bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of CMIP6 DECK Experiments With CNRM‐CM6‐1
Authors: Voldoire A. , Saint‐Martin D. , Sénési S. , Decharme B. , Alias A. , Chevallier M. , Colin J. , Guérémy J.‐F. , Michou M. , Moine M.‐P. , Nabat P. , Roehrig R. , Salas y Mélia D. , Séférian R. , Valcke S. , Beau I. , Belamari S. , Berthet S. , Cassou C. , Cattiaux J. , Deshayes J. , Douville H. , Ethé C. , Franchistéguy L. , Geoffroy O. , Lévy C. , Madec G. , Meurdesoif Y. , Msadek R. , Ribes A. , Sanchez‐Gomez E. , Terray L. , Waldman R.
Published: June 2019

This paper describes the main characteristics of CNRM‐CM6‐1, the fully coupled atmosphere‐ocean general circulation model of sixth generation jointly developed by Centre National de Recherches Météorologiques (CNRM) and Cerfacs for the sixth phase of the Coupled Model Intercomparison Project 6 (CMIP6). The paper provides a description of each component of CNRM‐CM6‐1, including the coupling method and the new online output software. We emphasize where model's components have been updated with respect to the former model version, CNRM‐CM5.1. In particular, we highlight major improvements in the representation of atmospheric and land processes. A particular attention has also been devoted to mass and energy conservation in the simulated climate system to limit long‐term drifts. The climate simulated by CNRM‐CM6‐1 is then evaluated using CMIP6 historical and Diagnostic, Evaluation and Characterization of Klima (DECK) experiments in comparison with CMIP5 CNRM‐CM5.1 equivalent experiments. Overall, the mean surface biases are of similar magnitude but with different spatial patterns. Deep ocean biases are generally reduced, whereas sea ice is too thin in the Arctic. Although the simulated climate variability remains roughly consistent with CNRM‐CM5.1, its sensitivity to rising CO2 has increased: the equilibrium climate sensitivity is 4.9 K, which is now close to the upper bound of the range estimated from CMIP5 models.
Mid‐Holocene, Coral‐Based Sea Surface Temperatures in the Western Tropical Atlantic
Authors: Rodriguez Luis G. , Cohen Anne L. , Ramirez Wilson , Oppo Delia W. , Pourmand Ali , Edwards R. Lawrence , Alpert Alice E. , Mollica Nathaniel
Published: June 2019

The Holocene is considered a period of relative climatic stability, but significant proxy data‐model discrepancies exist that preclude consensus regarding the postglacial global temperature trajectory. In particular, a mid‐Holocene Climatic Optimum, ~9,000 to ~5,000 years BP, is evident in Northern Hemisphere marine sediment records, but its absence from model simulations raises key questions about the ability of the models to accurately simulate climate and seasonal biases that may be present in the proxy records. Here we present new mid‐Holocene sea surface temperature (SST) data from the western tropical Atlantic, where twentieth‐century temperature variability and amplitude of warming track the twentieth‐century global ocean. Using a new coral thermometer Sr‐U, we first developed a temporal Sr‐U SST calibration from three modern Atlantic corals and validated the calibration against Sr‐U time series from a fourth modern coral. Two fossil corals from the Enriquillo Valley, Dominican Republic, were screened for diagenesis, U‐series dated to 5,199 ± 26 and 6,427 ± 81 years BP, respectively, and analyzed for Sr/Ca and U/Ca, generating two annually resolved Sr‐U SST records, 27 and 17 years long, respectively. Average SSTs from both corals were significantly cooler than in early instrumental (1870–1920) and late instrumental (1965–2016) periods at this site, by ~0.5 and ~0.75 °C, respectively, a result inconsistent with the extended mid‐Holocene warm period inferred from sediment records. A more complete sampling of Atlantic Holocene corals can resolve this issue with confidence and address questions related to multidecadal and longer‐term variability in Holocene Atlantic climate.
Multifunctional reduced graphene oxide-CVD graphene core–shell fibers
Authors: Choi Yong Seok , Yeo Chang-su , Kim Sang Jin , Lee Jin-Young , Kim Youngsoo , Cho Kang Rae , Ju Sanghyun , Hong Byung Hee , Park Sang Yoon
Published: June 2019

The graphene-based fiber structure with rGO cores and CVD graphene shells, showing an outstanding electrical conductivity and electrochemical performance with enhanced mechanical stability and durability.
Theoretical study on the charge transport and metallic conducting properties in organic complexes
Authors: Shi Ya-Rui , Liu Yu-Fang
Published: June 2019

The charge transfer process between substrate molecular and dopant always appears in doped organic semiconductors, so that molecular doping is a common method to improve the electrical properties by combining appropriate complexes of electron acceptor and donor molecules.
Descriptor–property relationships in heterogeneous catalysis: exploiting synergies between statistics and fundamental kinetic modelling
Authors: Pirro Laura , Mendes Pedro S. F. , Paret Stijn , Vandegehuchte Bart D. , Marin Guy B. , Thybaut Joris W.
Published: June 2019

Combined kinetic and statistical approach to shed light on the link between kinetically-relevant descriptors and easily tuneable catalyst properties.
Spectroscopic speciation of aqueous Am(iii)–oxalate complexes
Authors: Kim H.-K. , Jeong K. , Cho H.-R. , Jung E. C. , Kwak K. , Cha W.
Published: June 2019

Speciation, thermodynamic stability, and structural information of aqueous oxalato-Am(iii) complexes were resolved by combinatorial use of UV-Vis-LWCC, TRLFS, and DFT calculations.
A simple route to synthesize esterified lignin derivatives
Authors: Liu Li-Yang , Hua Qi , Renneckar Scott
Published: June 2019

Developed a simple esterification route to obtain lignin derivatives with tunable Tg's and low E-factor reactions.
Water-soluble pH neutral triazatruxene-based small molecules as hole injection materials for solution-processable organic light-emitting diodes
Authors: Chen Yonghong , Wu Xiaofu , Liu Yang , Chen Liang , Li Hua , Wang Weijie , Wang Shumeng , Tian Hongkun , Tong Hui , Wang Lixiang
Published: June 2019

Water-soluble and pH neutral triazatruxene-based small molecules have been used as hole injection materials in solution-processable organic light-emitting diodes, achieving even better performance compared with PEDOT:PSS.
Color tunable upconversion luminescent perovskite fluoride with long-/short-lived emissions toward multiple anti-counterfeiting
Authors: Han Xinxin , Song Enhai , Zhou Bo , Zhang Qinyuan
Published: June 2019

A color-tunable UC luminescent perovskite fluoride KCdF3:Yb3+,Mn2+,Ln3+with both long and short emission lifetimes has been demonstrated, showing high potential for multiple anti-counterfeiting with high throughput authentication rate.
Improving the Otsu method for MRA image vessel extraction via resampling and ensemble learning
Authors: Chang Yuchou
Published: June 2019

Accurate extraction of vessels plays an important role in assisting diagnosis, treatment, and surgical planning. The Otsu method has been used for extracting vessels in medical images. However, blood vessels in magnetic resonance angiography (MRA) image are considered as a sparse distribution. Pixels on vessels in MRA image are considered as an imbalanced data in classification of vessels and non‐vessel tissues. To extract vessels accurately, a novel method using resampling technique and ensemble learning is proposed for solving the imbalanced classification problem. Each pixel is sampled multiple times through multiple local patches within the image. Then, vessel or non‐vessel tissue is determined by the ensemble voting mechanism via a p‐tile algorithm. Experimental results show that the proposed method is able to outperform the traditional Otsu method by extracting vessels in MRA images more accurately.
Detection of trace heavy metals using atmospheric pressure glow discharge by optical emission spectra
Authors: Li Xiao , Yang De‐Zheng , Yuan Hao , Liang Jian‐Ping , Xu Tao , Zhao Zi‐Lu , Zhou Xiong‐Feng , Zhang Li , Wang Wen‐Chun
Published: June 2019

In this Letter, atmospheric pressure glow discharge based on a small discharge gap is excited by sine AC voltage in air on purpose of detecting trace heavy metal elements in solid samples, which makes the detection limits of trace heavy metal elements reach tens μg/kg. The waveforms of voltage and discharge current, discharge images, plasma gas temperature, and optical emission spectra are obtained to discuss the feasibility of atmospheric pressure glow discharge on detection of trace heavy metals. The formation mechanism of optical emission spectra and the strong emission intensity of heavy metal elements show that energetic electrons and excited metal atoms are easily generated by atmospheric pressure glow discharge. The effects of applied voltage and discharge gap on atmospheric pressure glow discharge are discussed to acquire the optimal experimental conditions. And a smaller discharge gap and applied voltage can restrain the transition from glow discharge to arc discharge. Besides, the limits of detections of Cu and Cd are about 0.0241 and 0.0318 μg/g, respectively, by using atmospheric pressure glow discharge with an applied voltage of 3.8 kV, discharge gap of 3.5 mm, and driving frequency of 10 kHz.
QoS mechanisms for MAC protocols in wireless sensor networks: a survey
Authors: Kaur Tarunpreet , Kumar Dilip
Published: June 2019

With the rapid development in ubiquitous smart sensors, wireless sensor networks (WSNs) have started to evolve into numerous applications including healthcare, military, agriculture, transportation, industry, internet of things (IOT), and smart cities. However, satisfying quality of service (QoS) requirements of various application domains remains a challenging issue due to the heterogeneous traffic flows, dynamic network conditions, and resource‐constrained nature of sensor nodes. In this regard, application‐specific QoS provisioning techniques have received considerable research attention at the medium access control (MAC) layer. This study presents a systematic review of the QoS mechanisms employed at the MAC layer in WSN and also highlights their open research issues. In addition, the survey presents a comparative analysis of various QoS‐aware MAC protocols with emphasis on their strengths and limitations. Finally, this survey discusses various potential directions for future research in the field of QoS provisioning at the MAC layer.
Mode selection map‐based vertical handover in D2D enabled 5G networks
Authors: Morattab Armin , Dziong Zbigniew , Sohraby Kazem
Published: June 2019

One of the promising features of 5G networks is device‐to‐device (D2D) communication that enables direct transmission between D2D user equipments (UEs). Besides the traditional cellular transmission mode, UEs can select between the reuse and dedicated modes. In this study the authors consider a scenario where a communicating D2D pair and a cellular UE that communicates with an evolved Node‐B can use the same spectrum. It is assumed that the cellular UE can move in the network while the D2D UEs are static. The movement of the cellular UE can affect the quality of the communication between the D2D pair. Therefore, the transmission mode between the D2D UEs might change to keep the best quality. In this study the authors propose a new mobility management and vertical handover algorithm that handles the transmission mode transition during the D2D connection to maximise the overall throughput. The algorithm uses distance from the border and critical direction set as mobility variables that are analytically determined. These variables are calculated using a mode selection map that is derived analytically when pathloss and fading models are used. Finally, in order to analyse the performance of the proposed handover algorithm, the authors analytically calculate handover rate and sojourn time metrics.
Random sequence encoded waveforms for covert asynchronous communications and radar
Authors: Kellett Daniel , Garmatyuk Dmitriy , Mudaliar Saba , Condict Nahlah , Qualls Isaiah
Published: June 2019

This work presents a random sequence coding scheme for joint radar‐communication waveforms in scenarios that require a high degree of data covertness. The authors’ goal is to embed the resultant signals in a parameter space of the probability density function of statistical distribution, leading to the samples of the underlying random process being used for waveform construction. The simulated performance shows that an unfriendly interceptor will be penalised significantly compared to an authorised receiver when the SNR is greater than −20 dB. The proposed method is well‐suited for asynchronous, ad‐hoc communications with a high low probability of intercept/low probability of detection potential. The authors also propose an algorithm to improve the performance of thus created communication signals when they are used simultaneously for radar. Experimental results for both communications and radar are also presented.
Computationally efficient TDOA and FDOA estimation algorithm in passive emitter localisation
Authors: Liu Zhixin , Wang Rui , Zhao Yongjun
Published: June 2019

This study addresses the joint time difference of arrival (TDOA) and frequency difference of arrival (FDOA) estimation problem in passive emitter localisation, involving range migration during the observation time. A computational efficient estimation algorithm based on scaled Fourier transformation is proposed. This method can effectively remove the RM and accomplish the parameter estimation. Cross‐terms suppression ability of the proposed method is also analysed and its characteristic indicates the applicability in the scenario of multi‐targets. The whole estimation step can be fast implemented by complex multiplications, fast Fourier transformation (FFT) and inverse FFT without any searching process. Compared with the ideal maximum likelihood estimator via extensive numerical experiments, the proposed method can achieve comparable estimation performance and have gained more than ten thousand times reduction in the computational cost, which helps practical application.
XLPE – layered silicate nanocomposites for high voltage insulation applications: dielectric characteristics, treeing behaviour and mechanical properties
Authors: Kavitha D. , Balachandran Meera
Published: June 2019

The study presented here investigates the performance of nano‐reinforced cross‐linked polyethylene (XLPE) for high‐voltage insulation applications with particular focus on dielectric characteristics, treeing behaviour and mechanical properties. The nanocomposites with varying content of organo‐modified layered silicate (nanoclay) were prepared by melt mixing of polyethylene, cross‐linking agent and nanoclay. X‐ray diffraction and atomic force microscopy studies showed that layered silicates were uniformly dispersed with exfoliation in XLPE matrix up to 5 wt% nanoclay content with formation of intercalated structures with slight agglomeration at higher nanofiller content. The dielectric loss, relative permittivity and dielectric strength of the nanocomposites increased with increasing nanoclay content, which was attributed to the inherent properties of XLPE and nanoclay, nanofiller dispersion and interfacial polarisation. The effect of frequency on the dielectric properties was also investigated. Incorporation of nanoclay in XLPE altered the electric field stress distribution in the material and consequently retarded water tree growth. The electric field distribution and the probability of water tree growth were studied by finite element method. Additionally, mechanical properties of the nanocomposite viz. tensile strength and modulus were also enhanced. The changes in the properties were correlated to the morphology of the nanocomposites, as well as polymer filler interactions.
Grid‐impedance estimation in high‐frequency range with a single signal injection using time–frequency distribution
Authors: AlyanNezhadi Mohammad Mahdi , Hassanpour Hamid , Zare Firuz
Published: June 2019

Grid impedance is an important parameter in most power system applications such as power quality analysis of smart grids. In this study, a new time–frequency distribution is employed for grid‐impedance estimation in high‐frequency range using a single rectangular pulse injection. There is no compatibility level for harmonics within the frequency range of 2–150 kHz which is the most important issue in the international standardisation committee. Compatibility level is defined based on harmonic emission and immunity levels of grid‐connected equipment. Therefore, knowledge of grid‐impedance characteristics over the frequency range of 2–150 kHz is very important to estimate the level of distortion caused by grid‐connected equipment and defines future regulations and standards. For impedance estimation, a pulse must be injected to the grid, then the current through and voltage at a point of common coupling are measured. The measurement duration must be long enough to consider the transient state. The most appropriate shortest measurement duration is selected from the time–frequency plane using Wiener entropy. Test and simulation results validate the accuracy of the proposed method for grid‐impedance estimation in high‐frequency range.
Performance of superconducting generators with different topologies under fault conditions
Authors: Guan Yang , Vedreño‐Santos Francisco , Azar Ziad , Thomas Arwyn S. , Li Guang‐Jin , Odavic Milijana , Zhu Zi‐Qiang
Published: June 2019

This paper compares the short‐circuit performance of superconducting (SC) generators with three different topologies, i.e. iron‐cored stator and rotor, iron‐cored stator and air‐cored rotor, and air‐cored stator and rotor. The analysis is based on three‐phase short‐circuit fault, and finite element analysis is used for simulation. Following the introduction of specifications of generators, the short‐circuit performances of different topologies are analysed and compared, with the field winding excited by voltage and current excitation sources, respectively. It shows that the short‐circuit performance can be improved by limiting the field current.
Transverse flux machines as an alternative to radial flux machines in an in‐wheel motor
Authors: Martinez‐Ocaña Iago , Baker Nick J. , Mecrow Barrie C. , Hilton Chris , Brockway Simon
Published: June 2019

This paper considers the use of transverse flux machines (TFMs) as an alternative to radial flux machines (RFMs) in an in‐wheel application for an electric vehicle. The base motor is an existing outer rotor surface‐mounted permanent magnet machine with fractional slot concentrated windings and liquid cooling. Two topologies of TFM are compared against this base machine. The first topology is a mutual flux path (TFM‐MP), while the second is a claw pole machine (TFM‐CP). First, the proposed TFM topologies are studied using FEA to understand the torque capability of both topologies. Second, a comparison between two different pole numbers of each topology is compared with the performance of the benchmarking machine (BMM). The machines will be compared in terms of torque density, losses, efficiency, and power factor (PF). Finally, it is presented as a comparison on the torque capabilities when constraining the magnet mass. It is shown that the TFMs selected can deliver higher torques than the base motor during continuous operation, but have failed to deliver the required overload torque. Furthermore, low PF and low efficiency make these machines unsuitable for the application of this in‐wheel traction motor.
Iron-rich object closely orbits a white dwarf
Authors: Berkowitz Rachel
Published: June 2019

The newly discovered object could be the core of a planet that survived the transition of its host star into a red giant.
Physical and mathematical approaches yield insights into how cancer develops and spreads
Authors: Feder Toni
Published: June 2019

Whether cancer cells survive, grow, or remain dormant depends in part on mechanical forces and other physical phenomena.
2
H/
1
H variation in microbial lipids is controlled by NADPH metabolism
Authors: Wijker Reto S. , Sessions Alex L. , Fuhrer Tobias , Phan Michelle
Published: June 2019

Significance

The deuterium/protium (
2
H/
1
H) ratio of microbial lipids varies substantially and appears to be correlated with the mode of metabolism in the host organism, with lipids from chemoautotrophs and photoautotrophs
2
H-depleted and heterotrophs in many cases
2
H-enriched. Such patterns suggest that the H-isotope ratios of lipids could be used to infer the metabolism of environmental organisms, with applications ranging from Earth history to global carbon cycling and ecology. Here, we learn to understand this information by using metabolic flux analysis. We show that the full range of lipid
2
H/
1
H ratios from a diverse set of aerobic heterotrophs can be quantitatively explained by fluxes through various NADP
+
-reducing reactions due to differences in their kinetic isotope effects.
Plant-derived coumarins shape the composition of an
Arabidopsis
synthetic root microbiome
Authors: Voges Mathias J. E. E. E. , Bai Yang , Schulze-Lefert Paul , Sattely Elizabeth S.
Published: June 2019

Significance

The root microbiome composition is largely determined by the soil inoculum, with a distinct contribution from the host. The molecular mechanisms with which the host influences its rhizobiome are only beginning to be discovered. Using a hydroponics-based synthetic community approach, we probe how root-exuded specialized metabolites sculpt the root microbiome. We uncover a role for coumarins in structuring the rhizobiome, particularly by limiting the growth of a
Pseudomonas
strain, for which we propose a mechanism of action involving reactive oxygen species. Our findings support the possibility that root-exuded coumarins form a part of the plant’s adaptive response to iron deficiency that goes beyond iron mobilization to modulate the rhizobiome, and highlight avenues toward engineering the rhizosphere for plant health.
Magnetic field-induced intermediate quantum spin liquid with a spinon Fermi surface
Authors: Patel Niravkumar D. , Trivedi Nandini
Published: June 2019

Significance

In a quantum spin liquid, the spins remain disordered down to zero temperature, and yet, it displays topological order that is stable against local perturbations. The Kitaev model with anisotropic interactions on the bonds of a honeycomb lattice is a paradigmatic model for a quantum spin liquid. We explore the effects of a magnetic field and discover an intermediate gapless spin liquid sandwiched between the known gapped Kitaev spin liquid and a polarized phase. We show that the gapless spin liquid harbors fractionalized neutral fermionic excitations, dubbed spinons, that remarkably form a Fermi surface in a charge insulator.
ArabidopsisABCG28 is required for the apical accumulation of reactive oxygen species in growing pollen tubes
Authors: Do Thanh Ha Thi , Choi Hyunju , Palmgren Michael , Martinoia Enrico , Hwang Jae-Ung , Lee Youngsook
Published: June 2019

Significance

Reactive oxygen species (ROS) are observed at the growing site of directional cell growth in many organisms, including the tip-growing pollen tubes. This work identifies an ABC transporter, AtABCG28, as a critical factor for ROS accumulation at the tip of the growingArabidopsis thalianapollen tube. This function of AtABCG28 is due to its involvement in accumulating secretory vesicles containing polyamines, precursors of ROS, to the growing tip. Thus, this study provides a mechanism underlying the spatial organization of ROS in a single cell, which is mediated by a transporter.
LSD1 destabilizes FBXW7 and abrogates FBXW7 functions independent of its demethylase activity
Authors: Lan Huiyin , Tan Mingjia , Zhang Qiang , Yang Fei , Wang Siyuan , Li Hua , Xiong Xiufang , Sun Yi
Published: June 2019

Significance

FBXW7 is a typical tumor suppressor by targeting many oncoproteins for ubiquitylation and degradation, whereas LSD1 has oncogenic activity. Whether and how FBXW7 and LSD1 interact, with what biological consequence, are unknown. Here, we report that LSD1 is a pseudosubstrate of FBXW7. Upon binding with FBXW7, LSD1, instead of being degraded, disrupts FBXW7 dimerization and promotes FBXW7 self-ubiquitylation and degradation via proteasome and lysosomal pathways in a manner independent of its demethylase activity. As such, LSD1 abrogates biological functions of FBXW7 in growth suppression, nonhomologous end-joining repair, and radioprotection. Our study reveals a novel oncogenic mechanism of LSD1 by targeting FBXW7 and provides a sound strategy to reactivate FBXW7 by PROTAC-based LSD1 degradation in human cancers harboring wild-type FBXW7 with overexpressed LSD1.
A major role for noncoding regulatory mutations in the evolution of enzyme activity
Authors: Loehlin David W. , Ames Jesse R. , Vaccaro Kathy , Carroll Sean B.
Published: June 2019

The quantitative evolution of protein activity is a common phenomenon, yet we know little about any general mechanistic tendencies that underlie it. For example, an increase (or decrease) in enzyme activity may evolve from changes in protein sequence that alter specific activity, or from changes in gene expression that alter the amount of protein produced. The latter in turn could arise via mutations that affect gene transcription, posttranscriptional processes, or copy number. Here, to determine the types of genetic changes underlying the quantitative evolution of protein activity, we dissected the basis of ecologically relevant differences in
Alcohol dehydrogenase
(
Adh
) enzyme activity between and within several
Drosophila
species. By using recombinant
Adh
transgenes to map the functional divergence of ADH enzyme activity in vivo, we find that amino acid substitutions explain only a minority (0 to 25%) of between- and within-species differences in enzyme activity. Instead, noncoding substitutions that occur across many parts of the gene (enhancer, promoter, and 5′ and 3′ untranslated regions) account for the majority of activity differences. Surprisingly, one substitution in a transcriptional Initiator element has occurred in parallel in two species, indicating that core promoters can be an important natural source of the tuning of gene activity. Furthermore, we show that both regulatory and coding substitutions contribute to fitness (resistance to ethanol toxicity). Although qualitative changes in protein specificity necessarily derive from coding mutations, these results suggest that regulatory mutations may be the primary source of quantitative changes in protein activity, a possibility overlooked in most analyses of protein evolution.
TOX and TOX2 transcription factors cooperate with NR4A transcription factors to impose CD8
+
T cell exhaustion
Authors: Seo Hyungseok , Chen Joyce , González-Avalos Edahí , Samaniego-Castruita Daniela , Das Arundhoti , Wang Yueqiang H. , López-Moyado Isaac F. , Georges Romain O. , Zhang Wade , Onodera Atsushi , Wu Cheng-Jang , Lu Li-Fan , Hogan Patrick G. , Bhandoola Avinash , Rao Anjana
Published: June 2019

T cells expressing chimeric antigen receptors (CAR T cells) have shown impressive therapeutic efficacy against leukemias and lymphomas. However, they have not been as effective against solid tumors because they become hyporesponsive (“exhausted” or “dysfunctional”) within the tumor microenvironment, with decreased cytokine production and increased expression of several inhibitory surface receptors. Here we define a transcriptional network that mediates CD8
+
T cell exhaustion. We show that the high-mobility group (HMG)-box transcription factors TOX and TOX2, as well as members of the NR4A family of nuclear receptors, are targets of the calcium/calcineurin-regulated transcription factor NFAT, even in the absence of its partner AP-1 (FOS-JUN). Using a previously established CAR T cell model, we show that TOX and TOX2 are highly induced in CD8
+
CAR
+
PD-1
high
TIM3
high
(“exhausted”) tumor-infiltrating lymphocytes (CAR TILs), and CAR TILs deficient in both TOX and TOX2 (
Tox
DKO) are more effective than wild-type (WT), TOX-deficient, or TOX2-deficient CAR TILs in suppressing tumor growth and prolonging survival of tumor-bearing mice. Like NR4A-deficient CAR TILs,
Tox
DKO CAR TILs show increased cytokine expression, decreased expression of inhibitory receptors, and increased accessibility of regions enriched for motifs that bind activation-associated nuclear factor κB (NFκB) and basic region-leucine zipper (bZIP) transcription factors. These data indicate that
Tox
and
Nr4a
transcription factors are critical for the transcriptional program of CD8
+
T cell exhaustion downstream of NFAT. We provide evidence for positive regulation of NR4A by TOX and of TOX by NR4A, and suggest that disruption of TOX and NR4A expression or activity could be promising strategies for cancer immunotherapy.
Criminal Incarceration, Statutory Bans on Food Assistance, and Food Security in Extremely Vulnerable Households: Findings from a Partnership with the North Texas Food Bank
Authors: McDonough Ian K. , Millimet Daniel L.
Published: June 2019

Leveraging a unique partnership with the North Texas Food Bank, we are able to collect original survey data from food pantry clients in North Texas to investigate a question that has received little attention due to a lack of data. Specifically, we assess the relationship between criminal incarceration and food security. Our analysis suggests minimal impact of incarceration, broadly defined, on household‐level food security. However, differentiating between drug‐ and non‐drug‐related incarceration, our analysis suggests a positive causal effect of drug‐related incarceration on food security, particularly among U.S. born households. This is consistent with an important role being played by the Supplemental Nutrition Assistance Program (SNAP) since many states ban participation by former drug offenders. To this end, we document a positive causal effect of incarceration on SNAP participation only among non‐drug related offenders. The results call into question the efficacy of statutory bans on program participation for those reintegrating into society.
Responses of community structure and diversity to nitrogen deposition and rainfall addition in contrasting steppes are ecosystem-dependent and dwarfed by year-to-year community dynamics
Authors: Yang Xuejun , Huang Zhenying , Dong Ming , Ye Xuehua , Liu Guofang , Hu Dandan , Tuvshintogtokh Indree , Tumenjargal Tsogtsaikhan , Cornelissen J Hans C
Published: June 2019

Background and Aims

Long-term studies to disentangle the multiple, simultaneous effects of global change on community dynamics are a high research priority to forecast future distribution of diversity. Seldom are such multiple effects of global change studied across different ecosystems.

Methods

Here we manipulated nitrogen deposition and rainfall at levels realistic for future environmental scenarios in three contrasting steppe types in Mongolia and followed community dynamics for 7 years.

Key Results

Redundancy analyses showed that community composition varied significantly among years. Rainfall and nitrogen manipulations did have some significant effects, but these effects were dependent on the type of response and varied between ecosystems. Community compositions of desert and meadow steppes, but not that of typical steppe, responded significantly to rainfall addition. Only community composition of meadow steppe responded significantly to nitrogen deposition. Species richness in desert steppe responded significantly to rainfall addition, but the other two steppes did not. Typical steppe showed significant negative response of species richness to nitrogen deposition, but the other two steppes did not. There were significant interactions between year and nitrogen deposition in desert steppe and between year and rainfall addition in typical steppe, suggesting that the effect of the treatments depends on the particular year considered.

Conclusions

Our multi-year experiment thus suggests that responses of community structure and diversity to global change drivers are ecosystem-dependent and that their responses to experimental treatments are dwarfed by the year-to-year community dynamics. Therefore, our results point to the importance of taking annual environmental variability into account for understanding and predicting the specific responses of different ecosystems to multiple global change drivers.
The Potential Role of Corticosteroid Prophylaxis for the Prevention of Microscopic Fat Embolism Syndrome in Gluteal Augmentations
Authors: Safran Tyler , Abi-Rafeh Jad , Alhalabi Becher , Davison Peter G
Published: June 2019

Background

Microscopic fat embolism syndrome (micro-FES) has been recently identified as a potentially fatal complication following gluteal augmentation utilizing autologous fat grafts; safety recommendations advocating for subcutaneous lipo-injections may be insufficient for its prevention.

Objectives

The authors of this systematic review evaluated the potential role of corticosteroid prophylaxis for the prevention of micro-FES in gluteal augmentation procedures.

Methods

The authors performed a systematic search employing the National Library of Medicine (PubMed), Medline, and Embase databases. Search terms were those pertaining to studies reporting the efficacy of prophylactic corticosteroid administration on micro-FES incidence in a high-risk surrogate population.

Results

Thirteen articles met the inclusion criteria for review, comprising 2 studies reporting on the efficacy of a single intravenous (IV) corticosteroid dose for the prophylaxis of micro-FES, 9 studies reporting on multiple prophylactic IV doses, and 2 additional studies reporting on the efficacy of inhaled corticosteroids in this context. All studies were identified from the orthopedic literature given that none were available directly from within plastic surgery. The prophylactic efficacy of multiple IV doses of methylprednisolone, or a single larger dose, was established, whereas the efficacy of inhaled corticosteroids remains elusive.

Conclusions

A single perioperative IV dose of methylprednisolone may be most appropriate for utilization by plastic surgeons; the safety and implication of this therapy on wound healing and fat graft survival are discussed. Further studies directly evaluating the efficacy of corticosteroid prophylaxis in the gluteal augmentation population are indicated. Finally, recommendations pertaining to the prevention, timely recognition, and effective management of micro-FES are discussed.
DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing
Authors: Torkamaneh Davoud , Laroche Jérôme , Boyle Brian , Belzile François
Published: June 2019

Motivation

Identification of DNA sequence variations such as single nucleotide polymorphisms (SNPs) is a fundamental step toward genetic studies. Reduced-representation sequencing methods have been developed as alternatives to whole genome sequencing to reduce costs and enable the analysis of many more individual. Amongst these methods, restriction site associated sequencing (RSAS) methodologies have been widely used for rapid and cost-effective discovery of SNPs and for high-throughput genotyping in a wide range of species. Despite the extensive improvements of the RSAS methods in the last decade, the estimation of the number of reads (i.e. read depth) required per sample for an efficient and effective genotyping remains mostly based on trial and error.

Results

Herein we describe a bioinformatics tool, DepthFinder, designed to estimate the required read counts for RSAS methods. To illustrate its performance, we estimated required read counts in six different species (human, cattle, spruce budworm, salmon, barley and soybean) that cover a range of different biological (genome size, level of genome complexity, level of DNA methylation and ploidy) and technical (library preparation protocol and sequencing platform) factors. To assess the prediction accuracy of DepthFinder, we compared DepthFinder-derived results with independent datasets obtained from an RSAS experiment. This analysis yielded estimated accuracies of nearly 94%. Moreover, we present DepthFinder as a powerful tool to predict the most effective size selection interval in RSAS work. We conclude that DepthFinder constitutes an efficient, reliable and useful tool for a broad array of users in different research communities.

Availability and implementation

https://bitbucket.org/jerlar73/DepthFinder

Supplementary information

Supplementary data are available at Bioinformatics online.
Success of alignment-free oligonucleotide (k-mer) analysis confirms relative importance of genomes not genes in speciation and phylogeny
Authors: Forsdyke Donald R
Published: June 2019

The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many 21st century practitioners. A path from the 19th century recognition of the informational basis of heredity to the modern era can be discerned. Crick’s DNA ‘unpairing postulate’ predicted that recombinational pairing of homologous DNAs during meiosis would be mediated by short k-mers in the loops of stem-loop structures extruded from classical duplex helices. The complementary ‘kissing’ duplex loops – like tRNA anticodon–codon k-mer duplexes – would seed a more extensive pairing that would then extend until limited by lack of homology or other factors. Indeed, this became the principle behind alignment-based methods that assessed similarity by degree of DNA–DNA reassociation in vitro. These are now seen as less sensitive than alignment-free methods that are closely consistent, both theoretically and mechanistically, with chromosomal anti-recombination models for the initiation of divergence into new species. The analytical power of k-mer differences supports the theses that evolutionary advance sometimes serves the needs of nucleic acids (genomes) rather than proteins (genes), and that such differences can play a role in early speciation events.
Systematically characterize the clinical and biological significances of 1p19q genes in 1p/19q non-codeletion glioma
Authors: Chai Rui-Chao , Zhang Ke-Nan , Chang Yu-Zhou , Wu Fan , Liu Yu-Qing , Zhao Zheng , Wang Kuan-Yu , Chang Yuan-Hao , Jiang Tao , Wang Yong-Zhi
Published: June 2019

1p/19q codeletion, which leads to the abnormal expression of 1p19q genes in oligodendroglioma, is associated with chemosensitivity and favorable prognosis. Here, we aimed to explore the clinical implications of 1p19q gene expression in 1p/19q non-codel gliomas. We analyzed expression of 1p19q genes in 668 1p/19q non-codel gliomas obtained from The Cancer Genome Atlas (n = 447) and the Chinese Glioma Genome Atlas (n = 221) for training and validation, respectively. The expression of 1p19q genes was significantly correlated with the clinicopathological features and overall survival of 1p/19q non-codel gliomas. Then, we derived a risk signature of 25 selected 1p19q genes that not only had prognosis value in total 1p/19q non-codel gliomas but also had prognosis value in stratified gliomas. The prognosis value of the risk signature was superior than known clinicopathological features in 1p/19q non-codel gliomas and was also highly associated with the following features: loss of CDKN2A/B copy number in mutant-IDH-astrocytoma; telomerase reverse transcriptase (TERT) promoter mutation, combined chromosome 7 gain/chromosome 10 loss and epidermal growth factor receptor amplification in wild-type-IDH-astrocytoma; classical and mesenchymal subtypes in glioblastoma. Furthermore, genes enriched in the biological processes of cell division, extracellular matrix, angiogenesis significantly correlated to the signature risk score, and this is also supported by the immunohistochemistry and cell biology experiments. In conclusion, the expression profile of 1p19q genes is highly associated with the malignancy and prognosis of 1p/19q non-codel gliomas. A 25-1p19q-gene signature has powerfully predictive value for both malignant molecular pathological features and prognosis across distinct subgroups of 1p/19q non-codel gliomas.
Early Forebrain Neurons and Scaffold Fibers in Human Embryos
Authors: Qin Jingwen , Wang Meizhi , Zhao Tianyun , Xiao Xue , Li Xuejun , Yang Jieping , Yi Lisha , Goffinet Andre M , Qu Yibo , Zhou Libing
Published: June 2019

Neural progenitor proliferation, neuronal migration, areal organization, and pioneer axon wiring are critical events during early forebrain development, yet remain incompletely understood, especially in human. Here, we studied forebrain development in human embryos aged 5 to 8 postconceptional weeks (WPC5–8), stages that correspond to the neuroepithelium/early marginal zone (WPC5), telencephalic preplate (WPC6 & 7), and incipient cortical plate (WPC8). We show that early telencephalic neurons are formed at the neuroepithelial stage; the most precocious ones originate from local telencephalic neuroepithelium and possibly from the olfactory placode. At the preplate stage, forebrain organization is quite similar in human and mouse in terms of areal organization and of differentiation of Cajal-Retzius cells, pioneer neurons, and axons. Like in mice, axons from pioneer neurons in prethalamus, ventral telencephalon, and cortical preplate cross the diencephalon–telencephalon junction and the pallial–subpallial boundary, forming scaffolds that could guide thalamic and cortical axons at later stages. In accord with this model, at the early cortical plate stage, corticofugal axons run in ventral telencephalon in close contact with scaffold neurons, which express CELSR3 and FZD3, two molecules that regulates formation of similar scaffolds in mice.
How Do Labor Representatives Affect Incentive Orientation of Executive Compensation?
Authors: Dyballa Katharina , Kraft Kornelius
Published: June 2019

Contrary to previous literature we hypothesize that labor’s interest may well—like that of shareholders—aim at securing the long-run survival of the firm. Consequently, employee representatives on the supervisory board could well have an interest in increasing incentive-based compensation to avoid management’s excessive risk taking and short-run oriented decisions. We compile unique panel data on executive compensation over the periods 2006–2011 for 405 listed companies and use a Hausman–Taylor approach to estimate the effect of codetermination on the compensation design. Finally, codetermination has a significantly positive effect on performance-based components of compensation, which supports our hypothesis. (JEL codes: J52, L20, G32, M12, C33)
A First Unexplained Invasive Encapsulated Bacterial Infection in Young Adults Associated With High Mortality and Readmission Rates
Authors: Jackson Niall , Sutton Tommy , Bedford Luke , Ugrinovic Sanja , Kumararatne Dinakantha , Gkrania-Klotsas Effrossyni
Published: June 2019

We find that patients <40 years old with a first invasive encapsulated bacterial infection have a high likelihood of death or readmission within 23 months. It is imperative to highlight them for immunological screening and initiate prophylactic interventions and treatment.
Factors affecting detection probability, effective area surveyed, and species misidentification in grassland bird point counts
Authors: Rigby Elizabeth A , Johnson Douglas H
Published: June 2019

We simulated bird surveys using recorded bird songs to assess factors affecting detection probability in grassland bird point counts. We used mixed effects logistic regression models to estimate effects of those factors and to estimate and visualize the variation in the area around the observer where birds can be perceived (the perception area). We simulated surveys with 8,926 binary opportunities for detection in Minnesota grasslands in 2011 and 2012. Species, distance to the observer, wind speed and direction, observer, and density of vegetation all affected detection of recorded bird songs. Species had a strong effect; the size of the predicted perception area around the observer differed by an order of magnitude among species. Wind also had a strong effect on detection. As wind speed increased, probability of detection downwind of the observer was reduced and the perception area around the observer became smaller and more asymmetrical. The effective distance at which an observer is more likely to detect a bird than not detect it may differ among species and angles to the wind, even within the same survey. Eight of 10 species had low probability of misidentification (≤0.03), but Grasshopper Sparrow (Ammodramus savannarum) and LeConte’s Sparrow (Ammospiza leconteii) were frequently misidentified (probability = 0.09–0.24 among observers), contributing to a low rate of correct detection for those species. We recommend collecting point-count data within distance bands so that data can be analyzed based on the effective radius for each species and standardizing surveys across wind conditions to reduce variation in detection probability.
The Transition to School Among Deaf/Hard-of-Hearing Children: Teacher and Parent Perspectives
Authors: Zaidman-Zait Anat , Poon Brenda T , Curle Deirdre , Jamieson Janet R , Norman Nancy
Published: June 2019

Although entry into the school system is a major milestone in the lives of young d/Deaf or hard-of-hearing (DHH) children and their families, relatively little is known about parents’ and teachers’ experiences and perspectives of this important transition. The aims of this study were to describe parents’ concerns during their children’s transition from early intervention to school, to describe practices available for families of DHH children, and to explore parents’ and teachers’ perspectives regarding practices that support a smooth transition to school. Parents (N = 40) and teachers (N = 37) of the deaf and hard of hearing completed surveys examining their experiences and perspectives on DHH children’s transition to school. Among concerns expressed among parents was their child’s ability to participate successfully in an inclusive school setting, as well as the level of supports their child would receive. Teachers reported numerous policies and practices that supported the transition to school, emphasizing high-intensity practices often used to gather information about the child and set accommodations in place. Parent and teacher reports on facilitators for the transition are compared and contrasted. Recommendations for research and practice are provided.