bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frogeye leaf spot caused by Cercospora sojina: A review
Authors: Barro Jhonatan P. , Neves Danilo L. , Del Ponte Emerson M. , Bradley Carl A. 
Published: June 2023

AbstractFrogeye leaf spot (FLS), caused by Cercospora sojina, is an economically important disease of soybean in many parts of the world where soybean is grown, including the United States and Argentina. Yield losses caused by FLS epidemics are mainly due to reduced photosynthetic leaf area, premature defoliation and reduced seed weight. Epidemics may be initiated from inoculum produced on infected plant residue where the pathogen can overwinter for up to two years. Many questions relating to population biology, genetic variability and pathotype structure remain unanswered. Race designations for C. sojina are under debate since the use of the 12 soybean differentials has produced inconsistent numbers of races in separate studies. Although a sexual stage for C. sojina has not been observed in either field or laboratory conditions, equal proportion of mating-type loci and high genotypic diversity suggest that populations of C. sojina are most likely to be undergoing cryptic sexual reproduction. Management practices for this disease include the use of cultivars with partial or complete resistance (Rcs genes), cultural practices (crop rotation and tillage) and foliar fungicide applications. However, resistance to quinone outside inhibitor (QoI) fungicides (caused by the G143A mutation in the Cytochrome b gene) has been reported since 2010, and resistant populations have become widespread across more than 20 soybean-producing states in the U.S. This review provides detailed information on the taxonomy, identification and genetic diversity of the pathogen. It also summarizes epidemiological aspects and strategies to combat this increasing threat to soybean crops worldwide.
Managing the Risk of COVID-19 Using Model Based Predictors: The Case of North Dakota
Authors: Sidhu Savita K. , Hohman Adam , Strand Mark A. , Shyllon Omobosinuola , Jansen Rick , McDonough Stephen 
Published: June 2023

AbstractObjective:North Dakota (ND) had the highest coronavirus disease 2019 (COVID-19) case and mortality rate in the United States for nearly 2 mo. This study aims to compare 3 metrics ND used to guide public health action across its 53 counties.Methods:Daily COVID-19 case and death totals in North Dakota were evaluated using data from the COVID-tracker website provided by the North Department of Health (NDDoH). It was reported as: active cases per 10,000, tests administered per 10,000, and test positivity rate (the North Dakota health metric). The COVID-19 Response press conferences provided data for the Governor’s metric. The Harvard model used daily new cases per 100,000. A chi-squared test was used to compare differences in these 3 metrics on July 1, August 26, September 23, and November 13, 2020.Results:On July 1, no significant difference between the metrics was found. By September 23, Harvard’s health metric indicated critical risk while ND’s health metric was moderate risk, and the Governor’s metric was still low risk.Conclusions:ND’s and the Governor’s metric underrepresented the risk of the COVID-19 outbreak in North Dakota. The Harvard metric reflected North Dakota’s increasing risk; it should be considered as a national standard in future pandemics.Public Health Implications:Model-based predictors could guide policy-makers to effectively control spread of infectious disease; proactive models could reduce risk of disease as it progresses in vulnerable communities.
Control systems and data management for high-power laser facilities
Authors: Feister Scott , Cassou Kevin , Dann Stephen , Döpp Andreas , Gauron Philippe , Gonsalves Anthony J. , Joglekar Archis , Marshall Victoria , Neveu Olivier , Schlenvoigt Hans-Peter , Streeter Matthew J. V. , Palmer Charlotte A. J. 
Published: June 2023

AbstractThe next generation of high-power lasers enables repetition of experiments at orders of magnitude higher frequency than what was possible using the prior generation. Facilities requiring human intervention between laser repetitions need to adapt in order to keep pace with the new laser technology. A distributed networked control system can enable laboratory-wide automation and feedback control loops. These higher-repetition-rate experiments will create enormous quantities of data. A consistent approach to managing data can increase data accessibility, reduce repetitive data-software development and mitigate poorly organized metadata. An opportunity arises to share knowledge of improvements to control and data infrastructure currently being undertaken. We compare platforms and approaches to state-of-the-art control systems and data management at high-power laser facilities, and we illustrate these topics with case studies from our community.
A strongly convergent algorithm for solving multiple set split equality equilibrium and fixed point problems in Banach spaces
Authors: Godwin E.C. , Mewomo O.T. , Alakoya T.O. 
Published: June 2023

AbstractIn this article, using an Halpern extragradient method, we study a new iterative scheme for finding a common element of the set of solutions of multiple set split equality equilibrium problems consisting of pseudomonotone bifunctions and the set of fixed points for two finite families of Bregman quasi-nonexpansive mappings in the framework of p-uniformly convex Banach spaces, which are also uniformly smooth. For this purpose, we design an algorithm so that it does not depend on prior estimates of the Lipschitz-type constants for the pseudomonotone bifunctions. Furthermore, we present an application of our study for finding a common element of the set of solutions of multiple set split equality variational inequality problems and fixed point sets for two finite families of Bregman quasi-nonexpansive mappings. Finally, we conclude with two numerical experiments to support our proposed algorithm.
Schwarz lemma for real harmonic functions onto surfaces with non-negative Gaussian curvature
Authors: Kalaj David , Mateljević Miodrag , Pinelis Iosif 
Published: June 2023

AbstractAssume that f is a real ρ-harmonic function of the unit disk $\mathbb{D}$ onto the interval $(-1,1)$, where $\rho(u,v)=R(u)$ is a metric defined in the infinite strip $(-1,1)\times \mathbb{R}$. Then we prove that $|\nabla f(z)|(1-|z|^2)\le \frac{4}{\pi}(1-f(z)^2)$ for all $z\in\mathbb{D}$, provided that ρ has a non-negative Gaussian curvature. This extends several results in the field and answers to a conjecture proposed by the first author in 2014. Such an inequality is not true for negatively curved metrics.
The entanglements of exchange in India
Authors: Jan Muhammad Ali 
Published: June 2023

AbstractIn thisModern Asian Studiesbook symposium, scholars of South Asia analyse the political, ethical, and epistemic aspects of market life, building on the volumeRethinking Markets in Modern India.1This interdisciplinary conversation approaches transactional realms from the disciplines of history, anthropology, development studies, and political economy. The symposium’s contributors examine a range of pertinent issues that encompass customary forms of exchange and capitalist aspects of trade. Among the topics discussed are those of market fetishism, bazaar knowledge, social embeddedness, forms of transactional representation and translation, and institutional and regulatory contexts for commerce.
Depth Moderates DOC Impact on Cold‐Water Refugia in Small, Northern Temperate Lakes
Authors: Gavin Amanda L. , Nelson Sarah J. , Saros Jasmine E. , SanClements Michael D. , Fernandez Ivan J. 
Published: June 2023

AbstractWidespread changes in dissolved organic carbon (DOC) concentrations in lakes of the Northern Hemisphere are well documented, and there is a need to understand the ecological implications for changes in cold‐water refugia. DOC controls thermal structure in small, wind‐sheltered lakes, thus influencing the volume and persistence of the hypolimnion and cold‐water habitat. We explored the relationship between the quantity and quality of DOC and the availability of cold‐water habitat over the course of summer stratification in small lakes of varying depths. The ratio of the hypolimnetic volume to total lake volume was calculated to assess the relative changes in cold‐water habitat availability in each lake over time. DOC concentration, maximum lake depth, and the interaction between DOC concentration and maximum lake depth explained 87% of the variability in percent change in hypolimnion volume ratio across studied lakes. Hypolimnion compression was greater in shallow, low DOC lakes, whereas deeper, intermediate DOC lakes had more persistent hypolimnion volumes over the course of summer stratification. These results demonstrate that depth moderates the effect of DOC on the volume and persistence of cold‐water refugia availability in north temperate lakes, advancing our understanding of differing lake sensitivity in a rapidly changing physical and chemical environment.
Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs
Authors: Pherribo Gordon J , Taga Michiko E 
Published: June 2023

Abstract
Microbial communities host many auxotrophs—organisms unable to synthesize one or more metabolites required for their growth. Auxotrophy is thought to confer an evolutionary advantage, yet auxotrophs must rely on other organisms that produce the metabolites they require. The mechanisms of metabolite provisioning by “producers” remain unknown. In particular, it is unclear how metabolites such as amino acids and cofactors, which are found inside the cell, are released by producers to become available to auxotrophs. Here, we explore metabolite secretion and cell lysis as two distinct possible mechanisms that result in the release of intracellular metabolites from producer cells. We measured the extent to which secretion or lysis of Escherichia coli and Bacteroides thetaiotaomicron amino acid producers can support the growth of engineered Escherichia coli amino acid auxotrophs. We found that cell-free supernatants and mechanically lysed cells provide minimal levels of amino acids to auxotrophs. In contrast, bacteriophage lysates of the same producer bacteria can support as many as 47 auxotroph cells per lysed producer cell. Each phage lysate released distinct levels of different amino acids, suggesting that in a microbial community the collective lysis of many different hosts by multiple phages could contribute to the availability of an array of intracellular metabolites for use by auxotrophs. Based on these results, we speculate that viral lysis could be a dominant mechanism of provisioning of intracellular metabolites that shapes microbial community structure.
Reconciling the biomedical data commons and the GDPR: three lessons from the EUCAN ELSI collaboratory
Authors: Bernier Alexander , Molnár-Gábor Fruzsina , Knoppers Bartha M. , Borry Pascal , Cesar Priscilla M. D. G. , Devriendt Thijs , Goisauf Melanie , Murtagh Madeleine , Jiménez Pilar Nicolás , Recuero Mikel , Rial-Sebbag Emmanuelle , Shabani Mahsa , Wilson Rebecca C. , Zaccagnini Davide , Maxwell Lauren 
Published: June 2023

AbstractThe coming-into-force of the EU General Data Protection Regulation (GDPR) is a watershed moment in the legal recognition of enforceable rights to informational self-determination. The rapid evolution of legal requirements applicable to data use, however, has the potential to outstrip the capabilities of networks of biomedical data users to respond to the shifting norms. It can also delegitimate established institutional bodies that are responsible for assessing and authorising the downstream use of data, including research ethics committees and institutional data custodians. These burdens are especially pronounced for clinical and research networks that are of transnational scale, because the legal compliance burden for outbound international data transfers from the EEA is especially high. Legislatures, courts, and regulators in the EU should therefore implement the following three legal changes. First, the responsibilities of particular actors in a data sharing network should be delimited through the contractual allocation of responsibilities between collaborators. Second, the use of data through secure data processing environments should not trigger the international transfer provisions of the GDPR. Third, the use of federated data analysis methodologies that do not provide analysis nodes or downstream users access to identifiable personal data as part of the outputs of those analyses should not be considered circumstances of joint controllership, nor lead to the users of non-identifiable data to be considered controllers or processors. These small clarifications of, or modifications to, the GDPR would facilitate the exchange of biomedical data amongst clinicians and researchers.
Evolutionary and functional history of the Escherichia coli K1 capsule
Authors: Arredondo-Alonso Sergio , Blundell-Hunter George , Fu Zuyi , Gladstone Rebecca A. , Fillol-Salom Alfred , Loraine Jessica , Cloutman-Green Elaine , Johnsen Pål J. , Samuelsen Ørjan , Pöntinen Anna K. , Cléon François , Chavez-Bueno Susana , De la Cruz Miguel A. , Ares Miguel A. , Vongsouvath Manivanh , Chmielarczyk Agnieszka , Horner Carolyne , Klein Nigel , McNally Alan , Reis Joice N. , Penadés José R. , Thomson Nicholas R. , Corander Jukka , Taylor Peter W. , McCarthy Alex J. 
Published: June 2023

AbstractEscherichia coliis a leading cause of invasive bacterial infections in humans. Capsule polysaccharide has an important role in bacterial pathogenesis, and the K1 capsule has been firmly established as one of the most potent capsule types inE. colithrough its association with severe infections. However, little is known about its distribution, evolution and functions across theE. coliphylogeny, which is fundamental to elucidating its role in the expansion of successful lineages. Using systematic surveys of invasiveE. coliisolates, we show that the K1-cpslocus is present in a quarter of bloodstream infection isolates and has emerged in at least four different extraintestinal pathogenicE. coli(ExPEC) phylogroups independently in the last 500 years. Phenotypic assessment demonstrates that K1 capsule synthesis enhancesE. colisurvival in human serum independent of genetic background, and that therapeutic targeting of the K1 capsule re-sensitizesE. colifrom distinct genetic backgrounds to human serum. Our study highlights that assessing the evolutionary and functional properties of bacterial virulence factors at population levels is important to better monitor and predict the emergence of virulent clones, and to also inform therapies and preventive medicine to effectively control bacterial infections whilst significantly lowering antibiotic usage.
Chemoproteomic target deconvolution reveals Histone Deacetylases as targets of (R)-lipoic acid
Authors: Lechner Severin , Steimbach Raphael R. , Wang Longlong , Deline Marshall L. , Chang Yun-Chien , Fromme Tobias , Klingenspor Martin , Matthias Patrick , Miller Aubry K. , Médard Guillaume , Kuster Bernhard 
Published: June 2023

AbstractLipoic acid is an essential enzyme cofactor in central metabolic pathways. Due to its claimed antioxidant properties, racemic (R/S)-lipoic acid is used as a food supplement but is also investigated as a pharmaceutical in over 180 clinical trials covering a broad range of diseases. Moreover, (R/S)-lipoic acid is an approved drug for the treatment of diabetic neuropathy. However, its mechanism of action remains elusive. Here, we performed chemoproteomics-aided target deconvolution of lipoic acid and its active close analog lipoamide. We find that histone deacetylases HDAC1, HDAC2, HDAC3, HDAC6, HDAC8, and HDAC10 are molecular targets of the reduced form of lipoic acid and lipoamide. Importantly, only the naturally occurring (R)-enantiomer inhibits HDACs at physiologically relevant concentrations and leads to hyperacetylation of HDAC substrates. The inhibition of HDACs by (R)-lipoic acid and lipoamide explain why both compounds prevent stress granule formation in cells and may also provide a molecular rationale for many other phenotypic effects elicited by lipoic acid.
Molecular mechanisms of Holliday junction branch migration catalyzed by an asymmetric RuvB hexamer
Authors: Rish Anthony D. , Shen Zhangfei , Chen Zhenhang , Zhang Nan , Zheng Qingfei , Fu Tian-Min 
Published: June 2023

AbstractThe Holliday junction (HJ) is a DNA intermediate of homologous recombination, involved in many fundamental physiological processes. RuvB, an ATPase motor protein, drives branch migration of the Holliday junction with a mechanism that had yet to be elucidated. Here we report two cryo-EM structures of RuvB, providing a comprehensive understanding of HJ branch migration. RuvB assembles into a spiral staircase, ring-like hexamer, encircling dsDNA. Four protomers of RuvB contact the DNA backbone with a translocation step size of 2 nucleotides. The variation of nucleotide-binding states in RuvB supports a sequential model for ATP hydrolysis and nucleotide recycling, which occur at separate, singular positions. RuvB’s asymmetric assembly also explains the 6:4 stoichiometry between the RuvB/RuvA complex, which coordinates HJ migration in bacteria. Taken together, we provide a mechanistic understanding of HJ branch migration facilitated by RuvB, which may be universally shared by prokaryotic and eukaryotic organisms.
CNK2 promotes cancer cell motility by mediating ARF6 activation downstream of AXL signalling
Authors: Serwe Guillaume , Kachaner David , Gagnon Jessica , Plutoni Cédric , Lajoie Driss , Duramé Eloïse , Sahmi Malha , Garrido Damien , Lefrançois Martin , Arseneault Geneviève , Saba-El-Leil Marc K. , Meloche Sylvain , Emery Gregory , Therrien Marc 
Published: June 2023

AbstractCell motility is a critical feature of invasive tumour cells that is governed by complex signal transduction events. Particularly, the underlying mechanisms that bridge extracellular stimuli to the molecular machinery driving motility remain partially understood. Here, we show that the scaffold protein CNK2 promotes cancer cell migration by coupling the pro-metastatic receptor tyrosine kinase AXL to downstream activation of ARF6 GTPase. Mechanistically, AXL signalling induces PI3K-dependent recruitment of CNK2 to the plasma membrane. In turn, CNK2 stimulates ARF6 by associating with cytohesin ARF GEFs and with a novel adaptor protein called SAMD12. ARF6-GTP then controls motile forces by coordinating the respective activation and inhibition of RAC1 and RHOA GTPases. Significantly, genetic ablation of CNK2 or SAMD12 reduces metastasis in a mouse xenograft model. Together, this work identifies CNK2 and its partner SAMD12 as key components of a novel pro-motility pathway in cancer cells, which could be targeted in metastasis.
A complete telomere-to-telomere assembly of the maize genome
Authors: Chen Jian , Wang Zijian , Tan Kaiwen , Huang Wei , Shi Junpeng , Li Tong , Hu Jiang , Wang Kai , Wang Chao , Xin Beibei , Zhao Haiming , Song Weibin , Hufford Matthew B. , Schnable James C. , Jin Weiwei , Lai Jinsheng 
Published: June 2023

AbstractA complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a complete genome assembly of maize with each chromosome entirely traversed in a single contig. The 2,178.6 Mb T2T Mo17 genome with a base accuracy of over 99.99% unveiled the structural features of all repetitive regions of the genome. There were several super-long simple-sequence-repeat arrays having consecutive thymine–adenine–guanine (TAG) tri-nucleotide repeats up to 235 kb. The assembly of the entire nucleolar organizer region of the 26.8 Mb array with 2,974 45S rDNA copies revealed the enormously complex patterns of rDNA duplications and transposon insertions. Additionally, complete assemblies of all ten centromeres enabled us to precisely dissect the repeat compositions of both CentC-rich and CentC-poor centromeres. The complete Mo17 genome represents a major step forward in understanding the complexity of the highly recalcitrant repetitive regions of higher plant genomes.
Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis
Authors: Shaw Dustin G. , Aguirre-Gamboa Raúl , Vieira Marcos C. , Gona Saideep , DiNardi Nicholas , Wang Anni , Dumaine Anne , Gelderloos-Arends Jody , Earley Zachary M. , Meckel Katherine R. , Ciszewski Cezary , Castillo Anabella , Monroe Kelly , Torres Joana , Shah Shailja C. , Colombel Jean-Frédéric , Itzkowitz Steven , Newberry Rodney , Cohen Russell D. , Rubin David T. , Quince Christopher , Cobey Sarah , Jonkers Iris H. , Weber Christopher R. , Pekow Joel , Wilson Patrick C. , Barreiro Luis B. , Jabri Bana 
Published: June 2023

AbstractPrimary sclerosing cholangitis (PSC) is an immune-mediated disease of the bile ducts that co-occurs with inflammatory bowel disease (IBD) in almost 90% of cases. Colorectal cancer is a major complication of patients with PSC and IBD, and these patients are at a much greater risk compared to patients with IBD without concomitant PSC. Combining flow cytometry, bulk and single-cell transcriptomics, and T and B cell receptor repertoire analysis of right colon tissue from 65 patients with PSC, 108 patients with IBD and 48 healthy individuals we identified a unique adaptive inflammatory transcriptional signature associated with greater risk and shorter time to dysplasia in patients with PSC. This inflammatory signature is characterized by antigen-driven interleukin-17A (IL-17A)+ forkhead box P3 (FOXP3)+ CD4 T cells that express a pathogenic IL-17 signature, as well as an expansion of IgG-secreting plasma cells. These results suggest that the mechanisms that drive the emergence of dysplasia in PSC and IBD are distinct and provide molecular insights that could guide prevention of colorectal cancer in individuals with PSC.
Clonal hematopoiesis is associated with protection from Alzheimer’s disease
Authors: Bouzid Hind , Belk Julia A. , Jan Max , Qi Yanyan , Sarnowski Chloé , Wirth Sara , Ma Lisa , Chrostek Matthew R. , Ahmad Herra , Nachun Daniel , Yao Winnie ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Bis Joshua , Psaty Bruce , Beiser Alexa , Bick Alexander G. , Bis Joshua C. , Fornage Myriam , Longstreth William T. , Lopez Oscar L. , Natarajan Pradeep , Psaty Bruce M. , Satizabal Claudia L. , Weinstock Joshua , Larson Eric B. , Crane Paul K. , Keene C. Dirk , Seshadri Sudha , Satpathy Ansuman T. , Montine Thomas J. , Jaiswal Siddhartha 
Published: June 2023

AbstractClonal hematopoiesis of indeterminate potential (CHIP) is a premalignant expansion of mutated hematopoietic stem cells. As CHIP-associated mutations are known to alter the development and function of myeloid cells, we hypothesized that CHIP may also be associated with the risk of Alzheimer’s disease (AD), a disease in which brain-resident myeloid cells are thought to have a major role. To perform association tests between CHIP and AD dementia, we analyzed blood DNA sequencing data from 1,362 individuals with AD and 4,368 individuals without AD. Individuals with CHIP had a lower risk of AD dementia (meta-analysis odds ratio (OR) = 0.64, P = 3.8 × 10−5), and Mendelian randomization analyses supported a potential causal association. We observed that the same mutations found in blood were also detected in microglia-enriched fraction of the brain in seven of eight CHIP carriers. Single-nucleus chromatin accessibility profiling of brain-derived nuclei in six CHIP carriers revealed that the mutated cells comprised a large proportion of the microglial pool in the samples examined. While additional studies are required to validate the mechanistic findings, these results suggest that CHIP may have a role in attenuating the risk of AD.