bluuebunny/crossref_metadata_2025 huggingface dataset:
Northern Hemisphere Heat Extremes in a Warmer Climate: More Probable but Less Colocated With Blocking
Authors: Narinesingh V. , Booth J. F. , Ming Y.
Published: January 2023

This work uses reanalysis and NOAA Geophysical Fluid Dynamics Laboratory's Coupled Model Intercomparison Project 6 model, CM4, to investigate the colocation of heat extremes and atmospheric blocking in the current climate and an end of 21st century, extreme‐emissions projection. In the present day, the colocation of heat events and blocking is greatest for the strongest heat events. Block‐heat extreme colocation is found to be less prevalent over ocean than land, exhibiting regional variation throughout the Northern Hemisphere. Over North America, colocation is greatest near the northwestern and northeastern coasts, minimizing near the center; over Eurasia, colocation is most prevalent in northern regions. In an RCP 8.5 projection, the historical 90th percentile temperature decreases to 0–70th percentile, depending on the region. This is primarily driven by mean state warming. Blocking is found to decrease along with the colocation of blocking and heat extremes, suggesting that in some regions, the mechanisms driving heat extremes will change in future climates.
How Is Time Distributed in a River Meander Belt?
Authors: Ielpi A. , Viero D. P. , Lapôtre M. G. A. , Graham A. , Ghinassi M. , Finotello A.
Published: January 2023

River meandering controls the age of floodplains through its characteristic paces of growth and eventual cutoff of channel bends, forming oxbows. Hence, floodplain‐age distributions should reflect a river's characteristic size and migration rate. This hypothesis has been previously tested in numerical simulations, yet without systematic comparisons with natural systems. Here we analyze oxbow spacing and timescales of bend evolution and abandonment in natural and numerically simulated meander belts. In both cases, a saturated state is achieved whereby oxbows are spaced ∼1 meander radius apart. At saturation, the distribution of floodplain ages and probability of sediment‐storage time can be constrained from characteristic timescales of bend evolution and abandonment. Owing to the similar relationships between floodplain width and characteristic timescales in natural and simulated rivers, we postulate that this approach should apply to unconfined meandering rivers elsewhere—a hypothesis to be tested with independent geo‐ or dendrochronological data.
Determining the Timing of Driver Influences on 1.8–3.5 MeV Electron Flux at Geosynchronous Orbit Using ARMAX Methodology and Stepwise Regression
Authors: Simms L. E. , Engebretson M. J. , Reeves G. D.
Published: January 2023

Although lagged correlations have suggested influences of solar wind velocity (V) and number density (N), Bz, ultralow frequency (ULF) wave power, and substorms (as measured by the auroral electrojet (AE) index) on MeV electron flux at geosynchronous orbit over an impressive number of hours and days, a satellite's diurnal cycle can inflate correlations, associations between drivers may produce spurious effects, and correlations between all previous time steps may create an appearance of additive influence over many hours. Autoregressive‐moving average transfer function (ARMAX) multiple regressions incorporating previous hours simultaneously can eliminate cycles and assess the impact of parameters, at each hour, while others are controlled. ARMAX influences are an order of magnitude lower than correlations uncorrected for time behavior. Most influence occurs within a few hours, not the many hours suggested by correlation. A log transformation accounts for nonlinearities. Over all hours, solar wind velocity (V) and number density (N) show an initial negative impact, with longer term positive influences over the 9 (V) or 27 (N) hr. Bz is initially a positive influence, with a longer term (6 hr) negative effect. ULF waves impact flux in the first (positive) and second (negative) hour before the flux measurement, with further negative influences in the 12–24 hr before. AE (representing electron injection by substorms) shows only a short term (1 hr) positive influence. However, when only recovery and after‐recovery storm periods are considered (using stepwise regression), there are positive influences of ULF waves, AE, and V, with negative influences of N and Bz.
An Algorithm to Separate Ionospheric Turbulence Radar Echoes From Those of Meteor Trails in Large Data Sets
Authors: Ivarsen Magnus F. , St‐Maurice Jean‐Pierre , Hussey Glenn C. , Galeschuk Draven , Lozinsky Adam , Pitzel Brian , McWilliams Kathryn A.
Published: January 2023

Coherent scatter echoes from disintegrating meteors and from the unstable ionospheric E‐region can overlap considerably between 90 and 110 km altitudes. As the physical origin of plasma irregularities produced by meteor trails differs starkly from that of E‐region auroral irregularities, this has consequences for winds as well as electrodynamic studies, thereby introducing a need to distinguish between the two types of echoes. To that goal, we have developed a novel separation algorithm to automatically sort through arbitrarily large data sets in the region of overlap. This proves very useful when the 3D location of echoes is available. The algorithm uses a definition of crowding, or clustering, in both time and space and has been developed and tested with a comprehensive data set obtained from the recently built Canadian icebear 3D radar. We discuss the characteristics belonging to the two classes of echoes, and present statistical results about the location of each type of echo as a function of conditions. Our proposed algorithm can be applied to any coherent scatter echo data with high resolution 3D location information.
OntoCAT - a simpler way to access ontology resources
Authors: Adamusiak Tomasz , Burdett Tony , van der Velde K Joeri , Abeygunawardena Niran , Antonakaki Despoina , Parkinson Helen , Swertz Morris
Published: January 2023

OntoCAT is an open source package developed to simplify the task of querying heterogeneous ontology resources. It supports local ontologies in OBO and OWL format as well as public repositories NCBO BioPortal and EBI Ontology Lookup Service (OLS). It is available from "http://ontocat.sourceforge.net":http://ontocat.sourceforge.net
Detection of Nonlinear Effects in Gene Expression Pathways
Authors: Mayr Andreas , Clevert Djork-Arne , Hochreiter Sepp
Published: January 2023

One of the main topics in systems biology is to model genetic pathways. Genes of a pathway, which show linear dependencies of their expression values, are easy to identify to belong to the pathway. However, if feedback loops or signal cascades are present, gene expression values of pathway genes can be nonlinearly dependent on the expression values of other genes in the pathway. In this situation such genes are hard to detect as belonging to the pathway because nonlinearity and noise must be distinguished.We propose an algorithm to infer nonlinear network elements in pathways from microarray data. Our model assumes, that gene expression values, belonging to one pathway, are mainly driven by one single latent factor. We expect that there are two groups of genes in a pathway: genes belonging to the first group are linearly dependent on the hidden factor, genes from the other group show a nonlinear dependence from the latent variable. The goal is to identify the kind of dependence from the hidden factor.Our algorithm for detecting nonlinear effects is an extension of linear Gaussian factor analysis. Nonlinearities are modelled by the square of the latent variable weighted by specific coefficients. We derived a novel model selection method for this generalization of factor analysis. To avoid the interpretation of noise as nonlinearity, we determine p-values that measure the probability of a linear gene being detected by chance as nonlinear. We apply our algorithm to microarray data of breast cancer samples, where we identified nonlinear dependencies of gene expression values in the p53 pathway.
The true story behind the annotation of a pathway
Authors: Dall’Olio Giovanni Marco , Laayouni Hafid
Published: January 2023

On 2010 we worked on the annotation of the N-Glycosylation pathway in the Reactome database. During this process, we found some unclear points and errors in other databases, and we reported and helped fix them. After we finished, we realized that the work of reporting errors to a database is basically not acknowledged by the scientific community: this is unfortunate because if only this process would be a bit more recognized and transparent, we could have better data in the databases and a more active community. Moreover, the fact that many databases tend to keep error reporting private creates great issues to the reproducibility of a work.Another way to look at this talk is: if you dedicate 6 months of your PhD thesis to annotate carefully a set of genes, in this case a pathway I have been studying, how many errors do you expect to find in other databases, or what should you be careful at?
Comments and Suggestions for Improvement of the Archon Genomics X PRIZE Validation Protocol
Authors: Zaranek Alexander Wait , Clegg Tom , Vandewege Ward , Thakuria Joseph
Published: January 2023

This document is a comment on the X PRIZE validation protocol written by Kedes et al. (2011). We propose several modifications which we think will improve the fairness and transparency of the contest while keeping the cost of the validation process under control.
Difference in response reliability predicted by STRFs in the cochlear nuclei of barn owls
Authors: Steinberg Louisa , Pena Jose
Published: January 2023

The brainstem auditory pathway is obligatory for all aural information. Brainstem auditory neurons must encode the level and timing of sounds, as well as their time-dependent spectral properties, the fine structure and envelope, which are essential for sound discrimination. This study focused on envelope coding in the two cochlear nuclei of the barn owl, nucleus angularis (NA) and nucleus magnocellularis (NM). NA and NM receive input from bifurcating auditory nerve fibers and initiate processing pathways specialized in encoding interaural time (ITD) and level (ILD) differences, respectively. We found that NA neurons, though unable to accurately encode stimulus phase, lock more strongly to the stimulus envelope than NM units. The spectrotemporal receptive fields (STRFs) of NA neurons exhibit a pre-excitatory suppressive field. Using multilinear regression analysis and computational modeling, we show that this feature of STRFs can account for enhanced across-trial response reliability, by locking spikes to the stimulus envelope. Our findings indicate a dichotomy in envelope coding between the time and intensity processing pathways as early as at the level of the cochlear nuclei. This allows the ILD processing pathway to encode envelope information with greater fidelity than the ITD processing pathway. Furthermore, we demonstrate that the properties of the neurons’ STRFs can be quantitatively related to spike timing reliability.
Voltage-sensitive dye imaging reveals tonotopic organization of auditory cortex spontaneous activity
Authors: Farley Brandon , Norena Arnaud
Published: January 2023

Imaging neural activity across a large (several mm) cortical area with high temporal and spatial resolution is desirable, for example in the auditory system to measure cortical processing across a broad frequency spectrum. Voltage-sensitive dye imaging (VSDI) has a unique combination of properties making this possible, but so far studies have been limited to studying simple sparsely-presented sensory stimuli. We demonstrate the feasibility of long-acquisition VSDI (using the dye RH-1691) in auditory cortex while presenting complex time-varying acoustic stimuli or silence. Using a dense array of partially-overlapping 50 ms tone pips (8 frequencies per octave spanning six octaves), we obtained high-resolution spectrotemporal receptive fields (STRFs) simultaneously across the majority of the guinea pig primary auditory cortical fields (A1 and DC). Long epochs of spontaneous activity were also measured, permitting a comparison of spontaneous activity patterns with functional architecture. By grouping all pixels in areas A1 and DC according to sound frequency preference (obtained from STRFs), we reveal that spontaneous activity (such as cortical spindles) show complex spatial patterns, which are organized according to sound frequency preference within and across cortical areas. More specifically, spontaneous activity correlation decreases as frequency preference diverges within A1 or DC; but additionally, pixels in A1 are also highly correlated with (even far-away) pixels in DC sharing similar frequency preference. These properties of patterned cortical spontaneous activity constrain mechanistic hypotheses regarding their genesis. Beyond these observations, the feasibility of VSDI with continuous stimulation or silence permits measuring population activity during long-lasting sound patterns, which is necessary for examining cortical dynamics and sensory-context dependent processing.
Optimal decision bounds for probabilistic population codes and time varying evidence
Authors: Drugowitsch Jan , Moreno-Bote Rubén , Pouget Alexandre
Published: January 2023

Decision making under time constraints requires the decision maker to trade off between making quick, inaccurate decisions and gathering more evidence for more accurate, but slower decisions. We have previously shown that, under rather general settings, optimal behavior can be described by a time-dependent decision bound on the decision maker’s belief of being correct (Drugowitsch, Moreno-Bote, Pouget, 2009). In cases where the reliability of sensory information remains constant over time, we have shown how to design diffusion models (DMs) with time-changing boundaries that feature such behavior. Such theories can be easily mapped onto simple neural models of decision making with two perfectly anti-correlated neurons, where they predict the existence of a stopping bound on the most active neurons. It is unclear however how the stopping bound would be implemented with more realistic neural population codes, particularly when the reliability of the evidence changes over time.Here we show that, under certain realistic conditions, we can apply the theory of optimal decision making to the biologically more plausible probabilistic population codes (PPCs; Ma et al. 2006). Our analysis shows that, with population codes, the optimal decision bounds are a function of the neural activity of all neurons in the population, rather than a previously postulated bound on its maximum activity. This theory predicts that the bound on the most active neurons would appear to shift depending on the firing rate of other neurons in the population, a puzzling behavior under the drift diffusion model as it would wrongly suggest that subjects change their stopping rule across conditions. This theory also applies to the case of time varying evidence, a case that cannot be handled by drift diffusion models without unrealistic assumptions.
Learning complex tasks with probabilistic population codes
Authors: Turner Richard , Berkes Pietro , Fiser Jozsef
Published: January 2023

Recent psychophysical experiments imply that the brain employs a neural representation of the uncertainty in sensory stimuli and that probabilistic computations are supported by the cortex. Several candidate neural codes for uncertainty have been posited including Probabilistic Population Codes (PPCs). PPCs support various versions of probabilistic inference and marginalisation in a neurally plausible manner. However, in order to establish whether PPCs can be of general use, three important limitations must be addressed. First, it is critical that PPCs support learning. For example, during cue combination, subjects are able to learn the uncertainties associated with the sensory cues as well as the prior distribution over the stimulus. However, previous modelling work with PPCs requires these parameters to be carefully set by hand. Second, PPCs must be able to support inference in non-linear models. Previous work has focused on linear models and it is not clear whether non-linear models can be implemented in a neurally plausible manner. Third, PPCs must be shown to scale to high-dimensional problems with many variables. This contribution addresses these three limitations of PPCs by establishing a connection with variational Expectation Maximisation (vEM). In particular, we show that the usual PPC update for cue combination can be interpreted as the E-Step of a vEM algorithm. The corresponding M-Step then automatically provides a method for learning the parameters of the model by adapting the connection strengths in the PPC network in an unsupervised manner. Using a version of sparse coding as an example, we show that the vEM interpretation of PPC can be extended to non-linear and multi-dimensional models and we show how the approach scales with the dimensionality of the problem. Our results provide a rigorous assessment of the ability of PPCs to capture the probabilistic computations performed in the cortex.
Critical functional lung volumes in neonatal intensive care: evidence and clinical applications
Authors: Dassios Theodore
Published: January 2023

Respiratory disease is common in premature and sick newborn infants and can often necessitate the initiation of intensive care. Newborn infants often suffer from conditions that are associated with decreased lung volumes that occur as a result of abnormal or incomplete lung development. Such conditions are prematurity and respiratory distress syndrome, preterm premature rupture of membranes and the ensuing pulmonary hypoplasia and congenital lung anomalies such as congenital diaphragmatic hernia. These diseases have a structural component manifesting with lower lung volumes and a functional component that can present with increased oxygen and ventilatory requirements. The corresponding decreased functional lung volume is possibly responsible for some unfavourable pulmonary outcomes. Some infants are unable to wean off invasive respiratory support and, in extreme cases, unable to sustain independent breathing that can lead to long-term invasive ventilation or subsequent death. The aim of this review is to summarise the available evidence behind the concept of a critical functional lung volume in neonatal intensive care and describe the clinical implications that arise from decreased functional lung volumes in the main high-risk populations of newborn infants.

Impact

Newborn infants suffer from diseases such as respiratory distress syndrome, pulmonary hypoplasia and congenital diaphragmatic hernia that are associated with a decrease in the total lung volume and impaired lung function.

Critically decreased functional lung volumes during neonatal care are associated with failure to wean off invasive respiratory support, increased mortality and possibly longer-term respiratory complications.
Circular RNA circPOFUT1 enhances malignant phenotypes and autophagy-associated chemoresistance via sequestrating miR-488-3p to activate the PLAG1-ATG12 axis in gastric cancer
Authors: Luo Ming , Deng Xiaofeng , Chen Zonglin , Hu Yongjun
Published: January 2023

Circular RNAs are key regulators in regulating the progression and chemoresistance of gastric cancer (GC), suggesting circular RNAs as potential therapeutic targets for GC. The roles of a novel circular RNA circPOFUT1 in GC are unknown. Here, we found that circPOFUT1 was upregulated in GC tissues and cells, and increased circPOFUT1 expression indicated poor prognosis. Overexpression of circPOFUT1 enhanced cell proliferation, migration, invasion and autophagy-associated chemoresistance in GC, which were suppressed by miR-488-3p overexpression. CircPOFUT1 reduced miR-488-3p expression via sponging miR-488-3p in GC cells. PLAG1 interacted with ATG12 and promoted its expression. MiR-488-3p bound to PLAG1 and suppressed the expression of PLAG1 and ATG12 in GC cells. Overexpression of circPOFUT1 enhanced autophagy-associated chemoresistance of GC cells in vivo, but it was inhibited by overexpression of miR-488-3p. Collectively, circPOFUT1 directly sponged miR-488-3p to activate the expression of PLAG1 and ATG12, thus enhancing malignant phenotypes and autophagy-associated chemoresistance in GC. Our findings show the potential of circPOFUT1 as biomarkers and targeting circPOFUT1 as a therapeutic strategy for GC.
Biophysical impacts of earth greening can substantially mitigate regional land surface temperature warming
Authors: Li Yitao , Li Zhao-Liang , Wu Hua , Zhou Chenghu , Liu Xiangyang , Leng Pei , Yang Peng , Wu Wenbin , Tang Ronglin , Shang Guo-Fei , Ma Lingling
Published: January 2023

Vegetation change can alter surface energy balance and subsequently affect the local climate. This biophysical impact has been well studied for forestation cases, but the sign and magnitude for persistent earth greening remain controversial. Based on long-term remote sensing observations, we quantify the unidirectional impact of vegetation greening on radiometric surface temperature over 2001–2018. Here, we show a global negative temperature response with large spatial and seasonal variability. Snow cover, vegetation greenness, and shortwave radiation are the major driving factors of the temperature sensitivity by regulating the relative dominance of radiative and non-radiative processes. Combined with the observed greening trend, we find a global cooling of −0.018 K/decade, which slows down 4.6 ± 3.2% of the global warming. Regionally, this cooling effect can offset 39.4 ± 13.9% and 19.0 ± 8.2% of the corresponding warming in India and China. These results highlight the necessity of considering this vegetation-related biophysical climate effect when informing local climate adaptation strategies.
The diverse meteorology of Jezero crater over the first 250 sols of Perseverance on Mars
Authors: Rodriguez-Manfredi J. A. , de la Torre Juarez M. , Sanchez-Lavega A. , Hueso R. , Martinez G. , Lemmon M. T. , Newman C. E. , Munguira A. , Hieta M. , Tamppari L. K. , Polkko J. , Toledo D. , Sebastian E. , Smith M. D. , Jaakonaho I. , Genzer M. , De Vicente-Retortillo A. , Viudez-Moreiras D. , Ramos M. , Saiz-Lopez A. , Lepinette A. , Wolff M. , Sullivan R. J. , Gomez-Elvira J. , Apestigue V. , Conrad P. G. , Del Rio-Gaztelurrutia T. , Murdoch N. , Arruego I. , Banfield D. , Boland J. , Brown A. J. , Ceballos J. , Dominguez-Pumar M. , Espejo S. , Fairén A. G. , Ferrandiz R. , Fischer E. , Garcia-Villadangos M. , Gimenez S. , Gomez-Gomez F. , Guzewich S. D. , Harri A.-M. , Jimenez J. J. , Jimenez V. , Makinen T. , Marin M. , Martin C. , Martin-Soler J. , Molina A. , Mora-Sotomayor L. , Navarro S. , Peinado V. , Perez-Grande I. , Pla-Garcia J. , Postigo M. , Prieto-Ballesteros O. , Rafkin S. C. R. , Richardson M. I. , Romeral J. , Romero C. , Savijärvi H. , Schofield J. T. , Torres J. , Urqui R. , Zurita S. ,   the MEDA team
Published: January 2023

NASA’s Perseverance rover’s Mars Environmental Dynamics Analyzer is collecting data at Jezero crater, characterizing the physical processes in the lowest layer of the Martian atmosphere. Here we present measurements from the instrument’s first 250 sols of operation, revealing a spatially and temporally variable meteorology at Jezero. We find that temperature measurements at four heights capture the response of the atmospheric surface layer to multiple phenomena. We observe the transition from a stable night-time thermal inversion to a daytime, highly turbulent convective regime, with large vertical thermal gradients. Measurement of multiple daily optical depths suggests aerosol concentrations are higher in the morning than in the afternoon. Measured wind patterns are driven mainly by local topography, with a small contribution from regional winds. Daily and seasonal variability of relative humidity shows a complex hydrologic cycle. These observations suggest that changes in some local surface properties, such as surface albedo and thermal inertia, play an influential role. On a larger scale, surface pressure measurements show typical signatures of gravity waves and baroclinic eddies in a part of the seasonal cycle previously characterized as low wave activity. These observations, both combined and simultaneous, unveil the diversity of processes driving change on today’s Martian surface at Jezero crater.
Laplacian renormalization group for heterogeneous networks
Authors: Villegas Pablo , Gili Tommaso , Caldarelli Guido , Gabrielli Andrea
Published: January 2023

The renormalization group is the cornerstone of the modern theory of universality and phase transitions and it is a powerful tool to scrutinize symmetries and organizational scales in dynamical systems. However, its application to complex networks has proven particularly challenging, owing to correlations between intertwined scales. To date, existing approaches have been based on hidden geometries hypotheses, which rely on the embedding of complex networks into underlying hidden metric spaces. Here we propose a Laplacian renormalization group diffusion-based picture for complex networks, which is able to identify proper spatiotemporal scales in heterogeneous networks. In analogy with real-space renormalization group procedures, we first introduce the concept of Kadanoff supernodes as block nodes across multiple scales, which helps to overcome detrimental small-world effects that are responsible for cross-scale correlations. We then rigorously define the momentum space procedure to progressively integrate out fast diffusion modes and generate coarse-grained graphs. We validate the method through application to several real-world networks, demonstrating its ability to perform network reduction keeping crucial properties of the systems intact.
Early Release Science of the exoplanet WASP-39b with JWST NIRSpec G395H
Authors: Alderson Lili , Wakeford Hannah R. , Alam Munazza K. , Batalha Natasha E. , Lothringer Joshua D. , Adams Redai Jea , Barat Saugata , Brande Jonathan , Damiano Mario , Daylan Tansu , Espinoza Néstor , Flagg Laura , Goyal Jayesh M. , Grant David , Hu Renyu , Inglis Julie , Lee Elspeth K. H. , Mikal-Evans Thomas , Ramos-Rosado Lakeisha , Roy Pierre-Alexis , Wallack Nicole L. , Batalha Natalie M. , Bean Jacob L. , Benneke Björn , Berta-Thompson Zachory K. , Carter Aarynn L. , Changeat Quentin , Colón Knicole D. , Crossfield Ian J. M. , Désert Jean-Michel , Foreman-Mackey Daniel , Gibson Neale P. , Kreidberg Laura , Line Michael R. , López-Morales Mercedes , Molaverdikhani Karan , Moran Sarah E. , Morello Giuseppe , Moses Julianne I. , Mukherjee Sagnick , Schlawin Everett , Sing David K. , Stevenson Kevin B. , Taylor Jake , Aggarwal Keshav , Ahrer Eva-Maria , Allen Natalie H. , Barstow Joanna K. , Bell Taylor J. , Blecic Jasmina , Casewell Sarah L. , Chubb Katy L. , Crouzet Nicolas , Cubillos Patricio E. , Decin Leen , Feinstein Adina D. , Fortney Joanthan J. , Harrington Joseph , Heng Kevin , Iro Nicolas , Kempton Eliza M.-R. , Kirk James , Knutson Heather A. , Krick Jessica , Leconte Jérémy , Lendl Monika , MacDonald Ryan J. , Mancini Luigi , Mansfield Megan , May Erin M. , Mayne Nathan J. , Miguel Yamila , Nikolov Nikolay K. , Ohno Kazumasa , Palle Enric , Parmentier Vivien , Petit dit de la Roche Dominique J. M. , Piaulet Caroline , Powell Diana , Rackham Benjamin V. , Redfield Seth , Rogers Laura K. , Rustamkulov Zafar , Tan Xianyu , Tremblin P. , Tsai Shang-Min , Turner Jake D. , de Val-Borro Miguel , Venot Olivia , Welbanks Luis , Wheatley Peter J. , Zhang Xi
Published: January 2023

Measuring the abundances of carbon and oxygen in exoplanet atmospheres is considered a crucial avenue for unlocking the formation and evolution of exoplanetary systems1,2. Access to the chemical inventory of an exoplanet requires high-precision observations, often inferred from individual molecular detections with low-resolution space-based3–5 and high-resolution ground-based6–8 facilities. Here we report the medium-resolution (R ≈ 600) transmission spectrum of an exoplanet atmosphere between 3 and 5 μm covering several absorption features for the Saturn-mass exoplanet WASP-39b (ref. 9), obtained with the Near Infrared Spectrograph (NIRSpec) G395H grating of JWST. Our observations achieve 1.46 times photon precision, providing an average transit depth uncertainty of 221 ppm per spectroscopic bin, and present minimal impacts from systematic effects. We detect significant absorption from CO2 (28.5σ) and H2O (21.5σ), and identify SO2 as the source of absorption at 4.1 μm (4.8σ). Best-fit atmospheric models range between 3 and 10 times solar metallicity, with sub-solar to solar C/O ratios. These results, including the detection of SO2, underscore the importance of characterizing the chemistry in exoplanet atmospheres and showcase NIRSpec G395H as an excellent mode for time-series observations over this critical wavelength range10.
Early Release Science of the exoplanet WASP-39b with JWST NIRISS
Authors: Feinstein Adina D. , Radica Michael , Welbanks Luis , Murray Catriona Anne , Ohno Kazumasa , Coulombe Louis-Philippe , Espinoza Néstor , Bean Jacob L. , Teske Johanna K. , Benneke Björn , Line Michael R. , Rustamkulov Zafar , Saba Arianna , Tsiaras Angelos , Barstow Joanna K. , Fortney Jonathan J. , Gao Peter , Knutson Heather A. , MacDonald Ryan J. , Mikal-Evans Thomas , Rackham Benjamin V. , Taylor Jake , Parmentier Vivien , Batalha Natalie M. , Berta-Thompson Zachory K. , Carter Aarynn L. , Changeat Quentin , dos Santos Leonardo A. , Gibson Neale P. , Goyal Jayesh M. , Kreidberg Laura , López-Morales Mercedes , Lothringer Joshua D. , Miguel Yamila , Molaverdikhani Karan , Moran Sarah E. , Morello Giuseppe , Mukherjee Sagnick , Sing David K. , Stevenson Kevin B. , Wakeford Hannah R. , Ahrer Eva-Maria , Alam Munazza K. , Alderson Lili , Allen Natalie H. , Batalha Natasha E. , Bell Taylor J. , Blecic Jasmina , Brande Jonathan , Caceres Claudio , Casewell S. L. , Chubb Katy L. , Crossfield Ian J. M. , Crouzet Nicolas , Cubillos Patricio E. , Decin Leen , Désert Jean-Michel , Harrington Joseph , Heng Kevin , Henning Thomas , Iro Nicolas , Kempton Eliza M.-R. , Kendrew Sarah , Kirk James , Krick Jessica , Lagage Pierre-Olivier , Lendl Monika , Mancini Luigi , Mansfield Megan , May E. M. , Mayne N. J. , Nikolov Nikolay K. , Palle Enric , Petit dit de la Roche Dominique J. M. , Piaulet Caroline , Powell Diana , Redfield Seth , Rogers Laura K. , Roman Michael T. , Roy Pierre-Alexis , Nixon Matthew C. , Schlawin Everett , Tan Xianyu , Tremblin P. , Turner Jake D. , Venot Olivia , Waalkes William C. , Wheatley Peter J. , Zhang Xi
Published: January 2023

The Saturn-mass exoplanet WASP-39b has been the subject of extensive efforts to determine its atmospheric properties using transmission spectroscopy1–4. However, these efforts have been hampered by modelling degeneracies between composition and cloud properties that are caused by limited data quality5–9. Here we present the transmission spectrum of WASP-39b obtained using the Single-Object Slitless Spectroscopy (SOSS) mode of the Near Infrared Imager and Slitless Spectrograph (NIRISS) instrument on the JWST. This spectrum spans 0.6–2.8 μm in wavelength and shows several water-absorption bands, the potassium resonance doublet and signatures of clouds. The precision and broad wavelength coverage of NIRISS/SOSS allows us to break model degeneracies between cloud properties and the atmospheric composition of WASP-39b, favouring a heavy-element enhancement (‘metallicity’) of about 10–30 times the solar value, a sub-solar carbon-to-oxygen (C/O) ratio and a solar-to-super-solar potassium-to-oxygen (K/O) ratio. The observations are also best explained by wavelength-dependent, non-grey clouds with inhomogeneous coverageof the planet’s terminator.
Early Release Science of the exoplanet WASP-39b with JWST NIRSpec PRISM
Authors: Rustamkulov Z. , Sing D. K. , Mukherjee S. , May E. M. , Kirk J. , Schlawin E. , Line M. R. , Piaulet C. , Carter A. L. , Batalha N. E. , Goyal J. M. , López-Morales M. , Lothringer J. D. , MacDonald R. J. , Moran S. E. , Stevenson K. B. , Wakeford H. R. , Espinoza N. , Bean J. L. , Batalha N. M. , Benneke B. , Berta-Thompson Z. K. , Crossfield I. J. M. , Gao P. , Kreidberg L. , Powell D. K. , Cubillos P. E. , Gibson N. P. , Leconte J. , Molaverdikhani K. , Nikolov N. K. , Parmentier V. , Roy P. , Taylor J. , Turner J. D. , Wheatley P. J. , Aggarwal K. , Ahrer E. , Alam M. K. , Alderson L. , Allen N. H. , Banerjee A. , Barat S. , Barrado D. , Barstow J. K. , Bell T. J. , Blecic J. , Brande J. , Casewell S. , Changeat Q. , Chubb K. L. , Crouzet N. , Daylan T. , Decin L. , Désert J. , Mikal-Evans T. , Feinstein A. D. , Flagg L. , Fortney J. J. , Harrington J. , Heng K. , Hong Y. , Hu R. , Iro N. , Kataria T. , Kempton E. M.-R. , Krick J. , Lendl M. , Lillo-Box J. , Louca A. , Lustig-Yaeger J. , Mancini L. , Mansfield M. , Mayne N. J. , Miguel Y. , Morello G. , Ohno K. , Palle E. , Petit dit de la Roche D. J. M. , Rackham B. V. , Radica M. , Ramos-Rosado L. , Redfield S. , Rogers L. K. , Shkolnik E. L. , Southworth J. , Teske J. , Tremblin P. , Tucker G. S. , Venot O. , Waalkes W. C. , Welbanks L. , Zhang X. , Zieba S.
Published: January 2023

Transmission spectroscopy1–3 of exoplanets has revealed signatures of water vapour, aerosols and alkali metals in a few dozen exoplanet atmospheres4,5. However, these previous inferences with the Hubble and Spitzer Space Telescopes were hindered by the observations’ relatively narrow wavelength range and spectral resolving power, which precluded the unambiguous identification of other chemical species—in particular the primary carbon-bearing molecules6,7. Here we report a broad-wavelength 0.5–5.5 µm atmospheric transmission spectrum of WASP-39b8, a 1,200 K, roughly Saturn-mass, Jupiter-radius exoplanet, measured with the JWST NIRSpec’s PRISM mode9 as part of the JWST Transiting Exoplanet Community Early Release Science Team Program10–12. We robustly detect several chemical species at high significance, including Na (19σ), H2O (33σ), CO2 (28σ) and CO (7σ). The non-detection of CH4, combined with a strong CO2 feature, favours atmospheric models with a super-solar atmospheric metallicity. An unanticipated absorption feature at 4 µm is best explained by SO2 (2.7σ), which could be a tracer of atmospheric photochemistry. These observations demonstrate JWST’s sensitivity to a rich diversity of exoplanet compositions and chemical processes.
Brominated lipid probes expose structural asymmetries in constricted membranes
Authors: Moss Frank R. , Lincoff James , Tucker Maxwell , Mohammed Arshad , Grabe Michael , Frost Adam
Published: January 2023

Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B and IST1, we observed leaflet-level and protein-localized structural lipid patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated stearoyl-docosahexanenoyl-phosphocholine showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.
Electrochemical micro-machining based on double feedback circuits
Authors: Xu Lizhong , Wang Jipeng , Zhao Chuanjun
Published: January 2023

Pulsed electrochemical micromachining accuracy predominantly depends on pulse duration. To obtain high accuracy, an expensive power source with ultra-short pulse duration is needed. An electrochemical micromachining method based on double feedback circuits is proposed in this work to achieve this aim. A positive feedback circuit plus a negative feedback circuit is used in the circuit of the pulsed electrochemical micromachining. Thus, the gains of the feedback circuits can control the pulse duration of the machining system. Experiments show that the machining resolution can be improved notably by an increase in the feedback gains. Using the method, one micro double cure beam is produced, and its accuracy gets to nanometer level under the condition of using an ordinary pulse duration power source.
Influence of non-uniform magnetic field on the thermal efficiency hydrodynamic characteristics of nanofluid in double pipe heat exchanger
Authors: Azizi Y. , Bahramkhoo M. , Kazemi A.
Published: January 2023

Enhancement of the heat transfer rate inside the double pipe heat exchangers is significant for industrial applications. In present work, the usage of non-uniform magnetic field on the heat transfer rate of the nanofluid flow streamed inside double pipe heat exchangers are comprehensively studied. Computational technique of CFD is used for the visualization of the nanofluid hydrodynamic in existence of the magnetic source. Influences of the magnetic intensity and nanofluid velocity on the heat transfer are also presented. Simple algorithm is used for the modeling of the incompressible nanofluid flow with addition of magnetic source. Presented results show that magnetic source intensifies the formation of the circulation in the gap of the inner tube and consequently, heat transfer is enhanced in our domain. Comparison of different geometries of tube reveals that the triangle tube is more efficient for improvement of the heat transfer of nanofluid flow. Our results indicate that heat transfer in the tube with triangular shape is more than other configurations and its performance is 15% more than smooth tube.
A preoperative magnetic resonance imaging-based model to predict biochemical failure after radical prostatectomy
Authors: Pan Minjie , Li Shouchun , Liu Fade , Liang Linghui , Shang Jinwei , Xia Wei , Cheng Gong , Hua Lixin
Published: January 2023

To investigate if a magnetic resonance imaging (MRI)-based model reduced postoperative biochemical failure (BF) incidence in patients with prostate cancer (PCa). From June 2018 to January 2020, we retrospectively analyzed 967 patients who underwent prostate bi-parametric MRI and radical prostatectomy (RP). After inclusion criteria were applied, 446 patients were randomized into research (n = 335) and validation cohorts (n = 111) at a 3:1 ratio. In addition to clinical variables, MRI models also included MRI parameters. The area under the curve (AUC) of receiver operating characteristic and decision curves were analyzed. The risk of postoperative BF, defined as persistently high or re-elevated prostate serum antigen (PSA) levels in patients with PCa with no clinical recurrence. In the research (age 69 [63–74] years) and validation cohorts (age 69 [64–74] years), the postoperative BF incidence was 22.39% and 27.02%, respectively. In the research cohort, the AUC of baseline and MRI models was 0.780 and 0.857, respectively, with a significant difference (P < 0.05). Validation cohort results were consistent (0.753 vs. 0.865, P < 0.05). At a 20% risk threshold, the false positive rate in the MRI model was lower when compared with the baseline model (31% [95% confidence interval (CI): 9–39%] vs. 44% [95% CI: 15–64%]), with the true positive rate only decreasing by a little (83% [95% CI: 63–94%] vs. 87% [95% CI: 75–100%]). 32 of 100 RPs can been performed, with no raise in quantity of patients with missed BF. We developed and verified a MRI-based model to predict BF incidence in patients after RP using preoperative clinical and MRI-related variables. This model could be used in clinical settings.
Joint modeling of longitudinal change of fasting blood sugar and systolic blood pressure with survival time to death among hypertension patients
Authors: Erango Markos Abiso
Published: January 2023

Hypertension is a universal public health challenge and a leading modifiable risk factor for cardiovascular disease and death. It is also called high blood pressure, described by two measured quantities systolic blood pressure (SBP) 140 mmHg or greater and diastolic blood pressure (DBP) 90 mmHg or greater. As the result, this study aims to use the joint model application to identify the factors that affect longitudinal changes in fasting blood sugar, SBP, and survival time to death of hypertension patients and their associations admitted to the Arba Minch General Hospital. We considered a total of 354 random samples of hypertension patients who had under follow-up at Arba Minch general hospital from January 2012 to February 2020. Among 2330 hypertension patients under follow-up, 354 were selected with a simple random sampling technique, and data was collected from the patient’s medical cards. After evaluating the longitudinal data with a linear mixed model and the baseline data with Cox proportional models, the joint models of both sub-models were assessed in R software version 4.2. According to the findings, the association between longitudinal changes (FBS, SBP, and time to death in hypertension patients was statistically significant. Ages, place of residence, lifestyle change, stages of hypertension, blood cholesterol level, related diseases, adherence to treatment, family history of hypertension patients, and DBP at baseline were associated factors that affect survival time and longitudinal measurement of FBS and SBP of the patients. The computed association parameters revealed subject-specific values. The subject-specific linear time slope of FBS and SBP was negatively related to the hazard rate of time to death of hypertension patients in Arba Minch general hospital. To reduce the risk of hypertension in patients, health professionals, governmental organizations, and non-governmental organizations must promote the implementation of community-based screening programs for early detection of hypertension.
Investigation of a robust pretreatment technique based on ultrasound-assisted, cost-effective ionic liquid for enhancing saccharification and bioethanol production from wheat straw
Authors: Ziaei-Rad Zhila , Pazouki Mohammad , Fooladi Jamshid , Azin Mehrdad , Gummadi Sathyanarayana N. , Allahverdi Abdollah
Published: January 2023

Application of cost-effective pretreatment of wheat straw is an important stage for massive bioethanol production. A new approach is aimed to enhance the pretreatment of wheat straw by using low-cost ionic liquid [TEA][HSO4] coupled with ultrasound irradiation. The pretreatment was conducted both at room temperature and at 130 °C with a high biomass loading rate of 20% and 20% wt water assisted by ultrasound at 100 W-24 kHz for 15 and 30 min. Wheat straw pretreated at 130 °C for 15 and 30 min had high delignification rates of 67.8% and 74.9%, respectively, and hemicellulose removal rates of 47.0% and 52.2%. Moreover, this pretreatment resulted in producing total reducing sugars of 24.5 and 32.1 mg/mL in enzymatic saccharification, respectively, which corresponds to saccharification yields of 67.7% and 79.8% with commercial cellulase enzyme CelluMax for 72 h. The ethanol generation rates of 38.9 and 42.0 g/L were attained for pretreated samples for 15 and 30 min, equivalent to the yields of 76.1% and 82.2% of the maximum theoretical yield following 48 h of fermentation. This demonstration provided a cheap and promising pretreatment technology in terms of efficiency and shortening the pretreatment time based on applying low-cost ionic liquid and efficient ultrasound pretreatment techniques, which facilitated the feasibility of this approach and could further develop the future of biorefinery.
Early response of Solanum nigrum L. to Lumax and castor oil combination in relation to antioxidant activity, osmolyte concentration and chlorophyll a fluorescence
Authors: Hassannejad Sirous , Fadaei Behrouz , Abbasvand Elham , Ghafarbi Soheila Porheidar , Nasirpour Zahra
Published: January 2023

Solanum nigrumL. (Black nightshade), is one of the most troublesome weeds of summer crops such as corn, soybean, sunflower, etc. To study the effect of combined Castor oil as an adjuvant with different doses of Lumax (Mesotrion + S-metolacholor + Terbuthylazine) on the physiological behavior of Solanum nigrum L., a greenhouse experiment was conducted in randomized complete block design with four replications in agricultural faculty of the University of Tabriz in 2021. A foliar application of Lumax increased proline, malondialdehyde, and hydrogen peroxide concentrations and superoxide dismutase, catalase, and peroxidase activity. The content of protein and photosynthetic pigments (Chlorophyll a, b, and carotenoids) also decreased significantly by using Lumax herbicide. Applying castor oil in combination with Lumax intensifies oxidative stress and lipid peroxidation. Results showed that by increasing the herbicide doses in comparison with control (non-herbicide), Area, Fm, Fv, Fv/Fm, Fv/F0, Sm, Sm/Tfm, and Fv/F0 decreased 48.32%, 19.52%, 27.95%, 10.47%, 50.90%, 28.34%, 79.38%, and 50.90%, respectively and F0, F0/Fm increased 46.76% and 82.38%, respectively. Castor oil showed a synergistic effect on Lumax herbicide and enhanced its efficacy onSolanum nigrum. The presented results supported the view that by evaluating chlorophyllafluorescence parameters, we would realize herbicide (alone or mixed with any adjacent) efficacy before the visual symptoms appear in the plant.
Deformation constitutive model of subgrade soil under intermittent cyclic loading
Authors: Zhang Bolang , Chen Kaisheng , Hu Xing , Zhang Xingwei , Luo Guofu , Chen Rongya
Published: January 2023

During the actual operation of subways, high-speed railway, and other infrastructure, subgrade soil will be subjected to periodic vibration and intermittent loading, i.e., intermittent cyclic load. To study the deformation characteristics of subgrade soil under intermittent cyclic loading, the Newtonian dashpot in the generalized Kelvin model is replaced by the fractional Abel dashpot, a fractional generalized Kelvin model is established. Then, a nonlinear viscoplastic body model considering damage is proposed, which is connected in series with the improved fractional generalized Kelvin model, and the deformation constitutive model of soil under intermittent cyclic loading is obtained. Finally, the effectiveness and applicability of the model are analyzed, and the model is compared with other constitutive models. The results show that the constitutive model established in the paper can reflect the combined effect of confining pressure, frequency, dynamic stress amplitude and other factors on the cumulative plastic strain of soil, and can well characterize the development law of three types of cumulative plastic strain curves of soil: stable, critical, and failure. The fitting parameters $$\alpha$$
α
and $$\eta$$
η
tend to decay and rise, respectively, with the increase in loading stage N, which reflects the rationality and accuracy of the model.