bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and transcriptomic characterization of theCollimonasquorum sensing genes and regulon
Authors: Uroz Stephane , Geisler Océane , Fauchery Laure , Lami Raphaël , Rodrigues Alice M S , Morin Emmanuelle , Leveau Johan H J , Oger Philippe 
Published: August 2022

AbstractCollimonads are well-adapted to nutrient-poor environments. They are known to hydrolyse chitin, produce antifungal metabolites, weather minerals, and are effective biocontrol agents protecting plants from fungal diseases. The production of N-acyl homoserine lactones (AHLs) was suggested to be a conserved trait of collimonads, but little is known about the genes that underlie this production or the genes that are controlled by AHLs. To improve our understanding of the role of AHLs in the ecology of collimonads, we carried out transcriptomic analyses, combined with chemical and functional assays, on strain Collimonas pratensis PMB3(1). The main AHLs produced by this strain were identified as 3-hydroxy-hexa- and octa-noyl-homoserine lactone. Genome analysis permitted to identify putative genes coding for the autoinducer synthase (colI) and cognate transcriptional regulator (colR). The ability to produce AHLs was lost in ΔcolI and ΔcolR mutants. Functional assays revealed that the two mutants metabolized glucose, formate, oxalate, and leucine better than the wild-type (WT) strain. Transcriptome sequencing analyses revealed an up-regulation of different metabolic pathways and of motility in the QS-mutants compared to the WT strain. Overall, our results provide insights into the role of the AHL-dependent regulation system of Collimonas in environment colonization, metabolism readjustment, and microbial interactions.
Investigations into metabolic properties and selected nutritional metabolic byproducts of different non-Saccharomyces yeast strains when producing nonalcoholic beer
Authors: Methner Yvonne , Weber Nadine , Kunz Oliver , Zarnkow Martin , Rychlik Michael , Hutzler Mathias , Jacob Fritz 
Published: August 2022

Abstract
Nonalcoholic beers are becoming increasingly popular, in part due to consumers’ awareness of a healthier lifestyle. Additionally, consumers are demanding diversification in the product range, which can be offered by producing nonalcoholic beers using non-Saccharomyces yeasts for fermentation to create a wide variety of flavors. So far, little is known about the nutritionally relevant byproducts that these yeasts release during wort fermentation and whether these yeasts can be considered safe for food fermentations. To gain insights into this, the B vitamins of four different nonalcoholic beers fermented with the yeast species Saccharomycodes ludwigii, Cyberlindnera saturnus (two strains), and Kluyveromyces marxianus were analyzed. Furthermore, a total of 16 beers fermented with different non-Saccharomyces yeast strains were analyzed for biogenic amines. Additionally, stress tolerance tests were performed at 37°C and in synthetic human gastric juice in vitro. B vitamins were found in the four nonalcoholic beers in nutritionally relevant amounts so they could serve as a supplement for a balanced diet. Biogenic amines remained below the limit of determination in all 16 beers, and thus likely had no influence, while the stress tolerance tests gave a first indication that seven yeast strains could possibly tolerate the human gastric juice milieu.
Statistical quantification of confounding bias in machine learning models
Authors: Spisak Tamas 
Published: August 2022

Abstract

Background
The lack of nonparametric statistical tests for confounding bias significantly hampers the development of robust, valid, and generalizable predictive models in many fields of research. Here I propose the partial confounder test, which, for a given confounder variable, probes the null hypotheses of the model being unconfounded.

Results
The test provides a strict control for type I errors and high statistical power, even for nonnormally and nonlinearly dependent predictions, often seen in machine learning. Applying the proposed test on models trained on large-scale functional brain connectivity data (N= 1,865) (i) reveals previously unreported confounders and (ii) shows that state-of-the-art confound mitigation approaches may fail preventing confounder bias in several cases.

Conclusions
The proposed test (implemented in the package mlconfound; https://mlconfound.readthedocs.io) can aid the assessment and improvement of the generalizability and validity of predictive models and, thereby, fosters the development of clinically useful machine learning biomarkers.
Data-driven multi-step self-de-aliasing approach for GRACE and GRACE-FO data processing
Authors: Abrykosov Petro , Murböck Michael , Hauk Markus , Pail Roland , Flechtner Frank 
Published: August 2022

SUMMARYTemporal aliasing errors resulting from the undersampling of non-tidal atmospheric as well as oceanic mass variations constitute the largest limitation towards the retrieval of monthly gravity solutions based on GRACE and GRACE-FO satellite gravity missions. Their mitigation is thus a primary goal of current research. Unfortunately, the two-step co-parametrization approach proposed for application in Bender-type gravity retrieval scenario in Wiese et al. yields no added value for a single satellite pair. A detailed study of this parametrization strategy is carried out and it is shown that the reason for this is the flawed central assumption of the proposed method, that is that signals of different spatial wavelengths can be perfectly captured and separated with respect to their temporal extent. Based on this finding, we derive a multi-step self-de-aliasing approach (DMD) which aims to rectify the shortcoming of the Wiese et al. method specifically for the single-pair case while retaining its independence from background-model-based de-aliasing of non-tidal atmosphere and ocean (AO) signal components. The functionality and added value of this novel approach is validated within a set of numerical closed-loop simulations as well as in real GRACE and GRACE-FO data processing. The simulation results show that the DMD may improve the gravity retrieval performance in the high-degree spectrum by more than one order of magnitude if one aims to retrieve the full AOHIS (i.e. atmosphere, ocean, hydrology, ice, solid earth) signal, and by at least a factor 5 if a priori AO de-aliasing is applied. Simultaneously, the DMD is shown to degrade the retrieval of the low degrees, but it is also demonstrated that this issue can be mitigated by introducing a constraint into the processing scheme. The simulation results are widely confirmed by results obtained from applying the DMD to real GRACE/GRACE-FO data of the test years 2007, 2014 and 2019. The applicability of the DMD is further shown for Bender-type gravity retrieval. It is demonstrated that in case of a double-pair-based gravity retrieval this approach is at least equivalent to the Wiese et al. method.
Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa
Authors: Johnson Rabia , Mangwana Noluxabiso , Sharma Jyoti R , Muller Christo J F , Malemela Kholofelo , Mashau Funanani , Dias Stephanie , Ramharack Pritika , Kinnear Craig , Glanzmann Brigitte , Viraragavan Amsha , Louw Johan , Surujlal-Naicker Swastika , Nkambule Sizwe , Webster Candice , Mdhluli Mongezi , Gray Glenda , Mathee Angela , Preiser Wolfgang , Vorster Alvera , Dalvie Shareefa , Street Renee 
Published: August 2022

Abstract
This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA in wastewater samples and clinical cases (r = 0.7749, P &lt; .0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven third wave, was significantly higher than during the Omicron-driven fourth wave. Whole-genome sequencing confirmed presence of Omicron lineage defining mutations in wastewater with the first occurrence reported 23 November 2021 (BA.1 predominant). The variant spread rapidly, with prevalence of Omicron-positive wastewater samples rising to &gt;80% by 10 January 2022 with BA.2 as the predominant sublineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. These findings demonstrate the value of wastewater-based epidemiology to monitor the spatiotemporal spread and potential origin of new Omicron sublineages.
Cancer Hazard Evaluations for Contemporary Needs: Highlights From New National Toxicology Program Evaluations and Methodological Advancements
Authors: Lunn Ruth M , Mehta Suril S , Jahnke Gloria D , Wang Amy , Wolfe Mary S , Berridge Brian R 
Published: August 2022

AbstractThe National Toxicology Program strives to raise awareness of cancer hazards in our environment. Identifying cancer hazards is key to primary prevention, informing public health decision making, and decreasing the global cancer burden. In December 2021, the US congressionally mandated 15th Report on Carcinogens was released, adding 8 new substances to the cumulative report. Chronic infection with Helicobacter pylori is listed as “known to be a human carcinogen.” Antimony trioxide and 6 haloacetic acids found as water disinfection by-products—dichloroacetic acid, dibromoacetic acid, bromochloroacetic acid, tribromoacetic acid, bromodichloroacetic acid, chlorodibromoacetic acid—are listed as “reasonably anticipated to be a human carcinogen.” A new dashboard provides interactive visualization and interrogation of the 256 listed substances, their uses, and associated cancers. Also, the National Toxicology Program recently published a Cancer Hazard Assessment Report on exposure scenarios associated with circadian disruption, concluding that persistent night shift work can cause breast cancer and certain lighting conditions may cause cancer. As highlighted in these reports and evaluations, we are evolving our approaches to meet contemporary challenges. These approaches include focusing on real-world exposures and advancing our methods to address challenges in cancer hazard assessments (eg, developing more structured approaches to evaluate mechanistic data and incorporating read-across approaches to assess chemicals lacking adequate human or animal cancer data). To promote public health, we provide information on environmental health disparities and disease prevention. Building on these efforts, we aim to continue our contributions to the war on cancer, declared 50 years ago.
A Logic for Desire Based on Causal Inference
Authors: Xie Kaibo , Yan Jialiang 
Published: August 2022

Abstract
Reasoning about desire plays a significant role in logic, artificial intelligence and philosophy, etc. In this paper, we propose an interpretation of desire that takes into account causal inference. To formalize this idea, we build a desire-causality model by combing the betterness model in preference logic and the causal model in the logic for causal reasoning. We then develop a logic for desire based on this semantics, and an axiomatization for our formal system is given.
Higher order initial conditions with massive neutrinos
Authors: Elbers Willem , Frenk Carlos S , Jenkins Adrian , Li Baojiu , Pascoli Silvia 
Published: August 2022

ABSTRACT
The discovery that neutrinos have mass has important consequences for cosmology. The main effect of massive neutrinos is to suppress the growth of cosmic structure on small scales. Such growth can be accurately modelled using cosmological N-body simulations, but doing so requires accurate initial conditions (ICs). There is a trade-off, especially with first-order ICs, between truncation errors for late starts and discreteness and relativistic errors for early starts. Errors can be minimized by starting simulations at late times using higher order ICs. In this paper, we show that neutrino effects can be absorbed into scale-independent coefficients in higher order Lagrangian perturbation theory (LPT). This clears the way for the use of higher order ICs for massive neutrino simulations. We demonstrate that going to higher order substantially improves the accuracy of simulations. To match the sensitivity of surveys like DESI and Euclid, errors in the matter power spectrum should be well below $1{{\ \rm per\ cent}}$. However, we find that first-order Zel’dovich ICs lead to much larger errors, even when starting as early as z = 127, exceeding $1{{\ \rm per\ cent}}$ at z = 0 for k &gt; 0.5 Mpc−1 for the power spectrum and k &gt; 0.1 Mpc−1 for the equilateral bispectrum in our simulations. Ratios of power spectra with different neutrino masses are more robust than absolute statistics, but still depend on the choice of ICs. For all statistics considered, we obtain $1{{\ \rm per\ cent}}$ agreement between 2LPT and 3LPT at z = 0.
The population of Galactic Centre filaments – III. Candidate radio and stellar sources
Authors: Yusef-Zadeh F , Arendt R G , Wardle M , Heywood I , Cotton W 
Published: August 2022

ABSTRACT
Recent MeerKAT radio continuum observations of the Galactic Centre at 20 cm show a large population of non-thermal radio filaments (NRFs) in the inner few hundred pc of the Galaxy. We have selected a sample of 57 radio sources, mainly compact objects, in the MeerKAT mosaic image that appear to be associated with NRFs. The selected sources are about four times the number of radio point sources associated with filaments than would be expected by random chance. Furthermore, an apparent correlation between bright IR stars and NRFs is inferred from their similar latitude distributions, suggesting that they both co-exist within the same region. To examine if compact radio sources are related to compact IR sources, we have used archival 2MASS, and Spitzer data to make spectral energy distribution of individual stellar sources coincident or close to radio sources. We provide a catalogue of radio and IR sources for future detailed observations to investigate a potential three-way physical association between NRFs, compact radio and IR stellar sources. This association is suggested by models in which NRFs are cometary tails produced by the interaction of a large-scale nuclear outflow with stellar wind bubbles in the Galactic Centre.
Human TRUB1 is a highly conserved pseudouridine synthase responsible for the formation of Ψ55 in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro
Authors: Jia Zidong , Meng Feilong , Chen Hui , Zhu Gao , Li Xincheng , He Yunfan , Zhang Liyao , He Xiao , Zhan Huisen , Chen Mengquan , Ji Yanchun , Wang Meng , Guan Min-Xin 
Published: August 2022

Abstract
Pseudouridine (Ψ) at position 55 in tRNAs plays an important role in their structure and function. This modification is catalyzed by TruB/Pus4/Cbf5 family of pseudouridine synthases in bacteria and yeast. However, the mechanism of TRUB family underlying the formation of Ψ55 in the mammalian tRNAs is largely unknown. In this report, the CMC/reverse transcription assays demonstrated the presence of Ψ55 in the human mitochondrial tRNAAsn, tRNAGln, tRNAGlu, tRNAPro, tRNAMet, tRNALeu(UUR) and tRNASer(UCN). TRUB1 knockout (KO) cell lines generated by CRISPR/Cas9 technology exhibited the loss of Ψ55 modification in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro but did not affect other 18 mitochondrial tRNAs. An in vitro assay revealed that recombinant TRUB1 protein can catalyze the efficient formation of Ψ55 in tRNAAsn and tRNAGln, but not in tRNAMet and tRNAArg. Notably, the overexpression of TRUB1 cDNA reversed the deficient Ψ55 modifications in these tRNAs in TRUB1KO HeLa cells. TRUB1 deficiency affected the base-pairing (18A/G-Ψ55), conformation and stability but not aminoacylation capacity of these tRNAs. Furthermore, TRUB1 deficiency impacted mitochondrial translation and biogenesis of oxidative phosphorylation system. Our findings demonstrated that human TRUB1 is a highly conserved mitochondrial pseudouridine synthase responsible for the Ψ55 modification in the mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro.
2′-O-Methylation of the second transcribed nucleotide within the mRNA 5′ cap impacts the protein production level in a cell-specific manner and contributes to RNA immune evasion
Authors: Drazkowska Karolina , Tomecki Rafal , Warminski Marcin , Baran Natalia , Cysewski Dominik , Depaix Anaïs , Kasprzyk Renata , Kowalska Joanna , Jemielity Jacek , Sikorski Pawel J 
Published: August 2022

Abstract
In mammals, m7G-adjacent nucleotides undergo extensive modifications. Ribose of the first or first and second transcribed nucleotides can be subjected to 2′-O-methylation to form cap1 or cap2, respectively. When the first transcribed nucleotide is 2′-O-methylated adenosine, it can be additionally modified to N6,2′-O-dimethyladenosine (m6Am). Recently, the crucial role of cap1 in distinguishing between ‘self’ and ‘non-self’ in mammalian cells during viral infection was revealed. Here, we attempted to understand the impact of cap methylations on RNA-related processes. Therefore, we synthesized tetranucleotide cap analogues and used them for RNA capping during in vitro transcription. Using this tool, we found that 2′-O-methylation of the second transcribed nucleotide within the mRNA 5′ cap influences protein production levels in a cell-specific manner. This modification can strongly hamper protein biosynthesis or have no influence on protein production levels, depending on the cell line. Interestingly, 2′-O-methylation of the second transcribed nucleotide and the presence of m6Am as the first transcribed nucleotide serve as determinants that define transcripts as ‘self’ and contribute to transcript escape from the host innate immune response. Additionally, cap methylation status does not influence transcript affinity towards translation initiation factor eIF4E or in vitro susceptibility to decapping by DCP2; however, we observe the resistance of cap2-RNA to DXO (decapping exoribonuclease)-mediated decapping and degradation.
Patterns in Mental Health Symptomatology and Cigarette, E-cigarette, and Marijuana Use Among Texas Youth and Young Adults Amid the Coronavirus Disease 2019 Pandemic
Authors: Clendennen Stephanie L , Chen Baojiang , Sumbe Aslesha , Harrell Melissa B 
Published: August 2022

Abstract

Introduction
This study examined patterns in mental health symptomatology and smoking and vaping behaviors among youth and young adults over a 1-year period from before to during the first year of the Coronavirus Disease 2019 (COVID-19) pandemic.

Aims and Methods
Participants (n = 2148) were 16–24-year-olds who completed three waves of the Texas Adolescent Tobacco and Marketing Surveillance Study (TATAMS). Descriptive statistics and mixed effects logistic regression models were used to examine changes in anxiety symptoms, depressive symptoms, perceived stress, and cigarette, e-cigarette, and marijuana use from before COVID-19 (fall 2019) to 6-month follow-up (spring 2020) and 12-month follow-up (fall 2020) periods during COVID-19. Longitudinal associations between mental health symptomatology and smoking and vaping were examined.

Results
Modest increases in symptoms of anxiety and depression were observed from before to during COVID-19. Perceived stress remained high and unchanged. Ever marijuana use increased at 6- and 12-month follow-up, while ever cigarette and e-cigarette use increased significantly only at 12-month follow-up. Marijuana use frequency increased significantly at 6- and 12-month follow-ups. Adjusting for sociodemographic factors, increased symptoms of anxiety and depression predicted increases in ever cigarette, e-cigarette, and marijuana use, and past 30-day cigarette and e-cigarette use, but not past 30-day marijuana use. Higher perceived stress predicted increases in ever use of cigarettes and e-cigarettes and past 30-day cigarette use.

Conclusions
Changes in mental health symptomatology and smoking and vaping behaviors among young people in Texas varied during this period of the COVID era. Increases in mental health symptomatology predicted increases in cigarette, e-cigarette, and marijuana use behaviors.

Implications
This study adds to the limited research on the longitudinal impact of anxiety symptoms, depressive symptoms, and perceived stress on cigarette, e-cigarette, and marijuana use from before to during the first year of the COVID-19 pandemic. Findings warrant health messaging and interventions that address the significant impact of worse mental health on increased smoking and vaping behavior, especially during crises like COVID-19 that may exacerbate mental health and substance use behaviors.
Towards a Poetic Sociology of Iran
Authors: Manoukian Setrag 
Published: August 2022

Abstract
Media and scholarly narratives often see an essential connection between Iranians and their poems and use poetry to explain Iranian politics, morality, and the self. Instead of this sociology of Iranian poetry, the chapter proposes a poetic sociology of Iran. Through an ethnography of poetic assemblies in the city of Shiraz, the chapter aims at describing a specific poetic modality of existence in several of its domains of relevance: geography, physics, logic, pedagogy, and sociology. In dialogue with the rich lineage of social studies of poetry in the Middle East and literary studies of Arabo-Persian traditions, the chapter suggests that the power of poetry in Iran, and perhaps elsewhere, resides in its potential to elide the constitutive opposition between norms and passions, between what a life should be and how it is, instituting an existential “bio-poetic” ground.
The Empty Tahrir Square
Authors: Raouf Ezzat Heba 
Published: August 2022

Abstract
The political implications of the changing urban maps that start from Tahrir Square and expand to the rest of Egypt need an interdisciplinary approach that combines political theory with traffic routes maps, and de-densification of Tahrir with the new urban forms emerging across the country.
The uprising in Egypt on the 25th of January and the following courses of revolution and counter-revolution entail a spatial dimension that is wider than dismantling the multitude in urban centers and securitizing the public space. Besides changing the geo-semiotics of Tahrir and their symbolism, a systematic de-densification of a wider plan de-densification in Cairo started unfolding, with traffic logics that are changing the urban and social fabric in the city. With the construction of a number of new cities, the new urban pattern emerging is polycentric, and coupled with constructing military bases in each region. The new map indicates a partial re-distribution of population, but also a high degree of urban segregation. To examine the unfolding changes and the political implications the flux between hierarchy and heterarchy is highlighted, as well as the relation between urban nodality and nodal security.