bluuebunny/crossref_metadata_2025 huggingface dataset:
Collision possibility analysis and collision avoidance for multi-object fibre-fed spectrographs with theta–phi positioners
Authors: Zhang Feifan , Wang Jianping , Liu Zhigang , Zhai Chao , Chu Jiaru
Published: July 2020

Multi-object spectroscopy has become a valuable technique in numerous modern astronomical facilities. Most spectrographs have thousands of fibre positioners packed at a focal plane with shared working space. Therefore, positioners might collide with each other, which can lead to them being damaged. In this study, we first analysed the types of collisions between hexagonal patterned theta–phi positioners and the possibility of these collisions. Based on this, we proposed a motion planning method by deploying a proposed ‘safety zone’ within the positioner patrol area. Simulated experiments validated that our method could completely solve collisions between positioners with equal arms, such as the Large-sky-Area Multi-Object fibre Spectroscopic Telescope (LAMOST) and the Dark Energy Spectroscopic Instrument (DESI), or between positioners with unequal arms, such as the Multi-Object Optical and Near-infrared Spectrograph (MOONS).
Testing the accuracy of 3D-HST photometric redshift estimates as reference samples for deep weak lensing studies
Authors: Raihan S F , Schrabback T , Hildebrandt H , Applegate D , Mahler G
Published: July 2020

Accurate weak lensing mass estimates of clusters are needed to calibrate mass proxies for the cosmological exploitation of galaxy cluster surveys. Such measurements require accurate knowledge of the redshift distribution of the weak lensing source galaxies. In this context, we investigate the accuracy of photometric redshifts (photo-zs) computed by the 3D-Hubble Space Telescope(HST) team for the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey fields, which provide a relevant photometric reference data set for deep weak lensing studies. Through the comparison to spectroscopic redshifts and photo-zs based on very deep data from the Hubble Ultra Deep Field, we identify catastrophic redshift outliers in the 3D-HST/CANDELS catalogue. These would significantly bias weak lensing results if not accounted for. We investigate the cause of these outliers and demonstrate that the interpolation of spectral energy distribution templates and a well-selected combination of photometric data can reduce the net impact for weak lensing studies.
Semi-analytic modelling of AGNs: autocorrelation function and halo occupation
Authors: Oogi Taira , Shirakata Hikari , Nagashima Masahiro , Nishimichi Takahiro , Kawaguchi Toshihiro , Okamoto Takashi , Ishiyama Tomoaki , Enoki Motohiro
Published: July 2020

The spatial clustering of active galactic nuclei (AGNs) is considered to be one of the important diagnostics for the understanding of the underlying processes behind their activities complementary to measurements of the luminosity function (LF). We analyse the AGN clustering from a recent semi-analytic model performed on a large cosmological N-body simulation covering a cubic gigaparsec comoving volume. We have introduced a new time-scale of gas accretion on to the supermassive black holes to account for the loss of the angular momentum on small scales, which is required to match the faint end of the observed X-ray LF. The large simulation box allows us accurate determination of the autocorrelation function of the AGNs. The model prediction indicates that this time-scale plays a significant role in allowing massive haloes to host relatively faint population of AGNs, leading to a higher bias factor for those AGNs. The model predictions are in agreement with observations of X-ray selected AGNs in the luminosity range $10^{41.5}~\mathrm{erg} \ \mathrm{s}^{-1} \le L_{2{-}10\mathrm{keV}} \le 10^{44.5}~\mathrm{erg} \ \mathrm{s}^{-1}$, with the typical host halo mass of $10^{12.5-13.5} h^{-1}\, {\rm M}_{\odot }$ at $z \lesssim 1$. This result shows that the observational clustering measurements impose an independent constraint on the accretion time-scale complementary to the LF measurements. Moreover, we find that not only the effective halo mass corresponding to the overall bias factor, but the extended shape of the predicted AGN correlation function shows remarkable agreement with those from observations. Further observational efforts towards the low-luminosity end at $z$ ∼ 1 would give us stronger constraints on the triggering mechanisms of AGN activities through their clustering.
X-ray spectroscopy of newly identified ULXs associated with M87’s globular cluster population
Authors: Dage Kristen C , Zepf Stephen E , Thygesen Erica , Bahramian Arash , Kundu Arunav , Maccarone Thomas J , Peacock Mark B , Strader Jay
Published: July 2020

We have identified seven ultraluminous X-ray sources (ULXs) that are coincident with globular cluster candidates (GC) associated with M87. ULXs in the old GC environment represent a new population of ULXs, and ones likely to be black holes. In this study, we perform detailed X-ray spectroscopic follow-up to seven GC ULXs across a wealth of archival Chandra observations and long time baseline of 16 yr. This study brings the total known sample of GC ULXs to 17. Two of these sources show variability in their X-ray luminosity of an order of magnitude over many years, and one of these sources shows intra-observational variability on the scale of hours. While the X-ray spectra of the majority of GC ULXs are best fit by single-component models, one of the sources studied in this paper is the second GC ULX to be best fit by a two-component model. We compare this new sample of GC ULXs to the previously studied sample, and compare the X-ray and optical properties counterparts across the samples. We find that the clusters that host ULXs in M87 have metallicities from g − z = 1.01 to g − z = 1.70. The best-fitting power-law indices of the X-ray spectra range from Γ = 1.37 to 2.21, and the best-fitting inner blackbody disc temperatures range from kT = 0.56 to 1.90 keV.
Targeted DNA oxidation by LSD1–SMAD2/3 primes TGF-β1/ EMT genes for activation or repression
Authors: Pezone Antonio , Taddei Maria Letizia , Tramontano Alfonso , Dolcini Jacopo , Boffo Francesca Ludovica , De Rosa Mariarosaria , Parri Matteo , Stinziani Stefano , Comito Giuseppina , Porcellini Antonio , Raugei Giovanni , Gackowski Daniel , Zarakowska Ewelina , Olinski Ryszard , Gabrielli Armando , Chiarugi Paola , Avvedimento Enrico Vittorio
Published: July 2020

The epithelial-to-mesenchymal transition (EMT) is a complex transcriptional program induced by transforming growth factor β1 (TGF-β1). Histone lysine-specific demethylase 1 (LSD1) has been recognized as a key mediator of EMT in cancer cells, but the precise mechanism that underlies the activation and repression of EMT genes still remains elusive. Here, we characterized the early events induced by TGF-β1 during EMT initiation and establishment. TGF-β1 triggered, 30–90 min post-treatment, a nuclear oxidative wave throughout the genome, documented by confocal microscopy and mass spectrometry, mediated by LSD1. LSD1 was recruited with phosphorylated SMAD2/3 to the promoters of prototypic genes activated and repressed by TGF-β1. After 90 min, phospho-SMAD2/3 downregulation reduced the complex and LSD1 was then recruited with the newly synthesized SNAI1 and repressors, NCoR1 and HDAC3, to the promoters of TGF-β1-repressed genes such as the Wnt soluble inhibitor factor 1 gene (WIF1), a change that induced a late oxidative burst. However, TGF-β1 early (90 min) repression of transcription also required synchronous signaling by reactive oxygen species and the stress-activated kinase c-Jun N-terminal kinase. These data elucidate the early events elicited by TGF-β1 and the priming role of DNA oxidation that marks TGF-β1-induced and -repressed genes involved in the EMT.
Anaplasmosis Presenting With Respiratory Symptoms and Pneumonitis
Authors: Rivera Jose E , Young Katelyn , Kwon Tae Sung , McKenzie Paula A , Grant Michelle A , McBride Darrell A
Published: July 2020

Anaplasmosis is a now common tick-borne illness that is characterized by the presence of fever, myalgias, thrombocytopenia, and elevated liver function tests. We report 4 cases with an atypical presentation with pulmonary symptoms and imaging findings, along with the characteristics of each patient, clinical course, and response to therapy.
Acquainted Strangers: Thwarted Interaction in Digitally Mediated Urban Gay Bars
Authors: Baldor Tyler
Published: July 2020

While some situations in sexual contexts facilitate interaction, others can make overtures difficult to negotiate. Furthermore, social media creates new challenges as individuals navigate sexualized spaces in an increasingly digital world. Drawing on fieldwork in Philadelphia gay bars and supplemental interviews with young gay club-goers, I find that men experience unexpected challenges that inhibit their ability to socialize with gay others and enact positive gay identities. I show how the social organization of particular bars, as well as the popularity of mobile dating applications, undermines the interactional accomplishment of positive outcomes such as identity affirmation and “having fun”: (1) men’s embodied work to evade effeminacy constrains their facial expressions, comportment, and speech; (2) gay bars’ multiple functions as sexual fields and community outposts render both social and sexual interaction difficult to initiate; (3) patrons struggle over whether and how to interact with other mobile dating app users, a novel social tie I conceptualize as acquainted strangers, in the bars. I discuss how these mechanisms—managing stigma corporeally, negotiating discrepant frames, and navigating ambiguous social ties—may thwart interactional achievements while reproducing inequalities in contexts beyond the gay bar.
Culex interfor and Culex saltanensis (Diptera: Culicidae) are susceptible and competent to transmit St. Louis encephalitis virus (Flavivirus: Flaviviridae) in central Argentina
Authors: Beranek Mauricio D , Quaglia Agustín I , Peralta Giovana C , Flores Fernando S , Stein Marina , Diaz Luis A , Almirón Walter R , Contigiani Marta S
Published: July 2020

Background

St. Louis encephalitis virus (SLEV) is endemic and autochthonous on the American continent. Culex pipiens quinquefasciatus is a vector of SLEV; however, Culex interfor and Culex saltanensis have also been found to be naturally infected with SLEV. The aim of this study was to determine the vector competence of C. interfor and C. saltanensis for SLEV from Argentina compared with C. p. quinquefasciatus.

Methods

Female of the Culex species were orally infected by feeding on viraemic chicks that had been inoculated with SLEV. Abdomens, legs and saliva blood-fed mosquitoes were analysed by viral plaque assay.

Results

Mosquitoes were susceptible to orally acquired infection, dissemination and transmission of SLEV in the saliva.

Conclusions

Our results demonstrate that C. saltanensis and C. interfor are susceptible to SLEV and competent for its transmission.
IV Chaucer
Authors: Simon-Jones Lindsey , Pitard Derrick , Twu Krista Sue-Lo
Published: July 2020

This chapter has six sections: 1. General; 2. The Canterbury Tales; 3. Troilus and Criseyde; 4. Other Works; 5. Reception; 6. Pedagogy. Section 1(a) is by Krista Sue-Lo Twu and Lindsey Simon-Jones (additions); sections 1(b) and 1(c) are by Krista Sue-Lo Twu; section 1(d) is by Lindsey Simon-Jones; section 2 is by Krista Sue-Lo Twu; sections 3 and 4 are by Derrick Pitard; sections 5 and 6 are by Lindsey Simon-Jones.
Integrating deep learning with microfluidics for biophysical classification of sickle red blood cells
Authors: Praljak Niksa , Iram Shamreen , Goreke Utku , Singh Gundeep , Hill Ailis , Gurkan Umut A. , Hinczewski Michael
Published: July 2020

Sickle cell disease (SCD), a group of inherited blood disorders with significant morbidity and early mortality, affects a sizeable global demographic largely of African and Indian descent. It is manifested in a mutated form of hemoglobin that distorts the red blood cells into a characteristic sickle shape with altered biophysical properties. Sickle red blood cells (sRBCs) show heightened adhesive interactions with inflamed endothelium, triggering obstruction of blood vessels and painful vaso-occlusive crisis events. Numerous studies have reported microfluidic-assay-based disease monitoring tools which rely on quantifying adhesion characteristics of adhered sRBCs from high resolution channel images. The current workflow for analyzing images from these assays relies on manual cell counting and detailed morphological characterization by a specially trained worker, which is time and labor intensive. Moreover manual counts by different individuals are prone to artifacts due to user bias. We present here a standardized and reproducible image analysis workflow designed to tackle these issues, using a two part deep neural network architecture that works in tandem for automatic, fast and reliable segmentation and classification into subtypes of adhered cell images. Our training utilized an exhaustive data set of images generated by the SCD BioChip, a microfluidic assay which injects clinical whole blood samples into protein-functionalized microchannels, mimicking physiological conditions in the microvasculature. The automated image analysis performs robustly in comparison to human classification: accuracies were similar to or better than those of the trained personnel, while the overall analysis time was improved by two orders of magnitude.
RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response
Authors: Birot Adrien , Kilchert Cornelia , Kus Krzysztof , Priest Emily , Alwash Ahmad Al , Castello Alfredo , Mohammed Shabaz , Vasiljeva Lidia
Published: July 2020

The nuclear RNA exosome plays a key role in mediating degradation and processing of multiple cellular RNAs. Recognition of the specific RNA substrates by the exosome is mediated by the RNA-binding co-factors. Transient binding of co-factors either to the exosome or the substrate RNAs as well as their rapid decay make identification of the co-factors challenging. Here, we employ a comparative poly(A)+ RNA interactome capture approach in the fission yeast exosome mutants to identify proteins that interact with poly(A)+ RNA in an exosome-dependent manner. Our analyses identified multiple proteins whose occupancy on RNA is altered in the exosome mutants including zinc-finger protein Mub1. Mub1 is required to maintain the levels of a subset of the exosome RNA substrates including mRNAs encoding for stress-responsive proteins. Removal of the zinc finger domain leads to loss of RNA suppression under non-stressed conditions, altered expression of heat shock genes in response to stress, and reduced growth at elevated temperature. These findings highlight importance of exosome-dependent mRNA degradation in buffering gene expression networks to mediate cellular adaptation to stress.
Senescent cell death as an aging resistance mechanism in naked mole-rat
Authors: Kawamura Yoshimi , Oka Kaori , Takamori Mayuko , Sugiura Yuki , Oiwa Yuki , Fujioka Shusuke , Homma Sayuri , Miyawaki Shingo , Narita Minoru , Fukuda Takaichi , Suematsu Makoto , Bono Hidemasa , Okano Hideyuki , Miura Kyoko
Published: July 2020

Naked mole-rats (NMRs) are the longest-lived rodents, showing minimal aging phenotypes. An unsolved paradox is that NMRs exhibit low intracellular anti-oxidant defence despite minimal aging. Here, we explained a link between these “contradicting” features by a phenomenon termed “senescent cell death (SCD)”—Senescence induced cell death in NMR cells due to their inherent vulnerability to reactive oxygen species and unique metabolic system. In NMR skin, we observed few senescent cells during aging or after ultraviolet irradiation, suggesting suppression of senescent cell accumulation in NMR tissue. We discovered that senescent NMR-fibroblasts induce SCD through retinoblastoma protein activation accompanied by autophagy dysregulation, increased oxidative damage and accelerated H2O2-releasing metabolic pathways. During senescence, NMR cells showed resistance to metabolic remodelling unlike mice. Our findings provide mechanistic insights into how extraordinary aging resistance is accomplished in NMR. This will contribute to the development of senolytic drugs to regulate age-related diseases.
Conserved conformational hierarchy across functionally divergent glycosyltransferases of the GT-B structural superfamily as determined from microsecond molecular dynamics
Authors: Ramirez-Mondragon Carlos A. , Nguyen Megin E. , Milicaj Jozafina , Tucci Frank J. , Muthyala Ramaiah , Taylor Erika A. , Sham Yuk Y.
Published: July 2020

It has long been understood that some proteins to undergo conformational transitions enroute to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the presence of ligand in the active site is necessary for the protein to crystalize in the closed conformation. Herein we describe microsecond molecular dynamics simulations of two evolutionarily unrelated glycosytransferases, HepI and GtfA. Simulations were performed using these proteins in the open and closed conformations, (respectively,) and we sought to identify the major dynamical modes and communication networks which allow conformational transition between the open and closed structures. We provide the first reported evidence (within the scope of our experimental parameters) that conformational hierarchy/directionality of the interconversion between open and closed conformations is a conserved feature of enzymes of the same structural superfamily. Additionally, residues previously identified to be important for substrate binding in HepI were shown to have strong negative correlations with non-ionizable residues distal to the active site. Mutagenesis of these residues produced mutants with altered enzymatic efficiency exhibiting lower Kmvalues, while the kcatis effectively unchanged. The negatively correlated motions of these residues are important for substrate binding and forming the Michaelis complex, without impacting the activation barrier for catalysis. This suggests that in the bi-domain HepI, the enzyme dynamics did not impact the transition state stabilization or chemistry, but rather earlier steps along the reaction coordinate, leading to the reorganization of the active site electrostatic environment required for catalysis.
Reduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer
Authors: Long Mark D , Singh Prashant K , Llimos Gerard , Jacobi Justine J , Rowsam Aryn M , Rosario Spencer R , Kirk Jason , Affronti Hayley C , Campbell Moray J , Smiraglia Dominic J
Published: July 2020

NCOR2 is frequently and significantly mutated in late stage androgen deprivation therapy resistant prostate cancer (ADT-RPCa). NCOR2 has been characterized as a transcriptional corepressor and has mechanistic links to DNA methylation, but its global functions and overall contributions to PCa progression remain enigmatic. In the current study, we utilize immunohistochemical staining of samples from over 700 PCa patients and reveal associations of reduced NCOR2 expression with correlates of aggressive primary PCa and recurrence in patients who received adjuvant androgen deprivation therapy. We mapped the dihydrotestosterone (DHT) dependent and independent effects of NCOR2 on the transcriptome, cistrome and DNA methylome in androgen sensitive (AS) and ADT-RPCa cells using the isogenic LNCaP and LNCaP-C4-2 (C4-2) cell models. Transcriptional profiling identified androgen dependent and independent regulatory roles of NCOR2, the latter of which was enhanced in the ADT-RPCa state and included neuronal differentiation. Interestingly, reduced expression of NCOR2 resulted in a striking global DNA hypermethylation pattern that significantly enriched at enhancer regions. ChIP-seq revealed that NCOR2 was more clearly associated with promoters in AS LNCaP cells, which was modestly enhanced by DHT treatment. However, in ADT-RPCa C4-2 cells, the NCOR2 cistrome was larger and more distal. Motif analyses and integration of large-scale public cistrome data revealed strong enrichment for FOXA1 in mediating NCOR2 binding, and included additional factors such as AR, E2F, TET2, MED1 and MBD2. Utilizing the CWR22 xenograft model, we demonstrate a direct role for NCOR2 in PCa progression as reduced NCOR2 expression attenuated the impact of ADT, and significantly accelerated recurrence of disease. Transcriptomic analyses in recurrent CWR22 tumors indicated NCOR2-dependent gene expression profiles during ADT that were enriched for neuroendocrine associated genes and also associated with worse survival in human patients with ADT-RPCa. DNA methylation profiles in CWR22 tumors with reduced NCOR2 expression recapitulated the hypermethylation observedin vitro, and further revealed that hypermethylation patterns are commonly associated with ADT-RPCa disease, which was also confirmed in human samples. These studies reveal robust roles for NCOR2 in regulating the PCa transcriptome and epigenome and underscore recent mutational studies linking NCOR2 loss of function to PCa disease progression.
HIF-stabilization prevents delayed fracture healing
Authors: Lang Annemarie , Helfmeier Sarah , Stefanowski Jonathan , Kuppe Aditi , Sunkara Vikram , Pfeiffenberger Moritz , Wolter Angelique , Damerau Alexandra , Hemmati-Sadeghi Shabnam , Ringe Jochen , Haag Rainer , Hauser Anja E. , Löhning Max , Perka Carsten , Duda Georg N. , Hoff Paula , Schmidt-Bleek Katharina , Gaber Timo , Buttgereit Frank
Published: July 2020

The initial phase of fracture healing decides on success of bone regeneration and is characterized by an inflammatory milieu and low oxygen tension (hypoxia). Negative interference with or prolongation of this fine-tuned initiation phase will ultimately lead to a delayed or incomplete healing such as non-unions which then requires an effective and gentle therapeutic intervention. Common reasons include a dysregulated immune response, immunosuppression or a failure in cellular adaptation to the inflammatory hypoxic milieu of the fracture gap and a reduction in vascularizing capacity by environmental noxious agents (e.g. rheumatoid arthritis, smoking). The hypoxia-inducible factor (HIF)-1α is responsible for the cellular adaptation to hypoxia, activating angiogenesis and supporting cell attraction and migration to the fracture gap. Here, we hypothesized that stabilizing HIF-1α could be a cost-effective and low-risk prevention strategy of fracture healing disorders. Therefore, we combined a well-known HIF-stabilizer – deferoxamine (DFO) – and a less known HIF-enhancer – macrophage migration inhibitory factor (MIF) – to synergistically induce improved fracture healing. Stabilization of HIF-1α enhanced calcification and osteogenic differentiation of MSCsin vitro.In vivo, the application of DFO with or without MIF during the initial healing phase accelerated callus mineralization and vessel formation in a clinically relevant mouse-osteotomy-model in a compromised healing setting. Our findings provide support for a promising preventive strategy towards bone healing disorders in patients with a higher risk due to e.g. delayed neovascularization by accelerating fracture healing using DFO and MIF to stabilize HIF-1α.
Unpacking the eagle collision risk model: practical guidance for wind energy
Authors: Evans Michael J. , Sporer Misti , Erickson Wally , Page Joy
Published: July 2020

Climate change is one of the greatest threats facing biodiversity, and solutions to reduce carbon emissions are needed to conserve species. Renewable energies are a prominent means to achieve this goal, but the potential for direct harm to wildlife has raised concerns as these technologies proliferate. To protect biodiversity, approaches that facilitate renewable energy development while protecting species are needed. In the United States wind energy developers must obtain a permit for any Bald or Golden eagles that might be killed at a facility. The U.S. Fish & Wildlife Service estimates fatalities using a Bayesian modeling framework, which combines pre-construction eagle surveys with prior information. The ways in which prior information is incorporated and how pre-construction monitoring affects model outcomes can be unclear to regulated entities and other stakeholders, creating uncertainty in the permitting process and retarding both the build-out of renewable energy and conservation measures for eagles. We conducted a simulation study quantifying the differences in predicted eagle fatalities obtained by incorporating prior information and using only site-specific survey data across a range of scenarios, evaluating the impact of survey effort on the magnitude of this effect. We identified predictable relationships between survey effort, eagle activity, facility size and discrepancies between estimates. We also translated these patterns into real-world financial costs, illustrating the interaction between pre-construction surveys, fatality estimates, and compensatory mitigation obligations in determining permit timing and expense.
Reduced Type-A Carbohydrate-Binding Module Interactions to Cellulose Leads to Improved Endocellulase Activity
Authors: Nemmaru Bhargava , Ramirez Nicholas , Farino Cindy J. , Yarbrough John M. , Kravchenko Nicholas , Chundawat Shishir P.S.
Published: July 2020

Dissociation of non-productively bound cellulolytic enzymes from cellulose is hypothesized to be a key rate-limiting factor impeding cost-effective biomass conversion to fermentable sugars. However, the role of carbohydrate-binding modules (CBMs) in enabling non-productive enzyme binding is not well understood. Here, we examine the subtle interplay of CBM binding and cellulose hydrolysis activity for three model Type-A CBMs (families 1, 3a, and 64) tethered to a multifunctional endoglucanase (CelE) on two distinct cellulose allomorphs (i.e., cellulose I and III). We generated a small-library of mutant CBMs with varying cellulose affinity, as determined by equilibrium binding assays, followed by monitoring cellulose hydrolysis activity of CelE-CBM fusion constructs. Finally, kinetic binding assays using quartz crystal microbalance with dissipation (QCM-D) were employed to measure CBM adsorption and desorption rate constantsKonandKoff, respectively, towards nanocrystalline cellulose derived from both allomorphs. Overall, our results indicate that reduced CBM equilibrium binding affinity towards cellulose I alone, resulting from increased desorption rates (Koff) and reduced effective adsorption rates (nKon), is correlated to overall improved endocellulase activity. Future studies could employ similar approaches to unravel the role of CBMs in non-productive enzyme binding and develop improved cellulolytic enzymes for industrial applications.
Inhibitors of the Bub1 spindle assembly checkpoint kinase: Synthesis of BAY-320 and comparison with 2OH-BNPP1
Authors: Amalina Ilma , Bennett Ailsa , Whalley Helen , Perera David , McGrail Joanne C. , Tighe Anthony , Procter David J , Taylor Stephen S.
Published: July 2020

Bub1 is a serine/threonine kinase proposed to function centrally in both mitotic chromosome alignment and the spindle assembly checkpoint (SAC), however its role remains controversial. Although it is well documented that Bub1 phosphorylation of Histone 2A at T120 (H2ApT120) recruits Sgo1/2 to kinetochores, the requirement of its kinase activity for chromosome alignment and the SAC is debated. As small-molecule inhibitors can be invaluable tools for investigation of kinase function, we decided to evaluate the relative potential of two agents (2OH-BNPPI and BAY-320) as Bub1 inhibitors. After confirming that both agents inhibit Bub1in vitro, we developed a cell based-assay to specifically measure Bub1 inhibitionin vivo. For this assay we overexpressed a fusion of Histone 2B and the Bub1 kinase region (Bub1C) tethering it in close proximity to H2A, which generated a strong ectopic H2ApT120 signal along chromosome arms. The ectopic signal generated from Bub1C activity was effectively inhibited by BAY-320, but not 2OH-BNPP1. In addition, only BAY-320 was able to inhibit endogenous Bub1-mediated Sgo1 localisation. Preliminary experiments using BAY-320 suggested a minor role for Bub1 kinase activity in chromosome alignment and the SAC, however results suggest that BAY-320 may exhibit off-target effects at the concentration required to demonstrate these outcomes. In conclusion, 2OH-BNPP1 may not be an effective Bub1 inhibitorin vivo, and while BAY-320 is able to inhibit Bub1in vivo, the high concentrations required and potential for off-target effects highlight the ongoing need for improved Bub1 inhibitors.
Authentic field experiences for STEM teachers: Collecting Florida fossils
Authors: MacFadden Bruce J. , Pirlo Jeanette , Abramowitz Brian , Killingsworth Stephanie , Ziegler Michael
Published: July 2020

The extensive sedimentary sequence of Florida preserves evidence of prehistoric life spanning some 40 million years into the past. This paper describes the results of a three-pronged professional development (PD) program conducted in November 2019 in which Florida teachers from eight counties gained knowledge and experience about the process and content of paleontology at an active field research site in northern Florida. Working alongside scientists, 15 elementary, middle, and high school teachers collected 5-million-year-old fossil vertebrates and made scientifically important discoveries that advance understanding of Florida’s prehistoric life. The PD included three components: (1) a pre-trip webinar; (2) a morning tour of our museum exhibits to scaffold teacher’s understanding of the kinds of fossils they would find; and (3) the actual day-long field experience collecting fossils. A post-PD evaluation revealed gains in knowledge about, and experience with, fossils and paleontology. We also found that overall satisfaction with the PD underscored the importance of each of the three components supporting one-another—resulting in a more informative and rewarding learning experience for the participants. Fossils and the science of paleontology are a gateway for STEM learning and this subject and its extensions are applicable to existing standards in earth and life sciences at many grade levels.
Single adeno-associated virus-based multiplexed CRISPR-Cas9 system to nullify core components of the mammalian molecular clock
Authors: Kim Boil , Kim Jihoon , Chun Minjeong , Park Inah , Choi Mijung , Kim Kyungjin , Choe Han Kyoung
Published: July 2020

The mammalian molecular clock is based on a transcription-translation feedback loop (TTFL) containing Period1, 2 (Per1, 2), Cryptochrome1, 2 (Cry1, 2), and Brain and Muscle ARNT-Like 1 (Bmal1). TTFL robustness is endowed by genetic complementation between these components; therefore, multiple genes must be knocked out to physiologically investigate the molecular clock, which requires extensive research resources. To facilitate molecular clock disruption, we developed a CRISPR-Cas9-based single adeno-associated viral (AAV) system targeting the circadian clock (CSAC) forPers, Crys, orBmal1. First, we designed single guide RNAs (sgRNAs) targeting individual clock genes using anin silicoapproach and validated their efficiency in Neuro2a cells. To target multiple genes, multiplex sgRNA plasmids were constructed using Golden Gate assembly and expressed in viral vectors. CSAC efficiency was demonstrated by decreased protein expressionin vitroand ablated molecular oscillationex vivo. We also measured locomotor activity and body temperature in Cas9-expressing mice injected with CSAC at the suprachiasmatic nucleus. Circadian rhythm disruption was observed under free-running conditions, indicating that CSAC can efficiently and robustly disrupt molecular circadian clock. Thus, CSAC is a simple and powerful tool for investigating the physiological role of the molecular clockin vivo.
Genetic ancestry changes in Stone to Bronze Age transition in the East European plain
Authors: Saag Lehti , Vasilyev Sergey V. , Varul Liivi , Kosorukova Natalia V. , Gerasimov Dmitri V. , Oshibkina Svetlana V. , Griffith Samuel J. , Solnik Anu , Saag Lauri , D’Atanasio Eugenia , Metspalu Ene , Reidla Maere , Rootsi Siiri , Kivisild Toomas , Scheib Christiana Lyn , Tambets Kristiina , Kriiska Aivar , Metspalu Mait
Published: July 2020

Transition from the Stone to the Bronze Age in Central and Western Europe was a period of major population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide sequence data from 28 individuals from the territory north of this source area – from the under-studied Western part of present-day Russia, including Stone Age hunter-gatherers (10,800–4,250 cal BC) and Bronze Age farmers from the Corded Ware complex called Fatyanovo Culture (2,900–2,050 cal BC). We show that Eastern hunter-gatherer ancestry was present in Northwestern Russia already from around 10,000 BC. Furthermore, we see a clear change in ancestry with the arrival of farming – the Fatyanovo Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe and European early farmer ancestry and thus likely originating from a fast migration towards the northeast from somewhere in the vicinity of modern-day Ukraine, which is the closest area where these ancestries coexisted from around 3,000 BC.
MORONET: Multi-omics Integration via Graph Convolutional Networks for Biomedical Data Classification
Authors: Wang Tongxin , Shao Wei , Huang Zhi , Tang Haixu , Zhang Jie , Ding Zhengming , Huang Kun
Published: July 2020

To fully utilize the advances in omics technologies and achieve a more comprehensive understanding of human diseases, novel computational methods are required for integrative analysis for multiple types of omics data. We present a novel multi-omics integrative method named Multi-Omics gRaph cOnvolutional NETworks (MORONET) for biomedical classification. MORONET jointly explores omics-specific learning and cross-omics correlation learning for effective multi-omics data classification. We demonstrate that MORONET outperforms other state-of-the-art supervised multi-omics integrative analysis approaches from a wide range of biomedical classification applications using mRNA expression data, DNA methylation data, and miRNA expression data. Furthermore, MORONET is able to identify important biomarkers from different omics data types that are related with the investigated diseases.
Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
Authors: Carrieri Anna Paola , Haiminen Niina , Maudsley-Barton Sean , Gardiner Laura-Jayne , Murphy Barry , Mayes Andrew , Paterson Sarah , Grimshaw Sally , Winn Martyn , Shand Cameron , Rowe Will , Hawkins Stacy , MacGuire-Flanagan Ashley , Tazzioli Jane , Kenny John , Parida Laxmi , Hoptroff Michael , Pyzer-Knapp Edward O.
Published: July 2020

Alterations in the human microbiome have been observed in a variety of conditions such has asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome’s role in our health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions.

We combine the effort of collecting a corpus of leg skin microbiome samples of two healthy cohorts of women with the development of anexplainable artificial intelligence (EAI)approach that provides accurate predictions of phenotypes and explanations. The explanations are expressed in terms of variations in the abundance of key microbes that drive the predictions.

We predict skin hydration, subject’s age, pre/post-menopausal status and smoking status from the leg skin microbiome. The key changes in microbial composition linked to skin hydration can accelerate the development of personalised treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring.

Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any conditions from microbiome samples and has the potential to accelerate the development of microbiome-based personalised therapeutics and non-invasive diagnostics.
Cocaine-dependent acquisition of locomotor sensitization and conditioned place preference requires D1 dopaminergic signaling through a cyclic AMP, NCS-Rapgef2, ERK and Egr-1/Zif268 pathway
Authors: Jiang Sunny Zhihong , Sweat Sean , Dahlke Sam , Loane Kathleen , Drossel Gunner , Xu Wenqin , Tejeda Hugo A. , Gerfen Charles R. , Eiden Lee E.
Published: July 2020

Elucidation of the underlying mechanism of dopamine signaling to ERK that underlies plasticity in dopamine D1 receptor expressingneurons leadingto acquired cocaine preference is incomplete. NCS-Rapgef2 is a novel cAMP effector, expressed in neuronal and endocrine cells in adult mammals, that is required for D1 dopamine receptor-dependent ERK phosphorylation in mouse brain. In this report, we studied the effects of abrogating NCS-Rapgef2 expression on cAMP-dependent ERK→Egr-1/zif268 signaling in cultured neuroendocrine cells; in D1 medium spiny neurons (MSNs) of nucleus accumbens slices; and in mouse brain in a region-specific manner. NCS-Rapgef2 gene deletion in the nucleus accumbens (NAc) in adult mice, using AAV-mediated expression of cre recombinase, eliminated cocaine-induced ERK phosphorylation and Egr-1/Zif268 upregulation in D1-MSNs and cocaine-induced behaviors including locomotor sensitization and conditioned place preference (CPP). Abrogation of NCS-Rapgef2 gene expression in medium prefrontal cortex and basolateral amygdala, by crossing mice bearing a floxed Rapgef2 allele with a cre mouse line driven by calcium/calmodulin-dependent kinase IIα promoter also eliminated cocaine-induced phospho-ERK activation and Egr-1/Zif268 induction, but without effect on the cocaine-induced behaviors. Our results indicate that NCS-Rapgef2 signaling to ERK in dopamine D1-receptor expressing neurons in the NAc, butnotin corticolimbic areas, contributes to cocaine-induced locomotor sensitization and CPP. Ablation of cocaine-dependent ERK activation by elimination of NCS-Rapgef2 occurred with no effect on phosphorylation of CREB in D1 dopaminoceptive neurons of NAc. This study reveals a new cAMP-dependent signaling pathway for cocaine-induced behavioral adaptations, mediated through NCS-Rapgef2/phospho-ERK activation, independently of PKA/CREB signaling.

SIGNIFICANCE STATEMENT

ERK phosphorylation in dopamine D1 receptor expressing neurons exerts a pivotal role in psychostimulant-induced neuronal gene regulation and behavioraladaptation, including locomotor sensitization and drug preference in rodents. In this study, we examined the role of dopamine signaling through the D1 receptor via a novel pathway initiated through the cAMP-activated guanine nucleotide exchange factor NCS-Rapgef2 in mice. NCS-Rapgef2 in the nucleus accumbens is required for activation of ERK and Egr-1/Zif268 in D1 dopaminoceptive neurons after acute cocaine administration, and subsequentenhanced locomotor response anddrugseeking behavior after repeated cocaine administration. This novel component in dopamine signaling provides a potential new target for intervention in psychostimulant-shaped behaviors, and new understanding of how D1-MSNs encode the experience of psychomotor stimulant exposure.
Arabidopsis poly(ADP-ribose)-binding protein RCD1 interacts with Photoregulatory Protein Kinases in nuclear bodies
Authors: Vainonen Julia P. , Shapiguzov Alexey , Krasensky-Wrzaczek Julia , Gossens Richard , Masi Raffaella De , Danciu Iulia , Puukko Tuomas , Battchikova Natalia , Jonak Claudia , Wirthmueller Lennart , Wrzaczek Michael , Kangasjärvi Jaakko
Published: July 2020

Continuous reprogramming of gene expression in response to environmental signals is required for plant survival in changing environment. One mechanism responsible for this is signaling through hub proteins that integrate external stimuli and transcriptional responses. RADICAL-INDUCED CELL DEATH1 (RCD1) functions as a nuclear hub protein, that interacts with a variety of transcription factors through its C-terminal RST domain and acts as a co-regulator of numerous stress responses in plants. Here, a previously unknown function for RCD1 as a novel plant poly(ADP-ribose) (PAR) reader protein is described. RCD1 localizes to specific locations inside the nucleus, in a PAR-dependent manner; its N-terminal WWE domain o binds PAR and together with the PARP-like domain determines its localization to nuclear bodies (NBs), which is prevented by inhibition of PAR synthesis. RCD1 also interacts with Photoregulatory Protein Kinases (PPKs) that co-localize with RCD1 in the NBs. The PPKs, that have been associated with circadian clock, abscisic acid, and light signaling pathways, phosphorylate RCD1 at multiple sites in the intrinsically disordered region between the WWE and PARP-like domains. This affects its stability and functions in the nucleus and1 provides a mechanism where the turnover of a PAR-binding transcriptional co-regulator is controlled by nuclear protein kinases.
Neural mechanisms underlying expectation-dependent inhibition of distracting information
Authors: van Moorselaar Dirk , Lampers Eline , Cordesius Elisa , Slagter Heleen A.
Published: July 2020

Predictions based on learned statistical regularities in the visual world have been shown to facilitate attention and goal-directed behavior by sharpening the sensory representation of goal-relevant stimuli in advance. Yet, how the brain learns to ignore predictable goal-irrelevant or distracting information is unclear. Here, we used EEG and a visual search task in which the predictability of a distractor’s location and/or spatial frequency was manipulated to determine how spatial and feature distractor expectations are neurally implemented and reduce distractor interference. We find that expected distractor features could not only be decoded pre-stimulus, but their representation differed from the representation of that same feature when part of the target. Spatial distractor expectations did not induce changes in preparatory neural activity, but a strongly reduced Pd, an ERP index of inhibition. These results demonstrate that neural effects of statistical learning critically depend on the task relevance and dimension (spatial, feature) of predictions.
Modeling collaterally sensitive drug cycles: shaping heterogeneity to allow adaptive therapy
Authors: Yoon Nara , Krishnan Nikhil , Scott Jacob
Published: July 2020

In previous work, we focused on the optimal therapeutic strategy with a pair of drugs which are collaterally sensitive to each other, that is, a situation in which evolution of resistance to one drug induces sensitivity to the other, and vice versa. [1] Here, we have extended this exploration to the optimal strategy with a collaterally sensitive drug sequence of an arbitrary length,N(≥ 2). To explore this, we have developed a dynamical model of sequential drug therapies withNdrugs. In this model, tumor cells are classified as one ofNsubpopulations represented as {Ri|i= 1,2,…,N}. Each subpopulation,Ri, is resistant to ‘Drug i’ and each subpopulation,Ri–1(orRN, ifi= 1), is sensitive to it, so that Riincreases under ‘Drug i’ as it is resistant to it, and after drug-switching, decreases under ‘Drug i+ 1’ as it is sensitive to that drug(s).

Similar to our previous work examining optimal therapy with two drugs, we found that there is an initial period of time in which the tumor is ‘shaped’ into a specific makeup of each subpopulation, at which time all the drugs are equally effective. After this shaping period, all the drugs are quickly switched with duration relative to their efficacy in order to maintain each subpopulation, consistent with the ideas underlying adaptive therapy. [2, 3]

Additionally, we have developed methodologies to administer the optimal regimen under clinical or experimental situations in which no drug parameters and limited information of trackable populations data (all the subpopulations or only total population) are known. The therapy simulation based on these methodologies showed consistency with the theoretical effect of optimal therapy.
Vascular dimorphism ensured by regulated proteoglycan dynamics favors rapid umbilical artery closure at birth
Authors: Nandadasa Sumeda , Szafron Jason M. , Pathak Vai , Murtada Sae-Il , Kraft Caroline M. , O’Donnell Anna , Norvik Christian , Hughes Clare , Caterson Bruce , Domowicz Miriam S. , Schwartz Nancy B. , Tran-Lundmark Karin , Veigl Martina , Sedwick David , Philipson Elliot H. , Humphrey Jay D. , Apte Suneel S.
Published: July 2020

The umbilical artery lumen occludes rapidly at birth, preventing blood loss, whereas the umbilical vein remains patent, providing the newborn with a placental infusion. Here, we identify differential arterial-venous proteoglycan dynamics as a determinant of these contrasting vascular responses. We show that the umbilical artery, unlike the vein, has an inner layer enriched in the hydrated proteoglycan aggrecan, external to which lie contraction-primed smooth muscle cells (SMC). At birth, SMC contraction drives inner layer buckling and centripetal displacement to occlude the arterial lumen, a mechanism elicited by biomechanical and computational analysis. Vascular dimorphism arises from spatially regulated proteoglycan expression and breakdown in umbilical vessels. Mice lacking aggrecan or the metalloprotease ADAMTS1, which degrades proteoglycans, demonstrated their opposing roles in umbilical cord arterial-venous dimorphism and contrasting effects on SMC differentiation. Umbilical vessel dimorphism is conserved in mammals, suggesting that their differential proteoglycan dynamics were a positive selection step in mammalian evolution.