bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs
Authors: Uckele Kathryn A. , Jahner Joshua P. , Tepe Eric J. , Richards Lora A. , Dyer Lee A. , Ochsenrider Kaitlin M. , Philbin Casey S. , Kato Massuo J. , Yamaguchi Lydia F. , Forister Matthew L. , Smilanich Angela M. , Dodson Craig D. , Jeffrey Christopher S. , Parchman Thomas L. 
Published: August 2021

AbstractFoundational hypotheses addressing plant–insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude 1H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other’s state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.
Location of the radial nerve along the humeral shaft between the prone and lateral decubitus positions at different elbow positions
Authors: Suwannaphisit Sitthiphong , Aonsong Wachirakorn , Suwanno Porames , Chuaychoosakoon Chaiwat 
Published: August 2021

AbstractIdentification of the radial nerve is important during the posterior approach to a humerus fracture. During this procedure, the patient can be placed in the prone or lateral decubitus position depending on the surgeon’s preference. The distance from the radial nerve to the osseous structures will be different in each position. The purpose of this study was to identify the safety zones in various patient and elbow flexion positions. The distances from the olecranon to the center of the radial groove and intermuscular septum and lateral epicondyle to the lateral intermuscular septum were measured using a digital Vernier caliper. The measurements were performed with cadavers in the lateral decubitus and prone positions at different elbow flexion angles. The distance from where the radial nerve crossed the posterior aspect of the humerus measured from the upper part of the olecranon to the center of the radial nerve in both positions at different elbow flexion angles varied from a mean maximum distance of 130.00 mm with the elbow in full extension in the prone position to a minimum distance of 121.01 mm with the elbow in flexion at 120° in the lateral decubitus position. The mean distance of the radial nerve from the upper olecranon to the lateral intermuscular septum varied from 107.13 to 102.22 mm. The distance from the lateral epicondyle to the lateral edge of the radial nerve varied from 119.92 to 125.38 mm. There was not significant contrast in the position of the radial nerve with osseous landmarks concerning different degrees of flexion, except for 120°, which is not significant, as this flexion angle is rarely used.
Role of charge accumulation in guided streamer evolution in helium DBD plasma jets
Authors: Pinchuk Mikhail , Nikiforov Anton , Snetov Vadim , Chen Zhaoquan , Leys Christophe , Stepanova Olga 
Published: August 2021

AbstractExperimental data are presented on the evolution of a helium atmospheric pressure plasma jet driven by a tailored voltage waveform generated as bunches of voltage pulses consisting of a superposition of $$\approx 43$$

≈
43

kHz bipolar square pulses and $$\approx 300$$

≈
300

kHz oscillations. The characteristics of directed ionization waves (guided streamers) are compared for bunches with different first pulse polarities and different bunch duty cycles. The longest and brightest streamers are achieved at the voltage bunch with the first negative pulse and a minimum duty cycle. The dynamics of streamers at the voltage bunch with the first positive pulse are characterized by the shortest length and a lower brightness. The plasma jet length can be smoothly changed by varying the number of pulses in the bunch and the polarity of the first pulse. It is thus possible to precisely localize the region of a strong field in space by combining the parameters of the applied voltage (the duty cycle and polarity of the first pulse of a bunch) with a stepwise propagation mode of a guided streamer.
Diagnostic value of IMP3 and p53 immunohistochemical staining in EUS-guided fine-needle aspiration for solid pancreatic tumors
Authors: Mikata Rintaro , Yasui Shin , Kishimoto Takashi , Kouchi Yusuke , Shingyoji Ayako , Senoo Junichi , Takahashi Koji , Nagashima Hiroki , Kusakabe Yuko , Ohyama Hiroshi , Ohno Izumi , Sugiyama Harutoshi , Chiba Tetsuhiro , Kato Jun , Kato Naoya 
Published: August 2021

AbstractWe previously identified insulin-like growth factor-II messenger ribonucleic acid-binding protein 3 (IMP3) as a valuable marker to distinguish malignant from benign lesions in pancreatic solid masses. The aim of this prospective study was to evaluate the usefulness of IMP3 and p53 immunohistochemical staining in endoscopic ultrasound-guided fine-needle aspiration (EUS–FNA) samples for pancreatic solid masses. The study recruited 90 consecutive patients with pancreatic masses, including 62 pancreatic ductal adenocarcinomas (PDACs), 11 benign tumors, and 17 other tumors, who underwent EUS–FNA, and conducted IMP3 and p53 immunohistochemical staining. The main outcome measurement was improved diagnostic utility using IMP3 and p53 immunohistochemical staining. IMP3 and p53 expressions were detected in 60.8% and 49.4% of malignant lesions, 69.4% and 58.1% of PDACs, and 0% of benign lesions, respectively. In PDAC and benign tumors, the use of IMP3 and/or p53 immunostaining increased the sensitivity of cytohistological analysis from 88.7 to 93.5%, although the difference was not statistically significant. The sensitivity of histological analysis combined with that of IMP3 staining was 91.9%, which was significantly greater than that of histology alone (80.6%). The use of IMP3 and p53 immunohistochemical staining did not significantly improve the sensitivity of cytohistological analysis; however, IMP3 staining may be helpful for the histological analysis of malignant pancreatic tumors.
Bovine innate immune phenotyping via a standardized whole blood stimulation assay
Authors: Reid Cian , Beynon Charlotte , Kennedy Emer , O’Farrelly Cliona , Meade Kieran G. 
Published: August 2021

AbstractCattle vary in their susceptibility to infection and immunopathology, but our ability to measure and longitudinally profile immune response variation is limited by the lack of standardized immune phenotyping assays for high-throughput analysis. Here we report longitudinal innate immune response profiles in cattle using a low-blood volume, whole blood stimulation system—the ImmunoChek (IChek) assay. By minimizing cell manipulation, our standardized system minimizes the potential for artefactual results and enables repeatable temporal comparative analysis in cattle. IChek successfully captured biological variation in innate cytokine (IL-1β and IL-6) and chemokine (IL-8) responses to 24-hr stimulation with either Gram-negative (LPS), Gram-positive (PamCSK4) bacterial or viral (R848) pathogen-associated molecular patterns (PAMPs) across a 4-month time window. Significant and repeatable patterns of inter-individual variation in cytokine and chemokine responses, as well as consistent high innate immune responder individuals were identified at both baseline and induced levels. Correlation coefficients between immune response read-outs (IL-1β, IL-6 and IL-8) varied according to PAMP. Strong significant positive correlations were observed between circulating monocytes and IL-6 levels for null and induced responses (0.49–0.61) and between neutrophils and cytokine responses to R848 (0.38–0.47). The standardized assay facilitates high-throughput bovine innate immune response profiling to identify phenotypes associated with disease susceptibility and responses to vaccination.
Resonance Raman enhancement by the intralayer and interlayer electron–phonon processes in twisted bilayer graphene
Authors: Moutinho M. V. O. , Eliel G. S. N. , Righi A. , Gontijo R. N. , Paillet M. , Michel T. , Chiu Po-Wen , Venezuela P. , Pimenta M. A. 
Published: August 2021

AbstractTwisted bilayer graphene is a fascinating system due to the possibility of tuning the electronic and optical properties by controlling the twisting angle $$\theta$$
θ
between the layers. The coupling between the Dirac cones of the two graphene layers gives rise to van Hove singularities (vHs) in the density of electronic states, whose energies vary with $$\theta$$
θ
. Raman spectroscopy is a fundamental tool to study twisted bilayer graphene (TBG) systems since the Raman response is hugely enhanced when the photons are in resonance with transition between vHs and new peaks appear in the Raman spectra due to phonons within the interior of the Brillouin zone of graphene that are activated by the Moiré superlattice. It was recently shown that these new peaks can be activated by the intralayer and the interlayer electron–phonon processes. In this work we study how each one of these processes enhances the intensities of the peaks coming from the acoustic and optical phonon branches of graphene. Resonance Raman measurements, performed in many different TBG samples with $$\theta$$
θ
between $$4^{\circ }$$

4
∘

and $$16^{\circ }$$

16
∘

and using several different laser excitation energies in the near-infrared (NIR) and visible ranges (1.39–2.71 eV), reveal the distinct enhancement of the different phonons of graphene by the intralayer and interlayer processes. Experimental results are nicely explained by theoretical calculations of the double-resonance Raman intensity in graphene by imposing the momentum conservation rules for the intralayer and the interlayer electron–phonon resonant conditions in TBGs. Our results show that the resonant enhancement of the Raman response in all cases is affected by the quantum interference effect and the symmetry requirements of the double resonance Raman process in graphene.
A novel and efficient approach to high-throughput production of HLA-E/peptide monomer for T-cell epitope screening
Authors: Vaurs Juliette , Douchin Gaël , Echasserieau Klara , Oger Romain , Jouand Nicolas , Fortun Agnès , Hesnard Leslie , Croyal Mikaël , Pecorari Frédéric , Gervois Nadine , Bernardeau Karine 
Published: August 2021

AbstractOver the past two decades, there has been a great interest in the study of HLA-E-restricted αβ T cells during bacterial and viral infections, including recently SARS-CoV-2 infection. Phenotyping of these specific HLA-E-restricted T cells requires new tools such as tetramers for rapid cell staining or sorting, as well as for the identification of new peptides capable to bind to the HLA-E pocket. To this aim, we have developed an optimal photosensitive peptide to generate stable HLA-E/pUV complexes allowing high-throughput production of new HLA-E/peptide complexes by peptide exchange. We characterized the UV exchange by ELISA and improved the peptide exchange readout using size exclusion chromatography. This novel approach for complex quantification is indeed very important to perform tetramerization of MHC/peptide complexes with the high quality required for detection of specific T cells. Our approach allows the rapid screening of peptides capable of binding to the non-classical human HLA-E allele, paving the way for the development of new therapeutic approaches based on the detection of HLA-E-restricted T cells.
First identification of ITM2B interactome in the human retina
Authors: Wohlschlegel J. , Argentini M. , Michiels C. , Letellier C. , Forster V. , Condroyer C. , He Z. , Thuret G. , Zeitz C. , Léger T. , Audo I. 
Published: August 2021

AbstractIntegral Membrane Protein 2 B (ITM2B) is a type II ubiquitous transmembrane protein which role remains unclear. ITM2B mutations have been associated with different disorders: mutations leading to longer mutant proteins have been reported in two distinct Alzheimer-like autosomal dominant disorders with early-onset progressive dementia and cerebellar ataxia. Both disorders share neurological features including severe cerebral amyloid angiopathy, non-neuritic plaques, and fibrillary tangles as in Alzheimer disease. Our group reported a missense mutation in ITM2B, in an unusual retinal dystrophy with no dementia. This finding suggests a specific role of ITM2B in the retina. As the identification of retinal-specific ITM2B partners could bring new insights into the cellular functions of ITM2B, we performed quantitative proteomics of ITM2B interactome of the human retina. Overall, 457 ITM2B partners were identified with 8 of them involved in visual transduction. In addition, bulk Gene Ontology analyses showed that many ITM2B partners are involved in several other biological functions, such as microtubule organization, protein translation and interestingly, mitochondrial homeostasis. These data represent the first report of the ITM2B interactome in the human retina and may serve as a valuable inventory of new potential ITM2B partners for future investigations of ITM2B physiological functions and dysfunctions.
Linguistic labels cue biological motion perception and misperception
Authors: Slivac Ksenija , Hervais-Adelman Alexis , Hagoort Peter , Flecken Monique 
Published: August 2021

AbstractLinguistic labels exert a particularly strong top-down influence on perception. The potency of this influence has been ascribed to their ability to evoke category-diagnostic features of concepts. In doing this, they facilitate the formation of a perceptual template concordant with those features, effectively biasing perceptual activation towards the labelled category. In this study, we employ a cueing paradigm with moving, point-light stimuli across three experiments, in order to examine how the number of biological motion features (form and kinematics) encoded in lexical cues modulates the efficacy of lexical top-down influence on perception. We find that the magnitude of lexical influence on biological motion perception rises as a function of the number of biological motion-relevant features carried by both cue and target. When lexical cues encode multiple biological motion features, this influence is robust enough to mislead participants into reporting erroneous percepts, even when a masking level yielding high performance is used.
Hydrolysis of a second Asp-Pro site at the N-terminus of NOTCH3 in inherited vascular dementia
Authors: Zhang Xiaojie , Lee Soo Jung , Wang Michael M. 
Published: August 2021

AbstractCerebrovascular pathology at the biochemical level has been informed by the study of cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), a vascular disorder caused by NOTCH3 mutations. Previous work in CADASIL described N-terminal proteolysis of NOTCH3 generated by specific non-enzymatic cleavage of the first Asp-Pro sequence of the protein. Here, we investigated whether the second Asp-Pro peptide bond (residues 121–122) of NOTCH3 is cleaved in CADASIL. Monospecific antibodies were generated that recognize the neo-epitope predicted to be generated by cleavage after Asp121. These antibodies were used to localize cleavage events at Asp121 in post-mortem CADASIL and control brain tissue and to investigate factors that regulate cleavage at Asp121. We report that cleavage at Asp121 occurs at a high level in the arterial media of CADASIL cerebral arteries. Leptomeningeal arteries demonstrated substantially more cleavage product than penetrating arteries in the white matter, and control vessels harbored only a small amount of cleaved NOTCH3. Proteolysis at Asp121 occurred in purified preparations of NOTCH3 ectodomain, was increased by acidic pH and reductive conditions, and required native protein conformation for cleavage. Increasing the concentration of NOTCH3 EGF-like domain protein elevated the level of proteolysis. On the other hand, several polyanionic chemicals potently blocked cleavage at Asp121. These studies demonstrate that the NOTCH3 protein in CADASIL is cleaved in multiple locations at labile Asp-Pro peptide bonds. As such, chronic brain vascular disease, like other neurodegenerative conditions, features proteolysis of pathological proteins at multiple sites which may generate small pathological peptides.
Dendritic cells play no significant role in the laser-induced choroidal neovascularization model
Authors: Droho Steven , Perlman Harris , Lavine Jeremy A. 
Published: August 2021

AbstractAge-related macular degeneration (AMD) is genetically associated with complement. Dendritic cells (DCs) play key roles during innate and adaptive immunity, and express complement components and their receptors. We investigated ocular DC heterogeneity and the role of DCs in the laser-induced choroidal neovascularization (CNV) model. In order to determine the function of DCs, we used two models of DC deficiency: the Flt3−/− and Flt3l−/− mouse. We identified three types of ocular DCs: plasmacytoid DC, classical DC-1, and classical DC-2. At steady-state, classical DCs were found in the iris and choroid but were not detectable in the retina. Plasmacytoid DCs existed at very low levels in iris, choroid, and retina. After laser injury, the number of each DC subset was up-regulated in the choroid and retina. In Flt3−/− mice, we found reduced numbers of classical DCs at steady-state, but each DC subset equally increased after laser injury between wildtype and Flt3−/− mice. In Flt3l−/− mice, each DC subsets was severely reduced after laser injury. Neither Flt3−/− or Flt3l−/− mice demonstrated reduced CNV area compared to wildtype mice. DCs do not play any significant role during the laser-induced CNV model of neovascular AMD.
Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.)
Authors: Medina Cesar Augusto , Samac Deborah A. , Yu Long-Xi 
Published: August 2021

AbstractAlfalfa is an important legume forage grown worldwide and its productivity is affected by environmental stresses such as drought and high salinity. In this work, three alfalfa germplasms with contrasting tolerances to drought and high salinity were used for unraveling the transcriptomic responses to drought and salt stresses. Twenty-one different RNA samples from different germplasm, stress conditions or tissue sources (leaf, stem and root) were extracted and sequenced using the PacBio (Iso-Seq) and the Illumina platforms to obtain full-length transcriptomic profiles. A total of 1,124,275 and 91,378 unique isoforms and genes were obtained, respectively. Comparative analysis of transcriptomes identified differentially expressed genes and isoforms as well as transcriptional and post-transcriptional modifications such as alternative splicing events, fusion genes and nonsense-mediated mRNA decay events and non-coding RNA such as circRNA and lncRNA. This is the first time to identify the diversity of circRNA and lncRNA in response to drought and high salinity in alfalfa. The analysis of weighted gene co-expression network allowed to identify master genes and isoforms that may play important roles on drought and salt stress tolerance in alfalfa. This work provides insight for understanding the mechanisms by which drought and salt stresses affect alfalfa growth at the whole genome level.
Bacterial resistance to CRISPR-Cas antimicrobials
Authors: Uribe Ruben V. , Rathmer Christin , Jahn Leonie Johanna , Ellabaan Mostafa Mostafa Hashim , Li Simone S. , Sommer Morten Otto Alexander 
Published: August 2021

AbstractIn the age of antibiotic resistance and precise microbiome engineering, CRISPR-Cas antimicrobials promise to have a substantial impact on the way we treat diseases in the future. However, the efficacy of these antimicrobials and their mechanisms of resistance remain to be elucidated. We systematically investigated how a target E. coli strain can escape killing by episomally-encoded CRISPR-Cas9 antimicrobials. Using Cas9 from Streptococcus pyogenes (SpCas9) we studied the killing efficiency and resistance mutation rate towards CRISPR-Cas9 antimicrobials and elucidated the underlying genetic alterations. We find that killing efficiency is not correlated with the number of cutting sites or the type of target. While the number of targets did not significantly affect efficiency of killing, it did reduce the emergence of chromosomal mutations conferring resistance. The most frequent target of resistance mutations was the plasmid-encoded SpCas9 that was inactivated by bacterial genome rearrangements involving translocation of mobile genetic elements such as insertion elements. This resistance mechanism can be overcome by re-introduction of an intact copy of SpCas9. The work presented here provides a guide to design strategies that reduce resistance and improve the activity of CRISPR-Cas antimicrobials.
Predation by avian predators may have initiated the evolution of myrmecomorph spiders
Authors: Veselý Petr , Dobrovodský Juraj , Fuchs Roman 
Published: August 2021

AbstractMyrmecomorphy is a strategy utilized by a variety of species, among which spiders are the most common. It is supposed that myrmecomorphy tends to be selected by predator avoidance of preying on ants rather than by blind ant workers. To date, this hypothesis has been tested mainly on invertebrate predators (mantises and spiders). We are the first to test whether an imperfect myrmecomorph spider (Phrurolithus festivus) gains protection against avian predators (wild adult great tits—Parus major) through its appearance. In a set of preferential trials, we showed that the ant model and the myrmecomorph spider are equally well protected against attack, though the attacked myrmecomorphs are usually eaten. This suggests that the mimicry of the myrmecomorph spiders is effective against avian predators and works in a Batesian manner. In this study, we have provided evidence toward the evolution of myrmecomorphy in response to selective pressure elicited by visually-oriented predators like birds.