bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plastic Moment: Kavi-Aitihāsik
Authors: Ghosh Ranjan 
Published: August 2024

Abstract
Working through what Ghosh calls the plastic rhythm, this chapter executes a close reading of Rabindranath Tagore’s writings on history; it tries to develop his theory of history and establish the character of his historical consciousness. Tagore’s philosophy of history can be distinguished from Western models of historical thinking and is resistant to any form of aligning with nationalist and revivalistic narratives that speak only of one culture, one nation, and one community. The chapter identifies plastic moments in historical thinking and works out a theoretical premise based on Tagore’s engagement with time, historical distance, the everyday, history as life view, historical fiction, historicality in literature, and the notion of the historical-now or presentism. Substantiated by the notion of a kavi-aitihāsik, ‘poet-historian’, Tagore’s historical theory works at the limits of ‘global history’, which is now often misappropriated through the principles of unifocality and bounded rationality. An inherent philosophy of plasticity frees Tagore’s sense of itihasa from the univocality of world history; it creates its own ‘worlding’, its historicality, enriching and disturbing our notions of global history.
The Plastic Kavi . . .
Authors: Ghosh Ranjan 
Published: August 2024

Abstract
This chapter reinvests the arguments in our understanding of plastic Tagore on different lines to make a resounding case for what we now accept as ‘the’ plastic kavi. In trying to do that, it commits to figure a few plastic moments in Tagore’s negotiations with nature. Plastic Tagore betrays an anxiety of a changing nature, a negative surplus that made him commit to a biocentric pedagogy or rural reconstruction within a nature–culture sambandha or a life amidst the nourishing and recuperative shelter of forests, trees, and plants—an inclusive and intensive green consciousness. He builds plastic lines that formulate new ideas of nature within the background of an anthropocenic unconscious and climaticenic becoming. The chapter in the end establishes the problematic of the plastic kavi and concludes that Tagore has never been outside the profound impacts of plasticity.
Volume electron microscopy analysis of synapses in primary regions of the human cerebral cortex
Authors: Cano-Astorga Nicolás , Plaza-Alonso Sergio , DeFelipe Javier , Alonso-Nanclares Lidia 
Published: August 2024

Abstract
Functional and structural studies investigating macroscopic connectivity in the human cerebral cortex suggest that high-order associative regions exhibit greater connectivity compared to primary ones. However, the synaptic organization of these brain regions remains unexplored. In the present work, we conducted volume electron microscopy to investigate the synaptic organization of the human brain obtained at autopsy. Specifically, we examined layer III of Brodmann areas 17, 3b, and 4, as representative areas of primary visual, somatosensorial, and motor cortex. Additionally, we conducted comparative analyses with our previous datasets of layer III from temporopolar and anterior cingulate associative cortical regions (Brodmann areas 24, 38, and 21). 9,690 synaptic junctions were 3D reconstructed, showing that certain synaptic characteristics are specific to particular regions. The number of synapses per volume, the proportion of the postsynaptic targets, and the synaptic size may distinguish one region from another, regardless of whether they are associative or primary cortex. By contrast, other synaptic characteristics were common to all analyzed regions, such as the proportion of excitatory and inhibitory synapses, their shapes, their spatial distribution, and a higher proportion of synapses located on dendritic spines. The present results provide further insights into the synaptic organization of the human cerebral cortex.
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants
Authors: Xu Chunhui , Shaw Trey , Choppararu Sai Akhil , Lu Yiwei , Farooq Shaik Naveed , Qin Yongfang , Hudson Matt , Weekley Brock , Fisher Michael , He Fei , Da Silva Nascimento Jose Roberto , Wergeles Nicholas , Joshi Trupti , Bates Philip D , Koo Abraham J , Allen Doug K , Cahoon Edgar B , Thelen Jay J , Xu Dong 
Published: August 2024

Abstract
FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features.
Database URL: https://www.fatplants.net/
Structure of the crust and upper mantle in Greenland and northeastern Canada: insights from anisotropic Rayleigh-wave tomography
Authors: Ajourlou Parviz , Darbyshire Fiona , Audet Pascal , Milne Glenn A 
Published: August 2024

SUMMARY
Seismic velocity models provide important constraints on Greenland’s deep structure, which, in turn, has profound implications for our understanding of the tectonic history of this region. However, the resolution of seismic models has been limited by a sparse network, particularly in northern and central Greenland. We address these limitations by generating new high-resolution Rayleigh-wave phase velocity maps encompassing Greenland and northeastern Canada by processing over three decades of teleseismic earthquake records and incorporating recently added stations in Greenland and Arctic Canada. These phase velocity maps are sensitive to structure from the lower crust down to the sub-lithospheric mantle (25–185 s period). We find significant heterogeneity and a strong correlation between isotropic and anisotropic seismic velocities with inferred geological structure. High seismic velocities associated with cratonic lithosphere are broadly divided into two regions, with a belt of reduced velocity spanning central Greenland, which we interpret as lithospheric erosion resulting from interaction between the Greenland continental keel and the Iceland plume. Within each region, we identify tectonic subdivisions that suggest fundamental differences between the blocks that make up Precambrian Greenland. In the south, the North Atlantic craton (NAC) has a high-velocity keel exhibiting anisotropic stratification. Between the NAC and the cratonic lithosphere further north, the Proterozoic Nagssugtoqidian orogenic belt shows a distinct signature of reduced seismic velocity to $\sim$75 s period, but then appears to pinch out at depth. The northern Greenland lithosphere exhibits significant isotropic heterogeneity, with a distinct core of high velocities in the northwest ($\sim$55–75 s period) giving way to a set of distinct east-west trending high-velocity belts at longer periods. At all periods sensitive to the lithospheric mantle in this region, anisotropic fast orientations are E–W, consistent with a north–south Precambrian assembly of the Greenland shield. In contrast to the NAC, there is no evidence of anisotropic stratification in the northern part of the cratonic keel. Based on both isotropic and anisotropic phase-velocity anomalies, we suggest that the Phanerozoic Caledonian and Ellesmerian-Franklinian fold belts are relatively thin-skinned features onshore Greenland, though the Caledonian belt may have a stronger signature off the east coast. At the longest periods, a prominent low-velocity anomaly initially centred on Iceland migrates northwards and spreads beneath central-eastern Greenland. Coupled with NW–SE trending anisotropy, this feature is interpreted as the effect of mantle flow radiating outward from the Iceland plume and interacting with the eroded Greenland lithosphere.
GLAD-M35: a joint P and S global tomographic model with uncertainty quantification
Authors: Cui Congyue , Lei Wenjie , Liu Qiancheng , Peter Daniel , Bozdağ Ebru , Tromp Jeroen , Hill Judith , Podhorszki Norbert , Pugmire David 
Published: August 2024

SUMMARY
We present our third and final generation joint P and S global adjoint tomography (GLAD) model, GLAD-M35, and quantify its uncertainty based on a low-rank approximation of the inverse Hessian. Starting from our second-generation model, GLAD-M25, we added 680 new earthquakes to the database for a total of 2160 events. New P-wave categories are included to compensate for the imbalance between P- and S-wave measurements, and we enhanced the window selection algorithm to include more major-arc phases, providing better constraints on the structure of the deep mantle and more than doubling the number of measurement windows to 40 million. Two stages of a Broyden–Fletcher–Goldfarb–Shanno (BFGS) quasi-Newton inversion were performed, each comprising five iterations. With this BFGS update history, we determine the model’s standard deviation and resolution length through randomized singular value decomposition.
Dust beyond the torus: revealing the mid-infrared heart of local Seyfert ESO 428-G14 with JWST/MIRI
Authors: Haidar Houda , Rosario David J , Alonso-Herrero Almudena , Pereira-Santaella Miguel , García-Bernete Ismael , Campbell Stephanie , Hönig Sebastian F , Ramos Almeida Cristina , Hicks Erin , Delaney Daniel , Davies Richard , Ricci Claudio , Harrison Chris M , Leist Mason , Lopez-Rodriguez Enrique , Garcia-Burillo Santiago , Zhang Lulu , Packham Chris , Gandhi Poshak , Audibert Anelise , Bellocchi Enrica , Boorman Peter , Bunker Andrew , Combes Françoise , Diaz Santos Tanio , Donnan Fergus R , Gonzalez Martin Omaira , Hermosa Muñoz Laura , Charidis Matthaios , Labiano Alvaro , Levenson Nancy A , May Daniel , Rigopoulou Dimitra , Rodriguez Ardila Alberto , Shimizu T Taro , Stalevski Marko , Ward Martin 
Published: August 2024

ABSTRACT
Polar dust has been discovered in a number of local active galactic nuclei (AGN), with radiation-driven torus models predicting a wind to be its main driver. However, little is known about its characteristics, spatial extent, or connection to the larger scale outflows. We present the first JWST/MIRI study aimed at imaging polar dust by zooming on to the centre of ESO 428-G14, part of the Galaxy Activity, Torus, and Outflow Survey (GATOS) survey of local AGN. We detect extended mid-infrared (MIR) emission within 200 pc from the nucleus. This polar structure is co-linear with a radio jet and lies perpendicular to a molecular gas lane that feeds and obscures the nucleus. Its morphology bears a striking resemblance to that of gas ionized by the AGN in the narrow-line region. We demonstrate that part of this spatial correspondence is due to contamination within the JWST filter bands from strong emission lines. Correcting for the contamination, we find the morphology of the dust continuum to be more compact, though still clearly extended out to $r\approx 100 \, \rm pc$. We estimate the emitting dust has a temperature of $\sim 120\, \rm K$. Using simple models, we find that the heating of small dust grains by the radiation from the central AGN and/or radiative jet-induced shocks is responsible for the extended MIR emission. Radiation-driven dusty winds from the torus is unlikely to be important. This has important implications for scales to which AGN winds can carry dust and dense gas out into their host galaxies.
Can early dark energy be probed by the high-redshift galaxy abundance?
Authors: Liu Weiyang , Zhan Hu , Gong Yan , Wang Xin 
Published: August 2024

ABSTRACT
The analysis of the cosmic microwave background data acquired by the Atacama Cosmology Telescope and the large-scale ($\ell \lesssim 1300$) Planck Telescope show a preference for the early dark energy (EDE) theory, which was set to alleviate the Hubble tension of the $\Lambda$ cold dark matter ($\Lambda$CDM) model by decreasing the sound horizon $r_{s}$, and gives $H_{0} \approx 72$ km s$^{-1}$ Mpc$^{-1}$. However, the EDE model is commonly questioned for exacerbating the $\sigma _8$ tension on top of the $\Lambda$CDM model, and its lack of preference from the late-time matter power spectrum observations, e.g. Baryon Oscillation Spectroscopic Survey. In light of the current obscurities, we inspect if the high redshift galaxy abundance, i.e. stellar mass function/density and luminosity function, can independently probe the EDE model. Our result shows that, compared to $\Lambda$CDM, the EDE model prediction at $z\gt 10$ displays better consistency with the unexpectedly high results observed by the JWST. At lower redshift, the EDE model only fits the most luminous/massive end, with the majority of the data presenting better consistency with $\Lambda$CDM, implying that adding an extra luminosity/mass-sensitive suppression mechanism of the galaxy formation is required for EDE to explain all data around $z\sim 7-10$.
Solar differential rotation coefficients fitted from synoptic magnetic maps
Authors: Chu Zhe , Gu Haihua 
Published: August 2024

ABSTRACT
Based on the consecutive synoptic magnetic maps, we devise a new method to calculate the solar differential rotation coefficients. This method is very easy to implement and has a high accuracy. Firstly, based on the two-term or three-term differential rotation formula, we simulate a synoptic map CR$_{n}$ evolves one Carrington Rotation (CR) time only under the effect of the differential rotation, and thereby a stretched synoptic map CR$_{n*}$ is obtained. Then, through searching the maximum covariance between the maps CR$_{n*}$ and CR$_{n+1}$ by the grid search method, the rotation coefficients can be determined. Based on the synoptic maps of CRs 1625 to 2278 (during the years 1975–2023), the two-term coefficients A and B for latitude region between $\pm 40^{\circ }$ are calculated. The rotation coefficient B shows an obvious 11-yr period. From the time series of B, we find that the Sun usually rotates more differentially in the rising phases of the sunspot cycles than in the falling phases. Moreover, the strong magnetic field corresponds to an increasing of B (note that B has a negative sign) or decreasing of differential. The evolutionary trend of B also indicates that there are several years until the maximum value of B will be reached in solar cycle 25, and the coefficient B will be still in the rising phase in the few coming years. The two-term rotation coefficients for the two hemispheres are also calculated separately, and in the studied time-scale, the largest N–S asymmetry of the rotation rate appeared in October 2007.
77 Impact of CBM588 on gut microbiome composition and dysbiosis in patients receiving frontline immune checkpoint inhibitor (ICI) combinations for metastatic renal cell carcinoma (mRCC)
Authors: Dizman Nazli , Ebrahimi Hedyeh , Barragan-Carrillo Regina , Meza Luis A , Bergerot Paulo , Dorff Tanya , BSc JoAnn Hsu , Zengin Zeynep , Castro Daniela , Chehrazi-Raffle Alex , Triphathi Abhishek , Trent Jeffrey , Takahashi Motomichi , Oka Kentaro , Higashi Seiya , Caporaso Gregory , Lee Keehoon , Pal Sumanta K 
Published: August 2024

Abstract

Background
Two recent randomized phase I clinical trials have provided compelling evidence that CBM588, a Clostridium butyricum-based live biotherapeutic, holds potential to enhance clinical outcomes in patients with mRCC receiving frontline ICI combinations (Dizman et al Nature Medicine 2022; Ebrahimi et al ASCO 2023). We examined the impact of CBM588 on gut microbiome composition in a combined cohort of these two studies to further investigate its impact on gut microbiome

Methods
We analyzed stool samples from two phase I randomized clinical trials that enrolled patients with mRCC treated with (1) nivolumab/ipilimumab (nivo/ipi) +/- CBM588 and (2) cabozantinib/nivolumab (cabo/nivo) +/- CBM588. We compared gut microbiome diversity and composition at baseline and week 12 between patients in the standard of care (SOC) arms (nivo/ipi or cabo/nivo) and those who received CBM588 in combination with a SOC regimen (SOC/CBM). Taxonomic profiling was performed using MetaPhlan v4, and changes in the abundances of clinically relevant microbial species from baseline to week 12 were assessed using the Wilcoxon matched pairs test. The ratio of Firmicutes/Bacteroidetes, a measure of gut dysbiosis, was computed across time points in the two cohorts.

Results
Among 58 patients included in the analysis, 38 received SOC/CBM588 as first-line treatment. The median age was 60 years (range: 36-90) and the majority of patients were male (71%), had clear cell mRCC (88%), and intermediate/poor risk disease (79%). In both the SOC and SOC/CBM cohorts, there were no statistically significant differences in alpha and beta diversity between baseline and week 12. Among clinically relevant species compared between baseline and week 12, Alistipes senegalensis was found to decrease in both the SOC and SOC/CBM cohorts (log fold change [LFC] -0.82 [P=0.004] and LFC -0.36 [P=0.007], respectively), while Eubacterium siraeum decreased only in the SOC cohort (LFC -1.75 [P=0.005]). The Firmicutes/Bacteroidetes ratio increased from 89.0% to 96.4% in the SOC cohort, whereas a notable decrease was observed in this ratio from 100.0% to 75.7%. in the SOC/CBM cohort.

Conclusions
CBM588 leads to a marked correction of gut dysbiosis and prevents the depletion of species previously associated with ICI response (i.e., Eubacterium siraeum). These findings provide a plausible mechanism for the enhanced clinical outcome with CBM588 now seen across two small, randomized trials. A phase III study is planned within the cooperative groups to evaluate the clinical activity and gut microbiome modulation capacity of CBM588 in combination with ICIs in mRCC.
29 Pilot study of an implantable microdevice forin vivo evaluation of drug response in renal cell carcinoma (NCT05700461)
Authors: Xu Wenxin , Bhagavatula Sharath , Steiner Clara , Zhong Caiwei , Mossanen Matthew , Chang Steven , Hirsch Michelle , Ahn Sebastian , Matthew Destiny , Berg Stephanie , Serzan Michael , McGregor Bradley , Hata Nobuhiko , Viswanathan Srinivas , Silverman Stuart , Jonas* Oliver , Choueiri* Toni 
Published: August 2024

Abstract

Background
There are multiple therapies for renal cell carcinoma (RCC), yet no personalized biomarkers exist that can guide optimal treatment for individual patients. We developed implantable microdevices (IMD) that can be placed within a target tumor using a standard small-gauge interventional needle under imaging guidance. The IMDs deliver spatially segregated microdoses of up to 20 different drugs and/or combinations over multiple days, and then are retrieved surgically with surrounding tissue. This allows for the assessment of tumor response to multiple drugs in vivo within the native tumor microenvironment, without exposing the patient to systemic drug toxicity. We are conducting a trial to evaluate the safety and feasibility of IMD implantation in RCC tumors and subsequent collection of drug response data on targeted, cytotoxic, and immune-modulatory agents.

Methods

Eligible patients have suspected or confirmed RCC and are planned for standard surgical resection of either their primary tumor or metastasis. Three days prior to surgery, one or more IMDs are implanted percutaneously into the tumor under CT guidance. Following nephrectomy or excision of a metastasis, the microdevices with surrounding tumor are removed en bloc; subsequently, the tissue is fixed, embedded and sectioned. The tumor/IMD cross-sections are analyzed for drug effect for each of the spatially separate treatment effects using a wide range of techniques, including immunohistochemistry for proliferation and pathway markers, spatial immune profiling using a panel of 25 tumor microenvironment markers, and spatial transcriptomics. Patients receive subsequent standard of care systemic treatment as per their oncologist’s discretion.
Five patients have been enrolled and a total of 16 IMDs have been implanted to date. Enrollment is ongoing for a planned total of 20 patients. Success is defined as meeting both safety and feasibility endpoints. Safety is defined as two or fewer safety failures out of 20 enrolled patients. Feasibility is defined as 16 or more patients with successful microdevice implantation and retrieval of interpretable data.
IMDs will be analyzed to explore spatially segregated drug effects on the tumor microenvironment including tumor cell death and immune cell activation, as well as evidence of differential tumor drug sensitivity across treatments and patients.

Conclusions
Implantation of microdevices in RCC tumors may be a useful approach to improve treatment selection and accelerate drug development. Trial enrollment is ongoing.
27 Spatial Clustering of Immunosuppressive Macrophages in Papillary Renal Cell Carcinoma
Authors: Soupir Alex , Hayes Mitchell , Laborde Jose , Sabitov Mr Kirill , Peak Taylor , Nguyen Mr Jonathan , Moran-Segura Carlos , Saeed-Vafa Daryoush , Lopez-Blanco Neale , Echevarria Ms Paola Ramos , Guske Christopher , Blasi Jodi , Dhillon Jasreman , Kim Youngchul , Mulé James , Fridley Brooke , Manley Brandon 
Published: August 2024

Abstract

Background
Papillary renal cell carcinoma (pRCC) accounts for up to 15% of all kidney cancer cases, yet our understanding of its tumor immune microenvironment (TIME) remains limited. We utilized multiplex immunofluorescence (mIF) and spatial transcriptomics (ST) to evaluate immune cell spatial architecture in pRCC and compared to that of clear cell RCC (ccRCC).

Methods
Surgical tumor specimens were obtained from localized RCC tumors, followed by mIF using markers for T cells, B cells, and tumor-associated macrophages (TAMs). Spatial data were derived in regions of interest (ROIs) manually selected from spatially distinct tissue compartments of the TIME. Single-cell ST was performed on a subset of patient samples, utilizing probes against 960 transcripts. Cell abundance, cell spatial clustering, and spatially varying gene expression were analyzed to identify unique features of the TIME in pRCC.

Results
Sixteen pRCC and 70 ccRCC patient samples underwent mIF. Compared to ccRCC, global pRCC immune cell abundance was statistically lower amongst functional CD8 T cells, while global cell spatial clustering was higher amongst M2-like macrophages as measured by mIF, including PDL1+ subsets. Using ST, seven genes were significantly associated with spatial clustering of M2-like macrophages in pRCC. Three of seven genes (CCL18, GPNMB, CD9) are known markers of lipid-associated TAMs (LAMs) (adjusted p-value &lt; 0.1).

Conclusions
Compared to ccRCC, pRCC has fewer T cells but greater M2-like macrophage spatial clustering. Using ST, we found that multiple LAM-associated genes are spatially enriched in pRCC. Additional resources should be dedicated to investigating myeloid biomarkers and the impact of myeloid modulating therapeutics in pRCC.