bluuebunny/crossref_metadata_2025_split huggingface dataset:
lydemapr: an R package to track the spread of the invasive Spotted Lanternfly (Lycorma delicatula, White 1845) (Hemiptera, Fulgoridae) in the United States
Authors: De Bona Sebastiano , Barringer Lawrence , Kurtz Paul , Losiewicz Jay , Parra Gregory R. , Helmus Matthew R. 
Published: January 2023

AbstractA crucial asset in the management of invasive species is the open-access sharing of data on the range of invaders and the progression of their spread. Such data should be current, comprehensive, consistent, and standardized, to support reproducible and comparable forecasting efforts among multiple researchers and managers. Here, we present thelydemaprR package containing spatiotemporal data and mapping functions to visualize the current spread of the spotted lanternfly (Lycorma delicatula, White 1841) in the Western Hemisphere. The spotted lanternfly is a forest and agricultural pest in the eastern Mid-Atlantic region of the U.S., where it was first discovered in 2014. As of 2022, it has been found in 12 states according to state and federal departments of agriculture. However, the lack of easily accessible, fine-scale data on its spread hampers research and management efforts. We obtained multiple memoranda-of-understanding from several agencies and citizen-science projects, gaining access to their internal data on spotted lanternfly point observations. We then cleaned, harmonized, anonymized, and combined the individual data sources into a single comprehensive dataset. The resulting dataset contains spatial data gridded at the 1 km2resolution, with yearly information on the presence/absence of spotted lanternflies, establishment status, and population density across 658,392 observations. Thelydemaprpackage will aid researchers, managers, and the public in their understanding, modeling, and managing of the spread of this invasive pest.
Altered transcriptomes, cell type proportions, and dendritic spine morphology in hippocampus of suicide deaths
Authors: Das Sujan C. , Schulmann Anton , Callor William B. , Jerominski Leslie , Panicker Mitradas M. , Christensen Erik D. , Bunney William E. , Williams Megan E. , Coon Hilary , Vawter Marquis P. 
Published: January 2023

AbstractSuicide is a condition resulting from complex environmental and genetic risks that affect millions of people globally. Both structural and functional studies identified the hippocampus as one of the vulnerable brain regions contributing to suicide risk. Here, we have identified the hippocampal transcriptomes, gene ontology, cell type proportions, dendritic spine morphology, and transcriptomic signature in iPSC-derived neuronal precursor cells (NPCs) and neurons in postmortem brain tissue from suicide deaths. The hippocampal tissue transcriptomic data revealed thatNPAS4gene expression was downregulated whileALDH1A2, NAAA, andMLXIPLgene expressions were upregulated in tissue from suicide deaths. The gene ontology identified 29 significant pathways includingNPAS4-associated gene ontology terms “excitatory post-synaptic potential”, “regulation of postsynaptic membrane potential” and “long-term memory” indicating alteration of glutamatergic synapses in the hippocampus of suicide deaths. The cell type deconvolution identified decreased excitatory neuron proportion and an increased inhibitory neuron proportion providing evidence of excitation/inhibition imbalance in the hippocampus of suicide deaths. In addition, suicide deaths had increased dendric spine density, due to an increase of thin (relatively unstable) dendritic spines, compared to controls. The transcriptomes of iPSC-derived hippocampal-like NPCs and neurons revealed 31 and 33 differentially expressed genes in NPC and neurons, respectively, of suicide deaths. The suicide-associated differentially expressed genes in NPCs wereRELN, CRH, EMX2, OXTR, PARM1andIFITM2which overlapped with previously published results. The previously-known suicide-associated differentially expressed genes in differentiated neurons wereCOL1A1, THBS1, IFITM2, AQP1, andNLRP2. Together, these findings would help better understand the hippocampal neurobiology of suicide for identifying therapeutic targets to prevent suicide.
Modified Robust Meta-Analytic-Predictive Priors for Incorporating Historical Controls in Clinical Trials
Authors: Zhao Qiang , Ma Haijun 
Published: January 2023

AbstractIncorporating historical information in clinical trials has been of much interest recently because of its potential to reduce the size and cost of clinical trials. Data-conflict is one of the biggest challenges in incorporating historical information. In order to address the conflict between historical data and current data, several methods have been proposed including the robust meta-analytic-predictive (rMAP) prior method. In this paper, we propose to modify the rMAP prior method by using an empirical Bayes approach to estimate the weights for the two components of the rMAP prior. Via numerical calculations, we show that this modification to the rMAP method improves its performance regarding multiple key metrics.
Revisit the Inhibitory Effects of Glucocorticoids on Immunocytes
Authors: Wu Shuting , Zhao Shushu , Zhong Yiwei , Wang Bin 
Published: January 2023

AbstractGlucocorticoids (GCs) are efficacious agents for reducing inflammation and suppressing immune responses, exerting various effects on immune cells through the intracellular glucocorticoid receptor (GR), and impacting both innate and adaptive immunity. In the context of COVID-19, glucocorticoids are often used to treat severe cases of patients by reducing inflammation, suppressing immune responses, and ameliorating the severity of COVID-19. However, the precise inhibitory effects on immune cells have yet to be comprehensively delineated. In this study, we extensively examined the inhibitory effects of treating Balb/c mice with dexamethasone (DEX) on lymphoid and myeloid cells. We observed that high doses of DEX treatment resulted in a reduction in the number of immunocytes and an attenuation of their activity. Particularly noteworthy, macrophages, DC cells, and monocytes were diminished by approximately 90% following high doses of DEX, while B cells experienced a reduction of about 70% and CD3 T cells were less affected. Furthermore, our findings demonstrated that DEX induces the inhibition of immune cells by engaging in high-affinity binding to GR. Consequently, we conclude that DEX treatments affect a broad range of immune cells, encompassing both lymphoid and myeloid cells, through depletion or the down-regulation of immune function, potentially acting via the GR signaling pathway. These findings may enhance the clinical applicability of DEX in achieving transient immune deficiency.
Trophic eggs affect caste determination in the antPogonomyrmex rugosus
Authors: Genzoni E. , Schwander T. , Keller L. 
Published: January 2023

AbstractUnderstanding how a single genome creates distinct phenotypes remains a fundamental challenge for biologists. Social insects provide a striking example of polyphenism, with queen and worker castes exhibiting morphological, behavioural, and reproductive differences. Here we show that trophic eggs, which do not contain an embryo and are primarily regarded as a source of food, play a role in the process of caste differentiation in the harvester antPogonomyrmex rugosus. When first instar larvae were given access to trophic eggs, they mostly developed into workers. By contrast, larvae without access to trophic eggs developed into queens. We found that trophic eggs differ in many ways from viable eggs, including texture, morphology and their contents of protein, triglycerides, glycogen, sugar and small RNAs. Moreover, comparison of miRNA fragment size distributions suggests differences in the composition of miRNAs between the two egg types. This is the first demonstration of trophic eggs playing a role in caste differentiation in social insects.
Live cell imaging and CLEM reveals effects of Mutant Huntingtin Aggregation Process
Authors: Yi̇ği̇t Esra Nur , Aydin Mehmet Şerif , Aksan Kurnaz Işıl , Eroğlu Emrah , Öztürk Gürkan 
Published: January 2023

AbstractHuntington’s disease is a neurodegenerative disease caused by expansion of CAG repeats in exon-1 ofHuntingtin (HTT)gene leading to production of mutant Huntingtin (mHtt) protein. Htt protein is known to play crucial roles in regulation of cytoskeletal dynamics and vesicular transport in physiological conditions. By combiningin vitrotime-lapse imaging and correlative light and electron microscopy (CLEM), we investigated the subcellular dynamics of mHtt during the process aggregate formation. Here we show that distribution of F-actin is affected by mHtt aggregation. F-actin tends to relocate from the peripheral to perinuclear area in cells with mHtt aggregates, possibly caused by sequestration of F-actin from cell membrane to aggregation zones. In accordance with this, mHtt in hippocampal neurons were aggregated into axonal varicosities together with F-actin as they have higher F-actin expression in their neurites compared to their soma. Additionally, correlative light and electron microscopy (CLEM) revealed increased mitochondrial accumulation at the periphery of mHtt aggregates which is surrounded by a F-actin mesh. Mitochondria targeted HyPerRed, a genetically encoded hydrogen peroxide sensor, revealed that oxidative stress in mHtt expressing cells increased. Thus, our findings give new insights about the pathology caused by mHtt through interplay of aggregates with F-actin cytoskeleton and mitochondrial oxidative stress.
α-synuclein preformed fibrils bind to β-neurexins and impair β-neurexin-mediated presynaptic organization
Authors: Feller Benjamin , Fallon Aurélie , Luo Wen , Nguyen Phuong Trang , Shlaifer Irina , Lee Alfred Kihoon , Karkout Samer , Bourgault Steve , Durcan Thomas M , Takahashi Hideto 
Published: January 2023

AbstractSynucleinopathies form a group of neurodegenerative diseases defined by misfolding and aggregation of alpha-synuclein (α-syn). Abnormal accumulation and spreading of α-syn aggregates lead to synapse dysfunction and neuronal cell death. Yet, little is known about synaptic mechanisms underlying α-syn pathology. Here we identified β-isoforms of neurexins (β-NRXs) as presynaptic organizing proteins that interact with α-syn preformed fibrils (α-syn PFFs), toxic α-syn aggregates, but not α-syn monomers. Our cell surface protein binding assays and surface plasmon resonance assays reveal that α-syn PFFs bind directly to β-NRX through their N-terminal histidine-rich domain (HRD) at nanomolar range (Kd: ~500 nM monomer equivalent). Furthermore, our artificial synapse formation assays show that α-syn PFFs diminish excitatory and inhibitory presynaptic organization induced by a specific isoform of neuroligin 1 that binds only β-NRXs, but not α-isoforms of neurexins. Thus, our data suggest that α-syn PFFs interact with β-NRXs to inhibit β-NRX-mediated presynaptic organization, providing novel molecular insight into how α-syn PFFs induce synaptic pathology in synucleinopathies such as Parkinson’s disease and dementia with Lewy bodies.
Network analysis reveals strain-dependent response to misfolded tau aggregates
Authors: Acri Dominic J. , You Yanwen , Tate Mason D. , McCord Brianne , Sharify A. Daniel , John Sutha , Karahan Hande , Kim Byungwook , Dabin Luke C. , Philtjens Stéphanie , Wijeratne H.R. Sagara , McCray Tyler J. , Smith Daniel C. , Bissel Stephanie J. , Lamb Bruce T. , Lasagna-Reeves Cristian A. , Kim Jungsu 
Published: January 2023

ABSTRACTMouse genetic backgrounds have been shown to modulate amyloid accumulation and propagation of tau aggregates. Previous research into these effects has highlighted the importance of studying the impact of genetic heterogeneity on modeling Alzheimer’s disease. However, it is unknown what mechanisms underly these effects of genetic background on modeling Alzheimer’s disease, specifically tau aggregate-driven pathogenicity. In this study, we induced tau aggregation in wild-derived mice by expressingMAPT(P301L). To investigate the effect of genetic background on the action of tau aggregates, we performed RNA sequencing with brains of 6-month-old C57BL/6J, CAST/EiJ, PWK/PhJ, and WSB/EiJ mice (n=64). We also measured tau seeding activity in the cortex of these mice. We identified three gene signatures: core transcriptional signature, unique signature for each wild-derived genetic background, and tau seeding-associated signature. Our data suggest that microglial response to tau seeds is elevated in CAST/EiJ and PWK/PhJ mice. Together, our study provides the first evidence that mouse genetic context influences the seeding of tau.Graphical AbstractSUMMARYSeeding of tau predates the phosphorylation and spreading of tau aggregates. Acri and colleagues report transcriptomic responses to tau and elevated tau seeds in wild-derived mice. This paper creates a rich resource by combining genetics, tau biosensor assays, and transcriptomics.
Too bad to be fraud, Midjourney has yet to embark in science
Authors: Cammer Michael 
Published: January 2023

AbstractArtificial Intelligence (AI) promises great benefits for data management, for image analysis, and for new discovery, but also creates unprecedented potential for fraud. This brief study explores whether images created by AI pose a threat to the integrity of figures in scientific publications. An attempt was made to use a leading AI image-generation engine, Midjourney, to create plausible facsimiles of images that are commonly depicted in manuscripts in the biological sciences. We conclude that a widely available AI for generated images is not a threat to integrity, yet, but may be in the near future.
Changes in biodiversity impact atmospheric chemistry and climate through plant volatiles and particles
Authors: Sanaei Anvar , Herrmann Hartmut , Alshaabi Loreen , Beck Jan , Ferlian Olga , Fomba Khanneh Wadinga , Haferkorn Sylvia , van Pinxteren Manuela , Quaas Johannes , Quosh Julius , Rabe René , Wirth Christian , Eisenhauer Nico , Weigelt Alexandra 
Published: January 2023

AbstractClimate extremes in tandem with biodiversity change affect emissions of biogenic volatile organic compounds (BVOCs) from plants and, as a result, the formation of biogenic secondary organic aerosols (BSOA). The resulting BSOA can have a wide variety of impacts, such as on Earth’s radiative balance or cloud- and precipitation formation. However, at present, it is unclear how changing biodiversity will lead to changes in BVOC emissions, BSOA formation and their corresponding effects. We present a conceptual framework of the relationships between biodiversity and BVOC emissions based on our current mechanistic understanding and combining knowledge from the fields of biology and atmospheric chemistry. Parts of this framework are tested in a case study using a tree diversity experiment with adjunct BVOC and BSOA characterisation. The relative differences in tree monocultures and mixtures show that the overall concentration of BVOCs decreases with increasing biodiversity (p< 0.01), but results for BSOA compounds are mixed and overall non-significant (p= 0.40). We suggest future studies should follow a multidisciplinary approach where the fields of biology, atmospheric chemistry and climate research interact.
Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution
Authors: Wang Kejun , Hua Guoying , Li Jingyi , Yang Yu , Zhang Chenxi , Yang Lan , Hu Xiaoyu , Scheben Armin , Wu Yanan , Gong Ping , Zhang Shuangjie , Fan Yanfeng , Zeng Tao , Lu Lizhi , Gong Yanzhang , Jiang Ruirui , Sun Guirong , Tian Yadong , Kang Xiangtao , Hu Haifei , Li Wenting 
Published: January 2023

ABSTRACTStructural variations (SVs) are a major source of domestication and improvement traits, however SV profiles of duck and their phenotypic impacts largely hidden. We present the first duck pan-genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (∼46.5X) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to duck’s domestication and improvement. By combining quantitative genetics with molecular experiments, we dissect how TE-derived SVs change gene expression ofIGF2BP1and generate a novel transcript ofMITF, shaping bodyweight and white plumage. In theIGF2BP1locus, the TE-derived SV explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). Our findings highlight the importance of using a pan-genome as a reference in genomics studies and explore the roles of TE-derived SVs in trait formation and in livestock breeding.
m6A Demethylase FTO Stabilizes LINK-A to Exert Oncogenic Roles via MCM3-Mediated Cell Cycle Progression and HIF-1α Activation
Authors: Nan Yabing , Liu Shi , Luo Qingyu , Wu Xiaowei , Zhao Pengfei , Chang Wan , Liu Zhihua 
Published: January 2023

AbstractRNAN6-methyladenosine (m6A) modification, balanced by methyltransferases and demethylases, has recently been shown to play critical roles in multiple cancers. However, the mechanism by which m6A modification regulates long noncoding RNA (lncRNA) stability and function during cancer progression remains unclear. Here, we show that m6A demethylase fat mass and obesity-associated protein (FTO) removes the m6A modification on long intergenic noncoding RNA for kinase activation (LINK-A) and stabilizes it to promote cell proliferation and cytotoxic chemotherapy resistance in esophageal squamous cell carcinoma (ESCC). Mechanistically, LINK-A enhances the interaction between minichromosome maintenance complex component 3 (MCM3) and cyclin-dependent kinase 1 (CDK1) to promote MCM3 phosphorylation by CDK1. MCM3 is a subunit of the hexameric protein complex and its phosphorylation facilitates loading of the MCM complex onto chromatin, which promotes cell cycle progression and subsequent cell proliferation. Meanwhile, LINK-A prevents the interaction of MCM3 and hypoxia-inducible factor 1α (HIF-1α), abrogates MCM3-mediated transcriptional repression of HIF-1α, and promotes glycolysis and chemoresistance of cancer cells. These results elucidate a mechanism whereby FTO-stabilized LINK-A plays oncogenic roles and present the FTO/LINK-A/MCM3/HIF-1α axis as a promising therapeutic target for ESCC.
Frequency and machine learning predictors of depressive, anxiety, obsessive-compulsive symptoms, and suicidal ideation among university students
Authors: Meda Nicola , Pardini Susanna , Rigobello Paolo , Visioli Francesco , Novara Caterina 
Published: January 2023

AbstractIntroductionProspective studies on mental health of students showed that young adults enroled in university are affected by poorer mental health than other working peers or adults, and this condition is responsible for a large proportion of disability-adjusted life-yearsMethodsWe enrolled 1388 students at the baseline (and 557 completed follow-up after six months) who reported their demographic information and completed self-report questionnaires on depressive, anxiety and obsessive-compulsive symptoms. We applied multiple regression modelling and supervised machine learning to evince associations and predict the risk factors of poorer mental health at baseline and follow-upResultsApproximately one out of five students reported severe depressive symptoms and/or suicidal ideation. An association of economic worry with depression was evidenced at the beginning of the study (when there was a high frequency of worry OR = 3.11 [1.88 – 5.15]) and during follow-up. Supervised machine learning exhibited high accuracy in predicting the students who maintained well-being (balanced accuracy = 0.85) or absence of suicidal ideation, but its performance was almost null in identifying those whose symptoms worsened.ConclusionsStudents’ severe mental health problems are reaching worrying percentages, and few demographic factors can be leveraged to predict poor mental health outcomes. Further research including people with lived experience is crucial to assess students’ needs and improve the prediction of those at risk of developing worse symptoms.
Probable transmission of SARS-CoV-2 from an African lion to zoo employees
Authors: Siegrist Audrey A. , Richardson Kira L. , Ghai Ria R. , Pope Brian , Yeadon Jamie , Culp Betsy , Behravesh Casey Barton , Liu Lixia , Brown Jennifer A. , Boyer Leslie V. 
Published: January 2023

AbstractAnimal to human transmission of SARS-CoV-2 has not previously been reported in a zoo setting. A vaccinated African lion with physical limitations requiring hand feeding tested positive for SARS-CoV-2 after development of respiratory signs. Zoo employees were screened, monitored prospectively for development of symptoms, then re-screened as indicated, with confirmation by RT-PCR and whole-genome virus sequencing when possible. Trace-back investigation narrowed the source of infection to one of five people. Three exposed employees subsequently developed symptoms, two with viral genomes identical to the lion’s. Forward contact tracing investigation confirmed probable lion-to-human transmission.Close contact with large cats is a risk factor for bidirectional zoonotic SARS-CoV-2 transmission that should be considered when occupational health and biosecurity practices at zoos are designed and implemented. SARS-CoV-2 rapid testing and detection methods in big cats and other susceptible animals should be developed and validated to facilitate timely implementation of One Health investigations.
Structural Elucidation of β1- and β2-Transferrin Using Microprobe-Capture In-Emitter Elution and High-Resolution Mass Spectrometry
Authors: Luo Ruben Yiqi , Pfaffroth Christopher , Yang Samuel , Hoang Kevin , Yeung Priscilla S.-W. , Zehnder James L. , Shi Run-Zhang 
Published: January 2023

AbstractBackgroundCerebrospinal fluid (CSF) leak is typically diagnosed by detecting a protein marker β2-transferrin (β2-Tf) in secretion samples. β2-Tf and β1-transferrin (β1-Tf) are glycoforms of human transferrin (Tf). A novel affinity capture technique for sample preparation, called microprobe-capture in-emitter elution (MPIE), was incorporated with high-resolution mass spectrometry (HR-MS) to analyze the Tf glycoforms and elucidate the structures of β1-Tf and β2-Tf.MethodsTo implement MPIE, an analyte is first captured on the surface of a microprobe, and subsequently eluted from the microprobe inside an electrospray emitter. The capture process is monitored in real-time via next-generation biolayer interferometry (BLI). When electrospray is established from the emitter to a mass spectrometer, the analyte is immediately ionized via electrospray ionization (ESI) for HR-MS analysis. Serum, CSF, and secretion samples were analyzed using MPIE-ESI-MS.ResultsBased on the MPIE-ESI-MS results, the structures of β1-Tf and β2-Tf were solved. As Tf glycoforms, β1-Tf and β2-Tf share the amino acid sequence but have varying N-glycans. β1-Tf, the major serum-type Tf, has two G2S2 N-glycans on Asn413 and Asn611. β2-Tf, the major brain-type Tf, has an M5 N-glycan on Asn413 and a G0FB N-glycan on Asn611.ConclusionsThe structures of β1-Tf and β2-Tf were successfully elucidated by MPIE-ESI-MS analysis. The resolving power of the novel MPIE-ESI-MS method was demonstrated in this study. On the other hand, knowing the N-glycan structures on β2-Tf allows for the design of other novel test methods for β2-Tf in the future.