bluuebunny/crossref_metadata_2025 huggingface dataset:
Triggering nuclear and galaxy activity in the Bullet cluster
Authors: Puccetti S. , Fiore F. , Bongiorno A. , Boutsia K. , Fassbender R. , Verdugo M.
Published: December 2019

The analysis of a cluster environment is a valuable instrument to investigate the origin of gas fuelling and trigger mechanisms in active galactic nuclei (AGN) and star-forming galaxies. To this purpose, we present a detailed analysis of the point-like X-ray sources in the Bullet cluster field. Based on ∼600 ks Chandra observations, we produced a catalogue of 381 X-ray point sources up to a distance of ∼1.5 virial radius and with flux limits ∼1 × 10−16 and ∼8 × 10−16 erg cm−2 s−1 in the 0.5–2 keV and 2–10 keV bands, respectively. We find a strong (up to a factor 1.5–2) and significant (≥4σ) over-density in the full region studied 0.3R200 <  R <  1.5R200. We identified optical (R band) and infrared (Spitzer IRAC) counterparts for ∼84% and ∼48% of the X-ray sources, respectively. We obtained new spectroscopic redshifts for 106 X-ray sources and collected from the literature additional 13 spectroscopic and 8 photometric redshifts of X-ray sources. Twenty-nine X-ray sources turned out to be cluster members. Spectroscopic and photometric redshifts of optical and infrared sources were also collected, and these sources were used as ancillary samples. We used these multi-wavelength data to characterise the nature of the Bullet cluster X-ray point sources. We find that the over-density in the region 0.3R200 <  R <  R200 is likely due to X-ray AGN (mostly obscured) and star-forming galaxies associated with the cluster, while in the more external region this over-density is likely to be mostly due to background AGN. The fraction of cluster galaxies hosting an X-ray detected AGN is 1.0 ± 0.4%, which is nearly constant with the radius; this fraction is similar to that reported in other clusters of galaxies at similar redshift. The fraction of X-ray bright AGN (L2 − 10 keV >  1043 ergs s−1) in the region 0.3R200 <  R <  R200 is 0.5−0.2+0.6%, which is higher than that in other clusters at similar redshift and more similar to the AGN fraction in the field. Finally, the spatial distributions of AGN and star-forming galaxies, which we selected for their infrared emission, appear similar, thus suggesting that both are triggered by the same mechanism.
The NGC 346 massive star census
Authors: Dufton P. L. , Evans C. J. , Lennon D. J. , Hunter I.
Published: December 2019

Previous analyses of two large spectroscopic surveys of early-type stars in the Large Magellanic Cloud (LMC) have found an excess of nitrogen enriched B-type targets with avesini ≤ 40 km s−1compared with the predictions of single star evolutionary models that incorporate rotational mixing. By contrast, the number of such targets with 40 <  vesini ≤ 80 km s−1was consistent with such models. We have undertaken a similar analysis for 61 B-type targets which lie towards the young cluster, NGC 346 in the Small Magellanic Cloud (SMC). These again have projected rotational velocities,vesini ≤ 80 km s−1, are not classified as supergiants, and are apparently single. Approximately 65% of these SMC targets could have nitrogen enhancements of less than 0.3 dex, which is consistent with them having experienced only small amounts of mixing due to their low rotational velocities. However, as with the previous LMC surveys, an excess of stars with low projected rotational velocities,vesini ≤ 40 km s−1, and significant nitrogen enrichments is found. This is estimated to be approximately 5% of the total population of apparently single B-type stars or 40% of all stars with current rotational velocities of less than 40 km s−1; these percentages are similar to those found previously for the two LMC samples. For all three surveys, the presence of undetected binaries and other uncertainties imply that these percentages might be underestimated and that it is indeed possible for all the single stars with current rotational velocities of less than 40 km s−1to be nitrogen enriched. Two possible explanations incorporate the effects of the magnetic field, via either a stellar merger followed by magnetic braking or the evolution of a single star with a large magnetic field. Both mechanisms would appear to be compatible with the observed frequency of nitrogen-enriched stars in the Magellanic Clouds. Differences in the properties of the nitrogen-enriched stars compared with the remainder of the sample would be consistent with the former mechanism. For the latter, a qualitative comparison with Galactic evolutionary models that incorporate magnetic fields is encouraging in terms of the amount of nitrogen enrichment and its presence in stars near the zero-age main sequence.
Relation entre taux de couverture du sol et biomasse de résidus de cultures : une simplification prédictive est envisageable
Authors: Thiebeau Pascal
Published: December 2019

En système d’agriculture de conservation, les résidus de cultures ne sont plus brassés dans un volume de sol labouré mais maintenus à la surface des sols ou partiellement enfouis. Leur présence contribue à la durabilité de ces systèmes par le maintien des équilibres agronomiques et environnementaux qu’ils induisent. Dans ce contexte, la connaissance de l’évolution de leur quantité à la surface d’un sol, de la récolte au semis de la culture suivante, devient un enjeu important de gestion des sols. Plusieurs auteurs ont établi une relation entre le taux de couverture du sol (TC) et la biomasse, propre à chaque espèce végétale, à partir d’un formalisme développé par Grégory (1982). Les objectifs de ce travail sont de tester sa validité dans le contexte pédoclimatique de la région Grand-Est (France), après récolte et au cours du processus de décomposition des résidus. Ce travail a été réalisé sur des exploitations pratiquant l’agriculture de conservation depuis plusieurs années. Les résidus ont été broyés lors de la récolte ou d’une opération spécifique. Les données de biomasse ont été collectées à l’aide de cadres de 0,5 m × 0,5 m, tandis que la couverture du sol a été étudiée à l’aide de photographies numériques. Le taux de couverture du sol a été calculé à l’aide d’un logiciel d’analyse d’images. Ce travail compare également deux périodes de mesure : en sortie d’hiver, plusieurs mois après la récolte, et juste après la récolte estivale. Les résultats montrent une très bonne correspondance entre le TC et la biomasse mesurée au sol, toutes espèces et période de mesures confondues, moyennant l’ajout d’un paramètre au formalisme de Grégory (1982). L’intégration de la variabilité spatiale au sol permet de proposer l’emploi d’un ajustement linéaire unique qui simplifie la prédiction du TC du sol ou « la prédiction » de la quantité de biomasse.
GRIN2A-Related Severe Epileptic Encephalopathy Treated with Memantine: An Example of Precision Medicine
Authors: Mir Ali , Qahtani Mohammed , Bashir Shahid
Published: December 2019

Epileptic spasm (ES) is one of the seizure types which is difficult to treat. Next-generation sequencing has facilitated rapid gene discovery that is linked to ES and GRIN2A being one of them. Genotype-driven precision medicine is on the horizon and is a targeted treatment approach toward the precise molecular cause of the disease. GRIN2A gene encodes for a subunit of N-methyl-D-aspartate (NMDA) receptor and it has been suggested from in vitro studies and few case reports that memantine, a NMDA receptor antagonist, was shown to reduce seizures in patients with GRIN2A mutations. Here, we describe a patient with a novel GRIN2A mutation and severe drug-resistant ES who became seizure free with memantine.
Spreading of fast-curing, thermosetting silicones
Authors: Xie Jingjin , Randolph Robert , Simmons Gary , Vinciguerra Michael , Suri Sahil , Bonini Nicholas , Root Anna , Hull Patrick V. , Mazzeo Aaron D.
Published: December 2019

This letter presents an experimental study and the associated numerical modeling of fast-curing, thermosetting droplets spreading on a heated surface. The results show a significant morphological dependence of the spreading droplets of Ecoflex 0050 (a heat-sensitive, platinum-catalyzed silicone material) on thermal conditions. Differential scanning calorimetry and rheometry provide quantifiable data for modeling the cure kinetics and rheological properties of the material. This work demonstrates an approach to developing a phenomenological model suitable for predicting the morphological variation of fast-curing, thermosetting materials without prior knowledge of their chemical composition. The developed multiphysics models for cure kinetics and chemorheology can serve as a functional tool for predictions requiring accurate dimensional control of free-forming thermosetting materials, such as nozzle-based additive manufacturing, centrifugal coating and forming, fabrication of soft robots, and soft lithography.
Emerging trends in modeling human liver disease in vitro
Authors: Underhill Gregory H. , Khetani Salman R.
Published: December 2019

The liver executes 500+ functions, such as protein synthesis, xenobiotic metabolism, bile production, and metabolism of carbohydrates/fats/proteins. Such functions can be severely degraded by drug-induced liver injury, nonalcoholic fatty liver disease, hepatitis B and viral infections, and hepatocellular carcinoma. These liver diseases, which represent a significant global health burden, are the subject of novel drug discovery by the pharmaceutical industry via the use of in vitro models of the human liver, given significant species-specific differences in disease profiles and drug outcomes. Isolated primary human hepatocytes (PHHs) are a physiologically relevant cell source to construct such models; however, these cells display a rapid decline in the phenotypic function within conventional 2-dimensional monocultures. To address such a limitation, several engineered platforms have been developed such as high-throughput cellular microarrays, micropatterned cocultures, self-assembled spheroids, bioprinted tissues, and perfusion devices; many of these platforms are being used to coculture PHHs with liver nonparenchymal cells to model complex cell cross talk in liver pathophysiology. In this perspective, we focus on the utility of representative platforms for mimicking key features of liver dysfunction in the context of chronic liver diseases and liver cancer. We further discuss pending issues that will need to be addressed in this field moving forward. Collectively, these in vitro liver disease models are being increasingly applied toward the development of new therapeutics that display an optimal balance of safety and efficacy, with a focus on expediting development, reducing high costs, and preventing harm to patients.
Equation of state and first principles prediction of the vibrational matrix shift of solid parahydrogen
Authors: Ibrahim Alexander , Wang Lecheng , Halverson Tom , Le Roy Robert J. , Roy Pierre-Nicholas
Published: December 2019

We generate the equation of state (EOS) of solid parahydrogen (para-H2) using a path-integral Monte Carlo (PIMC) simulation based on a highly accurate first-principles adiabatic hindered rotor potential energy curve for the para-H2 dimer. The EOS curves for the fcc and hcp structures of solid para-H2 near the equilibrium density show that the hcp structure is the more stable of the two, in agreement with experiment. To accurately reproduce the structural and energy properties of solid para-H2, we eliminated by extrapolation the systematic errors associated with the choice of simulation parameters used in the PIMC calculation. We also investigate the temperature dependence of the EOS curves, and the invariance of the equilibrium density with temperature is satisfyingly reproduced. The pressure as a function of density and the compressibility as a function of pressure are both calculated using the obtained EOS and are compared with previous simulation results and experiments. We also report the first ever a priori prediction of a vibrational matrix shift from first-principles two-body potential functions, and its result for the equilibrium state agrees well with experiment.
Fast-pulsing LED-enhanced NMR: A convenient and inexpensive approach to increase NMR sensitivity
Authors: Yang Hanming , Hofstetter Heike , Cavagnero Silvia
Published: December 2019

Low-concentration photochemically induced dynamic nuclear polarization (LC-photo-CIDNP) has recently emerged as a powerful technology for the detection of aromatic amino acids and proteins in solution in the low-micromolar to nanomolar concentration range. LC-photo-CIDNP is typically carried out in the presence of high-power lasers, which are costly and maintenance-heavy. Here, we show that LC-photo-CIDNP can be performed with light-emitting diodes (LEDs), which are inexpensive and much less cumbersome than lasers, laser diodes, flash lamps, or other light sources. When nuclear magnetic resonance (NMR) sample concentration is within the low-micromolar to nanomolar range, as in LC-photo-CIDNP, replacement of lasers with LEDs leads to no losses in sensitivity. We also investigate the effect of optical-fiber thickness and compare excitation rate constants of an Ar ion laser (488 nm) and a 466 nm LED, taking LED emission bandwidths into account. In addition, importantly, we develop a novel pulse sequence (13C RASPRINT) to perform ultrarapid LC-photo-CIDNP data collection. Remarkably, 13C RASPRINT leads to 4-fold savings in data collection time. The latter advance relies on the fact that photo-CID nuclear hyperpolarization does not suffer from the longitudinal-relaxation recovery requirements of conventional NMR. Finally, we combine both the above improvements, resulting in facile and rapid (≈16 s–2.5 min) collection of 1 and 2D NMR data on aromatic amino acids and proteins in solution at nanomolar to low micromolar concentration.
Solvent-dependent complex reaction pathways of bromoform revealed by time-resolved X-ray solution scattering and X-ray transient absorption spectroscopy
Authors: Kong Qingyu , Khakhulin Dmitry , Shkrob Ilya A. , Lee Jae Hyuk , Zhang Xiaoyi , Kim Jeongho , Kim Kyung Hwan , Jo Junbeom , Kim Jungmin , Kang Jaedong , Pham Van-Thai , Jennings Guy , Kurtz Charles , Spence Rick , Chen Lin X. , Wulff Michael , Ihee Hyotcherl
Published: December 2019

The photochemical reaction pathways of CHBr3 in solution were unveiled using two complementary X-ray techniques, time-resolved X-ray solution scattering (TRXSS) and X-ray transient absorption spectroscopy, in a wide temporal range from 100 ps to tens of microseconds. By performing comparative measurements in protic (methanol) and aprotic (methylcyclohexane) solvents, we found that the reaction pathways depend significantly on the solvent properties. In methanol, the major photoproducts are CH3OCHBr2 and HBr generated by rapid solvolysis of iso-CHBr2-Br, an isomer of CHBr3. In contrast, in methylcyclohexane, iso-CHBr2-Br returns to CHBr3 without solvolysis. In both solvents, the formation of CHBr2 and Br is a competing reaction channel. From the structural analysis of TRXSS data, we determined the structures of key intermediate species, CH3OCHBr2 and iso-CHBr2-Br in methanol and methylcyclohexane, respectively, which are consistent with the structures from density functional theory calculations.
An analysis of isomorphic RPMD in the golden rule limit
Authors: Lawrence Joseph E. , Manolopoulos David E.
Published: December 2019

We analyze the golden rule limit of the recently proposed isomorphic ring polymer (iso-RP) method. This method aims to combine an exact expression for the quantum mechanical partition function of a system with multiple electronic states with a pre-existing mixed quantum-classical (MQC) dynamics approximation, such as fewest switches surface hopping. Since the choice of the MQC method adds a degree of flexibility, we simplify the analysis by assuming that the dynamics used correctly reproduces the exact golden rule rate for a nonadiabatic (e.g., electron transfer) reaction in the high temperature limit. Having made this assumption, we obtain an expression for the iso-RP rate in the golden rule limit that is valid at any temperature. We then compare this rate with the exact rate for a series of simple spin-boson models. We find that the iso-RP method does not correctly predict how nuclear quantum effects affect the reaction rate in the golden rule limit. Most notably, it does not capture the quantum asymmetry in a conventional (Marcus) plot of the logarithm of the reaction rate against the thermodynamic driving force, and it also significantly overestimates the correct quantum mechanical golden rule rate for activationless electron transfer reactions. These results are analyzed and their implications discussed for the applicability of the iso-RP method to more general nonadiabatic reactions.
DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products
Authors: Merwin Nishanth J. , Mousa Walaa K. , Dejong Chris A. , Skinnider Michael A. , Cannon Michael J. , Li Haoxin , Dial Keshav , Gunabalasingam Mathusan , Johnston Chad , Magarvey Nathan A.
Published: December 2019

Significance

Natural products form the basis for most drugs in clinical use. Advances in genome sequencing and bioinformatic tools have revealed thousands of biosynthetic gene clusters encoding these products. However, linking natural products identified by genome mining to their corresponding products in untargeted metabolomics data remains a key challenge. Here we present a platform, DeepRiPP, which integrates genomic and metabolomic data to automate the discovery of new ribosomally synthesized posttranslationally modified peptides (RiPPs), a subclass of natural products with diverse chemistry and activities. We apply DeepRiPP to discover 3 novel RiPPs.
From thought to action: The brain–machine interface in posterior parietal cortex
Authors: Andersen Richard A. , Aflalo Tyson , Kellis Spencer
Published: December 2019

A dramatic example of translational monkey research is the development of neural prosthetics for assisting paralyzed patients. A neuroprosthesis consists of implanted electrodes that can record the intended movement of a paralyzed part of the body, a computer algorithm that decodes the intended movement, and an assistive device such as a robot limb or computer that is controlled by these intended movement signals. This type of neuroprosthetic system is also referred to as a brain–machine interface (BMI) since it interfaces the brain with an external machine. In this review, we will concentrate on BMIs in which microelectrode recording arrays are implanted in the posterior parietal cortex (PPC), a high-level cortical area in both humans and monkeys that represents intentions to move. This review will first discuss the basic science research performed in healthy monkeys that established PPC as a good source of intention signals. Next, it will describe the first PPC implants in human patients with tetraplegia from spinal cord injury. From these patients the goals of movements could be quickly decoded, and the rich number of action variables found in PPC indicates that it is an appropriate BMI site for a very wide range of neuroprosthetic applications. We will discuss research on learning to use BMIs in monkeys and humans and the advances that are still needed, requiring both monkey and human research to enable BMIs to be readily available in the clinic.
Primate optogenetics: Progress and prognosis
Authors: El-Shamayleh Yasmine , Horwitz Gregory D.
Published: December 2019

Monkeys are a premier model organism for neuroscience research. Activity in the central nervous systems of monkeys can be recorded and manipulated while they perform complex perceptual, motor, or cognitive tasks. Conventional techniques for manipulating neural activity in monkeys are too coarse to address many of the outstanding questions in primate neuroscience, but optogenetics holds the promise to overcome this hurdle. In this article, we review the progress that has been made in primate optogenetics over the past 5 years. We emphasize the use of gene regulatory sequences in viral vectors to target specific neuronal types, and we present data on vectors that we engineered to target parvalbumin-expressing neurons. We conclude with a discussion of the utility of optogenetics for treating sensorimotor hearing loss and Parkinson’s disease, areas of translational neuroscience in which monkeys provide unique leverage for basic science and medicine.
Attention can be subdivided into neurobiological components corresponding to distinct behavioral effects
Authors: Luo Thomas Zhihao , Maunsell John H. R.
Published: December 2019

Attention is a common but highly complex term associated with a large number of distinct behavioral and perceptual phenomena. In the brain, attention-related changes in neuronal activity are observed in widespread structures. The many distinct behavioral and neuronal phenomena related to attention suggest that it might be subdivided into components corresponding to distinct biological mechanisms. Recent neurophysiological studies in monkeys have isolated behavioral changes related to attention along the 2 indices of signal detection theory and found that these 2 behavioral changes are associated with distinct neuronal changes in different brain areas. These results support the view that attention is made up of distinct neurobiological mechanisms.
The mind–body problem: Circuits that link the cerebral cortex to the adrenal medulla
Authors: Dum Richard P. , Levinthal David J. , Strick Peter L.
Published: December 2019

Which regions of the cerebral cortex are the origin of descending commands that influence internal organs? We used transneuronal transport of rabies virus in monkeys and rats to identify regions of cerebral cortex that have multisynaptic connections with a major sympathetic effector, the adrenal medulla. In rats, we also examined multisynaptic connections with the kidney. In monkeys, the cortical influence over the adrenal medulla originates from 3 distinct networks that are involved in movement, cognition, and affect. Each of these networks has a human equivalent. The largest influence originates from a motor network that includes all 7 motor areas in the frontal lobe. These motor areas are involved in all aspects of skeletomotor control, from response selection to motor preparation and movement execution. The motor areas provide a link between body movement and the modulation of stress. The cognitive and affective networks are located in regions of cingulate cortex. They provide a link between how we think and feel and the function of the adrenal medulla. Together, the 3 networks can mediate the effects of stress and depression on organ function and provide a concrete neural substrate for some psychosomatic illnesses. In rats, cortical influences over the adrenal medulla and the kidney originate mainly from 2 motor areas and adjacent somatosensory cortex. The cognitive and affective networks, present in monkeys, are largely absent in rats. Thus, nonhuman primate research is essential to understand the neural substrate that links cognition and affect to the function of internal organs.
Alzheimer’s-like pathology in aging rhesus macaques: Unique opportunity to study the etiology and treatment of Alzheimer’s disease
Authors: Arnsten Amy F. T. , Datta Dibyadeep , Leslie Shannon , Yang Sheng-Tao , Wang Min , Nairn Angus C.
Published: December 2019

Although mouse models of Alzheimer’s disease (AD) have provided tremendous breakthroughs, the etiology of later onset AD remains unknown. In particular, tau pathology in the association cortex is poorly replicated in mouse models. Aging rhesus monkeys naturally develop cognitive deficits, amyloid plaques, and the same qualitative pattern and sequence of tau pathology as humans, with tangles in the oldest animals. Thus, aging rhesus monkeys can play a key role in AD research. For example, aging monkeys can help reveal how synapses in the prefrontal association cortex are uniquely regulated compared to the primary sensory cortex in ways that render them vulnerable to calcium dysregulation and tau phosphorylation, resulting in the selective localization of tau pathology observed in AD. The ability to assay early tau phosphorylation states and perform high-quality immunoelectron microscopy in monkeys is a great advantage, as one can capture early-stage degeneration as it naturally occurs in situ. Our immunoelectron microscopy studies show that phosphorylated tau can induce an “endosomal traffic jam” that drives amyloid precursor protein cleavage to amyloid-β in endosomes. As amyloid-β increases tau phosphorylation, this creates a vicious cycle where varied precipitating factors all lead to a similar phenotype. These data may help explain why circuits with aggressive tau pathology (e.g., entorhinal cortex) may degenerate prior to producing significant amyloid pathology. Aging monkeys therefore can play an important role in identifying and testing potential therapeutics to protect the association cortex, including preventive therapies that are challenging to test in humans.
The structural bases for agonist diversity in an
Arabidopsis thaliana
glutamate receptor-like channel
Authors: Alfieri Andrea , Doccula Fabrizio G. , Pederzoli Riccardo , Grenzi Matteo , Bonza Maria Cristina , Luoni Laura , Candeo Alessia , Romano Armada Neli , Barbiroli Alberto , Valentini Gianluca , Schneider Thomas R. , Bassi Andrea , Bolognesi Martino , Nardini Marco , Costa Alex
Published: December 2019

Arabidopsis thaliana
glutamate receptor-like (GLR) channels are amino acid-gated ion channels involved in physiological processes including wound signaling, stomatal regulation, and pollen tube growth. Here, fluorescence microscopy and genetics were used to confirm the central role of GLR3.3 in the amino acid-elicited cytosolic Ca
2+
increase in
Arabidopsis
seedling roots. To elucidate the binding properties of the receptor, we biochemically reconstituted the GLR3.3 ligand-binding domain (LBD) and analyzed its selectivity profile; our binding experiments revealed the LBD preference for
l
-Glu but also for sulfur-containing amino acids. Furthermore, we solved the crystal structures of the GLR3.3 LBD in complex with 4 different amino acid ligands, providing a rationale for how the LBD binding site evolved to accommodate diverse amino acids, thus laying the grounds for rational mutagenesis. Last, we inspected the structures of LBDs from nonplant species and generated homology models for other GLR isoforms. Our results establish that GLR3.3 is a receptor endowed with a unique amino acid ligand profile and provide a structural framework for engineering this and other GLR isoforms to investigate their physiology.
Teaching varies with task complexity in wild chimpanzees
Authors: Musgrave Stephanie , Lonsdorf Elizabeth , Morgan David , Prestipino Madison , Bernstein-Kurtycz Laura , Mundry Roger , Sanz Crickette
Published: December 2019

Significance

Understanding social influences on how apes acquire tool behaviors can help us model the evolution of culture and technology in humans. Humans scaffold novice tool skills with diverse strategies, including the transfer of tools between individuals. Chimpanzees transfer tools, and this behavior meets criteria for teaching. However, it is unclear how task complexity relates to this form of helping. Here, we find differences between 2 wild chimpanzee populations in rate, probability, and types of tool transfer during termite gathering. Chimpanzees showed greater helping in the population where termite gathering is a more complex tool task. In wild chimpanzees, as in humans, regular and active provisioning of learning opportunities may be essential to the cultural transmission of complex skills.
Shaping the learning landscape in neural networks around wide flat minima
Authors: Baldassi Carlo , Pittorino Fabrizio , Zecchina Riccardo
Published: December 2019

Learning in deep neural networks takes place by minimizing a nonconvex high-dimensional loss function, typically by a stochastic gradient descent (SGD) strategy. The learning process is observed to be able to find good minimizers without getting stuck in local critical points and such minimizers are often satisfactory at avoiding overfitting. How these 2 features can be kept under control in nonlinear devices composed of millions of tunable connections is a profound and far-reaching open question. In this paper we study basic nonconvex 1- and 2-layer neural network models that learn random patterns and derive a number of basic geometrical and algorithmic features which suggest some answers. We first show that the error loss function presents few extremely wide flat minima (WFM) which coexist with narrower minima and critical points. We then show that the minimizers of the cross-entropy loss function overlap with the WFM of the error loss. We also show examples of learning devices for which WFM do not exist. From the algorithmic perspective we derive entropy-driven greedy and message-passing algorithms that focus their search on wide flat regions of minimizers. In the case of SGD and cross-entropy loss, we show that a slow reduction of the norm of the weights along the learning process also leads to WFM. We corroborate the results by a numerical study of the correlations between the volumes of the minimizers, their Hessian, and their generalization performance on real data.
Long-term effects of cultural filtering on megafauna species distributions across China
Authors: Teng Shuqing N. , Xu Chi , Teng Licheng , Svenning Jens-Christian
Published: December 2019

Significance

Human activities have played an important role in driving biodiversity loss throughout history, but the nature of these dynamics remains unclear. Importantly, the role of cultural evolution is mostly ignored, despite strong societal changes over time worldwide. Here, we show that megafauna range contractions across China in the last 2 millennia have been dominated by the spread of farming and agricultural intensification, often associated with expansion of the Han culture, with little or no direct importance of climate change. Our findings demonstrate that cultural evolution is important for shaping the assembly of contemporary communities from historical regional species pools and has long overshadowed climate change in driving even broadscale biodiversity patterns.
Abortive herpes simplex virus infection of nonneuronal cells results in quiescent viral genomes that can reactivate
Authors: Cohen Efrat M. , Avital Nir , Shamay Meir , Kobiler Oren
Published: December 2019

Significance

Abortive viral infections are defined as cells that have been infected with a virus but did not produce any progeny virus as a result of the infection. Recent single-cell studies have shown that abortive infection is observed frequently even during infection of susceptible and permissive cell types. Here, we recovered populations of susceptible and permissive cells that survived infection with herpes simplex virus at high multiplicity of infection. We found that these abortive cells maintain viral genomes in a quiescent state at least for 5 wk. These viral genomes can reactivate to produce new progeny viruses. These findings suggest that abortive HSV-1 infection leads to spontaneous latency-like infection in nonneuronal cells, challenging the current paradigm of herpesviruses latency.
The olfactory basis of orchid pollination by mosquitoes
Authors: Lahondère Chloé , Vinauger Clément , Okubo Ryo P. , Wolff Gabriella H. , Chan Jeremy K. , Akbari Omar S. , Riffell Jeffrey A.
Published: December 2019

Mosquitoes are important vectors of disease and require sources of carbohydrates for reproduction and survival. Unlike host-related behaviors of mosquitoes, comparatively less is understood about the mechanisms involved in nectar-feeding decisions, or how this sensory information is processed in the mosquito brain. Here we show thatAedesspp. mosquitoes, includingAedes aegypti, are effective pollinators of thePlatanthera obtusataorchid, and demonstrate this mutualism is mediated by the orchid’s scent and the balance of excitation and inhibition in the mosquito’s antennal lobe (AL). TheP. obtusataorchid emits an attractive, nonanal-rich scent, whereas relatedPlatantheraspecies—not visited by mosquitoes—emit scents dominated by lilac aldehyde. Calcium imaging experiments in the mosquito AL revealed that nonanal and lilac aldehyde each respectively activate the LC2 and AM2 glomerulus, and remarkably, the AM2 glomerulus is also sensitive to N,N-diethyl-meta-toluamide (DEET), a mosquito repellent. Lateral inhibition between these 2 glomeruli reflects the level of attraction to the orchid scents. Whereas the enriched nonanal scent ofP. obtusataactivates the LC2 and suppresses AM2, the high level of lilac aldehyde in the other orchid scents inverts this pattern of glomerular activity, and behavioral attraction is lost. These results demonstrate the ecological importance of mosquitoes beyond operating as disease vectors and open the door toward understanding the neural basis of mosquito nectar-seeking behaviors.
Lessons from equilibrium statistical physics regarding the assembly of protein complexes
Authors: Sartori Pablo , Leibler Stanislas
Published: December 2019

Significance

In order to carry out their functions, most proteins assemble into multicomponent complexes. In the process of assembly, complexes need to discriminate their specific components from a mixture of hundreds of different proteins present in the cell. To assess some of the implications of this requirement, we develop a minimal model of self-assembly based on equilibrium statistical physics. We argue that the need to assemble reliably imposes fundamental constraints on the characteristics of complexes, which we support with analysis of available structural and compositional data. Our work constitutes only a step toward future theory of protein complex assembly, which will have to incorporate also nonequilibrium and kinetic aspects of this fundamental and rich, yet theoretically neglected, problem.
Trans-endocytosis of intact IL-15Rα–IL-15 complex from presenting cells into NK cells favors signaling for proliferation
Authors: Anton Olga M. , Peterson Mary E. , Hollander Michael J. , Dorward David W. , Arora Gunjan , Traba Javier , Rajagopalan Sumati , Snapp Erik L. , Garcia K. Christopher , Waldmann Thomas A. , Long Eric O.
Published: December 2019

Significance

Interleukin 15 (IL-15) is essential for natural killer (NK) cell survival and proliferation. The IL-15 receptor consists of 3 subunits: the α chain and the β and common γ (γc) chains, which are shared with the IL-2 receptor. NK cells express the β-γcchains and are activated intransby cells presenting IL-15 bound to IL-15Rα, such as dendritic cells. We show here that the release of soluble IL-15Rα–IL-15 complex from presenting cells contributes to efficient signaling for NK cell survival, whereas uptake of the entire membrane-associated-IL-15Rα–IL-15 complex from presenting cells into NK cells contributes to proliferation. Thus, outcomes are dictated not only by signal strength, but also by location where IL-15trans-presentation occurs in NK cells.
A low climate threshold for south Greenland Ice Sheet demise during the Late Pleistocene
Authors: Irvalı Nil , Galaasen Eirik V. , Ninnemann Ulysses S. , Rosenthal Yair , Born Andreas , Kleiven Helga (Kikki) F.
Published: December 2019

Significance

Understanding how warmer climates affected Greenland in the past helps in determining how future warming will impact it. The Greenland Ice Sheet (GIS) has retreated during recent interglacials, suggesting a critical survival threshold within a few degrees of modern temperatures. Defining this temperature threshold requires records of the past climates responsible for GIS demise. Using microfossil temperature reconstructions, we show that the current interglacial is unusually moderate and that all 4 previous interglacials were warmer than present near Greenland. Both magnitude and duration of past warmth were important influences on the ice sheet. Notably, the critical temperature threshold for past GIS decay will likely be surpassed this century. The duration for which this threshold is exceeded will determine Greenland’s fate.
Contributions of nonhuman primate research to understanding the consequences of human brain injury during development
Authors: Cacucci Francesca , Vargha-Khadem Faraneh
Published: December 2019

In this introductory review we first present a theoretical framework as well as a clinical perspective regarding the effects of early brain injury on the development of cognitive and behavioral functions in humans. Next, we highlight the contributions that nonhuman primate research make toward identifying some of the variables that influence long-term cognitive outcome after developmental disease, or damage. We start our review by arguing that in contrast to adult-onset injury, developmental brain insults alter the ontogenetic pattern of brain organization and circuit specialization depending on the variables of age at injury, the focality of the lesion, and the potential for reorganization. We then introduce the 2 nonhuman primate studies in this section (Kiorpes on vision; Bachevalier on cognitive memory), and highlight the relevance of their findings to our understanding of developmental conditions or injuries in humans, with the ultimate goal of improving the health and development of the young.
Quantitative microscopy reveals dynamics and fate of clustered IRE1α
Authors: Belyy Vladislav , Tran Ngoc-Han , Walter Peter
Published: December 2019

Significance

The endoplasmic reticulum (ER) is the site for folding and maturation of secreted and membrane proteins. When the ER protein-folding machinery is overwhelmed, misfolded proteins trigger ER stress, which is frequently linked to human diseases, including cancer and neurodegeneration. Inositol-requiring enzyme 1 (IRE1) is an ER membrane-resident sensor that assembles into large clusters of previously unknown organization upon its activation by unfolded peptides. We demonstrate that IRE1 clusters are topologically complex dynamic structures that remain contiguous with the ER membrane throughout their lifetime. The majority of clustered IRE1 molecules are diffusionally trapped inside the clusters until IRE1 signaling attenuates, at which point they are released back into the ER through a pathway that is functionally distinct from cluster assembly.
A genetically defined disease model reveals that urothelial cells can initiate divergent bladder cancer phenotypes
Authors: Wang Liang , Smith Bryan A. , Balanis Nikolas G. , Tsai Brandon L. , Nguyen Kim , Cheng Michael W. , Obusan Matthew B. , Esedebe Favour N. , Patel Saahil J. , Zhang Hanwei , Clark Peter M. , Sisk Anthony E. , Said Jonathan W. , Huang Jiaoti , Graeber Thomas G. , Witte Owen N. , Chin Arnold I. , Park Jung Wook
Published: December 2019

Small cell carcinoma of the bladder (SCCB) is a rare and lethal phenotype of bladder cancer. The pathogenesis and molecular features are unknown. Here, we established a genetically engineered SCCB model and a cohort of patient SCCB and urothelial carcinoma samples to characterize molecular similarities and differences between bladder cancer phenotypes. We demonstrate that SCCB shares a urothelial origin with other bladder cancer phenotypes by showing that urothelial cells driven by a set of defined oncogenic factors give rise to a mixture of tumor phenotypes, including small cell carcinoma, urothelial carcinoma, and squamous cell carcinoma. Tumor-derived single-cell clones also give rise to both SCCB and urothelial carcinoma in xenografts. Despite this shared urothelial origin, clinical SCCB samples have a distinct transcriptional profile and a unique transcriptional regulatory network. Using the transcriptional profile from our cohort, we identified cell surface proteins (CSPs) associated with the SCCB phenotype. We found that the majority of SCCB samples have PD-L1 expression in both tumor cells and tumor-infiltrating lymphocytes, suggesting that immune checkpoint inhibitors could be a treatment option for SCCB. We further demonstrate that our genetically engineered tumor model is a representative tool for investigating CSPs in SCCB by showing that it shares a similar a CSP profile with clinical samples and expresses SCCB–up-regulated CSPs at both the mRNA and protein levels. Our findings reveal distinct molecular features of SCCB and provide a transcriptional dataset and a preclinical model for further investigating SCCB biology.
Complexity-based approach for El Niño magnitude forecasting before the spring predictability barrier
Authors: Meng Jun , Fan Jingfang , Ludescher Josef , Agarwal Ankit , Chen Xiaosong , Bunde Armin , Kurths Jürgen , Schellnhuber Hans Joachim
Published: December 2019

Significance

Although El Niño events characterized by anomalous episodic warmings of the eastern equatorial Pacific can trigger disasters in various parts of the globe, reliable forecasts of their magnitude are still limited to about 6 mo ahead. A significant extension of this prewarning time would be instrumental for mitigating some of the worst damages. Here we introduce an approach relying on information entropy, which achieves some doubling of the prewarning time. The approach is based on our finding that the entropy in one calendar year exhibits a strong correlation with the magnitude of an El Niño that starts in the following year and thus allows us to forecast the onset and the magnitude of an El Niño event 1 y in advance.
Multiscale porous elastomer substrates for multifunctional on-skin electronics with passive-cooling capabilities
Authors: Xu Yadong , Sun Bohan , Ling Yun , Fei Qihui , Chen Zanyu , Li Xiaopeng , Guo Peijun , Jeon Nari , Goswami Shivam , Liao Yixuan , Ding Shinghua , Yu Qingsong , Lin Jian , Huang Guoliang , Yan Zheng
Published: December 2019

Significance

Point-of-care thermal management (e.g., joule heating, passive cooling) shows promising applications in body temperature regulations, which can improve human comfort and reduce energy consumption. On-skin electronics with joule-heating elements have been reported. However, the research of making on-skin electronics with passive-cooling functionalities is still rare. By using multiscale porous polystyrene-block-poly(ethylene-ran-butylene)-block-polystyrene as supporting substrates, we have developed multifunctional on-skin electronics with outstanding passive-cooling capabilities, delivering around 6 °C cooling effects under a solar intensity of 840 W⋅m−2. Other desired properties, rooted in porous SEBS substrates, include high breathability and outstanding waterproofing. In addition, a variety of bioelectronic devices are made on porous SEBS substrates via spray printing of silver nanowires (Ag NWs). The enabled devices demonstrate high performance and are recyclable.
Processes underlying the laser photochromic effect in colloidal plasmonic nanoparticle aggregates*
Authors: Ershov A E , Gerasimov V S , Isaev I L , Gavrilyuk A P , Karpov S V
Published: December 2019

We have studied the dynamic and static processes occurring in disordered multiparticle colloidal Ag aggregates with natural structure and affecting their plasmonic absorption spectra under pico- and nanosecond pulsed laser radiations, as well as the physical origin responsible for these processes. We have shown that depending on the duration of the laser pulse, the mechanisms of laser modification of such aggregates can be associated both with changes in the resonant properties of the particles due to their heating and melting (picosecond irradiation mode) and with the particle shifts in the resonant domains of the aggregates (nanosecond pulses) which depend on the wavelength, intensity, and polarization of the radiation. These mechanisms result in formation of a narrow dip in the plasmonic absorption spectrum of the aggregates near the laser radiation wavelength and affect the shape and position of the dip. The effect of polydispersity of nanoparticle aggregates on laser photochromic reaction has been studied.
A simple tight-binding approach to topological superconductivity in monolayer MoS2
Authors: Simchi H
Published: December 2019

Monolayer molybdenum disulfide (MoS2) has a honeycomb crystal structure. Here, with considering the triangular sublattice of molybdenum atoms, a simple tight-binding Hamiltonian is introduced (derived) for studying the phase transition and topological superconductivity in MoS2 under uniaxial strain. It is shown that spin-singlet p + ip wave phase is a topological superconducting phase with nonzero Chern numbers. When the chemical potential is greater (smaller) than the spin–orbit coupling (SOC) strength, the Chern number is equal to four (two) and otherwise it is equal to zero. Also, the results show that, if the superconductivity energy gap is smaller than the SOC strength and the chemical potential is greater than the SOC strength, the zero energy Majorana states exist. Finally, we show that the topological superconducting phase is preserved under uniaxial strain.
Synthesis of novel microencapsulated phase change material with SnO2/CNTs shell for solar energy storage and photo-thermal conversion
Authors: Ma Xiaochun , Liu Han , Chen Chen , Liu Yanjun , Zhang Lin , Xu Bin , Xiao Fan
Published: December 2019

In this study, In-situ precipitation reaction was used to prepare paraffin@SnO2/CNTs composite phase change materials. The paraffin@SnO2/CNTs composites material were prepared by using paraffin as a phase change core material, and tin dioxide and carbon nanotubes as composite shell materials. The microstructure, chemical composition and crystal phase structure of the composites were analyzed by Scanning electron microscope (SEM), Fourier infrared spectrum (FT-IR) and X-ray diffraction (XRD). The thermal performance and thermal stability of phase change materials were determined by differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The microcapsule has a core–shell structure with a diameter of 2–5 μm. The encapsulation efficiency of the paraffin@SnO2/CNTs composite was calculated to be 42.94%. The slurry is formed by dispersing microcapsules in water, which not only greatly improves the specific heat capacity, thermal conductivity, visible light absorption, but also makes the effective receiving efficiency reach 91.79% at 40 °C, indicating that it is a promising heat transfer working slurry in the field of Direct Absorption Solar Collectors (DASC) system.
Correcting the effect of the detection angular on laser-induced chlorophyll fluorescence
Authors: Yang Jian , Du Lin , Gong Wei , Shi Shuo , Sun Jia , Chen Biwu
Published: December 2019

Chlorophyll fluorescence has been widely used to monitor vegetation growth status and quantitative remote sensing monitoring of vegetation biochemical content. Therefore, it is significant to accurately measure the fluorescence information. In this study, the variation in fluorescence intensity of vivo vegetation leaf with the change in detection angle on the basis of laser-induced fluorescence technology was discussed. Experimental results demonstrated that the relationship between the emission fluorescence intensity and detection angles could be explained by the cosine expression. Then, two-step fluorescence intensity correction method was proposed. Firstly, the fluorescence intensity was corrected based on the changing of cosine expression. Secondly, the fluorescence ratio calculated based on the corrected fluorescence intensity. Results demonstrated that the effect of detection angles on fluorescence signals can be efficiently eliminated compared to the traditional spectral ratio method. Findings of this study may be valuable in promoting the applications of laser-induced fluorescence in remote sensing to achieve accurate chlorophyll fluorescence information for quantitative monitoring of plant nutrient stress.