bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hyperdirect insula-basal-ganglia pathway and adult-like maturity of global brain responses predict inhibitory control in children
Authors: Cai Weidong , Duberg Katherine , Padmanabhan Aarthi , Rehert Rachel , Bradley Travis , Carrion Victor , Menon Vinod 
Published: October 2019

AbstractInhibitory control is fundamental to children’s self-regulation and cognitive development. Here we investigate cortical-basal ganglia pathways underlying inhibitory control in children and their adult-like maturity. We first conduct a comprehensive meta-analysis of extant neurodevelopmental studies of inhibitory control and highlight important gaps in the literature. Second, we examine cortical-basal ganglia activation during inhibitory control in children ages 9–12 and demonstrate the formation of an adult-like inhibitory control network by late childhood. Third, we develop a neural maturation index (NMI), which assesses the similarity of brain activation patterns between children and adults, and demonstrate that higher NMI in children predicts better inhibitory control. Fourth, we show that activity in the subthalamic nucleus and its effective connectivity with the right anterior insula predicts children’s inhibitory control. Fifth, we replicate our findings across multiple cohorts. Our findings provide insights into cortical-basal ganglia circuits and global brain organization underlying the development of inhibitory control.
Protein folding while chaperone bound is dependent on weak interactions
Authors: Wu Kevin , Stull Frederick , Lee Changhan , Bardwell James C. A. 
Published: October 2019

AbstractIt is generally assumed that protein clients fold following their release from chaperones instead of folding while remaining chaperone-bound, in part because binding is assumed to constrain the mobility of bound clients. Previously, we made the surprising observation that the ATP-independent chaperone Spy allows its client protein Im7 to fold into the native state while continuously bound to the chaperone. Spy apparently permits sufficient client mobility to allow folding to occur while chaperone bound. Here, we show that strengthening the interaction between Spy and a recently discovered client SH3 strongly inhibits the ability of the client to fold while chaperone bound. The more tightly Spy binds to its client, the more it slows the folding rate of the bound client. Efficient chaperone-mediated folding while bound appears to represent an evolutionary balance between interactions of sufficient strength to mediate folding and interactions that are too tight, which tend to inhibit folding.
Ballistic transport and boundary resistances in inhomogeneous quantum spin chains
Authors: Biella Alberto , Collura Mario , Rossini Davide , De Luca Andrea , Mazza Leonardo 
Published: October 2019

AbstractTransport phenomena are central to physics, and transport in the many-body and fully-quantum regime is attracting an increasing amount of attention. It has been recently revealed that some quantum spin chains support ballistic transport of excitations at all energies. However, when joining two semi-infinite ballistic parts, such as the XX and XXZ spin-1/2 models, our understanding suddenly becomes less established. Employing a matrix-product-state ansatz of the wavefunction, we study the relaxation dynamics in this latter case. Here we show that it takes place inside a light cone, within which two qualitatively different regions coexist: an inner one with a strong tendency towards thermalization, and an outer one supporting ballistic transport. We comment on the possibility that even at infinite time the system supports stationary currents and displays a non-zero Kapitza boundary resistance. Our study paves the way to the analysis of the interplay between transport, integrability, and local defects.
Mechanical adaptability of artificial muscles from nanoscale molecular action
Authors: Lancia Federico , Ryabchun Alexander , Nguindjel Anne-Déborah , Kwangmettatam Supaporn , Katsonis Nathalie 
Published: October 2019

AbstractThe motion of artificial molecular machines has been amplified into the shape transformation of polymer materials that have been compared to muscles, where mechanically active molecules work together to produce a contraction. In spite of this progress, harnessing cooperative molecular motion remains a challenge in this field. Here, we show how the light-induced action of artificial molecular switches modifies not only the shape but also, simultaneously, the stiffness of soft materials. The heterogeneous design of these materials features inclusions of free liquid crystal in a liquid crystal polymer network. When the magnitude of the intrinsic interfacial tension is modified by the action of the switches, photo-stiffening is observed, in analogy with the mechanical response of activated muscle fibers, and in contrast to melting mechanisms reported so far. Mechanoadaptive materials that are capable of active tuning of rigidity will likely contribute to a bottom-up approach towards human-friendly and soft robotics.
Dopant-tuned stabilization of intermediates promotes electrosynthesis of valuable C3 products
Authors: Zhuang Tao-Tao , Nam Dae-Hyun , Wang Ziyun , Li Hui-Hui , Gabardo Christine M. , Li Yi , Liang Zhi-Qin , Li Jun , Liu Xiao-Jing , Chen Bin , Leow Wan Ru , Wu Rui , Wang Xue , Li Fengwang , Lum Yanwei , Wicks Joshua , O’Brien Colin P. , Peng Tao , Ip Alexander H. , Sham Tsun-Kong , Yu Shu-Hong , Sinton David , Sargent Edward H. 
Published: October 2019

AbstractThe upgrading of CO2/CO feedstocks to higher-value chemicals via energy-efficient electrochemical processes enables carbon utilization and renewable energy storage. Substantial progress has been made to improve performance at the cathodic side; whereas less progress has been made on improving anodic electro-oxidation reactions to generate value. Here we report the efficient electroproduction of value-added multi-carbon dimethyl carbonate (DMC) from CO and methanol via oxidative carbonylation. We find that, compared to pure palladium controls, boron-doped palladium (Pd-B) tunes the binding strength of intermediates along this reaction pathway and favors DMC formation. We implement this doping strategy and report the selective electrosynthesis of DMC experimentally. We achieve a DMC Faradaic efficiency of 83 ± 5%, fully a 3x increase in performance compared to the corresponding pure Pd electrocatalyst.
One thousand plant transcriptomes and the phylogenomics of green plants
Authors:   One Thousand Plant Transcriptomes Initiative
Published: October 2019

AbstractGreen plants (Viridiplantae) include around 450,000–500,000 species1,2of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
A cone-beam X-ray computed tomography data collection designed for machine learning
Authors: Der Sarkissian Henri , Lucka Felix , van Eijnatten Maureen , Colacicco Giulia , Coban Sophia Bethany , Batenburg Kees Joost 
Published: October 2019

AbstractUnlike previous works, this open data collection consists of X-ray cone-beam (CB) computed tomography (CT) datasets specifically designed for machine learning applications and high cone-angle artefact reduction. Forty-two walnuts were scanned with a laboratory X-ray set-up to provide not only data from a single object but from a class of objects with natural variability. For each walnut, CB projections on three different source orbits were acquired to provide CB data with different cone angles as well as being able to compute artefact-free, high-quality ground truth images from the combined data that can be used for supervised learning. We provide the complete image reconstruction pipeline: raw projection data, a description of the scanning geometry, pre-processing and reconstruction scripts using open software, and the reconstructed volumes. Due to this, the dataset can not only be used for high cone-angle artefact reduction but also for algorithm development and evaluation for other tasks, such as image reconstruction from limited or sparse-angle (low-dose) scanning, super resolution, or segmentation.
Classification of GABAergic interneurons by leading neuroscientists
Authors: Mihaljević Bojan , Benavides-Piccione Ruth , Bielza Concha , Larrañaga Pedro , DeFelipe Javier 
Published: October 2019

AbstractThere is currently no unique catalog of cortical GABAergic interneuron types. In 2013, we asked 48 leading neuroscientists to classify 320 interneurons by inspecting images of their morphology. That study was the first to quantify the degree of agreement among neuroscientists in morphology-based interneuron classification, showing high agreement for the chandelier and Martinotti types, yet low agreement for most of the remaining types considered. Here we present the dataset containing the classification choices by the neuroscientists according to interneuron type as well as to five prominent morphological features. These data can be used as crisp or soft training labels for learning supervised machine learning interneuron classifiers, while further analyses can try to pinpoint anatomical characteristics that make an interneuron especially difficult or especially easy to classify.
Validation of Reference Genes for Normalization of Relative qRT-PCR Studies in Papillary Thyroid Carcinoma
Authors: Razavi S. Adeleh , Afsharpad Mandana , Modarressi Mohammad Hossein , Zarkesh Maryam , Yaghmaei Parichehreh , Nasiri Shirzad , Tavangar S. Mohammad , Gholami Hanieh , Daneshafrooz Afsoon , Hedayati Mehdi 
Published: October 2019

AbstractQuantitative reverse transcription polymerase chain reaction (qRT-PCR) in thyroid tumors require accurate data normalization, however, there are no sufficient studies addressing the suitable reference genes for gene expression analysis in malignant and normal thyroid tissue specimens. The purpose of this study was to identify valid internal control genes for normalization of relative qRT-PCR studies in human papillary thyroid carcinoma tissue samples. The expression characteristics of 12 candidate reference genes (GAPDH, ACTB, HPRT1, TBP, B2M, PPIA, 18SrRNA, HMBS, GUSB, PGK1, RPLP0, and PGM1) were assessed by qRT-PCR in 45 thyroid tissue samples (15 papillary thyroid carcinoma, 15 paired normal tissues and 15 multinodular goiters). These twelve candidate reference genes were selected by a systematic literature search. GeNorm, NormFinder, and BestKeeper statistical algorithms were applied to determine the most stable reference genes. The three algorithms were in agreement in identifying GUSB and HPRT1 as the most stably expressed genes in all thyroid tumors investigated. According to the NormFinder software, the pair of genes including ‘GUSB and HPRT1’ or ‘GUSB and HMBS’ or ‘GUSB and PGM1’ were the best combinations for selection of pair reference genes. The optimal number of genes required for reliable normalization of qPCR data in thyroid tissues would be three according to calculations made by GeNorm algorithm. These results suggest that GUSB and HPRT1 are promising reference genes for normalization of relative qRT-PCR studies in papillary thyroid carcinoma.
Tracing microplastics in aquatic environments based on sediment analogies
Authors: Enders Kristina , Käppler Andrea , Biniasch Oliver , Feldens Peter , Stollberg Nicole , Lange Xaver , Fischer Dieter , Eichhorn Klaus-Jochen , Pollehne Falk , Oberbeckmann Sonja , Labrenz Matthias 
Published: October 2019

AbstractMicroplastics (MP) data collection from the aquatic environment is a challenging endeavour that sets apparent limitations to regional and global MP quantification. Expensive data collection causes small sample sizes and oftentimes existing data sets are compared without accounting for natural variability due to hydrodynamic processes governing the distribution of particles. In Warnow estuarine sediments (Germany) we found significant correlations between high-density polymer size fractions (≥500 µm) and sediment grain size. Among potential predictor variables (source and environmental terms) sediment grain size was the critical proxy for MP abundance. The MP sediment relationship can be explained by the force necessary to start particle transport: at the same level of fluid motion, transported sediment grains and MP particles are offset in size by one to two orders of magnitude. Determining grain-size corrected MP abundances by fractionated granulometric normalisation is recommended as a basis for future MP projections and identification of sinks and sources.
Estimating numbers of intracellular molecules through analysing fluctuations in photobleaching
Authors: Bakker Elco , Swain Peter S. 
Published: October 2019

AbstractThe impact of fluorescence microscopy has been limited by the difficulties of expressing measurements of fluorescent proteins in numbers of molecules. Absolute numbers enable the integration of results from different laboratories, empower mathematical modelling, and are the bedrock for a quantitative, predictive biology. Here we propose an estimator to infer numbers of molecules from fluctuations in the photobleaching of proteins tagged with Green Fluorescent Protein. Performing experiments in budding yeast, we show that our estimates of numbers agree, within an order of magnitude, with published biochemical measurements, for all six proteins tested. The experiments we require are straightforward and use only a wide-field fluorescence microscope. As such, our approach has the potential to become standard for those practising quantitative fluorescence microscopy.
Extended stable equilibrium invaded by an unstable state
Authors: Castillo-Pinto Camila , Clerc Marcel G. , González-Cortés Gregorio 
Published: October 2019

AbstractCoexistence of states is an indispensable feature in the observation of domain walls, interfaces, shock waves or fronts in macroscopic systems. The propagation of these nonlinear waves depends on the relative stability of the connected equilibria. In particular, one expects a stable equilibrium to invade an unstable one, such as occur in combustion, in the spread of permanent contagious diseases, or in the freezing of supercooled water. Here, we show that an unstable state generically can invade a locally stable one in the context of the pattern forming systems. The origin of this phenomenon is related to the lower energy unstable state invading the locally stable but higher energy state. Based on a one-dimensional model we reveal the necessary features to observe this phenomenon. This scenario is fulfilled in the case of a first order spatial instability. A photo-isomerization experiment of a dye-dopant nematic liquid crystal, allow us to observe the front propagation from an unstable state.
Impact of geography and surgical approach on recurrence in global pilonidal sinus disease
Authors: Doll Dietrich , Orlik Andriu , Maier Katharina , Kauf Peter , Schmid Marco , Diekmann Maja , Vogt Andreas P. , Stauffer Verena K. , Luedi Markus M. 
Published: October 2019

AbstractPilonidal sinus disease (PSD) is increasing globally. A recent meta-analysis and merged-data analysis showed that recurrence rates in PSD depend essentially on follow-up time and specific surgical procedures. However, the global distribution of surgical approaches and respective recurrence rates have never been studied in PSD. We aimed at studying the impact of geographic distribution of surgical approaches to treat PSD and subsequent geography-specific recurrence rates. We searched relevant databases as described previously. Recurrence rates were then associated with reported follow-up times and geographic origin. We simulated individual patients to enable analogy across data. Globally, recurrence rates range from 0.3% for Limberg/Dufourmentel approaches (95% CI 0.2–0.4) and flaps (95% CI 0.1–0.5) and up to 6.3% for incision (95% CI 3.2–9.3) at 12 months. Recurrence rates range from 0.3% for Karydakis/Bascom approaches (95% CI 0.0–0.8) up to 67.2% for incision (95% CI 7.5–100) in the USA, and 0.0% for primary asymmetric closure in Germany (95% CI 0.0–0.0). Our analysis shows that recurrence rates in PSD not only depend on therapeutic approaches and follow-up time but also on geography. Primary asymmetric closure and various flap techniques remain superior regardless of the geographical region. Some approaches have extraordinarily good outcomes in specific countries.
Acetic acid: a cost-effective agent for mitigation of seawater-induced salt toxicity in mung bean
Authors: Rahman Md. Mezanur , Mostofa Mohammad Golam , Rahman Md. Abiar , Islam Md. Robyul , Keya Sanjida Sultana , Das Ashim Kumar , Miah Md. Giashuddin , Kawser A. Q. M. Robiul , Ahsan S. M. , Hashem Abeer , Tabassum Baby , Abd_Allah Elsayed Fathi , Tran Lam-Son Phan 
Published: October 2019

AbstractThe current study sought the effective mitigation measure of seawater-induced damage to mung bean plants by exploring the potential roles of acetic acid (AA). Principal component analysis (PCA) revealed that foliar application of AA under control conditions improved mung bean growth, which was interlinked to enhanced levels of photosynthetic rate and pigments, improved water status and increased uptake of K+, in comparison with water-sprayed control. Mung bean plants exposed to salinity exhibited reduced growth and biomass production, which was emphatically correlated with increased accumulations of Na+, reactive oxygen species and malondialdehyde, and impaired photosynthesis, as evidenced by PCA and heatmap clustering. AA supplementation ameliorated the toxic effects of seawater, and improved the growth performance of salinity-exposed mung bean. AA potentiated several physio-biochemical mechanisms that were connected to increased uptake of Ca2+ and Mg2+, reduced accumulation of toxic Na+, improved water use efficiency, enhanced accumulations of proline, total free amino acids and soluble sugars, increased catalase activity, and heightened levels of phenolics and flavonoids. Collectively, our results provided new insights into AA-mediated protective mechanisms against salinity in mung bean, thereby proposing AA as a potential and cost-effective chemical for the management of salt-induced toxicity in mung bean, and perhaps in other cash crops.
Propagation and Scattering of Lamb Waves at Conical Points in Plates
Authors: Stobbe David M. , Grünsteidl Clemens M. , Murray Todd W. 
Published: October 2019

AbstractLamb waves exhibit conical dispersion at zero wave number when an accidental degeneracy occurs between thickness mode longitudinal and shear resonances of the same symmetry. Here we investigate the propagation of Lamb waves generated at the conical point frequency and the interaction of these waves with defects and interfaces. The group velocity and mode shapes of Lamb waves at the conical point are found, and it is shown that as the wavenumber gets close to zero, considerable group velocity is seen only for material properties supporting a degeneracy or near-degeneracy. The unusual wave propagation and mode conversion of Lamb waves generated at the conical point are elucidated through numerical simulations. Experimental measurements of near conical point Lamb wave interaction with holes in a plate demonstrate that these waves flow around defects while maintaining a constant phase of oscillation across that plate surface.
Systematic comparison between methods for the detection of influential spreaders in complex networks
Authors: Erkol Şirag , Castellano Claudio , Radicchi Filippo 
Published: October 2019

AbstractInfluence maximization is the problem of finding the set of nodes of a network that maximizes the size of the outbreak of a spreading process occurring on the network. Solutions to this problem are important for strategic decisions in marketing and political campaigns. The typical setting consists in the identification of small sets of initial spreaders in very large networks. This setting makes the optimization problem computationally infeasible for standard greedy optimization algorithms that account simultaneously for information about network topology and spreading dynamics, leaving space only to heuristic methods based on the drastic approximation of relying on the geometry of the network alone. The literature on the subject is plenty of purely topological methods for the identification of influential spreaders in networks. However, it is unclear how far these methods are from being optimal. Here, we perform a systematic test of the performance of a multitude of heuristic methods for the identification of influential spreaders. We quantify the performance of the various methods on a corpus of 100 real-world networks; the corpus consists of networks small enough for the application of greedy optimization so that results from this algorithm are used as the baseline needed for the analysis of the performance of the other methods on the same corpus of networks. We find that relatively simple network metrics, such as adaptive degree or closeness centralities, are able to achieve performances very close to the baseline value, thus providing good support for the use of these metrics in large-scale problem settings. Also, we show that a further 2–5% improvement towards the baseline performance is achievable by hybrid algorithms that combine two or more topological metrics together. This final result is validated on a small collection of large graphs where greedy optimization is not applicable.