bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic lags influence rapid evolution throughout a drought cycle
Authors: Branch Haley A. , Anstett Daniel N. , Angert Amy L. 
Published: August 2023

AbstractClimate anomalies pose strong selection which can lead to rapid evolution. These global mean trends occur on a backdrop of interannual variability that might weaken or even reverse selection. However, the impact of climatic interannual variability on rapid evolution is rarely considered. We study evolution through a seven-year period encompassing a severe drought across 12 populations ofMimulus cardinalis(scarlet monkeyflower). Plants were grown in a common greenhouse environment under wet and dry treatments, where specific leaf area and date of flowering were measured. We compare the ability of different climate metrics to explain the rapid evolution of trait values, examining different time-periods, including the collection year, prior years, and cumulative metrics across sequential years. We find that anomalies in mean annual precipitation best describe rapid evolution over our study period. Past climates, of one-to two-years ago, are often related to trait values in a conflicting direction to collection-year climate. Uncovering these complex climatic impacts on evolution is critical to better predict and interpret the impacts of climate change.
Neural signatures of attentional prioritization and facilitation in accessing repeated items in Visual Working memory
Authors: Narvaria Abhishek Singh , Banerjee Arpan , Roy Dipanjan 
Published: August 2023

AbstractThe top-down goal voluntarily maintains and selectively recalls items in visual working memory (VWM). In contrast, bottom-up attentional selection due to stimulus-driven selection by saliency or relational account, like in perceptually similar items has been found to prioritize items and facilitate recalling them in VWM involuntarily. However, there is a knowledge gap about whether repeated items, a relational property of stimuli can acquire prioritized access in VWM and act as a distractor that hinders recalling not-repeated items even if a valid probe facilitates them. To address this, we designed a novel VWM-based EEG study where human participants respond to a probe for an item’s presence or absence in a memory array containing repeated and not repeated items. Significantly slower response times and comparatively poor accuracy for recalling not-repeated items suggest that they are not prioritized, whereas repeated items are. Using spectral perturbation-based EEG analysis, we identified specific differences for sensor clusters in the power of beta, alpha and theta band as the neural correlate of probe matching for not-repeated vs. repeated conditions reflecting biased access to VWM items. For not-repeated item probe matching, delay in beta desynchronization shows poor memory-guided action selection behaviour. Whereas, higher frontal theta and parietal alpha power demonstrated a demand for stronger cognitive control for recalling items for not-repeated probe matching by shielding them from distracting repeated items. In summary, this opens up avenues for further investigations of distraction due to repetition like the relational property of stimuli and explaining the mechanisms of prioritized access of repeated items over goal-driven relevant not-repeated items in VWM.
NeuronalSNCAtranscription during Lewy body formation
Authors: Kon Tomoya , Forrest Shelley L. , Lee Seojin , Martinez-Valbuena Ivan , Li Jun , Nassir Nasna , Uddin Mohammed J. , Lang Anthony E. , Kovacs Gabor G. 
Published: August 2023

ABSTRACTBackgroundMisfolded α-synuclein (α-syn) is believed to contribute to neurodegeneration in Lewy body disease (LBD) based on considerable evidence including a gene-dosage effect observed in relation to point mutations and multiplication ofSNCAin familial Parkinson’s disease. A contradictory concept proposes early loss of the physiological α-syn as the major driver of neurodegeneration. There is a paucity of data onSNCAtranscripts in various α-syn immunoreactive cytopathologies.MethodsSNCAtranscripts in neurons without and with various α-syn immunoreactive cytopathologies in the substantia nigra and amygdala in LBD (n = 5) were evaluated using RNAscope combined with immunofluorescence for disease-associated α-syn. Single-nucleus RNA sequencing was performed to elucidate cell-type specificSNCAexpression in non-diseased frontal cortex (n = 3).ResultsSNCAtranscripts in neurons with punctate α-syn immunoreactivity were preserved both in the substantia nigra and amygdala but were reduced in neurons with compact α-syn inclusions. Only singleSNCAtranscripts were detected in astrocytes with or without α-syn immunoreactivity in the amygdala. Single-nucleus RNA sequencing revealed that excitatory and inhibitory neurons, oligodendrocyte progenitor cells, oligodendrocytes, and homeostatic microglia expressedSNCAtranscripts, while expression was largely absent in astrocytes and microglia.ConclusionsThe preserved cellularSNCAexpression in the more abundant non-Lewy body type α-syn cytopathologies provides a pool for local protein production that can aggregate and serve as a seed for misfolded α-syn. Successful segregation of disease-associated α-syn is associated with the exhaustion ofSNCAproduction in the terminal cytopathology, the Lewy body. Our observations support a therapeutic strategy incorporating a finely tuned dual approach targeting the elimination of misfolded α-syn along with the reduction of theSNCAtranscription to avoid feeding of pathological α-syn seeding.
The diversity and ecological significance of microbial traits potentially involved in B12biosynthesis in the global ocean
Authors: Zhou Jiayin , Qin Wei , Lu Xinda , Yang Yunfeng , Stahl David , Jiao Nianzhi , Zhou Jizhong , Liu Jihua , Tu Qichao 
Published: August 2023

AbstractCobalamin (B12), an essential nutrient and growth cofactor for many living organisms on the Earth, can be fully synthesized only by selected prokaryotes in nature. Therefore, microbial communities related with B12biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomy of complex functional assemblages. By anchoring microbial traits potentially involved in B12biosynthesis, we depict the biogeographic patterns of B12biosynthesis genes and their carrying taxa in the global ocean, in light of the limitation to detectde novoB12synthesizers via metagenomes alone. Both the taxonomic and functional composition of B12biosynthesis genes were strongly shaped by depth, differentiating epipelagic from mesopelagic zones. The functional genes were relatively stably distributed across different oceans, but their carrying taxa varied considerably, showing clear functional redundancy of microbial systems. Microbial taxa carrying B12biosynthesis genes in the surface water were influenced by environmental factors such as temperature, oxygen and nitrate. However, the composition of functional genes was weakly associated with these environmental factors. Null model analyses demonstrated that determinism governed the compositional variation of B12biosynthesis genes, whereas a higher degree of stochasticity was associated with taxonomic variations. Significant associations were observed between chlorophyllaconcentration and B12biosynthesis traits, indicating their importance in global ocean primary production. Conclusively, this study revealed an essential ecological mechanism governing the assembly of microbes in nature: the environment selects function rather than taxonomy; functional redundancy underlies stochastic community assembly.Impact StatementA central question in ecology is how a galaxy of microbial taxa is assembled and distributed across space and through time, executing essential ecosystem functions. By anchoring microbial functional traits potentially involved in B12biosynthesis and their carrying microbial taxa in the global ocean, this study addresses essential ecological questions from functional and taxonomic angles. Integrating multiple lines of evidence, we show that the ecosystem selects functional traits rather than taxonomic groups, and functional redundancy underlies stochastic taxonomic community assembly. Also, microbial communities potentially involved in B12biosynthesis are significantly associated with chlorophyllaconcentration, demonstrating their importance in global ocean primary production. This study provides valuable mechanistic insights into the complex microbial community assembly in natural ecosystems.
The phosphorylation landscape of infection-related development by the rice blast fungus
Authors: Cruz-Mireles Neftaly , Osés-Ruiz Miriam , Derbyshire Paul , Jégousse Clara , Ryder Lauren S. , Bautista Mark Jave , Eseola Alice Bisola , Sklenar Jan , Tang Bozeng , Yan Xia , Ma Weibin , Findlay Kim C. , Were Vincent , MacLean Dan , Talbot Nicholas J. , Menke Frank L.H. 
Published: August 2023

SUMMARYMany of the world’s most devastating crop diseases are caused by fungal pathogens which elaborate specialized infection structures to invade plant tissue. Here we present a quantitative mass spectrometry-based phosphoproteomic analysis of infection-related development by the rice blast fungusMagnaporthe oryzae, which threatens global food security. We mapped 8,005 phosphosites on 2,062 fungal proteins, revealing major re-wiring of phosphorylation-based signaling cascades during fungal infection. Comparing phosphosite conservation across 41 fungal species reveals phosphorylation signatures specifically associated with biotrophic and hemibiotrophic fungal infection. We then used parallel reaction monitoring to identify phosphoproteins directly regulated by the Pmk1 MAP kinase that controls plant infection byM. oryzae. We define 33 substrates of Pmk1 and show that Pmk1-dependent phosphorylation of a newly identified regulator, Vts1, is required for rice blast disease. Defining the phosphorylation landscape of infection therefore identifies potential therapeutic interventions for control of plant diseases.
Local activation of CA1 pyramidal cells induces theta phase precession
Authors: Sloin Hadas E. , Spivak Lidor , Levi Amir , Gattegno Roni , Someck Shirly , Stark Eran 
Published: August 2023

AbstractHippocampal theta phase precession is involved in spatiotemporal coding and generating multineural spike sequences, but how precession originates remains unresolved. To determine whether precession can be generated directly in CA1 and disambiguate multiple competing mechanisms, we used optogenetic activation to impose artificial place fields in pyramidal cells of mice running on a linear track. More than a third of the CA1 artificial fields exhibited synthetic precession that persisted for a full cycle. In contrast, artificial fields in the parietal cortex did not exhibit synthetic precession. The findings are incompatible with precession models based on inheritance, spreading activation, dual-input, or inhibition-excitation summation. Thus, a precession generator resides locally within CA1.
Identification of human skin microbiome odorants that manipulate mosquito landing behavior
Authors: Coutinho-Abreu Iliano V. , Jamshidi Omid , Raban Robyn , Atabakhsh Katayoon , Merriman Joseph A. , Fischbach Michael A. , Akbari Omar S. 
Published: August 2023

AbstractThe resident human skin microbiome is responsible for the production of most of the human scents that are attractive to mosquitoes. Hence, engineering the human skin microbiome to synthesize less of mosquito attractants or produce repellents could potentially reduce bites and prevent the transmission of deadly mosquito-borne pathogens. In order to further characterize the human skin volatilome, we quantified the major volatiles of 39 strains of skin commensals (StaphylococciandCorynebacterium). Importantly, to validate the behavioral activity of these volatiles, we first assessed landing behavior triggered by human skin bacteria volatiles. We demonstrated that this behavioral step is gated by the presence of carbon dioxide and L-(+)-lactic acid, similar to the combinatorial coding triggering short range attraction. Repellency behavior to selected skin volatiles and the geraniol terpene was tested in the presence of carbon dioxide and L-(+)-lactic acid. In a 2-choice landing behavior context, the skin volatiles 2- and 3-methyl butyric acids reduced mosquito landing by 62.0-81.6% and 87.1-99.6%, respectively. Similarly, geraniol was capable of reducing mosquito landing behavior by 74.9%. We also tested the potential repellency effects of geraniol on mosquitoes at short-range using a 4-port olfactometer. In these assays, geraniol reduced mosquito attraction (69-78%) to a mixture of key human kairomones carbon dioxide, L-(+)-lactic acid, and ammonia. These findings demonstrate that carbon dioxide and L-(+)-lactic acid changes the valence of other skin volatiles towards mosquito landing behavior. Moreover, this study offers candidate odorants to be targeted in a novel strategy to reduce attractants or produce repellents by the human skin microbiota that may curtail mosquito bites, and subsequent mosquito-borne disease.
The current quality and requirements of prehospital and emergency care in Indonesia and Malaysia: a cross-sectional multicenter survey
Authors: Tokita Akio , Nunokawa Hanako , Liu Keibun , Iwamoto Yuta , Sonoo Tomohiro , Hara Konan , Nakajima Mikio , Fukaguchi Kiyomitsu , Takeda Takanori , Sanip Amirudin , Juzar Dafsah A. , Harvendhar Singh Gurjeet Singh a/l , Condro Lukito , Tobing Monalisa , Hasan Muhammad Abdus-Syakur bin Abu , Rahman Nik Hisamuddin NA , Mahisa Orizanov , Zairinal Ramdinal Aviesena , Ramli Mohd Khairulizwan bin , Nor Mohd Afiq Mohd , Goto Tadahiro , Zakaria Mohd Idzwan bin 
Published: August 2023

AbstractBackgroundRapid economic growth in Southeast Asian countries has led to a significant gap between supply and demand of emergency care, which may negatively affect the health outcomes of local populations. The purpose of this study was to identify current challenges faced by emergency care systems in Indonesia and Malaysia.MethodsAn online survey was conducted between August and November 2022. Survey participants consisted of emergency department (ED) doctors, nurses, and other medical staff in 11 hospitals in Indonesia and Malaysia. The survey collected information on respondents’ characteristics, factors associated with the quality of prehospital or ED care, missing clinical information, and factors associated with patients’ length of stay at the ED.ResultsA total of 83 and 109 respondents from Indonesia and Malaysia, respectively, answered the survey. The most important factor affecting prehospital care quality in both countries was “inadequate amount of clinical information from the ambulance.” The most important factor affecting ED care quality was “crowdedness in the emergency room during night shifts.” The clinical information most frequently missing was family history, followed by estimated time of arrival to the hospital or medication history. The primary factor affecting the length of ED stay was diagnostic studies and their turnaround time.ConclusionsThis study identified common challenges in the emergency care systems of Indonesia and Malaysia. Our findings highlight the importance of recognizing both common and country-specific challenges to improve the quality of emergency care in Southeast Asia.
Clinical consequences of a polygenic predisposition to benign lower white blood cell counts
Authors: Mosley Jonathan D. , Shelley John P. , Dickson Alyson L. , Zanussi Jacy , Daniel Laura L. , Zheng Neil S. , Bastarache Lisa , Wei Wei-Qi , Shi Mingjian , Jarvik Gail P. , Rosenthal Elisabeth A. , Khan Atlas , Sherafati Alborz , Kullo Iftikhar J. , Walunas Theresa L. , Glessner Joe , Hakonarson Hakon , Cox Nancy J. , Roden Dan M. , Frangakis Stephan G. , Vanderwerff Brett , Stein C. Michael , Van Driest Sara L. , Borinstein Scott C. , Shu Xiao-Ou , Zawistowski Matthew , Chung Cecilia P. , Kawai Vivian K. 
Published: August 2023

ABSTRACTPolygenic variation unrelated to disease contributes to interindividual variation in baseline white blood cell (WBC) counts, but its clinical significance is undefined. We investigated the clinical consequences of a genetic predisposition toward lower WBC counts among 89,559 biobank participants from tertiary care centers using a polygenic score for WBC count (PGSWBC) comprising single nucleotide polymorphisms not associated with disease. A predisposition to lower WBC counts was associated with a decreased risk of identifying pathology on a bone marrow biopsy performed for a low WBC count (odds-ratio=0.55 per standard deviation increase in PGSWBC[95%CI, 0.30 - 0.94], p=0.04), an increased risk of leukopenia (a low WBC count) when treated with a chemotherapeutic (n=1,724, hazard ratio [HR]=0.78 [0.69 - 0.88], p=4.0×10-5) or immunosuppressant (n=354, HR=0.61 [0.38 – 0.99], p=0.04). A predisposition to benign lower WBC counts was associated with an increased risk of discontinuing azathioprine treatment (n=1,466, HR=0.62 [0.44 - 0.87], p=0.006). Collectively, these findings suggest that a WBC count polygenic score identifies individuals who are susceptible to escalations or alterations in clinical care that may be harmful or of little benefit.
Comparative Analysis of Salinity Response Transcriptomes in Salt-Tolerant Pokkali and Susceptible IR29 Rice
Authors: Geniza Matthew , Fox Samuel E. , Sage Abigail , Ansariola Mitra , Megraw Molly , Jaiswal Pankaj 
Published: August 2023

AbstractRice is a major cereal crop responsible for feeding the world’s population. To improve grain yield and quality, meet growing demand, and face the challenges posed by abiotic and biotic stress, it is imperative to explore genetic diversity in rice for candidate genes and loci that may contribute to stress tolerance. High salinity abiotic stress in the rice growth environment affects growth, yield, and quality. Therefore, we conducted a salt stress-responsive RNA-Seq-based transcriptome study of two rice (Oryza sativa) varieties, the salt-tolerant Pokkali and the salt-sensitive breeding line IR29. To identify early and late salinity response genes, we collected samples from the treated and untreated plants in this study at 1, 2, 5, 10, and 24 hours after treatment with 300 mM NaCl solution. We identified 7,209 and 6,595 salt-induced differentially expressed transcripts from Pokkali and IR29, respectively, over all time points. We identified ∼190,000 single nucleotide polymorphism (SNP) sites and ∼40,000 simple sequence repeat (SSR) sites, allowing analysis of their consequences on genetic diversity, transcript structure, gene function, and differential expression. We identified and validated the polymorphic SSRs in the differentially expressed salt-responsive genesRespiratory Burst Oxidase Homolog B (RBOHB)andRice Salt Sensitive 1 (RSS1)that underly nearby salt tolerance QTLs. This study provides insight into transcriptional programming during salt stress, evidence for improvingOryzagenome annotations, and reveals SNP and SSR sites associated with differential gene expression and potential gene function.
How to prevent chick culling in the poultry industry? Discovery of a new biomarker forin ovogender screening
Authors: Drouin Nicolas , Elfrink Hyung Lim , Bruins Wouter , Koval Slavik , Harms Amy C , Stutterheim Wil , Hankemeier Thomas 
Published: August 2023

AbstractChicken eggs are one of the most consumed foods worldwide. However, the practice of chicken culling in the poultry industry involves unnecessary animal suffering and finding a way to put an end to this has become a societal priority. One approach that has been propagated as acceptable is based on the selection of female eggs early in the incubation process and the devitalization of the male eggs.It is with this objective in mind that we searched for a biomarker for early gender screening in eggs. Applying an untargeted mass spectrometry approach, we profiled allantoic fluid of different day-old eggs and identified the feature 3-[(2-aminoethyl)sulfanyl]butanoic acid (ASBA) as a strong biomarker forin-ovogender prediction for day-9 old embryos. After validation using LC-APCI-MRM with an internal standard, we found ASBA can predict the female gender with a sensitivity and specificity well above 95% in our experiments.HighlightsDiscovery of a biomarker of chicken embryo gender in allantoic fluid from eggsDay 9 after laying was determined as optimum for sex prediction and animal welfare3-[(2-aminoethyl)sulfanyl]butanoic acid was identified using mass spectrometryThe biomarker was validated on large cohorts of different chicken speciesGraphical abstract
Insights into RAG evolution from the identification of “missing link” family ARAGLtransposons
Authors: Martin Eliza C. , Targa Lorlane Le , Tsakou-Ngouafo Louis , Fan Tzu-Pei , Lin Che-Yi , Xiao Jianxiong , Su Yi Hsien , Petrescu Andrei-Jose , Pontarotti Pierre , Schatz David G. 
Published: August 2023

ABSTRACTA series of “molecular domestication” events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1-RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order of these events is not well understood, in part because of a dearth of information regarding the invertebrateRAGL-Atransposon family. In contrast to the abundant and divergentRAGL-Btransposon family,RAGL-Amost closely resemblesRAGand is represented by a single orphanRAG1-like(RAG1L) gene in the genome of the hemichordatePtychodera flava(PflRAG1L-A). Here, we provide evidence for the existence of completeRAGL-Atransposons in the genomes ofP. flavaand several echinoderms. The predicted RAG1L-A and RAG2L-A proteins encoded by these transposons intermingle sequence features of jawed vertebrate RAG and RAGL-B transposases, leading to a prediction of DNA binding, catalytic, and transposition activities that are a hybrid of RAG and RAGL-B. Similarly, the terminal inverted repeats (TIRs) of theRAGL-Atransposons combine features of bothRAGL-Btransposon TIRs and RAG recombination signal sequences. Unlike all previously described RAG2L proteins, PflRAG2L-A and echinoderm RAG2L-A contain an acidic hinge region, which we demonstrate is capable of efficiently inhibiting RAG-mediated transposition. Our findings provide evidence for a critical intermediate in RAG evolution and argue that certain adaptations thought to be specific to jawed vertebrates (e.g., the RAG2 acidic hinge) actually arose in invertebrates, thereby focusing attention on other adaptations as the pivotal steps in the completion of RAG domestication in jawed vertebrates.