bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overexpression of Fibroblast Activation Protein (FAP) in stroma of proliferative inflammatory atrophy (PIA) and primary adenocarcinoma of the prostate
Authors: Caramella-Pereira Fernanda , Zheng Qizhi , Hicks Jessica L. , Roy Sujayita , Jones Tracy , Pomper Martin , Antony Lizamma , Meeker Alan K. , Yegnasubramanian Srinivasan , De Marzo Angelo M. , Brennen W. Nathaniel 
Published: April 2024

AbstractFibroblast activation protein (FAP) is a serine protease upregulated at sites of tissue remodeling and cancer that represents a promising therapeutic and molecular imaging target. In prostate cancer, studies of FAP expression using tissue microarrays are conflicting, such that its clinical potential is unclear. Furthermore, little is known regarding FAP expression in benign prostatic tissues. Here we demonstrated, using a novel iterative multiplex IHC assay in standard tissue sections, that FAP was nearly absent in normal regions, but was increased consistently in regions of proliferative inflammatory atrophy (PIA). In carcinoma, FAP was expressed in all cases, but was highly heterogeneous. High FAP levels were associated with increased pathological stage and cribriform morphology. We verified that FAP levels in cancer correlated with CD163+ M2 macrophage density. In this first report to quantify FAP protein in benign prostate and primary tumors, using standard large tissue sections, we clarify that FAP is present in all primary prostatic carcinomas, supporting its potential clinical relevance. The finding of high levels of FAP within PIA supports the injury/regeneration model for its pathogenesis and suggests that it harbors a protumorigenic stroma. Yet, high levels of FAP in benign regions could lead to false positive FAP-based molecular imaging results in clinically localized prostate cancer.
Investigating the biosynthesis and roles of the auxin phenylacetic acid duringPseudomonas syringae-Arabidopsis thalianapathogenesis
Authors: Lee Chia-Yun , Harper Christopher P. , Lee Soon Goo , Qi Yunci , Clay Taylor , Aoi Yuki , Jez Joseph M. , Kasahara Hiroyuki , Blodgett Joshua A. V. , Kunkel Barbara N. 
Published: April 2024

AbstractSeveral plant-associated microbes synthesize the auxinic plant growth regulator phenylacetic acid (PAA) in culture; however, the role of PAA in plant-pathogen interactions is not well understood. In this study, we investigate the role of PAA during interactions between the phytopathogenic bacteriumPseudomonas syringaestrainPtoDC3000 (PtoDC3000) and the model plant host,Arabidopsis thaliana. Previous work demonstrated that indole-3-acetaldehyde dehydrogenase A (AldA) ofPtoDC3000 converts indole-3-acetaldehyde (IAAld) to the auxin indole-3-acetic acid (IAA). Here, we further demonstrate the biochemical versatility of AldA, as it can use both IAAld and phenylacetaldehyde as substrates to produce IAA and PAA, respectively. We also show that during infection AldA-dependent synthesis of either IAA or PAA byPtoDC3000 does not contribute significantly to the increase in auxin levels inA. thalianaleaves. Using availablearogenate dehydratase(adt) mutant lines ofA. thalianacompromised for PAA synthesis, we observed that a reduction in PAA-Asp and PAA-Glu is correlated with elevated levels of IAA and increased susceptibility. These results provide evidence that PAA/IAA homeostasis inA. thalianainfluences the outcome of plant-microbial interactions.
Quantitative metabolic reference for healthy human cerebrum derived from group averaged 9.4T1H MRSI data
Authors: Wright Andrew Martin , Ziegs Theresia , Henning Anke 
Published: April 2024

AbstractDrawing inspiration from previous works using1H FID MRSI, this study quantifies metabolite concentrations at 9.4 T in the human cerebrum of a volunteer cohort and performs a respective group analysis to derive region specific metabolite concentrations. Voxel-specific corrections were performed for both water and individual metabolites, as well as used tissue specific T1-relaxation times. Anatomical and magnetic resonance spectroscopic imaging data were collected using MP2RAGE and FID MRSI sequences, and subsequent data underwent a series of preprocessing techniques. Results showed consistent metabolite maps for key metabolites (NAA, tCr, Glu, tCho and mI), while instability in data quality was noted for lower slices. This study not only showcases the potential of metabolite quantification and mapping at 9.4 T but also underscores the necessity for meticulous data processing to ensure accurate metabolite representations. Comparisons with earlier works and single voxel results validate the methodologies adopted.HighlightsQuantitative whole cerebrum metabolite maps in the human brain acquired at 9.4 T.Group averaged regional metabolite concentrations.Group summed regional metabolite spectra.
Detection of clade 2.3.4.4b highly pathogenic H5N1 influenza virus in New York City
Authors: Meade Philip S. , Bandawane Pooja , Bushfield Kaitlyn , Hoxie Irene , Azcona Karla R. , Burgos Daneidy , Choudhury Sadia , Diaby Adama , Diallo Mariama , Gaynor Kailani , Huang Aaron , Kante Kadiatou , Khan Shehryar N. , Kim William , Ajayi Paul Kehinde , Roubidoux Ericka , Nelson Sasha , McMahon Rita , Albrecht Randy A , Krammer Florian , Marizzi Christine 
Published: April 2024

AbstractHighly pathogenic avian influenza viruses of the H5N1 clade 2.3.4.4b arrived in North America in the winter of 2021/2022. These viruses have spread across the Americas causing morbidity and mortality in both wild and domestic birds as well as some mammalian species, including cattle. Many surveillance programs in wildlife as well as commercial poultry operations have detected these viruses. Here we conducted surveillance of avian species in the urban environment in New York City. We detected highly pathogenic H5N1 viruses in six samples from four different bird species and performed full genome sequencing. Sequence analysis showed the presence of multiple different genotypes. Our work highlights that the interface between animals and humans that may give rise to zoonotic infections or even pandemics is not limited to rural environments and commercial poultry operations but extends into the heart of our urban centers.ImportanceWhile surveillance for avian influenza viruses is often focused on migratory routes and their associated stop-over locations, or commercial poultry operations, many bird species – including migratory birds – frequent or live in urban green spaces and wetlands. This brings them into contact with a highly dense population of humans and pets providing an extensive urban animal-human interface in which the general public may have little awareness of circulating infectious diseases. This study focuses on virus surveillance at this interface, combined with culturally responsive science education and community outreach.
Temperature adaptation of yeast phospholipid molecular species at the acyl chain positional level
Authors: Kelso Celine , Maccarone Alan T. , de Kroon Anton I.P.M. , Mitchell Todd W. , Renne Mike F. 
Published: April 2024

AbstractThe budding yeastSaccharomyces cerevisiaeis a poikilothermic organism and adapts its lipid composition to the environmental temperature to maintain membrane physical properties. Studies addressing temperature-dependent adaptation of the lipidome in yeast have described changes in the phospholipid composition at the level of sum composition (e.g.PC 32:1) and molecular composition (e.g. PC 16:0_16:1). However, to date, there is no information at the level of positional isomers (e.g.PC 16:0/16:1versusPC 16:1/16:0). In this study, combined Collision- and Ozone-Induced Dissociation (CID/OzID) mass spectrometry was deployed to investigate homeoviscous adaptation of PC, PE, and PSsn-molecular species composition. We determined the main species to be 16:1/16:1, 16:0/16:1, 16:1/18:1, 16:0/18:1, and 18:0/16:1. In general, at higher culture temperature, thesn-1 position is increased in saturated acyl chains, whereas thesn-2 position mainly is increased in acyl chain length. PC mainly increases in 16:0/16:1 and 16:0/18:1, at the expense of 16:1/16:1, whereas PS and PE increase in 16:1/18:1, at the expense of 16:1/16:1 and 16:0/16:1. Our data suggest distinct adaptation mechanisms of thesn-1 andsn-2 acyl chains, and different manners ofsn-molecular species adaptation between PC and PE/PS.
A lytic transglycosylase connects bacterial focal adhesion complexes to the peptidoglycan cell wall
Authors: Ramírez Carbó Carlos A. , Faromiki Olalekan G. , Nan Beiyan 
Published: April 2024

AbstractThe Gram-negative bacteriumMyxococcus xanthusglides on solid surfaces. Dynamic bacterial focal adhesion complexes (bFACs) convert proton motive force from the inner membrane into mechanical propulsion on the cell surface. It is unclear how the mechanical force transmits across the rigid peptidoglycan (PG) cell wall. Here we show that AgmT, a highly abundant lytic PG transglycosylase homologous toEscherichia coliMltG, couples bFACs to PG. Coprecipitation assay and single-particle microscopy reveal that the gliding motors fail to connect to PG and thus are unable to assemble into bFACs in the absence of an active AgmT. Heterologous expression ofE. coliMltG restores the connection between PG and bFACs and thus rescues gliding motility in theM. xanthuscells that lack AgmT. Our results indicate that bFACs anchor to AgmT-modified PG to transmit mechanical force across the PG cell wall.
The impact of package selection and versioning on single-cell RNA-seq analysis
Authors: Rich Joseph M , Moses Lambda , Einarsson Pétur Helgi , Jackson Kayla , Luebbert Laura , Booeshaghi A. Sina , Antonsson Sindri , Sullivan Delaney K. , Bray Nicolas , Melsted Páll , Pachter Lior 
Published: April 2024

SummaryStandard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting raw read data into cell-gene count matrices through sequence alignment, followed by analyses including filtering, highly variable gene selection, dimensionality reduction, clustering, and differential expression analysis. Seurat and Scanpy are the most widely-used packages implementing such workflows, and are generally thought to implement individual steps similarly. We investigate in detail the algorithms and methods underlying Seurat and Scanpy and find that there are, in fact, considerable differences in the outputs of Seurat and Scanpy. The extent of differences between the programs is approximately equivalent to the variability that would be introduced in benchmarking scRNA-seq datasets by sequencing less than 5% of the reads or analyzing less than 20% of the cell population. Additionally, distinct versions of Seurat and Scanpy can produce very different results, especially during parts of differential expression analysis. Our analysis highlights the need for users of scRNA-seq to carefully assess the tools on which they rely, and the importance of developers of scientific software to prioritize transparency, consistency, and reproducibility for their tools.
Maturing giant kelp develop depth-specific microbiomes
Authors: Esaian Sevan , Bui An , DiFiore Bartholomew P. , Peters Joseph R. , Lepori-Bui Michelle , Husted Kelsey , Moeller Holly V. , Wilbanks Elizabeth G. 
Published: April 2024

AbstractGiant kelp (Macrocystis pyrifera) is a photosynthetic macroalga that produces dissolved organic carbon (DOC), essential for marine bacteria and food webs. The bacterial communities residing on giant kelp blades consume and compete for complex carbohydrates, contributing to the microbiome community structure. In this study, we investigate how the microbiome changes in response to the age and depth of giant kelp blades and assess how these changes relate to differences in the host’s photophysiology. We find that the microbial community increases in richness and evenness as kelp blades age. While the microbiomes of juvenile blades are stochastic, communities on mature blades coalesce into less variable, depth-specific community types. Differentially abundant genera in mature microbiomes include members ofBacteroidiaandGammaproteobacteria, known for carbohydrate degradation, andPlanctomycetes, which often produce protective secondary metabolites. These shifts in microbiome communities are associated with increased maximum quantum yield of photosystem II of mature blades; therefore, they may be linked to enhanced DOC exudation. By shedding light on these dynamics, our study contributes to a better understanding of the complex interplay between macroalgae, their respective microbiomes, and the surrounding marine environment.
T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome ofEscherichia coliduring infection through a phage-encoded decapping enzyme
Authors: Wolfram-Schauerte Maik , Moskalchuk Anastassiya , Pozhydaieva Nadiia , Rojas Adán Andrés Ramírez , Schindler Daniel , Kaiser Stefanie , Pazcia Nicole , Höfer Katharina 
Published: April 2024

ABSTRACTNicotinamide adenine dinucleotide (NAD) serves as a cap-like structure on cellular RNAs (NAD-RNAs) in all domains of life including the bacteriumEscherichia coli. NAD also acts as a key molecule in phage-host interactions, where bacterial immune systems deplete NAD to abort phage infection. Nevertheless, NAD-RNAs have not yet been identified during phage infections of bacteria and the mechanisms of their synthesis and degradation are unknown in this context. The T4 phage that specifically infectsE. colipresents an important model to study phage infections, but a systematic analysis of the presence and dynamics of NAD-RNAs during T4 phage infection is lacking. Here, we investigate the presence of NAD-RNAs during T4 phage infection in a dual manner. By applying time-resolved NAD captureSeq, we identify NAD-capped host and phage transcripts and their dynamic regulation during phage infection. We provide evidence that NAD-RNAs are – as reported earlier – generated by the host RNA polymerase by initiating transcription with NAD at canonical transcription start sites. In addition, we characterize NudE.1 – a T4 phage-encoded Nudix hydrolase – as the first phage-encoded NAD-RNA decapping enzyme. T4 phages carrying inactive NudE.1 display a delayed lysis phenotype. This study investigates for the first time the dual epitranscriptome of a phage and its host, thereby introducing epitranscriptomics as an important field of phage research.
Make China great again: the strategies of Confucian accountants
Authors: Wang Yuheng , Ahn Paul D. 
Published: April 2024

PurposeThis paper aims to offer insight into how strategies within the accounting profession, which has been becoming more global, might be changed by the recent outbreak of the Second Cold War between the West and the Rest of the World.Design/methodology/approachWe explore the strategies of those who called themselves “Confucian accountants” in China, a country which has recently discouraged its state-owned enterprises from using the services of the Big 4. We do this by employing qualitative research methods, including reflexive photo interviews, in which Big-4 accountants, recognised as the most Westernised accounting actors in China, and Confucian accountants are asked to take and explain photographs representing their professional lives. Bourdieu’s notions of “economy of practices” and “vision-of-division strategy” are drawn upon to understand who the Confucian accountants are and what they do strategically in their pursuit of a higher revenue stream and improved social standing in the Chinese social space.FindingsThe homegrown Confucian accountants share cultural-cognitive characteristics with neighbouring social actors, such as their clients and government officials, who have been inculcated with Confucianism and the state’s cultural confidence policy in pursuit of a “socialist market economy with Chinese characteristics”. Those accountants try to enhance their social standing and revenue stream by strategically demonstrating their difference from Big-4 accountants. For this purpose, they wear Confucian clothes, have Confucian props in their office, employ Confucian phrases in their everyday conversations, use Confucian business cards and construct and maintain guanxi with government officials and clients.Originality/valueThis paper is the first attempt to explore Confucian accountants’ strategies for increasing their revenue and social standing at the start of the Second Cold War.
A comparative study of capital structure compositions in grain marketing and input supply cooperatives
Authors: Grashuis Jasper , Jacobs Keri 
Published: April 2024

PurposeThe objective of the study is to explore explanations for the capital structure compositions of farmer cooperatives, which have a unique equity structure with allocated equity as well as unallocated equity.Design/methodology/approachData came from a panel of US grain marketing and input supply cooperatives for the 2010–2020 period. The study is concerned with the proportions of debt, allocated equity and unallocated equity, which requires the application of a fractional multinomial panel model to ensure predictions fall within the observed data range (i.e. 0–1).FindingsLarger cooperatives have relatively high debt proportions. Diversification of the product portfolio has a positive effect on the debt proportion. Profitability is associated with higher debt proportions in input supply cooperatives and higher allocated equity proportions in grain marketing cooperatives. Over time, the proportion of unallocated equity increased. Overall, some results differ across grain marketing and input supply cooperatives.Practical implicationsIncreasing proportions of unallocated equity warrant a debate about the future value of ownership and governance by members of farmer cooperatives.Originality/valuePrevious empirical investigations of the capital structure compositions of cooperatives lacked a distinction between allocated and unallocated equity. Our results show that the proportions of the two equity accounts respond differently to given predictors. Furthermore, much of the prior empirical literature fails to separate cooperatives on the basis of economic activities (i.e. marketing, supply and mixed).
An analysis of long-term and short-term impact of climate change on rice production in India
Authors: Singh Arshdeep , Arora Kashish , Babu Suresh Chandra 
Published: April 2024

PurposeClimate change-related weather events significantly affect rice production. In this paper, we investigate the impact of and interrelationships between agriculture inputs, climate change factors and financial variables on rice production in India from 1970–2021.Design/methodology/approachThis study is based on the time series analysis; the unit root test has been employed to unveil the integration order. Further, the study used various econometric techniques, including vector autoregression estimates (VAR), cointegration test, autoregressive distributed lag (ARDL) model and diagnostic test for ARDL, fully modified least squares (FMOLS), canonical cointegrating regression (CCR), impulse response functions (IRF) and the variance decomposition method (VDM) to validate the long- and short-term impacts of climate change on rice production in India of the scrutinized variables.FindingsThe study's findings revealed that the rice area, precipitation and maximum temperature have a significant and positive impact on rice production in the short run. In the long run, rice area (ß = 1.162), pesticide consumption (ß = 0.089) and domestic credit to private sector (ß = 0.068) have a positive and significant impact on rice production. The results show that minimum temperature and direct institutional credit for agriculture have a significant but negative impact on rice production in the short run. Minimum temperature, pesticide consumption, domestic credit to the private sector and direct institutional credit for agriculture have a negative and significant impact on rice production in the long run.Originality/valueThe present study makes valuable and original contributions to the literature by examining the short- and long-term impacts of climate change on rice production in India over 1970–2021. To the best of the authors’ knowledge, The majority of the studies examined the impact of climate change on rice production with the consideration of only “mean temperature” as one of the climatic variables, while in the present study, the authors have considered both minimum as well as maximum temperature. Furthermore, the authors also considered the financial variables in the model.
Oil price uncertainty and excess value of diversification
Authors: Singh Amanjot 
Published: April 2024

PurposeThis study examines the value implications of oil price uncertainty for investors in diversified firms using a sample of 922 USA firms from 2001 to 2019.Design/methodology/approachOur study employs a panel dataset to examine the value implications of oil price uncertainty for diversified firm investors. We consider several alternative specifications to account for unobserved factors and measurement errors that could potentially bias our results. In particular, we use alternative measures of the excess value of diversified firms and oil price uncertainty, additional control variables, fixed-effects models, the Oster test, impact threshold for confounding variable (ITCV) analysis, two-stage least square instrumental variable (2SLS-IV) analysis and the system-GMM model.FindingsWe find that the excess value of diversified firms, relative to a benchmark portfolio of single-segment firms, increases with high oil price uncertainty. The impact of oil price uncertainty is asymmetric, as corporate diversification is value-increasing for diversified firm investors only when the volatility is due to positive oil price changes and amidst supply-driven oil price shocks. The excess value increases irrespective of diversified firms’ financial constraints and oil usage. Diversified firms become conservative in their internal capital allocations with high oil price uncertainty. Such conservatism is value-increasing for diversified firm investors, as it supports higher performance in response to oil price uncertainty.Originality/valueOur study has three important implications: first, they are relevant to investors in understanding the portfolio value implications of oil price uncertainty. Second, they are helpful for firm managers while comprehending the value-relevant implications of internal capital allocations. Finally, our findings are policy relevant in the context of the future of diversified firms in developed markets.