bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultraviolet Dosage and Decontamination Efficacy was Widely Variable across 14 UV Devices after Testing a Dried Enveloped Ribonucleic Acid Virus Surrogate for SARS-CoV-2
Authors: Buhr Tony L. , Borgers-Klonkowski Erica , Gutting Bradford W. , Hammer Emlyn E. , Hamilton Shelia M. , Huhman Brett M. , Jackson Stuart L. , Kennihan Neil L. , Lilly Samuel D. , Little John D. , Luck Brooke B. , Matuczinski Emily A. , Miller Charles T. , Sides Rachel E. , Yates Vanessa L. , Young Alice A. 
Published: January 2022

AbstractAimsThe dosages and efficacy of 14 ultraviolet (UV) decontamination technologies were measured against a SARS-CoV-2 surrogate virus that was dried on to different materials for lab and field testing.Methods and ResultsA live enveloped, ribonucleic acid (RNA) virus surrogate for SARS- CoV-2 was dried on stainless steel 304 (SS304), Navy Top Coat-painted SS304 (NTC), cardboard, polyurethane, polymethyl methacrylate (PMMA), and acrylonitrile butadiene styrene (ABS) at > 8.0 log10 plaque-forming units (PFU) per test coupon. The coupons were then exposed to UV radiation during both lab and field testing. Commercial and prototype UV- emitting devices were measured for efficacy: 4 handheld devices, 3 room/surface-disinfecting machines, 5 air-disinfection devices, and 2 larger custom-made machines. UV device dosages ranged from 0.01-729 mJ cm-2. Anti-viral efficacy among the different UV devices ranged from no decontamination up to nearly achieving sterilization. Importantly, cardboard required far more dosage than SS304.ConclusionsEnormous variability in dosage and efficacy was measured among the different UV devices. Porous materials limit the utility of UV decontamination.Significance and Impact of the StudyUV devices have wide variability in dosages, efficacy, hazards, and UV output over time indicating that each UV device needs independent technical measurement and assessment for product development, prior to, and during use.
Shade-induced transcription of PIF-Direct-Target Genes precedes H3K4-trimethylation chromatin modification rises
Authors: Calderon Robert H. , Dalton Jutta , Zhang Yu , Quail Peter H. 
Published: January 2022

AbstractThe phytochrome (phy)-PIF (Phytochrome Interacting Factor) sensory module perceives and transduces light signals to Direct-Target Genes (DTGs), which then drive the adaptational responses in plant growth and development, appropriate to the prevailing environment. These signals include the first exposure of etiolated seedlings to sunlight upon emergence from subterranean darkness, and the change in color of the light that is filtered through, or reflected from, neighboring vegetation (‘shade’). Previously, we identified three broad categories of rapidly signal-responsive genes: those repressed by light and conversely induced by shade; those repressed by light, but subsequently unresponsive to shade; and those responsive to shade only. Here, we investigate the potential role of epigenetic chromatin modifications in regulating these contrasting patterns of phy-PIF module-induced expression of DTGs. Using RNA-seq and ChlP-seq, time-resolved profiling of transcript and histone 3 lysine 4 trimethylation (H3K4me3) levels, respectively, we show that, whereas the initial dark-to-light transition triggers a rapid, apparently temporally-coincident decline of both parameters, the light-to-shade transition induces similarly rapid increases in transcript levels that precede increases in H3K4me3 levels. Together with other recent findings, these data raise the possibility that, rather than being causal in the shade-induced expression changes, H3K4me3 may function to buffer the rapidly fluctuating shade/light switching that is intrinsic to vegetational canopies under natural sunlight conditions.
The T. ispahanicum elongated glume locus P2 maps to chromosome 6A and is associated with the ectopic expression of SVP-A1
Authors: Chen Yi , Liu Yinqi , Zhang Junli , Torrance Adam , Watanabe Nobuyoshi , Adamski Nikolai M. , Uauy Cristobal 
Published: January 2022

AbstractIn rice and wheat, glume and floral organ length are positively correlated with grain size, making them an important target to increase grain size and potentially yield. The wheat subspecies Triticum ispahanicum is known to develop elongated glumes and floral organs as well as long grains. These multiple phenotypic effects are controlled by the P2 locus, which was previously mapped to wheat chromosome 7B. Using three mapping populations, we show that the long glume locus P2 does not map to chromosome 7B, but instead maps to a 1.68 Mbp interval on chromosome 6A. Within this interval, we identified SVP-A1, a MADS box transcription factor which is the direct ortholog of the maize gene underlying the ‘pod corn’ Tunicate locus and is a paralog to the T. polonicum elongated glume P1 gene. In T. ispahanicum, we identified a private allele which has a 482-bp deletion in the SVP-A1 promoter and is associated with ectopic and higher expression of SVP-A1 in the elongated glumes and floral organs. We used near-isogenic lines (NILs) to show that P2 has a consistent positive effect on the length of glume, lemma, palea, spike and grain. Based on the mapping data, natural variation, biological function of SVP genes in cereals and expression analyses, we propose the MADS-box transcription factor SVP-A1 as a promising candidate for P2.Key messageWe propose the MADS-box transcription factor SVP-A1 as a promising candidate gene for the elongated glume locus P2, which maps to chromosome 6A instead of the previously proposed chromosome 7B.
STK25 inhibits PKA signaling by phosphorylating PRKAR1A
Authors: Zhang Xiaokan , Wang Bryan Z. , Kim Michael , Nash Trevor R. , Liu Bohao , Rao Jenny , Lock Roberta , Tamargo Manuel , Soni Rajesh Kumar , Belov John , Li Eric , Vunjak-Novakovic Gordana , Fine Barry 
Published: January 2022

SummaryIn the heart, Protein Kinase A (PKA) is critical for activating calcium handling and sarcomeric proteins in response to beta adrenergic stimulation leading to increased myocardial contractility and performance. The catalytic activity of PKA is tightly regulated by regulatory subunits which inhibit the catalytic subunit until released by cAMP binding. Phosphorylation of Type II regulatory subunits promotes PKA activation, however the role of phosphorylation in Type I regulatory subunits remain uncertain. Here we utilized human induced pluripotent stem cell cardiomyocytes (iPSC-CM) to identify STK25 as a kinase of the Type Ia regulatory subunit PRKAR1A. Phosphorylation of PRKAR1A led to inhibition of PKA kinase activity and increased binding to the catalytic subunit in the presence of cAMP. Stk25 knockout in mice diminished Prkar1a phosphorylation, increased Pka activity and augmented contractile response to beta adrenergic stimulation. Together, these data support STK25 as a negative regulator of PKA signaling through phosphorylation of PRKAR1A.
Reprogramming Alveolar Macrophage Responses to TGF-β Reveals CCR2+ Monocyte Activity that Promotes Bronchiolitis Obliterans Syndrome
Authors: Liu Zhiyi , Liao Fuyi , Zhu Jihong , Zhou Dequan , Heo Gyu Seong , Leuhmann Hannah P. , Scozzi Davide , Parks Antanisha , Hachem Ramsey , Byers Derek , Tague Laneshia K. , Kulkarni Hrishikesh S. , Cano Marlene , Wong Brian W. , Li Wenjun , Haung Howard J , Krupnick Alexander S. , Kreisel Daniel , Liu Yongjian , Gelman Andrew E. 
Published: January 2022

AbstractBronchiolitis obliterans syndrome (BOS) is a major impediment to lung transplant survival and is generally resistant to medical therapy. Extracorporeal photophoresis (ECP) is an immunomodulatory therapy that shows promise in stabilizing BOS patients but its mechanisms of action are unclear. In a mouse lung transplant model, we show that ECP blunts alloimmune responses and inhibits BOS through lowering airway TGF-β bioavailability without altering its expression. Surprisingly, ECP-treated leukocytes are engulfed primarily by alveolar macrophages (AM), which become reprogrammed to become less responsive to TGF-β and reduce TGF-β bioavailability through secretion of the TGF-β antagonist Decorin. In untreated recipients, high airway TGF-β activity stimulates AM to express CCL2 leading to CCR2+ monocyte-driven BOS development. Moreover, we find TGF-β receptor 2-dependent differentiation of CCR2+ monocytes is required for the generation of monocyte-derived AM, which in turn promote BOS by expanding tissue-resident memory CD8+ T cells that inflict airway injury through Blimp-1-mediated Granzyme B expression. Thus, through studying the effects of ECP, we have identified an AM functional plasticity that controls a TGF-β-dependent network, which couples CCR2+ monocyte recruitment and differentiation to alloimmunity and BOS. Alveolar macrophage plasticity can be harnessed to prevent Bronchiolitis Obliterans Syndrome.
A Guide for Quantifying and Optimizing Measurement Reliability for the Study of Individual Differences
Authors: Xu Ting , Cho Jae Wook , Kiar Gregory , Bridgeford Eric W. , Vogelstein Joshua T. , Milham Michael P. 
Published: January 2022

AbstractCharacterizing individual variations is central to interpreting individual differences in neuroscience and clinical studies. While the field has examined multifaceted individual differences in brain functional organization, it is only in recent years that neuroimaging researchers have begun to place a priority on its quantification and optimization. Here, we highlight a potential analytic pitfall that can lead to contaminated estimates of inter-individual differences. We define a two-dimensional individual variation field map to decipher sources of individual variation and their relation to fingerprinting and measures of reliability. We illustrate theoretical gradient flow that represents the most effective direction for optimization when measuring individual differences. We propose to use this general framework for dissecting within- and between-individual variation and provide a supporting online tool for the purposes of guiding optimization efforts in biomarker discovery.
Aeromonas hydrophilainduces skin disturbance through mucosal microbiota dysbiosis inPangasianodon hypophthalmus
Authors: Chen Li-Hsuan , Lin Chia-Hsuan , Siao Ru-Fang , Wang Liang-Chun 
Published: January 2022

ABSTRACTBacterial pathogens are well-equipped to adhere to and initiate infection in teleost fish. The fish skin mucus serves as the first barrier against environmental pathogens. The mucus harbors commensal microbes that form the microbiota, impacting the host physiological and immunological regulation. However, how the skin mucosal microbiota responds to the presence of pathogens remains largely unexplored. Thus, little is known about the status of skin mucus prior to the infection with noticeable symptoms. In this study, we aim to investigate the interaction between pathogen and skin mucosal microbiota, as well as the fish skin immune responses in the presence of pathogens. By challenging striped catfish (Pangasianodon hypophthalmus) with different concentrations of bacterial pathogenAeromonas hydrophila(AH), the skin immune response and the mucosal microbiota were examined by qPCR and 16S rRNA gene sequencing analysis. We found a pathogen concentration able to stimulate the skin immune response associated with the significant mucosal microbiota change and re-confirmed with theex vivofish skin model. Further analysis indicated that the change was attributed to the significant increase in opportunistic pathogens over AH. We concluded that the presence and increase of AH results in dysbiosis of mucosal microbiota that can stimulate skin immune response. We believe our work can shed some light on host-pathogen-commensal microbiota interaction and therefore contribute to aquaculture infection prevention.IMPORTANCEThe fish skin mucosal microbiota is essentially the first barrier in response to the presence of pathogens. This study is the first study to elucidate the interaction between the AH, the skin mucosal microbiota, and the striped catfish skin at the initiation stage of infection. Our study provides a platform to study both the correlation and causation of the interaction between pathogen, the fish skin, and the skin mucosal microbiota. This work provides information that changes in the AH-induced mucosal microbiota result in skin disturbance with immune stimulation.
Unified surface and volumetric projection of physiological imaging data
Authors: Kirk Thomas F. , Craig Martin S. , Chappell Michael A. 
Published: January 2022

AbstractProjection of volumetric data onto the cortical surface is an important precursor to performing surface-based analysis. Numerous projection methods have been reported in the literature, many of which make assumptions which tie them to use with specific modalities, notably blood oxygenation level dependent (BOLD) imaging. This means that they may not be appropriate for use with modalities where subcortical tissue contributes a signal of interest. This work details a new projection that provides a number of generalisations and extensions to existing methods. Namely, it may be used to project arbitrary data without making modality-specific assumptions and can produce unified surface and volumetric representations of data (a concept also known asgrayordinatesspace). When constrained to the same assumptions as existing methods, a comparison using simulation data shows that it produces similar outputs. When these assumptions are relaxed to project simulation data containing both cortical and subcortical signals to and from a unified surface and volume space, substantial and statistically significant differences in recovery of ground truth are observed compared to existing methods.
LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays
Authors: Nguyen Dat Thanh , Nguyen Quan Hoang , Duong Nguyen Thuy , Vo Nam Sy 
Published: January 2022

AbstractDespite the rapid development of sequencing technology, single-nucleotide polymorphism (SNP) array is still the most cost-effective genotyping solutions for large-scale genomic research and applications. Recent years have witnessed the rapid development of numerous genotyping platforms of different sizes and designs, but population-specific platforms are still lacking, especially for those in developing countries. We aim to develop methods to design SNP arrays for thse countries, so the arrays should be cost-effective (small size), yet can still generate key information needed to associate genotypes with traits. A key design principle for most current platforms is to improve genome-wide imputation so that more SNPs (imputed tag SNPs) not included in the array can be predicted. However, current tag SNP selection methods mostly focus on imputation accuracy and coverage, but not the functional content of the measured and imputed SNPs. It is those functional SNPs that are most likely associated to traits. Here, we propose LmTag, a novel method for tag SNP selection that not only improves imputation performance but also prioritizes highly functional SNP markers. We apply LmTag on a wide range of populations using both public and in-house whole genome sequencing databases. Our results showed that LmTag improved both functional marker prioritization and genome-wide imputation accuracy compared to existing methods. This novel approach could contribute to the next generation genotyping arrays that provide excellent imputation capability as well as facilitate array-based functional genetic studies. Such arrays are particularly suitable for under-represented populations in developing countries or non-model species, where little genomics data are available while investment in genome sequencing or high-density SNP arrays is limited.
Dynamics of Human Serum Transferrin in Varying Physicochemical Conditions Explored by Using Molecular Dynamics Simulations
Authors: Indrakumar Sowmya , Kulakova Alina , Harris Pernille , Peters Günther H. J. 
Published: January 2022

ABSTRACTConformational stability of human serum transferrin (Tf) at varying pH, salt, and excipient concentrations were investigated using molecular dynamics (MD) simulations and the results are compared with previously published small angle X-ray scattering (SAXS) experiments. SAXS study showed that at pH 5, Tf is predominantly present in partially open (PO) form, and the factions of PO differ based on the physicochemical condition and drifts towards closed form (HO) as the pH increases. Tf is a bilobal glycoprotein that is composed of homologous halves termed as N-lobe and C-lobe. The current study shows that the protonation of Y188 and K206 at pH 5 is the primary conformational drive into PO, which shifts towards the closed (HO) conformer as the pH increases. Furthermore, at pH 6.5, PO is unfavorable due to negative charge-charge repulsion at the N/C-lobe interface linker region causing increased hinge distance when compared to HO, which has favorable attractive electrostatics. Subsequently, the effect of salt concentration at 70 and 140 mM NaCl was studied. At 70 mM NaCl and pH 5, chloride ions bind strongly in the N-lobe iron-binding site, whereas these interactions are weak at pH 6.5. With increasing salt concentration at pH 5, regions surrounding the N-lobe iron-binding site are saturated and as a consequence sodium and chloride ions accumulate into the bulk. Additionally, protein-excipient interactions were investigated. At pH 5, excipients interact in similar loop regions, E89-T93, D416-D420, located in the C-lobe and N-lobe of the HO conformer, respectively. It is anticipated that interactions of additives in these two loop regions cause conformational changes that lead to iron coordinating residues in the N-lobe to drift away from iron and thus drive HO to PO conversion. Furthermore, at pH 6.5 and 140 mM histidine or phosphate, these interactions are negligible leading to the stabilization of HO.
Dendro-plexing single input spikes by multiple synaptic contacts enriches the computational capabilities of cortical neurons and reduces axonal wiring
Authors: Beniaguev David , Shapira Sapir , Segev Idan , London Michael 
Published: January 2022

AbstractA cortical neuron typically makes multiple synaptic contacts on the dendrites of its postsynaptic target neuron. The functional implications of this apparent redundancy are unclear. Due to dendritic cable filtering, proximal dendritic synapses generate brief somatic postsynaptic potentials (PSPs) whereas distal synapses give rise to broader PSPs. Consequently, with multiple synaptic contacts, a single presynaptic spike results in a somatic PSP composed of multiple temporal profiles. We developed a “Filter-and-Fire” (F&F) neuron model that incorporates multiple contacts and cable filtering; it demonstrates threefold increase in memory capacity as compared to a leaky Integrate-and-Fire (I&F) neuron, when trained to emit precisely timed spikes for specific input patterns. Furthermore, the F&F neuron can learn to recognize spatio-temporal input patterns, e.g., MNIST digits, where the I&F model completely fails. We conclude that “dendro-plexing” single input spikes by multiple synaptic contacts enriches the computational capabilities of cortical neurons and can dramatically reduce axonal wiring.
Lowering levels of reelin in entorhinal cortex layer II-neurons results in lowered levels of intracellular amyloid-β
Authors: Kobro-Flatmoen Asgeir , Battistin Claudia , Raveendran Rajeevkumar Nair , Bjorkli Christiana , Skender Belma , Kentros Cliff , Gouras Gunnar , Witter Menno P. 
Published: January 2022

AbstractProjection neurons in the anterolateral part of entorhinal cortex layer II (alEC LII) are the predominant cortical site for hyperphosphorylation of tau (p-tau) and formation of neurofibrillary tangles (NFTs) in brains of subjects with early-stage Alzheimer’s Disease (AD). A majority of alEC LII-neurons are unique among cortical excitatory neurons by expressing the protein reelin (Re+). In AD patients, and a rat model for AD overexpression mutated human APP, these Re+ excitatory projection-neurons are prone to accumulate intracellular amyloid-β (iAβ). Biochemical pathways that involve reelin-signaling regulate levels of p-tau, and iAβ has been shown to impair such reelin-signaling. We therefore used the rat model and set out to assess whether accumulation of iAβ in Re+ alEC LII projection neurons relates to the fact that these neurons express reelin. Here we show that in Re+ alEC LII-neurons, reelin and iAβ42 engage in a direct protein-protein interaction, and that microRNA-mediated lowering of reelin-levels in these neurons leads to a concomitant reduction of non-fibrillar iAβ ranging across three levels of aggregation. Our experiments are carried out several months before plaque pathology emerges in the rat model, and the reduction of iAβ occurs without any substantial associated changes in human APP-levels. We propose a model positioning reelin in a sequence of changes in functional pathways in Re+ alEC LII-neurons, explaining the region and neuron-specific initiation of AD pathology.SignificanceAnterolateral entorhinal cortex layer II (EC LII) neurons are the predominant cortical site for hyperphosphorylation of tau (p-tau) and formation of neurofibrillary tangles (NFTs) in brains of subjects with early-stage Alzheimer’s disease (AD). The same neurons are prone to very early accumulation of non-fibrillary forms of amyloid-β in the context of AD, and are unique among cortical excitatory neurons by expressing the protein reelin. We show that in such alEC LII-neurons, reelin and iAβ42 engage in a direct protein-protein interaction, and that selectively lowering levels of reelin leads to a concomitant reduction of non-fibrillar Aβ. We propose a model positioning reelin in a sequence of changes in functional pathways in reelin-expressing EC LII neurons, explaining the region and neuron specific initiation of AD.
Cross-linked natural IntegroPectin films from Citrus biowaste with intrinsic antimicrobial activity
Authors: Piacenza Elena , Presentato Alessandro , Alduina Rosa , Scurria Antonino , Pagliaro Mario , Albanese Lorenzo , Meneguzzo Francesco , Ciriminna Rosaria , Chillura Martino Delia F. 
Published: January 2022

AbstractPectin recovered via hydrodynamic cavitation (IntegroPectin) from lemon and grapefruit agri-food waste intrinsically containing antimicrobial bioactive substances (flavonoids, phenolic acids, terpenes, and terpenoids) was used to generate innovative and eco-compatible films that efficiently inhibit the growth of Gram-negative pathogens. Extensive characterization of films confirmed the presence of these substances, which differently interact with the polysaccharide polymer (pectin), plasticizer (glycerol), surfactant (Tween 60), and cross-linker (Ca2+), conferring to these films a unique structure. Besides, IntegroPectin-based films constitute sustained, controlled, and slow-release (up to 72h) systems for bioactive substances in an aqueous environment. This feature is crucial for the goodin vitroantimicrobial activity exerted by IntegroPectin films against three Gram-negative bacteria (two indicator pathogen strainsPseudomonas aeruginosaATCC 10145,P. aeruginosaPAO1, and the clinical isolateKlebsiella pneumoniae) that are involved in the global emergence of the antimicrobial resistance.