bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decadal Observations of Internal Wave Energy, Shear, and Mixing in the Western Arctic Ocean
Authors: Fine Elizabeth C. , Cole Sylvia T. 
Published: April 2022

AbstractAs Arctic sea ice declines, wind energy has increasing access to the upper ocean, with potential consequences for ocean mixing, stratification, and turbulent heat fluxes. Here, we investigate the relationships between internal wave energy, turbulent dissipation, and ice concentration and draft using mooring data collected in the Beaufort Sea during 2003–2018. We focus on the 50–300 m depth range, using velocity and CTD records to estimate near‐inertial shear and energy, a finescale parameterization to infer turbulent dissipation rates, and ice draft observations to characterize the ice cover. All quantities varied widely on monthly and interannual timescales. Seasonally, near‐inertial energy increased when ice concentration and ice draft were low, but shear and dissipation did not. We show that this apparent contradiction occurred due to the vertical scales of internal wave energy, with open water associated with larger vertical scales. These larger vertical scale motions are associated with less shear, and tend to result in less dissipation. This relationship led to a seasonality in the correlation between shear and energy. This correlation was largest in the spring beneath full ice cover and smallest in the summer and fall when the ice had deteriorated. When considering interannually averaged properties, the year‐to‐year variability and the short ice‐free season currently obscure any potential trend. Implications for the future seasonal and interannual evolution of the Arctic Ocean and sea ice cover are discussed.
A 20‐Year Study of Melt Processes Over Larsen C Ice Shelf Using a High‐Resolution Regional Atmospheric Model: 1. Model Configuration and Validation
Authors: Gilbert Ella , Orr Andrew , King John C. , Renfrew Ian A. , Lachlan‐Cope Thomas 
Published: April 2022

AbstractFollowing collapses of the neighboring Larsen A and B ice shelves, Larsen C has become a focus of increased attention. Determining how the prevailing meteorological conditions influence its surface melt regime is of paramount importance for understanding the dominant processes causing melt and ultimately for predicting its future. To this end, a new, high‐resolution (4 km grid spacing) Met Office Unified Model (MetUM) hindcast of atmospheric conditions and surface melt processes over the central Antarctic Peninsula is introduced. The hindcast is capable of simulating observed near‐surface meteorology and surface melt conditions over Larsen C. In contrast with previous model simulations, the MetUM captures the observed east‐west gradient in surface melting associated with foehn winds, as well as the interannual variability in melt shown in previous observational studies. As exemplars, we focus on two case studies—the months preceding the collapse of the Larsen B ice shelf in March 2002 and the high foehn, high melt period of March‐May 2016—to test the hindcast's ability to reproduce the atmospheric effects that contributed to considerable melting during those periods. The results suggest that the MetUM hindcast is a useful tool with which to explore the dominant causes of surface melting on Larsen C.
KLF6 facilitates differentiation of odontoblasts through modulating the expression of P21 in vitro
Authors: Chen Zhuo , Wu Wenzhi , Zheng Chen , Lan Yanhua , Xie Huizhi , Xie Zhijian 
Published: April 2022

AbstractMultiple signaling pathways are involved in the regulation of cell proliferation and differentiation in odontogenesis and dental tissue renewal, but the details of these mechanisms remain unknown. Here, we investigated the expression patterns of a transcription factor, Krüppel-like factor 6 (KLF6), during the development of murine tooth germ and its function in odontoblastic differentiation. KLF6 was almost ubiquitously expressed in odontoblasts at various stages, and it was co-expressed with P21 (to varying degrees) in mouse dental germ. To determine the function of Klf6, overexpression and knockdown experiments were performed in a mouse dental papilla cell line (iMDP-3). Klf6 functioned as a promoter of odontoblastic differentiation and inhibited the proliferation and cell cycle progression of iMDP-3 through p21 upregulation. Dual-luciferase reporter assay and chromatin immunoprecipitation showed that Klf6 directly activates p21 transcription. Additionally, the in vivo study showed that KLF6 and P21 were also co-expressed in odontoblasts around the reparative dentin. In conclusion, Klf6 regulates the transcriptional activity of p21, thus promoting the cell proliferation to odontoblastic differentiation transition in vitro. This study provides a theoretical basis for odontoblast differentiation and the formation of reparative dentine regeneration.
CS1 CAR-T targeting the distal domain of CS1 (SLAMF7) shows efficacy in high tumor burden myeloma model despite fratricide of CD8+CS1 expressing CAR-T cells
Authors: O’Neal Julie , Ritchey Julie K. , Cooper Matthew L. , Niswonger Jessica , Sofía González L. , Street Emily , Rettig Michael P. , Gladney Susan W. , Gehrs Leah , Abboud Ramzi , Prior Julie L. , Haas Gabriel J. , Jayasinghe Reyka G. , Ding Li , Ghobadi Armin , Vij Ravi , DiPersio John F. 
Published: April 2022

AbstractDespite improvement in treatment options for myeloma patients, including targeted immunotherapies, multiple myeloma remains a mostly incurable malignancy. High CS1 (SLAMF7) expression on myeloma cells and limited expression on normal cells makes it a promising target for CAR-T therapy. The CS1 protein has two extracellular domains – the distal Variable (V) domain and the proximal Constant 2 (C2) domain. We generated and tested CS1-CAR-T targeting the V domain of CS1 (Luc90-CS1-CAR-T) and demonstrated anti-myeloma killing in vitro and in vivo using two mouse models. Since fratricide of CD8 + cells occurred during production, we generated fratricide resistant CS1 deficient Luc90- CS1- CAR-T (ΔCS1-Luc90- CS1- CAR-T). This led to protection of CD8 + cells in the CAR-T cultures, but had no impact on efficacy. Our data demonstrate targeting the distal V domain of CS1 could be an effective CAR-T treatment for myeloma patients and deletion of CS1 in clinical production did not provide an added benefit using in vivo immunodeficient NSG preclinical models.
A silent two-photon imaging system for studying in vivo auditory neuronal functions
Authors: Song Xindong , Guo Yueqi , Chen Chenggang , Wang Xiaoqin 
Published: April 2022

AbstractTwo-photon laser-scanning microscopy has become an essential tool for imaging neuronal functions in vivo and has been applied to different parts of the neural system, including the auditory system. However, many components of a two-photon microscope, such as galvanometer-based laser scanners, generate mechanical vibrations and thus acoustic artifacts, making it difficult to interpret auditory responses from recorded neurons. Here, we report the development of a silent two-photon imaging system and its applications in the common marmoset (Callithrix Jacchus), a non-human primate species sharing a similar hearing range with humans. By utilizing an orthogonal pair of acousto-optical deflectors (AODs), full-frame raster scanning at video rate was achieved without introducing mechanical vibrations. Imaging depth can be optically controlled by adjusting the chirping speed on the AODs without any mechanical motion along the Z-axis. Furthermore, all other sound-generating components of the system were acoustically isolated, leaving the noise floor of the working system below the marmoset’s hearing threshold. Imaging with the system in awake marmosets revealed many auditory cortex neurons that exhibited maximal responses at low sound levels, which were not possible to study using traditional two-photon imaging systems. This is the first demonstration of a silent two-photon imaging system that is capable of imaging auditory neuronal functions in vivo without acoustic artifacts. This capacity opens new opportunities for a better understanding of auditory functions in the brain and helps isolate animal behavior from microscope-generated acoustic interference.
Psychosocial functioning in the balance between autism and psychosis: evidence from three populations
Authors: Abu-Akel Ahmad , Wood Stephen J. , Upthegrove Rachel , Chisholm Katharine , Lin Ashleigh , Hansen Peter C. , Gillespie Steven M. , Apperly Ian A. , Montag Christiane 
Published: April 2022

AbstractFunctional impairment is a core feature of both autism and schizophrenia spectrum disorders. While diagnostically independent, they can co-occur in the same individual at both the trait and diagnostic levels. The effect of such co-occurrence is hypothesized to worsen functional impairment. The diametric model, however, suggests that the disorders are etiologically and phenotypically diametrical, representing the extreme of a unidimensional continuum of cognition and behavior. A central prediction of this model is that functional impairment would be attenuated in individuals with mixed symptom expressions or genetic liability to both disorders. We tested this hypothesis in two clinical populations and one healthy population. In individuals with chronic schizophrenia and in individuals with first episode psychosis we evaluated the combined effect of autistic traits and positive psychotic symptoms on psychosocial functioning. In healthy carriers of alleles of copy number variants (CNVs) that confer risk for both autism and schizophrenia, we also evaluated whether variation in psychosocial functioning depended on the combined risk conferred by each CNV. Relative to individuals with biased symptom/CNV risk profiles, results show that functional impairments are attenuated in individuals with relatively equal levels of positive symptoms and autistic traits—and specifically stereotypic behaviors—, and in carriers of CNVs with relatively equal risks for either disorder. However, the pattern of effects along the “balance axis” varied across the groups, with this attenuation being generally less pronounced in individuals with high-high symptom/risk profile in the schizophrenia and CNV groups, and relatively similar for low-low and high-high individuals in the first episode psychosis group. Lower levels of functional impairments in individuals with “balanced” symptom profile or genetic risks would suggest compensation across mechanisms associated with autism and schizophrenia. CNVs that confer equal risks for both disorders may provide an entry point for investigations into such compensatory mechanisms. The co-assessment of autism and schizophrenia may contribute to personalized prognosis and stratification strategies.
Breast cancer in the era of integrating “Omics” approaches
Authors: Rossi Claudia , Cicalini Ilaria , Cufaro Maria Concetta , Consalvo Ada , Upadhyaya Prabin , Sala Gianluca , Antonucci Ivana , Del Boccio Piero , Stuppia Liborio , De Laurenzi Vincenzo 
Published: April 2022

AbstractWorldwide, breast cancer is the leading cause of cancer-related deaths in women. Breast cancer is a heterogeneous disease characterized by different clinical outcomes in terms of pathological features, response to therapies, and long-term patient survival. Thus, the heterogeneity found in this cancer led to the concept that breast cancer is not a single disease, being very heterogeneous both at the molecular and clinical level, and rather represents a group of distinct neoplastic diseases of the breast and its cells. Indubitably, in the past decades we witnessed a significant development of innovative therapeutic approaches, including targeted and immunotherapies, leading to impressive results in terms of increased survival for breast cancer patients. However, these multimodal treatments fail to prevent recurrence and metastasis. Therefore, it is urgent to improve our understanding of breast tumor and metastasis biology. Over the past few years, high-throughput “omics” technologies through the identification of novel biomarkers and molecular profiling have shown their great potential in generating new insights in the study of breast cancer, also improving diagnosis, prognosis and prediction of response to treatment. In this review, we discuss how the implementation of “omics” strategies and their integration may lead to a better comprehension of the mechanisms underlying breast cancer. In particular, with the aim to investigate the correlation between different “omics” datasets and to define the new important key pathway and upstream regulators in breast cancer, we applied a new integrative meta-analysis method to combine the results obtained from genomics, proteomics and metabolomics approaches in different revised studies.
Decreased thermal niche breadth as a trade-off of antibiotic resistance
Authors: Herren Cristina M , Baym Michael 
Published: April 2022

Abstract
Evolutionary theory predicts that adaptations, including antibiotic resistance, should come with associated fitness costs; yet, many resistance mutations seemingly contradict this prediction by inducing no growth rate deficit. However, most growth assays comparing sensitive and resistant strains have been performed under a narrow range of environmental conditions, which do not reflect the variety of contexts that a pathogenic bacterium might encounter when causing infection. We hypothesized that reduced niche breadth, defined as diminished growth across a diversity of environments, can be a cost of antibiotic resistance. Specifically, we test whether chloramphenicol-resistant Escherichia coli incur disproportionate growth deficits in novel thermal conditions. Here we show that chloramphenicol-resistant bacteria have greater fitness costs at novel temperatures than their antibiotic-sensitive ancestors. In several cases, we observed no resistance cost in growth rate at the historic temperature but saw diminished growth at warmer and colder temperatures. These results were consistent across various genetic mechanisms of resistance. Thus, we propose that decreased thermal niche breadth is an under-documented fitness cost of antibiotic resistance. Furthermore, these results demonstrate that the cost of antibiotic resistance shifts rapidly as the environment changes; these context-dependent resistance costs should select for the rapid gain and loss of resistance as an evolutionary strategy.
Stress-induced pro- and anti-inflammatory cytokine concentrations in female PTSD and depressive patients
Authors: Renner Vanessa , Schellong Julia , Bornstein Stefan , Petrowski Katja 
Published: April 2022

AbstractAlterations of the hypothalamus pituitary-axis on one hand and heightened rates of somatic diseases and mortality on the other hand are consistently found for PTSD and MDD patients. A possible link between these factors might be the immune system, in particular pro- and anti-inflammatory cytokines. A ‘low-grade inflammation’ in PTSD and MDD patients was found, whereas the influence of acute stress and the role of anti-inflammatory cytokines was rarely examined. In this study, 17 female PTSD patients participated in the Trier social stress test while serum cytokine levels (IL-6, IL-10) were assessed. Cytokine levels of PTSD patients were compared with levels of female depressive patients (n = 18) and female healthy controls (n = 18). Group differences were assessed using a 3 (group) x 8 (time: −15, −1, +1, +10, +20, +30, +45, +60 min) ANCOVA for repeated measures with baseline values as covariates. There was no group difference regarding IL-6 levels (p = 0.920) but PTSD patients showed significantly higher levels of IL-10 compared with depressive patients (p < 0.001, d = 0.16) and healthy controls (p = 0.001, d = 0.38). Under acute stress, PTSD patients did not show the widely found elevated IL-6 levels but showed an increase of anti-inflammatory IL-10. Therefore, acute stress seems to promote an imbalance of pro- and anti-inflammatory cytokine levels in PTSD and might indicate a hyperreactive immune response. This should be considered in future studies to further understand the role of the immune system as a link between stress response and somatic diseases.
Chromosome evolution and the genetic basis of agronomically important traits in greater yam
Authors: Bredeson Jessen V. , Lyons Jessica B. , Oniyinde Ibukun O. , Okereke Nneka R. , Kolade Olufisayo , Nnabue Ikenna , Nwadili Christian O. , Hřibová Eva , Parker Matthew , Nwogha Jeremiah , Shu Shengqiang , Carlson Joseph , Kariba Robert , Muthemba Samuel , Knop Katarzyna , Barton Geoffrey J. , Sherwood Anna V. , Lopez-Montes Antonio , Asiedu Robert , Jamnadass Ramni , Muchugi Alice , Goodstein David , Egesi Chiedozie N. , Featherston Jonathan , Asfaw Asrat , Simpson Gordon G. , Doležel Jaroslav , Hendre Prasad S. , Van Deynze Allen , Kumar Pullikanti Lava , Obidiegwu Jude E. , Bhattacharjee Ranjana , Rokhsar Daniel S. 
Published: April 2022

AbstractThe nutrient-rich tubers of the greater yam,Dioscorea alataL., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly ofD. alatacombined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in theDioscorealineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.
The downward spiralling nature of the North Atlantic Subtropical Gyre
Authors: Berglund Sara , Döös Kristofer , Groeskamp Sjoerd , McDougall Trevor J. 
Published: April 2022

AbstractThe Atlantic Meridional Overturning Circulation (AMOC) regulates the heat distribution and climate of Earth. Here we identify a new feature of the circulation within the North Atlantic Subtropical Gyre that is associated with the northward flowing component of the AMOC. We find that 70% of the water that flows northwards as part of the AMOC circulates the Gyre at least once before it can continue northwards. These circuits are needed to achieve an increase of density and depth through a combination of air-sea interaction and interior mixing processes, before water can escape the latitudes of the Gyre and join the northern upper branch of the AMOC. This points towards an important role of the Gyre circulation in determining the strength and variability of the AMOC and the northward heat transport. Understanding this newly identified role of the North Atlantic Subtropical Gyre is needed to properly represent future changes of the AMOC.
Hidden information on protein function in censuses of proteome foldedness
Authors: Cox Dezerae , Ang Ching-Seng , Nillegoda Nadinath B. , Reid Gavin E. , Hatters Danny M. 
Published: April 2022

AbstractMethods that assay protein foldedness with proteomics have generated censuses of apparent protein folding stabilities in biological milieu. However, different censuses poorly correlate with each other. Here, we show that the reason for this is that methods targeting foldedness through monitoring amino acid sidechain reactivity also detect changes in conformation and ligand binding, which can be a substantial fraction of the data. We show that the reactivity of only one quarter of cysteine or methionine sidechains in proteins in a urea denaturation curve of mammalian cell lysate can be confidently explained by a two-state unfolding isotherm. Contrary to that expected from unfolding, up to one third of the cysteines decreased reactivity. These cysteines were enriched in proteins with functions relating to unfolded protein stress. One protein, chaperone HSPA8, displayed changes arising from ligand and cofactor binding. Unmasking this hidden information using the approaches outlined here should improve efforts to understand both folding and the remodeling of protein function directly in complex biological settings.
Membrane marker selection for segmenting single cell spatial proteomics data
Authors: Dayao Monica T. , Brusko Maigan , Wasserfall Clive , Bar-Joseph Ziv 
Published: April 2022

AbstractThe ability to profile spatial proteomics at the single cell level enables the study of cell types, their spatial distribution, and interactions in several tissues and conditions. Current methods for cell segmentation in such studies rely on known membrane or cell boundary markers. However, for many tissues, an optimal set of markers is not known, and even within a tissue, different cell types may express different markers. Here we present RAMCES, a method that uses a convolutional neural network to learn the optimal markers for a new sample and outputs a weighted combination of the selected markers for segmentation. Testing RAMCES on several existing datasets indicates that it correctly identifies cell boundary markers, improving on methods that rely on a single marker or those that extend nuclei segmentations. Application to new spatial proteomics data demonstrates its usefulness for accurately assigning cell types based on the proteins expressed in segmented cells.
Deep learning enhanced Rydberg multifrequency microwave recognition
Authors: Liu Zong-Kai , Zhang Li-Hua , Liu Bang , Zhang Zheng-Yuan , Guo Guang-Can , Ding Dong-Sheng , Shi Bao-Sen 
Published: April 2022

AbstractRecognition of multifrequency microwave (MW) electric fields is challenging because of the complex interference of multifrequency fields in practical applications. Rydberg atom-based measurements for multifrequency MW electric fields is promising in MW radar and MW communications. However, Rydberg atoms are sensitive not only to the MW signal but also to noise from atomic collisions and the environment, meaning that solution of the governing Lindblad master equation of light-atom interactions is complicated by the inclusion of noise and high-order terms. Here, we solve these problems by combining Rydberg atoms with deep learning model, demonstrating that this model uses the sensitivity of the Rydberg atoms while also reducing the impact of noise without solving the master equation. As a proof-of-principle demonstration, the deep learning enhanced Rydberg receiver allows direct decoding of the frequency-division multiplexed signal. This type of sensing technology is expected to benefit Rydberg-based MW fields sensing and communication.
Interactive single-cell data analysis using Cellar
Authors: Hasanaj Euxhen , Wang Jingtao , Sarathi Arjun , Ding Jun , Bar-Joseph Ziv 
Published: April 2022

AbstractCell type assignment is a major challenge for all types of high throughput single cell data. In many cases such assignment requires the repeated manual use of external and complementary data sources. To improve the ability to uniformly assign cell types across large consortia, platforms and modalities, we developed Cellar, a software tool that provides interactive support to all the different steps involved in the assignment and dataset comparison process. We discuss the different methods implemented by Cellar, how these can be used with different data types, how to combine complementary data types and how to analyze and visualize spatial data. We demonstrate the advantages of Cellar by using it to annotate several HuBMAP datasets from multi-omics single-cell sequencing and spatial proteomics studies. Cellar is open-source and includes several annotated HuBMAP datasets.