bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vertical Distribution of Aerosols and Hazes Over Jupiter's Great Red Spot and Its Surroundings in 2016 From HST/WFC3 Imaging
Authors: Anguiano‐Arteaga Asier , Pérez‐Hoyos Santiago , Sánchez‐Lavega Agustín , Sanz‐Requena José Francisco , Irwin Patrick G. J. 
Published: October 2021

AbstractIn this work, we have analyzed images provided by the Hubble Space Telescope's Wide Field Camera 3 (HST/WFC3) in December 2016, with a spectral coverage from the ultraviolet to the near infrared. We have obtained the spectral reflectivity of the GRS and its surroundings, with particular emphasis on selected, dynamically interesting regions. A spectral characterization of the GRS area is performed following two different procedures: (a) in terms of Altitude/Opacity and Color Indices (AOI and CI); (b) by means of automatic spectral classification. We used the NEMESIS radiative transfer suite to retrieve the main atmospheric parameters (e.g., particle vertical and size distributions, refractive indices) that are able to explain the observed spectral reflectivity. The optimal a priori model atmosphere used for the retrievals is obtained from a grid of about 12,000 different atmospheric models, and choosing the one that best fits South Tropical Zone (STrZ) spectra and its observed limb‐darkening. We conclude that the spectral reflectivity of the GRS area is well reproduced with the following layout: (a) a stratospheric haze with its base near the 100 mbar level, with optical depths at 900 nm of the order of unity and particles with a size of 0.3 μm; (b) a more vertically extended tropospheric haze, with τ (900 nm) ∼10 down to 500 mbar and micron sized particles. Both haze layers show a stronger short wavelength absorption, and thus both act as chromophores. The altitude difference between clouds tops in the GRS and surrounding areas is ∼10 km.
Middle Miocene (∼14 Ma) and Late Miocene (∼6 Ma) Paleogeographic Boundary Conditions
Authors: He Zhilin , Zhang Zhongshi , Guo Zhengtang , Scotese Christopher R. , Deng Chenglong 
Published: October 2021

AbstractDuring the Miocene, major global cooling occurred during two intervals: the middle Miocene (∼14–13 Ma) and the late Miocene (∼7‐6 Ma). The Antarctic Ice Sheet expanded substantially at ∼14–13 Ma, and glaciation in the Northern Hemisphere was initiated at ∼7–6 Ma. Although the causes of these two global cooling events remain unclear, paleoclimate modeling provides an important approach for investigating the mechanisms. However, paleoclimate modeling relies on paleogeographic boundary conditions, and many uncertainties remain regarding the land–sea distribution, topography, and bathymetry of the Miocene; specifically, previous published paleogeographic reconstructions for the middle and late Miocene show several discrepancies with each other. Here, we present two new sets of global topographic and bathymetric boundary conditions for the middle Miocene (∼14 Ma) and late Miocene (∼6 Ma). Our new reconstructions use a published plate kinematics model, oceanic lithospheric paleo‐ages, and oceanic sediment thicknesses and incorporate global fossil records, stratigraphy, lithofacies, paleoenvironment, and paleoelevation data. With these data, we further constrain the conditions of several important intercontinental and marginal seas surrounding Eurasia and the Arctic, the depth of major seaways in tropical latitudes and middle‐high latitudes of the Northern Hemisphere, and global paleotopography, especially that of the Tibetan Plateau and the Andes.
Column Relative Humidity and Primary Condensation Rate as Two Useful Supplements to Atmospheric River Analysis
Authors: Mo Ruping , So Rita , Brugman Melinda M. , Mooney Curtis , Liu Anthony Q. , Jakob Matthias , Castellan Armel , Vingarzan Roxanne 
Published: October 2021

AbstractLandfalling atmospheric rivers (ARs) frequently trigger heavy and sometimes prolonged precipitation, especially in regions with favored orographic enhancement. The presence and strength of ARs are often described using the integrated water vapor (IWV) and the integrated vapor transport (IVT). However, the associated precipitation is not directly correlated with these two variables. Instead, the intensity of precipitation is mainly determined by the net convergence of moisture flux and the initial degree of saturation of the air column. In this study, a simple algorithm is proposed for estimating the heavy precipitation attributable to the IVT convergence. Bearing a strong resemblance to the Kuo‐Anthes parameterization scheme for cumulus convection, the proposed algorithm calculates the large‐scale primary condensation rate (PCR) as a proportion of the IVT convergence, with a reduction to account for the general moistening in the atmosphere. The amount of reduction is determined by the column relative humidity (CRH), which is defined as the ratio of IWV to its saturation counterpart. Our analysis indicates that the diagnosable PCR compares well to the forecast precipitation rate given by a numerical weather prediction model. It is also shown that the PCR in an air column with CRH 0.50 is negligibly small. The usefulness of CRH and PCR as two complements to standard AR analysis is illustrated in three case studies. The potential application of PCR to storm classification is also explored.
Solving Challenges of Assimilating Microwave Remote Sensing Signatures With a Physical Model to Estimate Snow Water Equivalent
Authors: Merkouriadi Ioanna , Lemmetyinen Juha , Liston Glen E. , Pulliainen Jouni 
Published: October 2021

AbstractGlobal monitoring of seasonal snow water equivalent (SWE) has advanced significantly over the past decades. However, challenges remain when estimating SWE from passive and active microwave signatures, because a priori characterization of snow properties is required for SWE retrievals. Numerical experiments have shown that utilizing physical snow models to acquire snowpack characterization can potentially improve microwave‐based SWE retrievals. This study aims to identify the challenges of assimilating active and passive microwave signatures with physical snow models, and to examine solutions to those challenges. Guided by observations from a point‐based study, we designed a sensitivity experiment to quantify the effects of changes in the physically modeled SWE—and of corresponding changes to other snowpack properties—to the microwave‐based SWE retrievals. The results indicate that assimilating microwave signatures with physical snow models face some critical challenges associated with the physical relationship between SWE and snow microstructure. We demonstrate these challenges can be overcome if the microwave algorithms account for these relationships.
Diverse ‘just-right’ levels of chromosomal instability and their clinical implications in neoadjuvant treated gastric cancer
Authors: Kohlruss Meike , Krenauer Marie , Grosser Bianca , Pfarr Nicole , Jesinghaus Moritz , Slotta-Huspenina Julia , Novotny Alexander , Hapfelmeier Alexander , Schmidt Thomas , Steiger Katja , Gaida Matthias M. , Reiche Magdalena , Bauer Lukas , Ott Katja , Weichert Wilko , Keller Gisela 
Published: October 2021

Abstract
Background
The Cancer Genome Atlas (TCGA) consortium described EBV positivity(+), high microsatellite instability (MSI-H), genomic stability (GS) and chromosomal instability (CIN) as molecular subtypes in gastric carcinomas (GC). We investigated the predictive and prognostic value of these subtypes with emphasis on CIN in the context of neoadjuvant chemotherapy (CTx) in GC.

Methods
TCGA subgroups were determined for 612 resected adenocarcinomas of the stomach and gastro-oesophageal junction (291 without, 321 with CTx) and 143 biopsies before CTx.
EBV and MSI-H were analysed by standard assays. CIN was detected by multiplex PCRs analysing 22 microsatellite markers. Besides the TCGA classification, CIN was divided into four CIN-subgroups: low, moderate, substantial, high. Mutation profiling was performed for 52 tumours by next-generation sequencing.

Results
EBV(+) (HR, 0.48; 95% CI, 0.23–1.02), MSI-H (HR, 0.56; 95% CI, 0.35–0.89) and GS (HR, 0.72; 95% CI, 0.45–1.13) were associated with increased survival compared to CIN in the resected tumours. Considering the extended CIN-classification, CIN-substantial was a negative prognostic factor in uni- and multivariable analysis in resected tumours with CTx (each p < 0.05). In biopsies before CTx, CIN-high predicted tumour regression (p = 0.026), but was not prognostically relevant.

Conclusion
A refined CIN classification reveals tumours with different biological characteristics and potential clinical implications.
Extracellular vesicles in pancreatic cancer progression and therapies
Authors: Chang Chao-Hui , Pauklin Siim 
Published: October 2021

AbstractPancreatic cancer (PC) is one of the leading causes of cancer-related death worldwide due to delayed diagnosis and limited treatments. More than 90% of all pancreatic cancers are pancreatic ductal adenocarcinoma (PDAC). Extensive communication between tumour cells and other cell types in the tumour microenvironment have been identified which regulate cancer hallmarks during pancreatic tumorigenesis via secretory factors and extracellular vesicles (EVs). The EV-capsuled factors not only facilitate tumour growth locally, but also enter circulation and reach distant organs to construct a pre-metastatic niche. In this review, we delineate the key factors in pancreatic ductal adenocarcinoma derived EVs that mediate different tumour processes. Also, we highlight the factors that are related to the crosstalk with cancer stem cells/cancer-initiating cells (CSC/CIC), the subpopulation of cancer cells that can efficiently metastasize and resist currently used chemotherapies. Lastly, we discuss the potential of EV-capsuled factors in early diagnosis and antitumour therapeutic strategies.
Population structure, biogeography and transmissibility of Mycobacterium tuberculosis
Authors: Freschi Luca , Vargas Roger , Husain Ashaque , Kamal S. M. Mostofa , Skrahina Alena , Tahseen Sabira , Ismail Nazir , Barbova Anna , Niemann Stefan , Cirillo Daniela Maria , Dean Anna S. , Zignol Matteo , Farhat Maha Reda 
Published: October 2021

AbstractMycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4939 pan-susceptible strains, and find 30 new genetically distinct clades that we validate in a dataset of 4645 independent isolates. We find a consistent geographically restricted or unrestricted pattern for 20 groups, including three groups of Lineage 1. The distribution of terminal branch lengths across the M. tuberculosis phylogeny supports the hypothesis of a higher transmissibility of Lineages 2 and 4, in comparison with Lineages 3 and 1, on a global scale. We define an expanded barcode of 95 single nucleotide substitutions that allows rapid identification of 69 M. tuberculosis sub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of the M. tuberculosis phylogeny and biogeography.
Spared perilesional V1 activity underlies training-induced recovery of luminance detection sensitivity in cortically-blind patients
Authors: Barbot Antoine , Das Anasuya , Melnick Michael D. , Cavanaugh Matthew R. , Merriam Elisha P. , Heeger David J. , Huxlin Krystel R. 
Published: October 2021

AbstractDamage to the primary visual cortex (V1) causes homonymous visual-field loss long considered intractable. Multiple studies now show that perceptual training can restore visual functions in chronic cortically-induced blindness (CB). A popular hypothesis is that training can harness residual visual functions by recruiting intact extrageniculostriate pathways. Training may also induce plastic changes within spared regions of the damaged V1. Here, we link changes in luminance detection sensitivity with retinotopic fMRI activity before and after visual discrimination training in eleven patients with chronic, stroke-induced CB. We show that spared V1 activity representing perimetrically-blind locations prior to training predicts the amount of training-induced recovery of luminance detection sensitivity. Additionally, training results in an enlargement of population receptive fields in perilesional V1, which increases blind-field coverage and may support further recovery with subsequent training. These findings uncover fundamental changes in perilesional V1 cortex underlying training-induced restoration of conscious luminance detection sensitivity in CB.
Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants
Authors: Han Pengcheng , Su Chao , Zhang Yanfang , Bai Chongzhi , Zheng Anqi , Qiao Chengpeng , Wang Qing , Niu Sheng , Chen Qian , Zhang Yuqin , Li Weiwei , Liao Hanyi , Li Jing , Zhang Zengyuan , Cho Heecheol , Yang Mengsu , Rong Xiaoyu , Hu Yu , Huang Niu , Yan Jinghua , Wang Qihui , Zhao Xin , Gao George Fu , Qi Jianxun 
Published: October 2021

AbstractMultiple SARS-CoV-2 variants of concern (VOCs) have been emerging and some have been linked to an increase in case numbers globally. However, there is yet a lack of understanding of the molecular basis for the interactions between the human ACE2 (hACE2) receptor and these VOCs. Here we examined several VOCs including Alpha, Beta, and Gamma, and demonstrate that five variants receptor-binding domain (RBD) increased binding affinity for hACE2, and four variants pseudoviruses increased entry into susceptible cells. Crystal structures of hACE2-RBD complexes help identify the key residues facilitating changes in hACE2 binding affinity. Additionally, soluble hACE2 protein efficiently prevent most of the variants pseudoviruses. Our findings provide important molecular information and may help the development of novel therapeutic and prophylactic agents targeting these emerging mutants.
Experimental demonstration of peripherally-excited antenna arrays
Authors: Dorrah Ayman H. , Eleftheriades George V. 
Published: October 2021

AbstractEmerging technologies such as 5G communication systems, autonomous vehicles and satellite Internet have led to a renewed interest in 2D antennas that are capable of generating fixed/scannable pencil beams. Although traditional active phased arrays are technologically suitable for these applications, there are cases where other alternatives are more attractive, especially if they are simpler and less costly to design and fabricate. Recently, the concept of the Peripherally-Excited (PEX) antenna array has been proposed, promising a sizable reduction in the active-element count, especially when compared with traditional phased arrays. Albeit at the price of exhibiting some constraints on the possible beam-pointing directions. Here, we demonstrate the first practical implementation of the PEX antenna concept, and the proposed design is capable of generating single or multiple independently scannable pencil beams at broadside and tilted radiation directions, from a shared radiating aperture. The proposed structure is also easily scalable to higher millimeter-wave frequencies, and can be particularly useful in MIMO and duplex antenna applications, commonly encountered in automotive radars, among others.
Influence of historical changes in tropical reef habitat on the diversification of coral reef fishes
Authors: Leprieur Fabien , Pellissier Loic , Mouillot David , Gaboriau Théo 
Published: October 2021

AbstractPast environmental changes are expected to have profoundly impacted diversity dynamics through time. While some previous studies showed an association between past climate changes or tectonic events and important shifts in lineage diversification, it is only recently that past environmental changes have been explicitly integrated in diversification models to test their influence on diversification rates. Here, we used a global reconstruction of tropical reef habitat dynamics during the Cenozoic and phylogenetic diversification models to test the influence of (i) major geological events, (ii) reef habitat fragmentation and (iii) reef area on the diversification of 9 major clades of tropical reef fish (Acanthuridae, Balistoidea, Carangoidea, Chaetodontidae, Haemulinae, Holocentridae, Labridae, Pomacentridae and Sparidae). The diversification models revealed a weak association between paleo-habitat changes and diversification dynamics. Specifically, the fragmentation of tropical reef habitats over the Cenozoic was found to be a driver of tropical reef fish diversification for 2 clades. However, overall, our approach did not allow the identification of striking associations between diversification dynamics and paleo-habitat fragmentation in contrast with theoretical model’s predictions.
Vitamin D deficiency during late pregnancy mediates placenta-associated complications
Authors: Raia-Barjat Tiphaine , Sarkis Camille , Rancon Florence , Thibaudin Lise , Gris Jean-Christophe , Alfaidy Nadia , Chauleur Céline 
Published: October 2021

AbstractDuring pregnancy, maternal vitamin D insufficiency could increase the risk of preeclampsia. Aim of the study was to evaluate the relationship between vitamin D status and the occurrence of placenta-mediated complications (PMCs) in a population at high risk. A prospective multicenter cohort study of 200 pregnant patients was conducted. The vitamin D level of patients with placenta-mediated complications was lower at 32 weeks compared to uncomplicated pregnancies (P = 0.001). At 32 weeks, the risk of occurrence of PMCs was five times higher in patients with vitamin D deficiency (RR: 5.14 95% CI (1.50–17.55)) compared to patients with normal vitamin D levels. There was a strong, inverse relationship between serum 25(OH)D levels at 32 weeks and the subsequent risk of PMCs (P = 0.001). At 32 weeks, the vitamin D level of patients with late-onset PMCs was lower than the one of patients with early-onset PMCs and of patients without PMCs (P < 0.0001). These results suggest a role of vitamin D in the maintenance of placental performance and therefore in the prevention of the onset of late PMC.
Genetic transformation and growth index determination of the Larix olgensis LoHDZ2 transcription factor gene in tobacco
Authors: An Peiqi , Wang Chen , Cao Qing , Zhao Qingrong , Qin Ruofan , Zhang Lei , Zhang Hanguo 
Published: October 2021

AbstractHomeodomain-leucine zippers (HD-Zip) are plant-specific transcription factors that participate in different plant development processes and differentially regulate metabolic processes. LoHDZ2 is an HD-ZipII subfamily transcription factor gene that we identified from a transcriptomic analysis of Larix olgensis. To understand its function, we built a LoHDZ2 expression vector and then inserted it into tobacco by genetic transformation. Transgenic plants were identified at the DNA and RNA levels. Phenotypic index analysis of transgenic tobacco showed dwarfed growth with larger leaves and earlier flowering than the wild type. LoHDZ2 was expressed differently after hormone treatment with IAA, MeJA and 2,4-D. The results suggested that LoHDZ2 may respond to hormones and be involved in regulating growth and metabolism. These results helped us better understand the function of LoHDZ2 and provided a candidate gene for Larix olgensis molecular breeding.
Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean
Authors: Andrews Adam J. , Puncher Gregory N. , Bernal-Casasola Darío , Di Natale Antonio , Massari Francesco , Onar Vedat , Toker Nezir Yaşar , Hanke Alex , Pavey Scott A. , Savojardo Castrense , Martelli Pier Luigi , Casadio Rita , Cilli Elisabetta , Morales-Muñiz Arturo , Mantovani Barbara , Tinti Fausto , Cariani Alessia 
Published: October 2021

AbstractAtlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.
Detecting initial correlations via correlated spectroscopy in hybrid quantum systems
Authors: Jatakia Parth , Vinjanampathy Sai , Saha Kasturi 
Published: October 2021

AbstractGeneric mesoscopic quantum systems that interact with their environment tend to display appreciable correlations with environment that often play an important role in the physical properties of the system. However, the experimental methods needed to characterize such systems either ignore the role of initial correlations or scale unfavourably with system dimensions. Here, we present a technique that is agnostic to system–environment correlations and can be potentially implemented experimentally. Under a specific set of constraints, we demonstrate the ability to detect and measure specific correlations. We apply the technique to two cases related to Nitrogen Vacancy Centers (NV). Firstly, we use the technique on an NV coupled to a P1 defect centre in the environment to demonstrate the ability to detect dark spins. Secondly, we implement the technique on a hybrid quantum system of NV coupled to an optical cavity with initial correlations. We extract the interaction strength and effective number of interacting NVs from the initial correlations using our technique.