bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo generation of hit-like molecules from gene expression signatures using artificial intelligence
Authors: Méndez-Lucio Oscar , Baillif Benoit , Clevert Djork-Arné , Rouquié David , Wichard Joerg 
Published: January 2020

AbstractFinding new molecules with a desired biological activity is an extremely difficult task. In this context, artificial intelligence and generative models have been used for molecular de novo design and compound optimization. Herein, we report a generative model that bridges systems biology and molecular design, conditioning a generative adversarial network with transcriptomic data. By doing so, we can automatically design molecules that have a high probability to induce a desired transcriptomic profile. As long as the gene expression signature of the desired state is provided, this model is able to design active-like molecules for desired targets without any previous target annotation of the training compounds. Molecules designed by this model are more similar to active compounds than the ones identified by similarity of gene expression signatures. Overall, this method represents an alternative approach to bridge chemistry and biology in the long and difficult road of drug discovery.
African cratonic lithosphere carved by mantle plumes
Authors: Celli Nicolas Luca , Lebedev Sergei , Schaeffer Andrew J. , Gaina Carmen 
Published: January 2020

AbstractHow cratons, the ancient cores of continents, evolved since their formation over 2.5 Ga ago is debated. Seismic tomography can map the thick lithosphere of cratons, but its resolution is low in sparsely sampled continents. Here we show, using waveform tomography with a large, newly available dataset, that cratonic lithosphere beneath Africa is more complex and fragmented than seen previously. Most known diamondiferous kimberlites, indicative of thick lithosphere at the time of eruption, are where the lithosphere is thin today, implying surprisingly widespread lithospheric erosion over the last 200 Ma. Large igneous provinces, attributed to deep-mantle plumes, were emplaced near all lithosphere-loss locations, concurrently with or preceding the loss. This suggests that the cratonic roots foundered once modified by mantle plumes. Our results imply that the total volume of cratonic lithosphere has decreased since its Archean formation, with the fate of each craton depending on its movements relative to plumes.
Parkinson’s disease: proteinopathy or lipidopathy?
Authors: Fanning Saranna , Selkoe Dennis , Dettmer Ulf 
Published: January 2020

AbstractLipids play a more significant role in Parkinson’s disease and its related brain disorders than is currently recognized, supporting a “lipid cascade”. The 14 kDa protein α-synuclein (αS) is strongly associated with Parkinson’s disease (PD), dementia with Lewy bodies (DLB), other synucleinopathies such as multiple system atrophy, and even certain forms of Alzheimer’s disease. Rigorously deciphering the biochemistry of αS in native systems is the key to developing treatments. αS is highly expressed in the brain, the second most lipid-rich organ, and has been proposed to be a lipid-binding protein that physiologically interacts with phospholipids and fatty acids (FAs). αS-rich cytoplasmic inclusions called Lewy bodies and Lewy neurites are the hallmark lesions of synucleinopathies. Excess αS–membrane interactions may trigger proteinaceous αS aggregation by stimulating its primary nucleation. However, αS may also exert its toxicity prior to or independent of its self-aggregation, e.g., via excessive membrane interactions, which may be promoted by certain lipids and FAs. A complex αS-lipid landscape exists, which comprises both physiological and pathological states of αS. As novel insights about the composition of Lewy lesions occur, new lipid-related PD drug candidates emerge, and genome-wide association studies (GWAS) increasingly validate new hits in lipid-associated pathways, it seems timely to review our current knowledge of lipids in PD and consider the roles for these pathways in synucleinopathies.
NHC-gold compounds mediate immune suppression through induction of AHR-TGFβ1 signalling in vitro and in scurfy mice
Authors: Cheng Xinlai , Haeberle Stefanie , Shytaj Iart Luca , Gama-Brambila Rodrigo. A. , Theobald Jannick , Ghafoory Shahrouz , Wölker Jessica , Basu Uttara , Schmidt Claudia , Timm Annika , Taškova Katerina , Bauer Andrea S. , Hoheisel Jörg , Tsopoulidis Nikolaos , Fackler Oliver T. , Savarino Andrea , Andrade-Navarro Miguel A. , Ott Ingo , Lusic Marina , Hadaschik Eva N. , Wölfl Stefan. 
Published: January 2020

AbstractGold compounds have a long history of use as immunosuppressants, but their precise mechanism of action is not completely understood. Using our recently developed liver-on-a-chip platform we now show that gold compounds containing planarN-heterocyclic carbene (NHC) ligands are potent ligands for the aryl hydrocarbon receptor (AHR). Further studies showed that the lead compound (MC3) activates TGFβ1 signaling and suppresses CD4+T-cell activation in vitro, in human and mouse T cells. Conversely, genetic knockdown or chemical inhibition of AHR activity or of TGFβ1-SMAD-mediated signaling offsets the MC3-mediated immunosuppression. In scurfy mice, a mouse model of human immunodysregulation polyendocrinopathy enteropathy X-linked syndrome, MC3 treatment reduced autoimmune phenotypes and extended lifespan from 24 to 58 days. Our findings suggest that the immunosuppressive activity of gold compounds can be improved by introducing planar NHC ligands to activate the AHR-associated immunosuppressive pathway, thus expanding their potential clinical application for autoimmune diseases.
Living with the Unknown: A Qualitative Study of Parental Experience of Prognostic Uncertainty in the Neonatal Intensive Care Unit
Authors: Krick Jeanne A. , Weiss Elliott Mark , Snyder Anna , Haldar Shefali , Campelia Georgina D. , Opel Douglas J. 
Published: January 2020

Abstract
Objective This study aims to characterize the experience of prognostic uncertainty for neonatal intensive care unit (NICU) parents.
Study Design We conducted a qualitative interview study of current and former NICU parents regarding their experience with prognostic uncertainty in the NICU. Interviews were transcribed and analyzed using a grounded theory methodology.
Results Twenty-four parents were interviewed before achieving thematic saturation. Three phases of the parental experience of prognostic uncertainty emerged: shock, gray daze, and looking forward. These phases often, but not always, occurred sequentially. In shock, parents felt overwhelmed by uncertainty and were unable to visualize a future for their family. In gray daze, parents felt frustrated by the continued uncertainty. While accepting the possibility of a future for their family, they could not conceptualize a path by which to achieve it. In looking forward, parents accepted uncertainty as inevitable and incorporated it into their vision of the future.
Conclusion While each parent experienced the prognostic uncertainty in the neonatal intensive care unit in their own way, we found three common experiential phases. By understanding how a parent experiences prognostic uncertainty in these phases, providers may become better able to communicate and form therapeutic relationships with parents.
High-resolution deep view microscopy of cells and tissues
Authors: Schneckenburger H. , Richter V. , Gelleri M. , Ritz S. , Vaz Pandolfo R. , Schock F. , von Hase J. , Birk U. , Cremer C. 
Published: January 2020

Abstract
Methods, experimental setups and perspectives of three-dimensional deep view imaging microscopy of cell or tissue samples are reported. Preliminary biophysical and clinically relevant examples are presented.
Laser speckle contrast imaging of blood microcirculation in pancreatic tissues during laparoscopic interventions
Authors: Potapova E.V. , Seryogina E.S. , Dremin V.V. , Stavtsev D.D. , Kozlov I.O. , Zherebtsov E.A. , Mamoshin A.V. , Ivanov Yu.V. , Dunaev A.V. 
Published: January 2020

AbstractLaser speckle contrast imaging of the microcirculatory bed of the pancreas is performed, which allows its condition to be assessed and thereby is an additional valuable tool for making a diagnostic decision and dynamically monitoring the effectiveness of the treatment for pathology of the abdominal organs. Laparoscopic operations on the pancreas are low-traumatic and in most cases avoid open surgical interventions. For the first time an experimental system for recording speckle images, combined with a commercially available five-millimetre rigid laparoscope, is presented. The sensitivity of the system to the fluid motion in a capillary at different velocities is determined, and the possibility of finding areas of blood microcirculation disturbance in modelling pancreatic ischemia in an experiment on laboratory animals is revealed. The laparoscope illumination channel is verified by comparison with speckle dynamics under external illumination of the studied object.
Structural and optical properties of nanoparticles formed by laser ablation of porous silicon in liquids: Perspectives in biophotonics
Authors: Zabotnov S.V. , Kurakina D.A. , Kashaev F.V. , Skobelkina A.V. , Kolchin A.V. , Kaminskaya T.P. , Khilov A.V. , Agrba P.D. , Sergeeva E.A. , Kashkarov P.K. , Kirillin M.Yu. , Golovan L.A. 
Published: January 2020

Abstract
The paper discusses the possibility of manufacturing silicon nanoparticles, which are suitable for contrasting biological tissues imaged by optical coherence tomography, by femtosecond laser ablation of porous silicon in various liquids. The manufactured nanoparticles are characterised by average sizes of 87, 112, and 102 nm for cases of ablation in water, ethanol, and liquid nitrogen, respectively, as well as a relatively narrow size distribution, which provides additional advantages for subsequent delivery into biological tissues. Electrochemical etching, which results in the formation of layers of porous silicon, allows the yield of ablation products to be increased several-fold by lowering the ablation threshold, thereby increasing the light scattering efficiency of the prepared suspensions compared with the case of using crystalline silicon as targets. The possibility of obtaining high-contrast images of a biotissue phantom based on an agar gel with embedded nanoparticles is shown. The magnitude of the contrast depends on the liquid used for ablation and correlates with the values of the reduced scattering coefficient of the studied suspensions.
Comparative analysis of the methods for quantitative determination of water content in skin from diffuse reflectance spectroscopy data
Authors: Yakimov B.P. , Davydov D.A. , Fadeev V.V. , Budylin G.S. , Shirshin E.A. 
Published: January 2020

Abstract
The predictive properties of methods aimed for estimating the water content in skin from the spectral diffuse reflection characteristics near the water absorption line in the near-IR spectral range are analysed. Numerical simulation data, experimental data on diffuse reflection from human skin phantoms, and data from the reference data set of human skin reflectance spectra are used to consider the possibility of gaining additional information about the water distribution in skin. The influence of variations in the scattering coefficient and oxyhaemoglobin concentration on the water content estimates is investigated.
Control of the optical properties of gum and dentin tissue of a human tooth at laser spectral lines in the range of 200 – 800 nm
Authors: Selifonov A.A. , Tuchin V.V. 
Published: January 2020

AbstractA change in the optical properties of the tissue of the gums and dentin of a human tooth is experimentally investigatedin vitrowith the application of a 99.5 % glycerol solution. The kinetics of the total transmittance in the spectral range of 200 – 800 nm on characteristic laser lines is studied. It is shown that the effectiveness of optical clearing, expressed as a relative increase in the total transmittance, for gum tissue in the laser radiation range of 200 – 800 nm can vary significantly (by an order of magnitude). In this case, the absolute values of optical transmittance in the UV region are relatively small due to the strong absorption by the endogenous chromophores of the studied tissues, and in the visible and NIR regions, on the contrary, they are significant, which is due to the absence of strongly absorbing chromophores. The effectiveness of dentin clearing in the entire visible and NIR spectral regions is on average 25 % for 300 minutes of immersion of the sample in a 99.5 % glycerol solution. The presented results are necessary for increasing the efficiency of laser therapy and methods for optical monitoring of morphological changes in biological tissues for the purpose of early diagnosis of diseases.
Role-space in VRS and VRI
Authors: Lee Robert G. 
Published: January 2020

Abstract
This chapter explores issues related to Video Relay Services
(VRS), a telephone access service for Deaf people and Video Remote
Interpreting (VRI). First there is a discussion of Deaf people and
specifically users of sign language and how they negotiate remote
communicative interactions (initially without direct access to audio-only
technologies such as the telephone). Similarities and differences between
VRS services for Deaf people and remote interpreted interactions (which can
involve signed and spoken or solely spoken language interlocutors) are then
explored.
The concept of role-space (Llewellyn-Jones and Lee 2014) is then introduced as a lens
through which these interactions can be analysed. A discussion of VRI
situations through the role-space dimensions of interaction management,
participant alignment and presentation of self is presented. Finally,
recommendations for factors to be considered to make VRI situations more
effective are presented.
On the role of the interlocutor in second
language development
Authors: Philp Jenefer , Gurzynski-Weiss Laura 
Published: January 2020

Abstract
In this chapter we examine
the role of the interlocutor in second language
(L2) learning and use from a
cognitive-interactionist perspective,
concentrating on oral interaction in face-to-face
and (written and/or video) chat-based contexts. We
center our discussion on the ways relationship,
status, proficiency, or familiarity between
interlocutors impact L2 interaction and
opportunities for development, as well as how
interlocutor individual differences play a part in
the interaction. Finally, we outline ways to
continue this line of work, including suggestions
for researchers, teachers, and students alike.
Variationist perspective(s) on interlocutor
individual differences
Authors: Geeslin Kimberly L. 
Published: January 2020

Abstract
The variationist
perspective provides tools for modeling language
use in context by incorporating the influences of
social and linguistic factors in the interactional
setting. These influencing factors include speaker
characteristics (age, regional origin),
characteristics of the setting (formality), and
characteristics of other participants in the
interaction (Geeslin & Long, 2014). In second
language research, these factors can describe
change over time (i.e., development) and the
acquisition of sociolinguistic competence (i.e.,
the ability to modify one’s speech in socially
acceptable ways across settings) (Canale & Swain,
1980; Tarone, 2007). While the variationist
perspective is well equipped for addressing the
role of the interlocutor, the potential of
variationist tools has not been fully exploited.
The present chapter reviews existing variationist
research, provides a new model that includes these
interlocutor-related factors, and proposes a
research agenda for moving forward.
Complexity Theory
Authors: Larsen-Freeman Diane 
Published: January 2020

Abstract
Complexity theorists are interested in
understanding the relations among
components in a complex system and how individual
differences in the components affect their
relationship to other components. Specific to our
interests here, the ability of speakers to adjust
their speech depends on the relationship with the person with whom they
interact. Further, all interactions involve mutual
influence (Ricca, 2012). Larsen-Freeman and Cameron
(2008a) call this bidirectional influence
“co-adaptation.”
Existing research on interaction
is briefly surveyed before turning to the view of
interlocutor interaction that Complexity Theory inspires.
Before concluding, research attesting to the
effect of interlocutor individual differences
(age, experience, sex, status, similarity,
identity, first language) is reviewed. Finally,
four considerations for enhancing future research
on interlocutor individual differences are
proposed.
Impact of growth kinetics on the interface morphology and magnetization in La1/3Sr2/3FeO3/La2/3Sr1/3MnO3 heterostructures
Authors: Waschk M , Sarkar A , Barthel J , Voigt J , Schröder S , Zakalek P , Schmitz M , Kirby B J , Pütter S , Schubert J , Brückel T 
Published: January 2020

Abstract
The ability to create atomically perfect, epitaxial heterostructures of correlated complex perovskite oxides using state-of-art thin film deposition techniques has generated new physical phenomena at engineered interfaces. Here we report on the impact of growth kinetics on the magnetic structure and exchange coupling at the interface in heterostructures combining layers of antiferromagnetic La1/3Sr2/3FeO3 (LSFO) and ferromagnetic La2/3Sr1/3MnO3 (LSMO) on (0 0 1)-oriented SrTiO3 (STO) substrates. Two growth orders are investigated, (a) LSMO/LSFO/STO(0 0 1) and (b) LSFO/LSMO/STO(0 0 1), where the LSFO layer is grown by molecular beam epitaxy and the LSMO layer by high oxygen pressure sputtering. The interface has been investigated using electron microscopy and polarized neutron reflectometry. Interdiffusion over seven monolayers is observed in LSMO/LSFO (a) with an almost 50% reduction in magnetization at the interface and showing no exchange coupling. However, the exchange bias effect (

mT at 10 K) could be realized when the interface is atomically sharp, as in LSFO/LSMO (b). Our study therefore reveals that, even for well ordered and lattice-matched structures, the kinetics involved in the growth processes drastically influences the interface quality with a strong correlation to the magnetic properties.
A soft gripper with programmable effective length, tactile and curvature sensory feedback
Authors: Hao Yufei , Liu Zemin , Liu Jiaqi , Fang Xi , Fang Bin , Nie Shilin , Guan Yingchun , Sun Fuchun , Wang Tianmiao , Wen Li 
Published: January 2020

Abstract
Soft grippers based on fluidic elastomer actuators have the characteristics of gentle and adaptable grasping that is difficult to realize by rigid grippers. However, it remains challenging to implement a compact gripping device that has multiple bending configurations to exert appropriate force, and sensory capabilities to evaluate the grasping state. Here, we present a soft gripper with variable effective lengths (VELs) that is achieved by rapidly softening selective shape memory polymer sections (within 0.6 s) via a flexible heater. A vortex tube is used to jet cold airflow to accelerate the stiffening process (within 14 s). We show that the soft gripper can not only identify objects but also exert higher gripping force by setting appropriate length according to pneumatic-thermal hybrid actuation. We further propose a touch-reconfiguration-grasp strategy to showcase the synergy of VELs and sensory feedback. The gripper first touches the object under the fully softened state and evaluates the grasping condition based on the sensors’ feedback, then reconfigures the bending length and grasps the object until successful. We envision that soft grippers with sensing ability and reconfigurable grasping configurations would be promising for future applications in unconstructed environments.
Strategies of object polarization and their role in electrosensory information gathering
Authors: Caputi Angel A , Aguilera Pedro A 
Published: January 2020

AbstractWeakly electric fish polarize the nearby environment with a stereotyped electric field and gain information by detecting the changes imposed by objects with tuned sensors. Here we focus on polarization strategies as paradigmatic bioinspiring mechanisms for sensing devices. We begin this research developing a toy model that describes three polarization strategies exhibited by three different groups of fish. We then report an experimental analysis which confirmed predictions of the model and in turn predicted functional consequences that were explored in behavioral experiments in the pulse fishGymnotus omarorum. In the experiments, polarization was evaluated by estimating the object’s stamp (i.e. the electric source that produces the same electric image as the object) as a function of object impedance, orientation, and position. Signal detection and discrimination was explored inG. omarorumby provoking novelty responses, which are known to reflect the increment in the electric image provoked by a change in nearby impedance. To achieve this, we stepped the longitudinal impedance of a cylindrical object between two impedances (either capacitive or resistive). Object polarization and novelty responses indicate thatG. omarorumhas two functional regions in the electrosensory field. At the front of the fish, there is a foveal field where object position and orientation are encoded in signal intensity, while the qualia associated with impedance is encoded in signal time course. On the side of the fish there is a peripheral field where the complexity of the polarizing field facilitates detection of objects oriented in any angle with respect to the fish´s longitudinal axis. These findings emphasize the importance of articulating field generation, sensor tuning and the repertoire of exploratory movements to optimize performance of artificial active electrosensory systems.
Kit’s development for automation mechanical transmission of a cargo vehicle
Authors: Vashurin A S , Butin D A , Yarzhemsky A D 
Published: January 2020

Abstract
The article describes the electric drive design for clutch control. A feature of the developed electric drive is the compensation mechanism use that allowed reducing the electric motor drive power. The developed electric drive controls the car clutch via a standard hydraulic system. The electric hydraulic clutch control does not have a pump and a flow control valve, but it is based on the piston movement in the main clutch cylinder. The main design steps were: determination of the diaphragm clutch spring parameters and operating cycles; choice of the compensation mechanism power characteristics; electric motor and gear ratio selection. The device operation was tested by simulation in a computer programs package. The calculation showed that the use of the compensation mechanism allowed to reduce the electric motor power in the electric drive by 5.7 times. This enabled to decrease energy consumption during the electric drive operation as well as to reduce its dimensions and cost.
Modified extreme learning machine based motion control of robotic manipulators
Authors: Kapoor Neha , Ohri Jyoti 
Published: January 2020

Abstract
Precise trajectory tracking is a difficult task due to partially known and unknown dynamics and the disturbances present in the system. For improving the tracking performance of the robotic manipulator, this work proposes a novel PSO optimized kernel based Extreme Learning Machine (PSO-KELM) learning algorithm in which PSO is used to get the optimal values of the free kernel-parameters in KELM. The simulation results represent the good generalized performance and PSO-KELM outperforms the KELM and ELM based control techniques for the manipulator trajectory tracking. Comparative analysis of the proposed control schemes have been done with NN and SVM based controllers and various ELM based variants for the trajectory tracking problem in robotic manipulator.