra A. 
Published: September 2018

Abstract:During the 1970s and 1980s, southern African liberation movements lent rhetorical and sometimes material support to Central American guerilla groups. Such action represented both change and continuity within the previous decade’s non-aligned solidarities. This paper explores these connections and attempts to explain their significance on both sides of the ocean. It draws upon research in southern African and American archives in order to re-examine both spaces’ historiographies. Finally, it asks what these solidarities tell us about the nature of Cold War trans-oceanic linkages, fits them into debates over the nature of the discursive Atlantic, and ponders whether previous scholarship has effectively explored their significance.
Molecular investigation of the Pfmdr1 gene of Plasmodium falciparum isolates in Henan Province imported from Africa
Authors: Yang Chengyun , Zhou Ruimin , Liu Ying , Li Suhua , Qian Dan , Zhao Yuling , Zhang Hongwei , Xu Bianli 
Published: September 2018

AbstractEfficacious antimalarial drugs are important for malaria control and elimination, and continuous monitoring of their efficacy is essential. The prevalence and distribution of Pfmdr1 were evaluated in African migrant workers in Henan Province. Among 632 isolates, 13 haplotypes were identified, NYSND (39.87%, 252/632), YYSND (2.85%, 18/632), NFSND (31.01%, 196/632), NYSNY (0.47%, 3/632), YFSND (13.77%, 87/632), NFSNY (0.32%, 2/632), YYSNY (2.06%, 13/632), YFSNY (0.16%, 1/632), N/Y YSND (1.90%, 12/632), N Y/F SND (6.17%, 39/632), N/Y Y/F SND (0.47%, 3/632), YYSN D/Y (0.16%, 1/632) and N/Y FSND (0.79%, 5/632). The highest frequency of NYSND was observed in individuals from North Africa (63.64%, 7/11), followed by South Africa (61.33%, 111/181), Central Africa (33.33%, 56/168), West Africa (28.94%, 68/235) and East Africa (27.03%, 10/37) (χ2 = 54.605, P < 0.05). The highest frequency of NFSND was observed in East Africa (48.65%, 18/37), followed by West Africa (39.14%, 92/235), Central Africa (26.79%, 45/168), South Africa (22.65%, 41/181) and North Africa (9.09%, 1/11) (χ2 = 22.368 P < 0.05). The mutant prevalence of codons 86 and 184 decreased. These data may provide complementary information on antimalarial resistance that may be utilized in the development of a treatment regimen for Henan Province.
Infection patterns of trematodes across size classes of an invasive snail species using field and laboratory studies
Authors: Bachtel Rebecca Z. , Rittenhouse Matthew , Sandland Gregory J. , Koop Jennifer A. H. 
Published: September 2018

AbstractIn the Upper Mississippi River Region, invasive faucet snails (Bithynia tentaculata) and their trematode parasites have been implicated in more than 182 000 waterfowl deaths since 1996. Estimating transmission potential depends on accurate assessments of susceptible host population size. However, little is known about the mechanisms underlying snail–host susceptibility in this system. Prior field studies suggest that very small, likely young, faucet snails are less suitable secondary intermediate hosts. Here, we test whether the patterns observed in the field are because small snails (1) are refractory to infection by cercariae, (2) die from infection and are removed from sampled populations, and/or (3) are not preferred by cercariae. Our own field collections were consistent with the observation that smaller faucet snails exhibit lower metacercarial infection prevalence and abundance than larger snails. However, laboratory-based experiments show that smaller snails were actually more susceptible to infection than larger snails. Moreover, the smallest snail size class had significantly higher mortality than larger snails following infection, which may explain their reduced infection levels observed in the field. Our study demonstrates the importance of pairing field and laboratory studies to better understand mechanisms underlying patterns of infection.
Psychological origins of the Industrial Revolution
Authors: Baumard Nicolas 
Published: September 2018

AbstractSince the Industrial Revolution, human societies have experienced high and sustained rates of economic growth. Recent explanations of this sudden and massive change in economic history have held that modern growth results from an acceleration of innovation. But it is unclear why the rate of innovation drastically accelerated in England in the eighteenth century. An important factor might be the alteration of individual preferences with regard to innovation resulting from the unprecedented living standards of the English during that period, for two reasons. First, recent developments in economic history challenge the standard Malthusian view according to which living standards were stagnant until the Industrial Revolution. Pre-industrial England enjoyed a level of affluence that was unprecedented in history. Second, behavioral sciences have demonstrated that the human brain is designed to respond adaptively to variations in resources in the local environment. In particular, Life History Theory, a branch of evolutionary biology, suggests that a more favorable environment (high resources, low mortality) should trigger the expression of future-oriented preferences. In this paper, I argue that some of these psychological traits – a lower level of time discounting, a higher level of optimism, decreased materialistic orientation, and a higher level of trust in others – are likely to increase the rate of innovation. I review the evidence regarding the impact of affluence on preferences in contemporary as well as past populations, and conclude that the impact of affluence on neurocognitive systems may partly explain the modern acceleration of technological innovations and the associated economic growth.
Value-based provider payment: towards a theoretically preferred design
Authors: Cattel Daniëlle , Eijkenaar Frank , Schut Frederik T. 
Published: September 2018

AbstractWorldwide, policymakers and purchasers are exploring innovative provider payment strategies promoting value in health care, known as value-based payments (VBP). What is meant by ‘value’, however, is often unclear and the relationship between value and the payment design is not explicated. This paper aims at: (1) identifying value dimensions that are ideally stimulated by VBP and (2) constructing a framework of a theoretically preferred VBP design. Based on a synthesis of both theoretical and empirical studies on payment incentives, we conclude that VBP should consist of two components: a relatively large base payment that implicitly stimulates value and a relatively small payment that explicitly rewards measurable aspects of value (pay-for-performance). Being the largest component, the base payment design is essential, but often neglected when it comes to VBP reform. We explain that this base payment ideally (1) is paid to a multidisciplinary provider group (2) for a cohesive set of care activities for a predefined population, (3) is fixed, (4) is adjusted for the population’s risk profile and (5) includes risk-mitigating measures. Finally, some important trade-offs in the practical operationalisation of VBP are discussed.
Modeling Trench Sediment‐Controlled Flow in Subduction Channels: Implications for the Topographic Evolution of the Central Andean Fore Arc
Authors: Cosentino N. J. , Morgan J. P. , Jordan T. E. 
Published: September 2018

AbstractThe high elevation of the onshore fore‐arc platform in northern Chile cannot be accounted for by previously proposed tectonic mechanisms such as coastal underplating and coseismic deformation, whose topographic effects are restricted to the coastal zone. Subduction channels have been recognized both in modern and fossil noncollisional convergent margins, yet their role on fore‐arc surface elevation has not been sufficiently explored. Long‐term viscoelastic flow in a strengthened, finite‐thickness subduction channel promotes coupled offshore fore‐arc subsidence and onshore fore‐arc platform uplift. We propose that the onset of protracted hyperaridity in the coastal zone of northern Chile starved the trench of sediments, inducing a rise in shear stress at the top of the subduction channel sufficient to trigger hundreds of meters of uplift of the onshore fore‐arc basin surface, most of which took place by the middle Miocene. This is consistent with latitudinal correlations between coastal precipitation, trench sediment thickness and onshore fore‐arc topography along the Chilean margin, and with available paleoclimatic and paleotopographic evidence in northern Chile.
Up to What Extent Can We Characterize Ocean Eddies Using Present‐Day Gridded Altimetric Products?
Authors: Amores Angel , Jordà Gabriel , Arsouze Thomas , Le Sommer Julien 
Published: September 2018

AbstractThe most common methodology used to detect and characterize mesoscale eddies in the global ocean is to analyze altimetry‐based sea‐level gridded products with an automatic eddy detection and tracking algorithm. However, a careful look at the location of altimetry tracks shows that their separation is often larger than the Rossby radius of deformation. This implies that gridded products based on the information obtained along track would potentially be unable to characterize the mesoscale variability and, in particular, the eddy field. In this study, we analyze up to what extent sea‐level gridded products are able to characterize mesoscale eddies with a special focus on the North Atlantic Ocean and the Mediterranean Sea. In order to perform this task, we have generated synthetic sea level anomaly maps using along‐track data extracted from realistic high‐resolution ocean model simulations and applying an optimal interpolation procedure. Then, we have used an eddy detection and tracking algorithm to the gridded synthetic product and to the original model outputs and compared the characteristics of the resulting eddy fields. Our results suggest that gridded products largely underestimate the density of eddies, capturing only between 6% and 16% of the total number of eddies. The main reason is that the spatial resolution of the gridded products is not enough to capture the small‐scale eddies that are the most abundant. Also, the unresolved structures are aliased into larger structures in the gridded products, so those products show an unrealistic number of large eddies with overestimated amplitudes.
Three‐Dimensional Turbulence‐Resolving Modeling of the Venusian Cloud Layer and Induced Gravity Waves: Inclusion of Complete Radiative Transfer and Wind Shear
Authors: Lefèvre M. , Lebonnois S. , Spiga A. 
Published: September 2018

AbstractVenus' convective cloud layers and associated gravity waves strongly impact the local and global budget of heat, momentum, and chemical species. Here we use for the first time three‐dimensional turbulence‐resolving dynamical integrations of Venus' atmosphere from the surface to 100‐km altitude, coupled with fully interactive radiative transfer computations. We show that this enables to correctly reproduce the vertical position (46‐ to 55‐km altitude) and thickness (9 km) of the main convective cloud layer measured by Venus Express and Akatsuki radio occultations, as well as the intensity of convective plumes (3 m/s) measured by VEGA balloons. Both the radiative forcing in the visible and the large‐scale dynamical impact play a role in the variability of the cloud convective activity with local time and latitude. Our model reproduces the diurnal cycle in cloud convection observed by Akatsuki at the low latitudes and the lack thereof observed by Venus Express at the equator. The observed enhancement of cloud convection at high latitudes is simulated by our model, although underestimated compared to observations. We show that the influence of the vertical shear of horizontal superrotating winds must be accounted for in our model to allow for gravity waves of the observed intensity (>1 K) and horizontal wavelength (up to 20 km) to be generated through the obstacle effect mechanism. The vertical extent of our model also allows us to predict for the first time a 7‐km‐thick convective layer at the cloud top (70‐km altitude) caused by the solar absorption of the unknown ultraviolet absorber.
The antibacterial efficacy of a foam mouthwash and its ability to remove biofilms
Authors: Jones Siân B. , West Nicola X. , Nesmiyanov Pavel P. , Krylov Sergey E. , Klechkovskaya Vera V. , Arkharova Natalya A. , Zakirova Svetlana A. 
Published: September 2018

Abstract
Objectives/Aims
To evaluate the antimicrobial activity of a newly developed foam mouthwash containing a modified lactoperoxidase system in vitro.

Materials and methods
Biofilms of five bacterial species were developed on hydrophobic and hydrophilic surfaces whilst salivary-based biofilm was grown on tooth enamel. Each surface was exposed to the foam mouthwash or saline in vitro. Optical density and scanning electron microscopy (SEM) was used to determine retention of the biofilm following 5 or 30 s exposure time.

Results
The foam mouthwash was active against biofilms formed by S. aureus, K. rhizophila, M. thailandicus, E. coli, and C. violaceum and eliminated significant amount of biofilm from each surface; immature 4 h biofilm was less resistant than 24 h biofilm. A 30 s rinse showed best performance, with removal of up to 66% of biofilm from the hydrophilic surface. SEM imaging confirmed oral biofilm removal from the enamel surface after a 5 s rinse with the foam mouthwash.

Discussion
Foam mouthwash demonstrated a significant impact on growing biofilm when compared against saline solution. Growing biofilms were more susceptible to the action of the foam mouthwash, which justifies after-meal use of the mouthwash when traditional dentifrices may not be accessible.

Conclusions
Foam mouthwash can be a convenient on-the-go format of oral care products that can be used after meals or when needed to reduce the risk of biofilm-associated oral conditions.
Bi-directional cell-pericellular matrix interactions direct stem cell fate
Authors: Ferreira Silvia A. , Motwani Meghna S. , Faull Peter A. , Seymour Alexis J. , Yu Tracy T. L. , Enayati Marjan , Taheem Dheraj K. , Salzlechner Christoph , Haghighi Tabasom , Kania Ewa M. , Oommen Oommen P. , Ahmed Tarek , Loaiza Sandra , Parzych Katarzyna , Dazzi Francesco , Varghese Oommen P. , Festy Frederic , Grigoriadis Agamemnon E. , Auner Holger W. , Snijders Ambrosius P. , Bozec Laurent , Gentleman Eileen 
Published: September 2018

AbstractModifiable hydrogels have revealed tremendous insight into how physical characteristics of cells’ 3D environment drive stem cell lineage specification. However, in native tissues, cells do not passively receive signals from their niche. Instead they actively probe and modify their pericellular space to suit their needs, yet the dynamics of cells’ reciprocal interactions with their pericellular environment when encapsulated within hydrogels remains relatively unexplored. Here, we show that human bone marrow stromal cells (hMSC) encapsulated within hyaluronic acid-based hydrogels modify their surroundings by synthesizing, secreting and arranging proteins pericellularly or by degrading the hydrogel. hMSC’s interactions with this local environment have a role in regulating hMSC fate, with a secreted proteinaceous pericellular matrix associated with adipogenesis, and degradation with osteogenesis. Our observations suggest that hMSC participate in a bi-directional interplay between the properties of their 3D milieu and their own secreted pericellular matrix, and that this combination of interactions drives fate.