bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calmodulin inhibition as a mode of action of antifungal imidazole pharmaceuticals in non-target organisms
Authors: Breitholtz Magnus , Ivanov Pavel , Ek Karin , Gorokhova Elena 
Published: May 2020

AbstractTo improve assessment of risks associated with pharmaceutical contamination of the environment, it is crucial to understand effects and mode of action of drugs in non-target species. The evidence is accumulating that species with well-conserved drug targets are prone to be at risk when exposed to pharmaceuticals. An interesting group of pharmaceuticals released into the environment is imidazoles, antifungal agents with inhibition of ergosterol synthesis as a primary mode of action in fungi. However, imidazoles have also been identified as competitive antagonists of calmodulin (CaM), a calcium-binding protein with phylogenetically conserved structure and function. Therefore, imidazoles would act as CaM inhibitors in various organisms, including those with limited capacity to synthesize sterols, such as arthropods. We hypothesized that effects observed in crustaceans exposed to imidazoles are related to the CaM inhibition and CaM-dependent nitric oxide (NO) synthesis. To test this hypothesis, we measured (i) CaM levels and its gene expression, (ii) NO accumulation and (iii) gene expression of NO synthase (NOS1 and NOS2), in the cladoceran Daphnia magna exposed to miconazole, a model imidazole drug. Whereas significantly increased CaM gene expression and its cellular allocation were observed, supporting the hypothesized mode of action, no changes occurred in either NO synthase expression or NO levels in the exposed animals. These findings suggest that CaM inhibition by miconazole leads to protein overexpression that compensates for the loss in the protein activity, with no measurable downstream effects on NO pathways. The inhibition of CaM in D. magna may have implications for effect assessment of exposure to mixtures of imidazoles in aquatic non-target species.
Traumatic Brain Injury among football players in 2017 Series A Brazilian Football Championship – The gap between concussion protocols and the current medical practices
Authors: Salvarani Cármine Porcelli , de Medeiros Lucas Ribeiro , Sotocorno Leonardo Henrique Micheletti , Tomazini Vinícius Simon , de Castro Diego Ciotta , Dias Eduardo Almeida , da Costa Paulo Sérgio Teixeira , Pimenta Bruno Bueno , de Oliveira Diego Almeida , da Silva Eduardo Vinícius Colman , Sapatero Fernando Henrique 
Published: May 2020

ABSTRACTBackgroundSideline assessment of football players with a potential concussion is a challenging concern. Video analysis is an important tool to recognize traumatic brain injury (TBI), including sports-related concussions, among football players.AimTo report the characteristics of TBI among football players in 2017 Brazilian Series A Football Championship and to discuss the evaluation protocols of football players with concussion.MethodsThis is an observational study concerning video analysis of all matches on 2017 Series A Brazilian Football Championship. The videos were first analyzed by a team of 10 trained medical students. All suspected TBIs were reviewed by the research’s coordinator. Concussion diagnosis was defined by one of the following events: lying motionless, loss of responsiveness, impact seizure, disorientation and motor incoordination. The length of sideline medical assessment was systematically recorded.ResultsIn a whole of 380 matches, it was verified 374 TBIs. The most common etiology was “head-to-head” impact. Twelve players were replaced after TBI. Thirteen players (3,5% of TBIs) had concussion, but only four of them were replaced. The overall mean time for medical assessment was 1’35” (range: 48” to 7’40”). Considering the twelve players who had a concussion and the thirteen players who were replaced, the mean time for medical evaluation was 3’19” and 3’26”, respectively.ConclusionThis study confirms that there is a gap between formal protocols for concussion assessment on sideline in Brazilian Elite Football and current medical practices. It also discusses changes on football rules of player replacement to an adequate sideline medical evaluation.
T cells expanded from renal cell carcinoma are tumor-reactive but fail to produce IFN-γ, TNF-α or IL-2
Authors: van Asten Saskia D. , de Groot Rosa , van Loenen Marleen M. , de Jong Jeroen , Monkhorst Kim , Haanen John B.A.G. , Amsen Derk , Bex Axel , Spaapen Robbert M. , Wolkers Monika C. 
Published: May 2020

AbstractMetastatic renal cell carcinoma (RCC) has a poor prognosis. Recent advances have shown beneficial responses to immune checkpoint inhibitors, such as anti-PD-1 or anti-PD-L1 antibodies. As only a subset of RCC patients respond, alternative strategies should be explored. Patients refractory to anti-PD-1 therapy may benefit from autologous tumor infiltrating lymphocyte (TIL) therapy. Even though efficient TIL expansion was reported from RCC lesions, it is not well established how many RCC TIL products are tumor-reactive, how well they produce pro-inflammatory cytokines in response to autologous tumors, and whether their response correlates with the presence of specific immune cells in the tumor lesions.We here compared the immune infiltrate composition of RCC lesions with that of autologous kidney tissue of 18 RCC patients. T cell infiltrates were increased in the tumor lesions, and CD8+T cell infiltrates were primarily of effector memory phenotype. Nine out of 16 (56%) tested TIL products we generated were tumor-reactive, as defined by CD137 upregulation after exposure to autologous tumor digest. Tumor reactivity was found in particular in TIL products originating from tumors with a high percentage of infiltrated T cells compared to autologous kidney, and coincided with increasedex vivoCD25 expression on CD8+T cells. Importantly, although TIL products had the capacity to produce the key effector cytokines IFN-γ, TNF-α or IL-2, they failed to do so in response to autologous tumor digests. In conclusion, TIL products from RCC lesions contain tumor-reactive T cells. Their lack of tumor-specific cytokine production requires further investigation of immunosuppressive factors in RCC and subsequent optimization of RCC-derived TIL culture conditions.
Unique habitat and macroinvertebrate assemblage structures in spring-fed stream: a comparison among clastic lowland tributaries and mainstreams in northern Japan
Authors: Sakai Masaru , Iwabuchi Katsuya , Bauman David 
Published: May 2020

AbstractThe stable flow and temperature regimes of spring-fed streams are distinct from the dynamic regimes of other streams. We investigated differences in habitat and macroinvertebrate assemblages among three stream types (spring-fed tributary, non-spring-fed tributary and mainstream) in a clastic lowland of northern Japan. Current velocity was the slowest in the spring-fed reach, where the percent of fine sediment deposition was also 3.8–11.4 times higher than in the other stream types. The standing stock of detritus was also greater in the spring-fed reach. These results suggest that the stable flow regime in the spring-fed stream leads to the accumulation of fine sediment and detritus on the streambed. Oligochaeta and chironomids, which are burrower-gatherers, were remarkably abundant in the spring-fed reach. Total macroinvertebrate abundance was 3.8–12.2 times greater in the spring-fed reach than in the other stream types. Sprawler-grazer ephemeropterans were the most abundant in the mainstream reaches, likely due to higher primary productivity.Allomyiasp, which depend on cool spring-fed habitats, were found only in the spring-fed reach. The indicator species analysis also indicated multiple taxa of detritivores andAllomyiasp. for the spring-fed tributary. The macroinvertebrate assemblage in the spring-fed reach was characterized by numerous burrowers, collector-gatherers, and crenobiont taxa, highlighting the uniqueness and its contribution to enhance beta diversity in river networks.
Visualizing the itch-sensing skin arbors
Authors: Xing Yanyan , Steel Haley R. , Hilley Henry B. , Lawson Katy , Niehoff Taylor , Han Liang 
Published: May 2020

ABSTRACTDiverse sensory neurons exhibit distinct neuronal morphologies with a variety of axon terminal arborizations used to subserve their functions. Due to its clinical significance, the molecular and cellular mechanisms of itch are being intensely studied. However, a complete analysis of itch-sensing terminal arborization morphology is missing. Using a novelMrgprC11CreERT2transgenic mouse line, we labeled a small subset of itch-sensing neurons that express multiple itch-related molecules including MrgprA3, MrgprC11, histamine receptor H1, IL-31 receptor, 5-HT receptor 1F, natriuretic precursor peptide B, and neuromedin B. By combining sparse genetic labeling and whole-mount PLAP histochemistry, we found that itch-sensing skin arbors exhibit free endings with extensive axonal branching in the superficial epidermis and large receptive fields. These results revealed the unique morphological characteristics of itch-sensing neurons and provide novel insights into the basic mechanisms of itch transmission.
GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers
Authors: Bianco Gaia , Coto-Llerena Mairene , Gallon John , Taha-Mehlitz Stephanie , Kancherla Venkatesh , Konantz Martina , Srivatsa Sumana , Montazeri Hesam , Panebianco Federica , De Menna Marta , Paradiso Viola , Ercan Caner , Dahmani Ahmed , Montaudon Elodie , Beerenwinkel Niko , Kruithof-de Julio Marianna , Terracciano Luigi M. , Lengerke Claudia , Bidard François-Clément , Jeselsohn Rinath M. , Marangoni Elisabetta , Ng Charlotte K. Y. , Piscuoglio Salvatore 
Published: May 2020

SummarySynthetic lethal interactions, where the simultaneous but not individual inactivation of two genes is lethal to the cell, have been successfully exploited to treat cancer.GATA3is frequently mutated in estrogen receptor (ER)-positive breast cancers and its deficiency defines a subset of patients with poor response to hormonal therapy and poor prognosis. However, GATA3 is not targetable. Here we show thatGATA3andMDM2are synthetically lethal in ER-positive breast cancer. Depletion and pharmacological inhibition of MDM2 induce apoptosis inGATA3-deficient modelsin vitro, in vivoand in patient-derived organoids (PDOs) harboringGATA3somatic mutation. The synthetic lethality requires p53 and acts via the PI3K/Akt/mTOR pathway. Our results present MDM2 as a novel therapeutic target in the substantial cohort of ER-positive,GATA3-mutant breast cancer patients. With MDM2 inhibitors widely available, our findings can be rapidly translated into clinical trials to evaluate in-patient efficacy.
Evolutionary transition to XY sex chromosomes associated with Y-linked duplication of a male hormone gene in a terrestrial isopod
Authors: Russell Aubrie , Borrelli Sevarin , Fontana Rose , Laricchiuta Joseph , Pascar Jane , Becking Thomas , Giraud Isabelle , Cordaux Richard , Chandler Christopher H. 
Published: May 2020

AbstractSex chromosomes are highly variable in some taxonomic groups, but the evolutionary mechanisms underlying this diversity are not well understood. In terrestrial isopod crustaceans, evolutionary turnovers in sex chromosomes are frequent, possibly caused byWolbachia, a vertically-transmitted endosymbiont causing male-to-female sex reversal. Here, we use surgical manipulations and genetic crosses, plus genome sequencing, to examine sex chromosomes in the terrestrial isopodTrachelipus rathkei. Although an earlier cytogenetics study suggested a ZZ/ZW sex chromosome system in this species, we surprisingly find multiple lines of evidence that in our study population, sex is determined by an XX/XY system. Consistent with a recent evolutionary origin for this XX/XY system, the putative male-specific region of the genome is small. The genome shows evidence of Y-linked duplications of the gene encoding the androgenic gland hormone, a major component of male sexual differentiation in isopods. Our analyses also uncover sequences horizontally acquired from pastWolbachiainfections, consistent with the hypothesis thatWolbachiamay have interfered with the evolution of sex determination inT. rathkei. Overall, these results provide evidence for the co-occurrence of multiple sex chromosome systems withinT. rathkei, further highlighting the relevance of terrestrial isopods as models for the study of sex chromosome evolution.
A homodimeric aptamer variant generated from ligand-guided selection activates T-cell receptor cluster of differentiation three complex
Authors: Freage Lina , Jamal Deana , Williams Nicole , Mallikaratchy Prabodhika R. 
Published: May 2020

AbstractRecently, immunotherapeutic modalities with engineered cells and monoclonal antibodies have been effective in treating several malignancies. However, growing evidence suggests that immune-related adverse events (irAE) lead to severe and long-term side effects. Most iRAEs involve prolonged circulation of antibodies. To address this problem, nucleic acid aptamers can serve as alternative molecules to design immunotherapeutics with high functional diversity and predictable circulation times. Here, we report the first synthetic prototype consisting of DNA aptamers, which can activate T-cell receptor cluster of differentiation 3 (TCR-CD3) complex in cultured T-cells. We show that activation potential is similar to that of a monoclonal antibody (mAb) against TCR-CD3, suggesting the potential of aptamers in developing efficacious synthetic immunomodulators. The synthetic prototype of anti-TCR-CD3ε, as described herein, was designed using aptamer ZUCH-1 against TCR-CD3ε, generated by Ligand Guided Selection (LIGS). Aptamer ZUCH-1 was truncated and modified with nuclease-resistant RNA analogs to enhance stability. Several dimeric analogs with truncated and modified variants were designed with variable linker lengths to investigate the activation potential of each construct. Among them, dimeric aptamer with approximate dimensions similar to those of an antibody showed the highest T-cell-activation, suggesting the importance of optimizing linker lengths in engineering functional aptamers. The observed activation potential of dimeric aptamers shows the vast potential of aptamers in designing synthetically versatile immunomodulators with tunable pharmacokinetic properties, expanding immunotherapeutic designs with the use of nucleic acid-based ligands such as aptamers.
Microbubble-Mediated Cavitation Promotes Apoptosis and Suppresses Invasion in AsPC-1 Cells
Authors: Cao J. , Zhou H. , Qiu F. , Chen J. , Diao F. , Huang P. 
Published: May 2020

AbstractThis study aimed to identify the potential and mechanisms of microbubble-mediated cavitation in promoting apoptosis and suppressing invasion in cancer cells. AsPC-1 cells were used and divided into four groups: control group, microbubble-only (MB) group, ultrasound-only (US) group, and ultrasound combined with microbubbles (US+MB) group. Pulse ultrasound was used with a frequency of 360 kHz and an intensity of 0.7 W/cm2for 1 min (duty rate=50%). Then cells in four groups were cultured for 24 h. Cell counting kit‑8 illustrated that US+MB could decrease cell viability. Western blot confirmed that US+MB increased cleaved Caspase‑3, Bcl-2-associated X protein (BAX), and decreased the B‑cell lymphoma‑2 (Bcl-2) levels. Besides, US+MB increased intracellular calcium ions and down-regulated cleaved Caspase-8. For proliferation ability, cells in US+MB group had a lower expression of Ki67 and the weakened colony formation ability. The transwell invasion assay showed that US+MB could decrease invasion ability in AsPC-1 cells. Further evidence showed that cells conducted with US+MB had the lower level of hypoxia-inducible factor-1α (HIF-1α) and Vimentin and the higher expression of E-cadherin than the other three groups. Finally, cells conducted with US+MB had less invadopodia formation. In conclusion, these results suggested that microbubble-mediated cavitation promoted apoptosis and suppressed invasion in AsPC-1 cells.SignificanceCancer cells have a high rate of cell division and a high rate of cell division can speed up the development of hypoxia which lead to promote cancer invasion and metastasis. Here we used microbubble-mediated cavitation to generate a mechanical shock wave which could effectively kill cancer cells through physical damage and intrinsic signaling pathway. Furthermore, effective killing of cancer cells could restrain the development of hypoxia and prevent invasion ability of cancer cells.
A Purkinje cell model that simulates complex spikes
Authors: Burroughs Amelia , Cerminara Nadia L. , Apps Richard , Houghton Conor 
Published: May 2020

AbstractPurkinje cells are the principal neurons of the cerebellar cortex. One of their distinguishing features is that they fire two distinct types of action potential, called simple and complex spikes, which interact with one another. Simple spikes are stereotypical action potentials that are elicited at high, but variable, rates (0 – 100 Hz) and have a consistent waveform. Complex spikes are composed of an initial action potential followed by a burst of lower amplitude spikelets. Complex spikes occur at comparatively low rates (~ 1 Hz) and have a variable waveform. Although they are critical to cerebellar operation a simple model that describes the complex spike waveform is lacking. Here, a novel single-compartment model of Purkinje cell electrodynamics is presented. The simpler version of this model, with two active conductances and a leak channel, can simulate the features typical of complex spikes recordedin vitro. If calcium dynamics are also included, the model can capture the pause in simple spike activity that occurs after complex spike events. Together, these models provide an insight into the mechanisms behind complex spike spikelet generation, waveform variability and their interactions with simple spike activity.
O-Pair Search with MetaMorpheus for O-glycopeptide Characterization
Authors: Lu Lei , Riley Nicholas M. , Shortreed Michael R. , Bertozzi Carolyn R. , Smith Lloyd M. 
Published: May 2020

AbstractWe report O-Pair Search, a new approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides using an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. O-Pair Search is freely available:https://github.com/smith-chem-wisc/MetaMorpheus.
sangeranalyseR: simple and interactive analysis of Sanger sequencing data in R
Authors: Chao Kuan-Hao , Barton Kirston , Palmer Sarah , Lanfear Robert 
Published: May 2020

AbstractSummarysangeranalyseR is an interactive R/Bioconductor package and two associated Shiny applications designed for analysing Sanger sequencing from data from theABIFfile format in R. It allows users to go from loading reads to saving aligned contigs in a few lines of R code. sangeranalyseR provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, viewing chromatograms, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. sangeranalyseR comes with extensive online documentation, and outputs detailed interactive HTML reports.Availability and implementationsangeranalyseR is implemented in R and released under an MIT license. It is available for all platforms on Bioconductor (https://bioconductor.org/packages/sangeranalyseR) and on Github (https://github.com/roblanf/sangeranalyseR).Contactkuanhao.chao@gmail.comSupplementary informationDocumentation athttps://sangeranalyser.readthedocs.io/.
Radiosynthesis and Preclinical Evaluation of [68Ga]Ga-NOTA-Folate for PET Imaging of Folate Receptor β Positive Macrophages
Authors: Moisio Olli , Palani Senthil , Virta Jenni , Elo Petri , Liljenbäck Heidi , Tolvanen Tuula , Käkelä Meeri , Miner Maxwell G. , Herre Erika Atencio , Marjamäki Päivi , Örd Tiit , Heinäniemi Merja , Kaikkonen-Määttä Minna , Zhang Fenghua , Srinivasarao Madduri , Knuuti Juhani , Low Philip S. , Saraste Antti , Li Xiang-Guo , Roivainen Anne 
Published: May 2020

ABSTRACTFolate receptor β (FR-β) is one of the markers expressed on macrophages and a promising target for imaging of inflammation. Here, we report the radiosynthesis and preclinical evaluation of [68Ga]Ga-NOTA-folate (68Ga-FOL). First, we determined the affinity of68Ga-FOL using human FR-β expressing cells. Then, we studied atherosclerotic mice with68Ga-FOL and18F-FDG PET/CT. After sacrifice, the tissues excised were measured with a γ-counter forex vivobiodistribution. Further, the tracer distribution and co-localization with macrophages in aorta cryosections were studied using autoradiography, hematoxylin-eosin staining and immunostaining with anti-Mac-3 antibody. Specificity of68Ga-FOL was assessed in a blocking study with excess of folate glucosamine. As a last step, human radiation doses were extrapolated from rat PET data. We were able to produce68Ga-FOL at high radioactivity concentration, with high molar activity and radiochemical purity. The cell binding studies showed high (5.1 ± 1.1 nM) affinity of68Ga-FOL to FR-β. The myocardial uptake of68Ga-FOL (SUV 0.43 ± 0.06) was 20-folds lower compared to18F-FDG (SUV 10.6 ± 1.8,P= 0.001). The autoradiography and immunohistochemistry of aorta revealed that68Ga-FOL radioactivity co-localized with Mac-3-positive macrophage-rich atherosclerotic plaques. The plaque-to-healthy vessel wall ratio of68Ga-FOL (2.44 ± 0.15) was significantly higher than that of18F-FDG (1.93 ± 0.22,P= 0.005). Blocking studies verified68Ga-FOL specificity to FR. As estimated from rat data the human effective dose was 0.0105 mSv/MBq. The organ with highest absorbed dose was kidney (0.1420 mSv/MBq). In conclusion,68Ga-FOL is a promising new FR-β-targeted tracer for imaging macrophage-associated inflammation.TABLE OF CONTENT/ABSTRACT GRAPHIC
Integrated multi-omics reveals common properties underlying stress granule and P-body formation
Authors: Kershaw Christopher J. , Nelson Michael G. , Lui Jennifer , Bates Christian P. , Jennings Martin D. , Hubbard Simon J. , Ashe Mark P. , Grant Chris M. 
Published: May 2020

ABSTRACTNon-membrane-bound compartments such as P-bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically determined the protein and mRNA composition of PBs and SGs formed in response to a common stress condition imposed by glucose depletion. We find that high molecular weight (HMW) complexes exist prior to glucose depletion that may act as seeds for the further condensation of proteins forming mature PBs and SGs. Both before and after glucose depletion, these HMW complexes are enriched for proteins containing low complexity and RNA binding domains. The mRNA content of these HMW complexes is enriched for long, structured mRNAs that become more poorly translated following glucose depletion. Many proteins and mRNAs are shared between PBs and SGs including several multivalent RNA binding proteins that may promote condensate interactions during liquid-liquid phase separation. Even where the precise identity of mRNAs and proteins localizing to PBs and SGs is distinct, the mRNAs and proteins share common biophysical and chemical features that likely trigger their phase separation.