bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster
Authors: Cotto Irmarie , Vilardi Katherine J. , Huo Linxuan , Fogarty Emily C. , Khunjar Wendell , Wilson Christopher , De Clippeleir Haydee , Gilmore Kevin , Bailey Erika , Lücker Sebastian , Pinto Ameet J. 
Published: June 2022

AbstractStudies have found Ca. Nitrospira nitrosa-like bacteria to be the principal or sole comammox bacteria in nitrogen removal systems for wastewater treatment. In contrast, multiple populations of strict ammonia and nitrite oxidizers co-exist in similar systems. This apparent lack of diversity is surprising and could impact the feasibility of leveraging comammox bacteria for nitrogen removal. We used full-length 16S rRNA gene sequencing and genome-resolved metagenomics to compare population-level (i.e., species) diversity of comammox bacteria with that of strict nitrifiers in full-scale wastewater treatment systems and assess whether these observations were consistent or diverged at the strain-level. Full-length 16S rRNA gene sequencing indicated that while Nitrosomonas-like bacteria exhibited higher population-level diversity, the effective microdiversity of most Nitrospira-like bacteria were comparatively higher except for one Nitrospira Lineage II population. Comammox bacterial metagenome assembled genomes (MAGs) were associated with Ca. Nitrospira nitrosa. The average amino acid identity between comammox bacterial MAGs (93% ± 3) across systems was significantly higher than that of the Nitrosomonas-like ammonia oxidizers (73%±8) and the Nitrospira-like nitrite oxidizer MAGs (75%±13), suggesting that the same comammox population was detected in all systems. Comammox bacteria and some ammonia oxidizers MAGs were significantly less microdiverse than most ammonia and nitrite oxidizers. Interestingly, strain-resolved analysis also indicates that different nitrogen removal systems harbor different comammox bacterial strains within the Ca. Nitrospira nitrosa cluster. These results suggest that comammox bacteria associated with Ca. Nitrospira nitrosa have low species- and strain-level diversity in nitrogen removal systems and may thus harbor specific adaptations to the wastewater ecosystem.
Noisy circumnutations facilitate self-organized shade avoidance in sunflowers
Authors: Nguyen Chantal , Dromi Imri , Kempinski Aharon , Gall Gabriella E. C. , Peleg Orit , Meroz Yasmine 
Published: June 2022

AbstractCircumnutations are widespread in plants and typically associated with exploratory movements, however a quantitative understanding of their role remains elusive. In this study we report, for the first time, the role of noisy circumnutations in facilitating an optimal growth pattern within a crowded group of mutually shading plants. We revisit the problem of self-organization observed for sunflowers, mediated by shade response interactions. Our analysis reveals that circumnutation movements conform to a bounded random walk characterized by a remarkably broad distribution of velocities, covering three orders of magnitude. In motile animal systems such wide distributions of movement velocities are frequently identified with enhancement of behavioral processes, suggesting that circumnutations may serve as a source of functional noise. To test our hypothesis, we developed a Langevin-type parsimonious model of interacting growing disks, informed by experiments, successfully capturing the characteristic dynamics of individual and multiple interacting plants. Employing our simulation framework we examine the role of circumnutations in the system, and find that the observed breadth of the velocity distribution represents a sharp transition in the force-noise ratio, conferring advantageous effects by facilitating exploration of potential configurations, leading to an optimized arrangement with minimal shading. These findings represent the first report of functional noise in plant movements, and establishes a theoretical foundation for investigating how plants navigate their environment by employing computational processes such as task-oriented processes, optimization, and active sensing. Since plants move by growing, space and time are coupled, and dynamics of self-organization lead to emergent 3D patterns. As such this system provides conceptual insight for other interacting growth-driven systems such fungal hyphae, neurons and self-growing robots, as well as active matter systems where agents interact with past trajectories of their counterparts, such as stigmergy in social insects. This foundational insight has implications in statistical physics, ecological dynamics, agriculture, and even swarm robotics.One sentence summary of paperThe study highlights noisy circumnutations as a strategy plants use for optimizing growth in crowded conditions.
Cooperation between Imp2p and Cdc15p imparts stiffness to the constricting contractile ring in fission yeast
Authors: Bellingham-Johnstun Kimberly , Commer Blake , Levesque Brié , Tyree Zoe L. , Laplante Caroline 
Published: June 2022

ABSTRACTThe contractile ring must anchor to the plasma membrane and cell wall to transmit its tension to the plasma membrane. F-BAR domain containing proteins including Cdc15p and Imp2p in fission yeast are likely candidate anchoring proteins based on their mutant phenotypes. Cdc15p is a node component, links the actin bundle to the plasma membrane, recruits Bgs1p to the division plane, prevents contractile ring sliding, and contributes to the stiffness of the contractile ring. Less is known about Imp2p. We found that similarly to Cdc15p, Imp2p contributes to the stiffness of the contractile ring and assembles into protein clusters. Imp2p clusters contain ∼8 Imp2p dimers and depend on the actin network for their stability at the division plane. Importantly, Imp2p and Cdc15p reciprocally affect the amount of the other in the contractile ring indicating that the two proteins influence each other during cytokinesis and may explain their similar phenotypes.
Increased volatile thiol release during beer fermentation using constructed interspecies yeast hybrids
Authors: Krogerus Kristoffer , Rettberg Nils , Gibson Brian 
Published: June 2022

AbstractInterspecies hybridization has been shown to be a powerful tool for developing and improving brewing yeast in a number of industry-relevant respects. Thanks to the popularity of heavily hopped ‘India Pale Ale’-style beers, there is an increased demand from brewers for strains that can boost hop aroma. Here, we explored whether hybridization could be used to construct strains with an enhanced ability to release hop-derived flavours through β-lyase activity, which releases desirable volatile thiols. Wild Saccharomyces strains were shown to possess high β-lyase activity compared to brewing strains, however, they also produced phenolic off-flavours (POF) and showed poor attenuation. To overcome these limitations, interspecies hybrids were constructed by crossing pairs of one of three brewing and one of three wild Saccharomyces strains (S. uvarum and S. eubayanus). Hybrids were screened for fermentation ability and β-lyase activity, and selected hybrids showed improved fermentation and formation of both volatile thiols (4MMP, 3MH and 3MH acetate) and aroma-active esters compared to the parent strains. Undesirable traits (e.g. POF) could be removed from the hybrid by sporulation. To conclude, it was possible to boost the release of desirable hop-derived thiols in brewing yeast by hybridization with wild yeast. This allows production of beer with boosted hop aroma with less hops (thus improving sustainability issues).
Single-Cell RNA-seq Uncovers Dynamic Processes Orchestrated by RNA-Binding Protein DDX43 in Chromatin Remodeling during Spermiogenesis
Authors: Tan Huanhuan , Wang Weixu , Zhou Chongjin , Wang Yanfeng , Zhang Shu , Yang Pinglan , Guo Rui , Chen Wei , Ye Lan , Cui Yiqiang , Ni Ting , Zheng Ke 
Published: June 2022

AbstractAdvances in single-cell RNA sequencing (scRNA-seq) have allowed for elucidating biological mechanisms at cell state level. Mammalian spermatogenic process showcases dynamic switches of gene expression pattern with delicate morphological and functional alterations of germ cells, but it is unclear how such dynamics is genetically controlled. Here we demonstrate that mouse testis-enriched RNA helicase DDX43, as well as its ATP hydrolysis site, is required for spermiogenesis. Genetic mutation of Ddx43 renders spermatids heterogeneously defective in multiple steps of chromatin remodeling, resulting in incomplete substitution of transition protein by protamine and less condensed sperm nucleus. Through scRNA-seq analyses of testicular cells derived from adult wild-type and Ddx43 mutant testes in mice, we reveal that the DDX43 deficiency-elicited perturbation in the dynamic RNA regulatory processes underlies the differentiation deficiency of spermatids. Further, focused analyses on early-stage spermatids combined with enhanced CLIP sequencing (eCLIP-seq) identify Elfn2 as DDX43-targeted hub gene, whose in vivo knockdown shows similar phenotypic defects as Ddx43 mutant. Our study illustrates an essential role for DDX43 in post-meiotic chromatin remodeling and highlights the single cell-based strategy for a refined dissection of stage-specific regulation of germline differentiation.
CRISPR/Cas9 and FLP-FRT mediated multi-modular engineering of the cis-regulatory landscape of the bithorax complex of Drosophila melanogaster
Authors: Hajirnis Nikhil , Pandey Shubhanshu , Mishra Rakesh K 
Published: June 2022

AbstractThe Homeotic genes or Hox define the anterior-posterior (AP) body axis formation in bilaterians and are often present on the chromosome in an order which is collinear to their function across the AP axis. The expression pattern of Hox genes is attributed to the cis-regulatory modules (CRMs) that regulate the genes in a segment-specific manner. In the bithorax complex (BX-C), one of the two Hox complexes in Drosophila melanogaster, even the CRMs consisting of enhancers, initiators, insulators, and Polycomb/trithorax response elements are organized in order that is collinear to their function in the thoracic and abdominal region. Much of these findings are based on the analysis of hundreds of mutations in the BX-C. However, targeted genomic rearrangements comprising of duplications, inversions, etc., that can reveal the basis of collinearity and the number of regulatory modules with respect to body segments have not been reported. In the present study, we generated a series of transgenic lines with the insertion of FRT near the regulatory domain boundaries, to shuffle the CRMs associated with the posterior Hox, Abd-B, of the BX-C. Using these FRT lines, we created several alterations such as deletion, duplication, or inversion of multiple CRMs to comprehend their peculiar genomic arrangement and numbers in the BX-C.
Intrabacterial regulation of a cytotoxic effector by its cognate metaeffector promotes Legionella pneumophila virulence
Authors: Chauhan Deepika , Joseph Ashley M. , Shames Stephanie R. 
Published: June 2022

AbstractLegionella pneumophila is a natural pathogen of unicellular protozoa that can opportunistically infect macrophages and cause Legionnaires’ Disease. Intracellular replication is driven by hundreds of bacterial effector proteins that are translocated into infected host cells by a Dot/Icm type IV secretion system. L. pneumophila effectors are temporally regulated in part by a unique family of translocated regulatory effectors, termed metaeffectors, which bind and modulate the function of a cognate effector in host cells. We discovered that regulation of the cytotoxic effector SidI by its metaeffector, MesI, is critical for L. pneumophila virulence in natural and opportunistic hosts. MesI binds and negatively regulates SidI activity in vitro but how dysregulation of SidI impairs L. pneumophila intracellular replication is unclear. Using a chromosomally-encoded inducible expression system, we discovered that dysregulation of SidI, via loss of MesI, was toxic to L. pneumophila. SidI enzymatic activity was required for toxicity since L. pneumophila growth was unaffected by induced expression of a catalytically inactive sidI allele. We found MesI translocation into host cells was dispensable for intracellular replication and that MesI-deficient bacteria were rapidly degraded within host cells. Together, our data suggest a unique role for intrabacterial effector regulation by a translocated metaeffector in L. pneumophila virulence.ImportanceLegionella pneumophila replicates within phagocytic host cells using hundreds of effector protein virulence factors, which canonically subvert the function of host proteins and pathways. L. pneumophila encodes a unique family of translocated effectors called metaeffectors, which bind and regulate the function of a cognate effector in host cells. The metaeffector MesI promotes L. pneumophila virulence by regulating the cytotoxic effector SidI; however, the MesI regulatory mechanism is poorly understood. We discovered a unique intrabacterial role for MesI in L. pneumophila virulence. When uncoupled from MesI, SidI was toxic to L. pneumophila in vitro and triggered robust bacterial degradation in host cells. Importantly, translocation of MesI was dispensable for intracellular replication, demonstrating that intrabacterial regulation of SidI contributes to L. pneumophila virulence. These data show a unique and important role for MesI regulation of SidI within the bacterium, which challenges the dogma that effectors function exclusively within host cells.
Intelligibility and cellularity in the villas of Palladio and Le Corbusier: examining Rowe's observations
Authors: Dawes Michael J. , Lee Ju Hyun , Ostwald Michael J. 
Published: June 2022

PurposeIn the 1947 article, The Mathematics of the Ideal Villa, Colin Rowe famously compared the spatial and geometric properties of buildings by two architects: Palladio and Le Corbusier. Many of Rowe's observations in this article have since been extensively debated but not rigorously tested. This paper examines Rowe's proposition that Palladio's villa plans possess greater intelligibility and cellularity than Le Corbusier's villa plans.Design/methodology/approachTwo established computational techniques, axial line analysis and isovist analysis, are adopted in this paper to quantify and compare the properties of intelligibility and cellularity in the four villas that Rowe used to construct his argument: Malcontenta, Rotunda, Stein, and Savoye.FindingsWhile acknowledging methodological limitations, the results of this paper do not support Rowe's claims, but they do lead to a unique quantitative examination of spatial configurations and properties of four famous villa plans.Originality/valueThis is the first paper to quantitatively examine Rowe's claims that Palladian villas possess greater intelligibility and cellularity than Le Corbusier's villas.
Forming an academic program review learning community: description of a conceptual model
Authors: Hoare Alana , Dishke Hondzel Catharine , Wagner Shannon 
Published: June 2022

PurposeHigher education institutions are required to evaluate program quality through cyclical program review processes. Despite often being considered the “gold standard” of academic review, there persists dissatisfaction with the lack of integration of program review findings into other planning processes, such as budgeting, assessment and strategic planning. As a result, the notion of program review action plans “collecting dust on the shelf” is so ubiquitous that the concept is normalized as an expected outcome. The purpose of this paper is to describe a conceptual model whereby teams of faculty members receive education and training from quality assurance practitioners and educational developers, access to institutional resources, opportunities for cross-departmental collaborations and collective advocacy to increase the capacity of faculty members to implement improvement goals resulting from program reviews.Design/methodology/approachThe authors theorize that a professional learning community is a meaningful approach to program review and present a conceptual model – the Academic Program Review Learning Community (PRLC) – as an antidote to hierarchical, fragmented, compliance-oriented processes. The authors suggest that the PRLC offers a reliable institutional framework for learning through formalized structures and nested support services, including peer learning and external coaching, which can enhance the catalytic capacity of reviews.FindingsThe authors argue that postsecondary institutions should create formal structures for incorporating learning communities because, without a reliable infrastructure for collective learning, decision-making may be fragmented oridiosyncratic because of shifting demands, priorities or disconnected faculty.Originality/valueA learning community model for program review fits well with a new way to think about program review because faculty are most engaged when they feel ownership over the process. Furthermore, few models exist for conducting program review; as a result, chairs and academics often struggle to conduct reviews without a coherent framework to draw upon.
Deep learning framework for true amplitude imaging: Effect of conditioners and initial models
Authors: Kaur Harpreet , Sun Junzhe , Aharchaou Mehdi , Baumstein Anatoly , Fomel Sergey 
Published: June 2022

ABSTRACTWe propose a workflow to correct migration amplitudes by estimating the inverse Hessian operator weights using a neural network–based framework. We train the network such that it learns the transformation between the migration output and true amplitude reflectivity constrained by different conditioners. We analyse the network output with a velocity model and with source illumination as a conditioner. Compared to the velocity model, source illumination as a conditioner performs better because source illumination encodes the geometrical spreading information and accounts for non‐stationarity. We further use the output of the deep neural network as a starting model for accelerating the convergence of iterative least‐squares reverse time migration. Using a deep learning framework, the proposed method combines the model domain and data domain least‐squares migration approaches to recover images with interpretable amplitudes, attenuated migration artefacts, better signal‐to‐noise ratio and improved resolution. We compare the output of the proposed algorithm with conventional least‐squares output and show that the proposed workflow is more robust, especially in the areas with weak illumination.
Pharmacological characterization of linzagolix, a novel, orally active, non‐peptide antagonist of gonadotropin‐releasing hormone receptors
Authors: Tezuka Motohiro , Tamai Yasuaki , Kuramochi Yu , Kobayashi Kaoru , Fushimi Nobuhiko , Kiguchi Sumiyoshi 
Published: June 2022

AbstractControl of gonadotropin‐releasing hormone (GnRH) signalling is an effective strategy for the treatment of sex hormone‐dependent diseases. GnRH analogues have been widely used for treating these diseases; however, initial stimulation or complete suppression of GnRH signalling by GnRH analogues results in the occurrence of several distinct adverse effects. Accordingly, we aimed to discover small molecule GnRH antagonists with superior pharmacokinetic and pharmacodynamic profiles. Linzagolix is a potent, orally available, and selective GnRH antagonist. Here, we reported the pharmacological characterization of linzagolix in vitro and in vivo. Linzagolix selectively binds to the GnRH receptor and inhibits GnRH‐stimulated signalling, in a manner comparable to cetrorelix, a peptide GnRH antagonist. Because the inhibitory effect of the gonad axis is useful for the treatment of gynaecological conditions such as endometriosis and uterine fibroids, we investigated the effect of orally administrated linzagolix on the gonadal axis in ovariectomized and intact cynomolgus monkeys. In ovariectomized monkeys, linzagolix immediately suppressed the serum luteinizing hormone concentration at doses over 1 mg/kg, indicating dose‐dependent inhibition that correlated with serum linzagolix concentrations. In intact female monkeys, repeated linzagolix administration suppressed hormone surges and ceased or prolonged menstrual cycles. Furthermore, all animals presenting arrested menstrual cycles following linzagolix treatment showed recovery of hormone secretion and regular menstrual cycles after administration periods ended. Our results demonstrated that linzagolix has potential as a novel agent for reproductive‐age women suffering from sex hormone‐dependent diseases.
Risk governance during the COVID‐19 pandemic: A quantitative content analysis of governors' narratives on twitter
Authors: Zahry Nagwan R. , McCluskey Michael , Ling Jiying 
Published: June 2022

AbstractThe current study addresses the communication aspect of risk governance during the COVID‐19 pandemic by examining whether governors' tweets differ by political party, gender and crisis phase. Drawing on the Centers for Disease Control and Prevention's Crisis Emergency Risk Communication (CERC) model and framing literature, we examined the salience of five CERC's communication objectives, namely acknowledge crisis with empathy, promote protective actions, describe preparedness/response efforts, address rumours and misunderstanding and segment audience. Using a deductive and inductive approach, we analysed 7000 Twitter messages sent by the 50 US state governors during the period of 13 March 2020 to 17 August 2020. Our findings suggest that governors' tweets aligned with CERC's communication objectives to a varying degree. We found main and interaction effects of political party, gender and crisis phase on governors' communication objectives. New emergent communication objectives included attention to mental health, call for social influencers and promoting hope. Implications are discussed.
Predictors of mortality in COVID‐19 induced acute kidney injury
Authors: Yüksel Enver , Arac Songül , Deniz Altintaş Derya 
Published: June 2022

AbstractBackgroundWe aimed to investigate the predictors of mortality in patients with COVID‐19‐induced acute kidney injury (COV‐AKI).MethodsWe enrolled 803 patients who developed COV‐AKI. The patients were divided into two groups: survivors and nonsurvivors.ResultsA multivariate logistic regression analysis showed that age (p < 0.001), increased admission C‐reactive protein (p = 0.016), procalcitonin (p = 0.019), creatine kinase (p = 0.04), KDIGO stage 1 versus 2 AKI (p < 0.001), KDIGO stage 1 versus 3 (p < 0.001), the need for renal replacement therapy (p = 0.002) and highest creatinine (p = 0.004) were significantly associated with increased inhospital mortality. However, the mortality of patients with AKI on admission (p = 0.002) was found to be lower than those who developed AKI after hospitalization.ConclusionsAmong patients with COV‐AKI, high‐inflammatory response and severe AKI were associated with significantly higher mortality.