bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic evaluation of ESBL-producingEscherichia coliurinary isolates in Otago, New Zealand
Authors: Hapuarachchi Isuri U , Hannaway Rachel F , Roman Tabatha , Biswas Ambarish , Dyet Kristin , Morgan Xochitl , Ussher James E 
Published: September 2021

AbstractObjectivesThe incidence of infections with ESBL-producing Escherichia coli (ESBL-Ec) in New Zealand is increasing. ESBL-Ec most commonly cause urinary tract infections and are seen in both community and hospitalized patients. The reason for the increasing incidence of ESBL-Ec infections is unknown.MethodsIn this study, 65 urinary ESBL-Ec isolates from the Otago region in 2015 were fully genetically characterized to understand the mechanisms of transmission. The ESBL gene, E. coli STs, plasmid types and genetic context (e.g. insertion sequences) of ESBL genes were determined by a combination of whole genome and plasmid sequencing. The phylogenetic relationships of the isolates were compared with ESBL-Ec isolates sequenced as part of the 2016 nationwide survey.ResultsSignificant diversity of E. coli strains, plasmids, and the genetic context of ESBL genes was seen. However, there was evidence of common mobile genetic elements in unrelated ESBL-Ec.ConclusionsMultiple introductions of ESBL resistance genes or resistant bacterial strains with limited horizontal transmission of mobile genetic elements accounts for the increased incidence of ESBL-Ec in this low prevalence area. Future studies should investigate modes of transmission of ESBL-Ec in the Otago region.
Genome-wide Analysis of Alternative Gene Splicing Associated with Virulence in the Brown Planthopper Nilaparvata lugens (Hemiptera: Delphacidae)
Authors: Liu Kai , Su Qin , Kang Kui , Chen Meng , Wang Wei-Xia , Zhang Wen-Qing , Pang Rui 
Published: September 2021

Abstract
Alternative splicing of protein coding genes plays a profound role in phenotypic variation for many eukaryotic organisms. The development of high-throughput sequencing and bioinformatics algorithms provides the possibility of genome-wide identification of alternative splicing events in eukaryotes. However, for the brown planthopper Nilaparvata lugens, a destructive pest of rice crops, whole-genome distribution of alternative splicing events and the role of alternative splicing in the phenotypic plasticity of virulence have not previously been estimated. Here, we developed an analysis pipeline to identify alternative splicing events in the genome of N. lugens. Differential expression analysis and functional annotation were performed on datasets related to different virulence phenotypes. In total, 27,880 alternative splicing events corresponding to 9,787 multi-exon genes were detected in N. lugens. Among them, specifically expressed alternative splicing transcripts in the virulent Mudgo population were enriched in metabolic process categories, while transcripts in the avirulent TN1 population were enriched in regulator activity categories. In addition, genes encoding odorant receptor, secreted saliva protein and xenobiotic metabolic P450 monooxygenase showed different splicing patterns between Mudgo population and TN1 population. Host change experiment also revealed that an isoform of a P450 gene could be specially induced by the stimulation of resistant rice variety Mudgo. This research pioneered a genome-wide study of alternative gene splicing in the rice brown planthopper. Differences in alternative splicing between virulent and avirulent populations indicated that alternative splicing might play an important role in the formation of virulence phenotypes in N. lugens.
Beyond Agency as Good: Complicity and Displacement after the Siege of Sarajevo
Authors: GoluboviĆ Jelena 
Published: September 2021

AbstractForced migration scholars have increasingly documented the agency of displaced persons. However, this scholarship has attended primarily to the positive or constructive dimensions of agency, documenting migrants’ capacities for resilience, resistance, and problem-solving. In this paper, I argue that forced migration scholarship should extend to recognize the darker dimensions of agency, such as complicity in acts of violence. Drawing on emerging work on ‘complex victimhood’ in conflict studies scholarship, which grapples with the difficult simultaneity of victimhood and complicity, I begin to articulate a figure of the ‘complex migrant’. As a case study, I draw on fieldwork with Bosnian Serb women who were part of the 1996 displacement of Serbs from Sarajevo, when the divided city was re-unified following nearly four years of siege by Bosnian Serb forces. Against the figure of the ideal refugee/victim, I outline the numerous deviations that made Serbs illegible as refugees. I also demonstrate how my interlocutors asserted the qualities of the ideal victim in their narratives to make their losses legible. I argue that a complex victimhood framework is useful for analysing other understudied retributive displacements. I also suggest that it can work to gradually disempower discourses that blame migrants when they fail to live up to the ideal of the good victim.
Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato
Authors: Zheng Fangyan , Cui Long , Li Changxing , Xie Qingmin , Ai Guo , Wang Junqiang , Yu Huiyang , Wang Taotao , Zhang Junhong , Ye Zhibiao , Yang Changxian 
Published: September 2021

Abstract
Trichomes are specialized glandular or non-glandular structures that provide physical or chemical protection against insect and pathogen attack. Trichomes in Arabidopsis have been extensively studied as typical non-glandular structures. By contrast, the molecular mechanism underlying glandular trichome formation and elongation remains largely unknown. We previously demonstrated that Hair is essential for the formation of type I and type VI trichomes. Here, we found that overexpression of Hair increased the density and length of tomato trichomes. Biochemical assays revealed that Hair physically interacts with its close homolog SlZFP8-like (SlZFP8L), and SlZFP8L also directly interacts with Woolly. SlZFP8L-overexpressing plants showed increased trichome density and length. We further found that the expression of SlZFP6, which encodes a C2H2 zinc finger protein, is positively regulated by Hair. Using chromatin immunoprecipitation, yeast one-hybrid, and dual-luciferase assays we identified that SlZFP6 is a direct target of Hair. Similar to Hair and SlZFP8L, the overexpression of SlZFP6 also increased the density and length of tomato trichomes. Taken together, our results suggest that Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato.
Fibrational bisimulations and quantitative reasoning: Extended version
Authors: Sprunger David , Katsumata Shin-ya , Dubut Jérémy , Hasuo Ichiro 
Published: September 2021

Abstract
Bisimulation and bisimilarity are fundamental notions in comparing state-based systems. Their extensions to a variety of systems have been actively pursued in recent years, a notable direction being quantitative extensions. In this paper we enhance a categorical framework for such extended (bi)simulation notions. We use coalgebras as system models and fibrations for organizing predicates—following the seminal work by Hermida and Jacobs. Endofunctor liftings are crucial predicate-forming ingredients; the first contribution of this work is to extend several extant lifting techniques from particular fibrations to $\textbf {CLat}_\wedge $-fibrations over $\textbf {Set}$. The second contribution of this work is to introduce endolifting morphisms as a mechanism for comparing predicates between fibrations. We apply these techniques by deriving some known properties of the Hausdorff pseudometric and approximate bisimulation in control theory.
Widely distributed exogenic materials of varying compositions and morphologies on asteroid (101955) Bennu
Authors: Tatsumi Eri , Popescu Marcel , Campins Humberto , de León Julia , García Juan Luis Rizos , Licandro Javier , Simon Amy A , Kaplan Hannah H , DellaGiustina Daniella N , Golish Dathon R , Lauretta Dante S 
Published: September 2021

ABSTRACTUsing the multiband imager MapCam on board the OSIRIS-REx (Origins, Spectral Interpretation, Resource Identification, and Security–Regolith Explorer) spacecraft, we identified 77 instances of proposed exogenic materials distributed globally on the surface of the B-type asteroid (101955) Bennu. We identified materials as exogenic on the basis of an absorption near 1 $\mu$m that is indicative of anhydrous silicates. The exogenic materials are spatially resolved by the telescopic camera PolyCam. All such materials are brighter than their surroundings, and they are expressed in a variety of morphologies: homogeneous, breccia-like, inclusion-like, and others. Inclusion-like features are the most common. Visible spectrophotometry was obtained for 46 of the 77 locations from MapCam images. Principal component analysis indicates at least two trends: (i) mixing of Bennu's average spectrum with a strong 1-$\mu$m band absorption, possibly from pyroxene-rich material, and (ii) mixing with a weak 1-$\mu$m band absorption. The end member with a strong 1-$\mu$m feature is consistent with Howardite-Eucrite-Diogenite (HED) meteorites, whereas the one showing a weak 1-$\mu$m feature may be consistent with HEDs, ordinary chondrites, or carbonaceous chondrites. The variation in the few available near-infrared reflectance spectra strongly suggests varying compositions among the exogenic materials. Thus, Bennu might record the remnants of multiple impacts with different compositions to its parent body, which could have happened in the very early history of the Solar system. Moreover, at least one of the exogenic objects is compositionally different from the exogenic materials found on the similar asteroid (162173) Ryugu, and they suggest different impact tracks.
Profile comparison of the 6–9 μm polycyclic aromatic hydrocarbon bands in starburst-dominated galaxies
Authors: Canelo Carla M , Sales Dinalva A , Friaça Amâncio C S , Pastoriza Miriani , Menéndez-Delmestre Karín 
Published: September 2021

ABSTRACT
Polycyclic aromatic hydrocarbons (PAHs) are of great astrochemical and astrobiological interest due to their potential to form prebiotic molecules. We analyse the 7.7 and 8.6 $\mu$m PAH bands in 126 pre-dominantly starburst-dominated galaxies extracted from the Spitzer/IRS ATLAS project. Based on the peak positions of these bands, we classify them into the different A, B, and C Peeters’ classes, which allows us to address the potential characteristics of the PAH-emitting population. We compare this analysis with previous work focused on the 6.2 $\mu$m PAH band for the same sample. For the first time in the literature, this statistical analysis is performed on a sample of galaxies. In our sample, the 7.7 $\mu$m complex is equally distributed in A and B object’s class while the 8.6 $\mu$m band presents more class B sources. Moreover, 39 per cent of the galaxies were distributed into A class objects for both 6.2 and 7.7 $\mu$m bands and only 18 per cent received the same A classification for the three bands. The ‘A A A’ galaxies presented higher temperatures and less dust in their interstellar medium. Considering the redshift range covered by our sample, the distribution of the three bands into the different Peeters’ classes reveals a potential cosmological evolution in the molecular nature of the PAHs that dominate the interstellar medium in these galaxies, where B class objects seem to be more frequent at higher redshifts and, therefore, further studies have to be addressed.
Inelastic rate coefficients for collisions of C4H− with H2
Authors: Balança Christian , Quintas-Sánchez Ernesto , Dawes Richard , Dumouchel Fabien , Lique François , Feautrier Nicole 
Published: September 2021

ABSTRACT
Carbon-chain anions were recently detected in the interstellar medium. These very reactive species are used as tracers of the physical and chemical conditions in a variety of astrophysical environments. However, the local thermodynamic equilibrium conditions are generally not fulfilled in these environments. Therefore, collisional as well as radiative rates are needed to accurately model the observed emission lines. We determine in this work the state-to-state rate coefficients of C4H− in collision with both ortho- and para-H2. A new ab initio 4D potential energy surface was computed using explicitly correlated coupled-cluster procedures. This surface was then employed to determine rotational excitation and de-excitation cross-sections and rate coefficients for the first 21 rotational levels (up to rotational level j1 = 20) using the close-coupling method, while the coupled-state approximation was used to extend the calculations up to j1 = 30. State-to-state rate coefficients were obtained for the temperature range 2–100 K. The differences between the ortho- and para-H2 rate coefficients are found to be small.
Galaxy assembly bias and large-scale distribution: a comparison between IllustrisTNG and a semi-analytic model
Authors: Hadzhiyska Boryana , Liu Sonya , Somerville Rachel S , Gabrielpillai Austen , Bose Sownak , Eisenstein Daniel , Hernquist Lars 
Published: September 2021

ABSTRACT
In this work, we compare large scale structure observables for stellar mass selected samples at z = 0, as predicted by two galaxy models, the hydrodynamical simulation IllustrisTNG and the Santa-Cruz semi-analytic model (SC-SAM). Although both models have been independently calibrated to match observations, rather than each other, we find good agreement between the two models for two-point clustering and galaxy assembly bias signatures. The models also show a qualitatively similar response of occupancy and clustering to secondary halo parameters other than mass, such as formation history and concentration, although with some quantitative differences. Thus, our results demonstrate that the galaxy–halo relationships in SC-SAM and TNG are quite similar to first order. However, we also find areas in which the models differ. For example, we note a strong correlation between halo gas content and environment in TNG, which is lacking in the SC-SAM, as well as differences in the occupancy predictions for low-mass haloes. Moreover, we show that higher order statistics, such as cumulants of the density field, help us to accurately describe the galaxy distribution and discriminate between models that show degenerate behaviour for two-point statistics. Our results suggest that SAMs are a promising cost-effective and intuitive method for generating mock catalogues for next generation cosmological surveys.
The MOSDEF survey: the dependence of H α-to-UV SFR ratios on SFR and size at z ∼ 2
Authors: Fetherolf Tara , Reddy Naveen A , Shapley Alice E , Kriek Mariska , Siana Brian , Coil Alison L , Mobasher Bahram , Freeman William R , Sanders Ryan L , Price Sedona H , Shivaei Irene , Azadi Mojegan , de Groot Laura , Leung Gene C K , Zick Tom O 
Published: September 2021

ABSTRACT
We perform an aperture-matched analysis of dust-corrected H α and UV star formation rates (SFRs) using 303 star-forming galaxies with spectroscopic redshifts 1.36 &lt; zspec &lt; 2.66 from the MOSFIRE Deep Evolution Field survey. By combining H α and H β emission line measurements with multiwaveband resolved Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey/3D-HST imaging, we directly compare dust-corrected H α and UV SFRs, inferred assuming a fixed attenuation curve shape and constant SFHs, within the spectroscopic aperture. Previous studies have found that H α and UV SFRs inferred with these assumptions generally agree for typical star-forming galaxies, but become increasingly discrepant for galaxies with higher SFRs (≳100 M⊙ yr−1), with H α-to-UV SFR ratios being larger for these galaxies. Our analysis shows that this trend persists even after carefully accounting for the apertures over which H α and UV-based SFRs (and the nebular and stellar continuum reddening) are derived. Furthermore, our results imply that H α SFRs may be higher in the centres of large galaxies (i.e. where there is coverage by the spectroscopic aperture) compared to their outskirts, which could be indicative of inside-out galaxy growth. Overall, we suggest that the persistent difference between nebular and stellar continuum reddening and high H α-to-UV SFR ratios at the centres of large galaxies may be indicative of a patchier distribution of dust in galaxies with high SFRs.
PL03.3.A Development and characterization of CD317-specific CAR T cells as an innovative immunotherapeutic strategy against glioblastoma
Authors: Hänsch L , Peipp M , Myburgh R , Silginer M , Weiss T , Gramatzki D , Vasella F , Manz M , Weller M , Roth P 
Published: September 2021

Abstract

BACKGROUND
Due to the limited success of existing therapies for gliomas, innovative therapeutic options are urgently needed. Chimeric antigen receptor (CAR) T cell therapy has been successful in patients with hematological malignancies. However, using this treatment against solid tumors such as glioblastomas is more challenging. Here, we generated CAR T cells targeting the transmembrane protein CD317 (BST-2, HM1.24) which is overexpressed in glioma cells and may therefore serve as a novel target antigen for CAR T cell-based immunotherapy.

MATERIAL AND METHODS
CAR T cells targeting CD317 were generated by lentiviral transduction of human T cells from healthy donors. The anti-glioma activity of CD317-CAR T cells was determined in lysis assays using different glioma target cell lines with varying CD317 expression levels. The efficiency of CD317-CAR T cells to control tumor growth in vivo was evaluated in clinically relevant orthotopic xenograft glioma mouse models.

RESULTS
We created a second-generation CAR construct targeting CD317 and observed strong anti-glioma activity of CD317-CAR T cells in vitro. Glioma cells with a CRISPR/Cas9-mediated CD317 knockout were resistant to CD317-specific CAR T cells, demonstrating their target antigen-specificity. Since CD317 is also expressed by T cells, transduction with a CD317-directed CAR resulted in fratricide of the transduced T cells. Silencing of CD317 in CAR T cells by integrating a specific shRNA into the CAR vector significantly increased the viability, proliferation and cytotoxic function of the CAR T cells. Importantly, intratumoral treatment with CD317-CAR T cells prolonged the survival and cured a significant fraction of glioma-bearing nude mice.

CONCLUSION
We demonstrate strong CD317-specific anti-tumor activity of CD317-CAR T cells against various glioma cell lines in vitro and in xenograft glioma models in vivo. These data lay a scientific basis for the subsequent evaluation of this therapeutic strategy in clinical neuro-oncology.
KS01.5.A Allergic airway inflammation impacts tumor take and delays experimental glioblastoma progression
Authors: Poli A , Oudin A , Muller A , Hunewald O , Domingues O , Nazarov P V , Puard V , Baus V , Azuaje F , Dittmar G , Zimmer J , Michel T , Niclou S P , Ollert M 
Published: September 2021

Abstract

BACKGROUND
Numerous epidemiological studies have highlighted the protective role of immunoglobulin E-mediated allergic diseases on glioblastoma (GBM) susceptibility and prognosis. However, the mechanistic explanations behind these phenomena remain unexplored. Our objective was to set up a preclinical model and investigate the mechanisms underlying such protection to improve our understanding of the crosstalk between immune system and brain tumor development.

MATERIAL AND METHODS
A mouse model of allergic airway inflammation (AAI) induced by repeated nasal instillation of House Dust Mite extract was initiated before intracranial implantation of GL261 glioma cells, in both immunocompetent (C57BL/6) and immunodeficient (RAG-KO) mice. Tumor take and tumor growth were monitored by MRI. Central (microglia) and peripheral (spleen, bone marrow) immune cells were characterized by flow cytometry. The response of microglia was further assessed by RNA sequencing. Impact of candidate genes on patient survival was characterized by Cox regression analysis using data from TCGA and CGGA.

RESULTS
Following AAI induction in C57BL/6 mice, engraftment of GL261 cells in the brain was delayed and tumor growth rate was reduced. This correlated with an increase in survival of the mice and was accompanied by increased effector memory T-cells in the circulation. Of note, the survival benefit was lost in RAG-KO mice devoid of adaptive immunity. At the level of the brain, we observed enhanced secretion of TNFα and IL6 in microglia ex vivo. AAI induced a transcriptional reprogramming of microglia towards a pro-inflammatory-like state. We identified an allergy-related microglia gene signature that is associated with improved prognosis of glioma patients.

CONCLUSION
Our results demonstrate that AAI limits both tumor take and GBM progression in mice, providing a preclinical model to study the role of allergic inflammation in GBM susceptibility and prognosis, respectively. At the functional level, we identify a potentiation of microglial and adaptive anti-tumoral immunity. Further investigations are warranted to shed light on the reciprocal crosstalk between microglial reprogramming and peripheral immunity in the context of allergies and brain tumors.
OS06.7A METPlatform identifies brain metastasis vulnerabilities and predicts patient response to therapy
Authors: Zhu L , Blanco-Aparicio C , Bertero L , Soffietti R , Weiss T , Muñoz J , Sepúlveda J , Weller M , Pastor J , Valiente M 
Published: September 2021

Abstract

BACKGROUND
The diagnosis of brain metastasis involves high morbidity and mortality and remains an unmet clinical need in spite of being the most common tumor in the brain. Exclusion of these cancer patients from clinical trials is a major cause of their limited therapeutic options.

MATERIAL AND METHODS
We report a novel drug-screening platform (METPlatform) based on organotypic cultures which allows identifying effective anti-metastasis agents in the presence of the organ microenvironment. We have applied this approach to clinically relevant stages of brain metastasis using both experimental models and human tumor tissue (by performing patient-derived organotypic cultures - PDOCs -). We have also used METPlatform to perform unbiased proteomics of brain metastases in situ to identify potential novel mediators of this disease and explore resistance mechanisms to targeted therapy. Finally, we have exploited METPlatform as “avatars” to predict response to therapy in patients with primary brain tumors.

RESULTS
We identified heat shock protein 90 (HSP90) as a promising therapeutic target for brain metastasis. DEBIO-0932, a blood-brain barrier permeable HSP90 inhibitor, shows high potency against mouse and human brain metastases from different primary origin and oncogenomic profile at clinically relevant stages of the disease, including a novel model of local relapse after neurosurgery. Furthermore, in situ proteomic analysis of brain metastases treated with the chaperone inhibitor revealed non-canonical clients of HSP90 as potential novel mediators of brain metastasis and actionable mechanisms of resistance driven by autophagy. Combined therapy using HSP90 and autophagy inhibitors showed synergistic effects compared to sublethal concentrations of each monotherapy, demonstrating the potential of METPlatform to design and test rationale combination therapies to target metastasis more effectively. Finally, we show that brain tumor PDOCs predict the response of the corresponding patient to standard of care, thus proving the potential of METPlatform for improving personalized care in cancer.

CONCLUSION
Our work validates METPlatform as a potent resource for metastasis research integrating drug-screening and unbiased omic approaches that is fully compatible with human samples and questions the rationale of excluding patients with brain metastasis from clinical trials. We envision that METPlatform will be established as a clinically relevant strategy to personalize the management of metastatic disease in the brain and elsewhere.