bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian parameter inference for shallow subsurface modeling using field data and impacts on geothermal planning
Authors: Kreitmair Monika J. , Makasis Nikolas , Menberg Kathrin , Bidarmaghz Asal , Farr Gareth J. , Boon David P. , Choudhary Ruchi
Published: November 2022

Understanding the subsurface is crucial in building a sustainable future, particularly for urban centers. Importantly, the thermal effects that anthropogenic infrastructure, such as buildings, tunnels, and ground heat exchangers, can have on this shared resource need to be well understood to avoid issues, such as overheating the ground, and to identify opportunities, such as extracting and utilizing excess heat. However, obtaining data for the subsurface can be costly, typically requiring the drilling of boreholes. Bayesian statistical methodologies can be used towards overcoming this, by inferring information about the ground by combining field data and numerical modeling, while quantifying associated uncertainties. This work utilizes data obtained in the city of Cardiff, UK, to evaluate the applicability of a Bayesian calibration (using GP surrogates) approach to measured data and associated challenges (previously not tested) and to obtain insights on the subsurface of the area. The importance of the data set size is analyzed, showing that more data are required in realistic (field data), compared to controlled conditions (numerically-generated data), highlighting the importance of identifying data points that contain the most information. Heterogeneity of the ground (i.e., input parameters), which can be particularly prominent in large-scale subsurface domains, is also investigated, showing that the calibration methodology can still yield reasonably accurate results under heterogeneous conditions. Finally, the impact of considering uncertainty in subsurface properties is demonstrated in an existing shallow geothermal system in the area, showing a higher than utilized ground capacity, and the potential for a larger scale system given sufficient demand.
Bénard convection in a slowly rotating penny-shaped cylinder subject to constant heat flux boundary conditions
Authors: Soward A.M. , Oruba L. , Dormy E.
Published: November 2022

We consider axisymmetric Boussinesq convection in a shallow cylinder of radius

$L$

and depth

$H (\ll L)$

, which rotates with angular velocity

$\varOmega$

about its axis of symmetry aligned to the vertical. Constant heat flux boundary conditions, top and bottom, are adopted, for which the onset of instability occurs on a long horizontal length scale provided that

$\varOmega$

is sufficiently small. We investigate the nonlinear development by well-established two-scale asymptotic expansion methods. Comparisons of the results with the direct numerical simulations (DNS) of the primitive governing equations are good at sufficiently large Prandtl number

$\sigma$

. As

$\sigma$

is reduced, the finite amplitude range of applicability of the asymptotics reduces in concert. Though the large meridional convective cell, predicted by the DNS, is approximated adequately by the asymptotics, the azimuthal flow fails almost catastrophically, because of significant angular momentum transport at small

$\sigma$

, exacerbated by the cylindrical geometry. To appraise the situation, we propose hybrid methods that build on the meridional streamfunction

$\psi$

derived from the asymptotics. With

$\psi$

given, we solve the now linear azimuthal equation of motion for the azimuthal velocity

$v$

by DNS. Our ‘hybrid’ methods enable us to explain features of the flow at large Rayleigh number, found previously by Oruba et al. (J. Fluid Mech., vol. 812, 2017, pp. 890–904).
Occurrence of baleen whales in the New York Bight, 1998–2017: insights from opportunistic data
Authors: Chou Emily , Rekdahl Melinda L. , Kopelman Arthur H. , Brown Danielle M. , Sieswerda Paul L. , DiGiovanni Robert A. , Rosenbaum Howard C.
Published: November 2022

The New York Bight is undergoing rapid anthropogenic change amidst an apparent increase in baleen whale sightings. Though survey efforts have increased in recent years, the lack of published knowledge on baleen whale occurrence prior to these efforts impedes effective assessments of distributional or behavioural shifts due to increasing human activities. Here we synthesize opportunistic sightings of baleen whales from 1998–2017, which represent the majority of sightings data prior to recent survey efforts, and which are largely unpublished. Humpback and fin whales were the most commonly sighted species, followed by North Atlantic right whales and North Atlantic minke whales. Important behaviours such as feeding and nursing were observed, and most species (including North Atlantic right whales) were seen during all seasons. Baleen whales overlapped with multiple anthropogenic use areas, and all species, but of particular importance North Atlantic right whales, were sighted outside the spatial and temporal bounds of the Seasonal Management Areas for North Atlantic right whales. These opportunistic data are vital for providing a baseline and context of baleen whales in the New York Bight prior to broad-scale efforts and facilitate interpretation of current and future observations and trends, which can more accurately inform effective management and mitigation efforts.
The 0161 rap gap: the marginalisation of Black rap musicians in Manchester's live music scene
Authors: Reisner Latoya , Rymajdo Kamila
Published: November 2022

Focusing on Manchester, the largest city in the north of England, this paper explores why and how Black rap practitioners have been excluded from performing and promoting rap music in its city centre during the last 20 years. Discussing the intersecting factors of policing of venues and racial bias and class stigma among Manchester's venue owners and promoters, while also scrutinising the city's neoliberal urban expansion and gentrification, the paper analyses the ways in which Black rappers and practitioners have been marginalised but also how they have attempted to resist and overcome these conditions. Drawing on cultural studies, critical race theory and urban geography, while employing qualitative research methods of in-depth interviews, this paper builds on existing research on the marginalisation of Black rap musicians and promoters. It builds on and moves beyond the scholarly emphasis on the policing of rap genres in London to argue that discrimination faced by Black rap practitioners extends far outside the capital and is part of a wider problem of racial capitalism of which policing is but one agent.
Spectral Mechanics and the Technical Failures of the Monograph
Authors: Catenella Pallas
Published: November 2022

In 2018, Maria Callas rose from the dead. During a series of tours dubbed Callas in Concert, local orchestras performed with a three-dimensional hologram of the departed diva as she re-sounded arias of her past. This virtual manifestation of Callas put on a convincing show. Listeners were struck by the quality of the diva's voice – ‘from heart-breaking vulnerability to imposing strength’ – and marvelled at foley effects such as the clicking of her heels and rustling of her gown. Notably, however, the performance fell victim to repeated technical failures. In Chicago, a glitch caused her final encore to end prematurely; in Blacksburg, Virginia, audience members were distracted by the transparent nature of the hologram, which gave Callas an ‘especially ghostly appearance’. The performances set the operatic sphere atwitter with questions of ethics and taste, debates over classical music's obligations to the living and devotions to the dead. Anthony Tommasini likened the performances to a grand séance, an act of operatic necrophilia. Catherine Womack interpreted the spectral shows as a sign that ‘in the twenty-first century, living and breathing are not prerequisites for a successful performing career’. However, as Deirdre Loughridge, Gundula Kreuzer and Gabriela Cruz demonstrate in their monographs, Callas in Concert is not a phenomenon unique to the twenty-first century. Indeed, the authors show that technologically mediated resurrections of the dead, operatic appeals to nostalgia, and illusion-busting technical failures are instead part of a long operatic tradition, one which began well before the holographic revitalisations of Maria Callas.
Doors, privacy and the public sphere: a conceptual discussion on the spatial structure of early modern Istanbul
Authors: Şavk Serkan
Published: November 2022

The aim of this article is to offer a new conceptual framework for the study of various spaces in Istanbul during the seventeenth and the eighteenth centuries. I contend that rather than the sharp distinction manifested with the public–private dichotomy, we need to focus on gradations of privacy. I offer qāpū and bāb as two new concepts borrowed from the period's own repertoire for representing the macro and micro ends of the spatial gradation. Theoretically, I draw on George Simmel's definition of doors as the interfaces of spatial formation.
Children’s Perspectives on Fairness and Inclusivity in the Classroom
Authors: Kaufman Elise Marie , Killen Melanie
Published: November 2022

School represents an important context for children’s social, moral, and identity development. Research indicates that supportive teacher-student relationships are significantly related to positive student academic achievement. Unfortunately, teacher bias as well as peer exclusion based on group identity (gender, race, ethnicity, and nationality) pervade many school contexts. The presence of these biases in the classroom is negatively related to students’ academic development, especially for children who are minoritized and marginalized. Very little research has connected teacher bias and children’s reasoning about bias and inequalities in the classroom context. The classroom is a complex environment in which to examine children’s social and moral reasoning about bias, given teachers’ position of authority which often includes power, status, and prestige. We propose that understanding both teacher bias and peer intergroup exclusion are essential for promoting more fair classrooms. This paper reviews foundational theory as well as the social reasoning developmental model as a framework for studying how children think about fairness and bias in the classroom context. We then discuss current research on children’s social-cognitive and moral capacities, particularly in the contexts of societal inequality and social inclusion or exclusion. Finally, this article proposes new directions for research to promote fairness and inclusivity in schools and suggests how these new lines of research might inform school-based interventions.
Weed detection to weed recognition: reviewing 50 years of research to identify constraints and opportunities for large-scale cropping systems
Authors: Coleman Guy R.Y. , Bender Asher , Hu Kun , Sharpe Shaun M. , Schumann Arnold W. , Wang Zhiyong , Bagavathiannan Muthukumar V. , Boyd Nathan S. , Walsh Michael J.
Published: November 2022

The past 50 yr of advances in weed recognition technologies have poised site-specific weed control (SSWC) on the cusp of requisite performance for large-scale production systems. The technology offers improved management of diverse weed morphology over highly variable background environments. SSWC enables the use of nonselective weed control options, such as lasers and electrical weeding, as feasible in-crop selective alternatives to herbicides by targeting individual weeds. This review looks at the progress made over this half-century of research and its implications for future weed recognition and control efforts; summarizing advances in computer vision techniques and the most recent deep convolutional neural network (CNN) approaches to weed recognition. The first use of CNNs for plant identification in 2015 began an era of rapid improvement in algorithm performance on larger and more diverse datasets. These performance gains and subsequent research have shown that the variability of large-scale cropping systems is best managed by deep learning for in-crop weed recognition. The benefits of deep learning and improved accessibility to open-source software and hardware tools has been evident in the adoption of these tools by weed researchers and the increased popularity of CNN-based weed recognition research. The field of machine learning holds substantial promise for weed control, especially the implementation of truly integrated weed management strategies. Whereas previous approaches sought to reduce environmental variability or manage it with advanced algorithms, research in deep learning architectures suggests that large-scale, multi-modal approaches are the future for weed recognition.
Lifetime and Current Self-Harm Thoughts and Behaviors and Their Relationship to Parent and Peer Attachment
Authors: Janssens Julie J. , Myin-Germeys Inez , Lafit Ginette , Achterhof Robin , Hagemann Noëmi , Hermans Karlijn S. F. M. , Hiekkaranta Anu P. , Lecei Aleksandra , Kirtley Olivia J.
Published: November 2022

Abstract: Background: Previous research suggests attachment is a vulnerability factor for self-harm thoughts and behaviors in adults. Yet, few studies have investigated this relationship during adolescence, although adolescence is a critical period for changes in attachment relationships and self-harm onset. Whether and how attachment relates to self-harm thoughts and behaviors as measured in daily life is also unknown. Aims: To investigate whether and how paternal, maternal, and peer attachment are associated with lifetime and current adolescent self-harm thoughts and behaviors. Additionally, to examine how different attachment bonds interact in relation to lifetime and current adolescent self-harm thoughts and behaviors. Method: Pre-existing data from N = 1,913 adolescents of the SIGMA study were used. Attachment and lifetime history of self-harm thoughts and behaviors were measured via retrospective questionnaires. Current self-harm thoughts and behaviors were assessed 10 times per day for 6 days using the experience sampling method (ESM). Results: Paternal and maternal attachments were associated with lifetime self-harm thoughts and behaviors and current self-harm thoughts. No significant associations were found between peer attachment and self-harm outcomes. Limitations: Some analyses were underpowered. Conclusion: Our results highlight the importance of parent–child attachment relationships, which may be intervention targets for prevention and treatment of adolescent self-harm.
Salt Spray May Stifle Lightning over the Sea
Authors: Wilke Carolyn
Published: November 2022

New research suggests that sea-salt aerosols seed large raindrops that starve clouds of water needed to make lightning. But not all scientists are convinced it’s simply about salt spray.
Geometric-phase intraocular lenses with multifocality
Authors: Lee Seungmin , Park Gayeon , Kim Seonho , Ryu Yeonghwa , Yoon Jae Woong , Hwang Ho Sik , Song In Seok , Lee Chang Sun , Song Seok Ho
Published: November 2022

We demonstrate a new type of multifocal and extended depth of focus (EDOF) intraocular lenses (IOLs) embedding μm-thin geometric phase (GP) lens layers. As an emerging approach for lens phase design, the GP modulated IOLs outperform conventional diffractive IOLs in multifocality while completely avoiding the clinically undesirable demand for additional surface patterns to standard monofocal IOL designs. The number of foci and light splitting ratio of the GP IOLs are adjusted by changing the number of stacked GP layers and the thickness of each layer. Bifocal and trifocal GP IOLs are fabricated by radial alignment of anisotropic orientation in UV-curable liquid crystal polymers. After characterizing the defocus image and modulation transfer function of the GP IOLs, it is expected that GP IOLs will alleviate the most common problems associated with multifocal and EDOF IOLs, blurred vision and photic phenomena caused by light scattering and posterior capsule opacification.
Ultrasonically actuated neural probes for reduced trauma and inflammation in mouse brain
Authors: Chen Po-Cheng , Young Catharine G. , Schaffer Chris B. , Lal Amit
Published: November 2022

Electrical neural recordings measured using direct electrical interfaces with neural tissue suffer from a short lifespan because the signal strength decreases over time. The inflammatory response to the inserted microprobe can create insulating tissue over the electrical interfaces, reducing the recorded signal below noise levels. One of the factors contributing to this inflammatory response is the tissue damage caused during probe insertion. Here, we explore the use of ultrasonic actuation of the neural probe during insertion to minimize tissue damage in mice. Silicon neural microprobes were designed and fabricated with integrated electrical recording sites and piezoelectric transducers. The microprobes were actuated at ultrasonic frequencies using integrated piezoelectric transducers. The microprobes were inserted into mouse brains under a glass window over the brain surface to image the tissue surrounding the probe using two-photon microscopy. The mechanical force required to penetrate the tissue was reduced by a factor of 2–3 when the microprobe was driven at ultrasonic frequencies. Tissue histology at the probe insertion site showed a reduced area of damage and decreased microglia counts with increasing ultrasonic actuation of the probes. Two-photon imaging of the microprobe over weeks demonstrated stabilization of the inflammatory response. Recording of electrical signals from neurons over time suggests that microprobes inserted using ultrasound have a higher signal-to-noise ratio over an extended time period.
Cholinergic basal forebrain degeneration due to sleep-disordered breathing exacerbates pathology in a mouse model of Alzheimer’s disease
Authors: Qian Lei , Rawashdeh Oliver , Kasas Leda , Milne Michael R. , Garner Nicholas , Sankorrakul Kornraviya , Marks Nicola , Dean Matthew W. , Kim Pu Reum , Sharma Aanchal , Bellingham Mark C. , Coulson Elizabeth J.
Published: November 2022

Although epidemiological studies indicate that sleep-disordered breathing (SDB) such as obstructive sleep apnea is a strong risk factor for the development of Alzheimer’s disease (AD), the mechanisms of the risk remain unclear. Here we developed a method of modeling SDB in mice that replicates key features of the human condition: altered breathing during sleep, sleep disruption, moderate hypoxemia, and cognitive impairment. When we induced SDB in a familial AD model, the mice displayed exacerbation of cognitive impairment and the pathological features of AD, including increased levels of amyloid-beta and inflammatory markers, as well as selective degeneration of cholinergic basal forebrain neurons. These pathological features were not induced by chronic hypoxia or sleep disruption alone. Our results also revealed that the cholinergic neurodegeneration was mediated by the accumulation of nuclear hypoxia inducible factor 1 alpha. Furthermore, restoring blood oxygen levels during sleep to prevent hypoxia prevented the pathological changes induced by the SDB. These findings suggest a signaling mechanism whereby SDB induces cholinergic basal forebrain degeneration.
Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level
Authors: Sefer Anna , Kallis Eleni , Eilert Tobias , Röcker Carlheinz , Kolesnikova Olga , Neuhaus David , Eustermann Sebastian , Michaelis Jens
Published: November 2022

Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1’s multi-domain organization. Here, we directly probe this process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1’s N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state.
HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex
Authors: Leisegang Matthias S. , Bains Jasleen Kaur , Seredinski Sandra , Oo James A. , Krause Nina M. , Kuo Chao-Chung , Günther Stefan , Sentürk Cetin Nevcin , Warwick Timothy , Cao Can , Boos Frederike , Izquierdo Ponce Judit , Haydar Shaza , Bednarz Rebecca , Valasarajan Chanil , Fuhrmann Dominik C. , Preussner Jens , Looso Mario , Pullamsetti Soni S. , Schulz Marcel H. , Jonker Hendrik R. A. , Richter Christian , Rezende Flávia , Gilsbach Ralf , Pflüger-Müller Beatrice , Wittig Ilka , Grummt Ingrid , Ribarska Teodora , Costa Ivan G. , Schwalbe Harald , Brandes Ralf P.
Published: November 2022

DNA:DNA:RNA triplexes that are formed through Hoogsteen base-pairing of the RNA in the major groove of the DNA duplex have been observed in vitro, but the extent to which these interactions occur in cells and how they impact cellular functions remains elusive. Using a combination of bioinformatic techniques, RNA/DNA pulldown and biophysical studies, we set out to identify functionally important DNA:DNA:RNA triplex-forming long non-coding RNAs (lncRNA) in human endothelial cells. The lncRNA HIF1α-AS1 was retrieved as a top hit. Endogenous HIF1α-AS1 reduces the expression of numerous genes, including EPH Receptor A2 and Adrenomedullin through DNA:DNA:RNA triplex formation by acting as an adapter for the repressive human silencing hub complex (HUSH). Moreover, the oxygen-sensitive HIF1α-AS1 is down-regulated in pulmonary hypertension and loss-of-function approaches not only result in gene de-repression but also enhance angiogenic capacity. As exemplified here with HIF1α-AS1, DNA:DNA:RNA triplex formation is a functionally important mechanism of trans-acting gene expression control.
Barium content of Archaean continental crust reveals the onset of subduction was not global
Authors: Huang Guangyu , Mitchell Ross N. , Palin Richard M. , Spencer Christopher J. , Guo Jinghui
Published: November 2022

Earth’s earliest continental crust is dominated by tonalite–trondhjemite–granodiorite (TTG) suites, making these rocks key to unlocking the global geodynamic regime operating during the Archaean (4.0–2.5 billion years ago [Ga]). The tectonic setting of TTG magmatism is controversial, with hypotheses arguing both for and against subduction. Here we conduct petrological modeling over a range of pressure–temperature conditions relevant to the Archaean geothermal gradient. Using an average enriched Archaean basaltic source composition, we predict Ba concentrations in TTG suites, which is difficult to increase after magma generated in the source. The results indicate only low geothermal gradients corresponding to hot subduction zones produce Ba-rich TTG, thus Ba represents a proxy for the onset of subduction. We then identify statistically significant increases in the Ba contents of TTG suites worldwide as recording the diachronous onset of subduction from regional at 4 Ga to globally complete sometime after 2.7 Ga.
Endothelial dysfunction markers and immune response indices in cosmonauts’ blood after long-duration space flights
Authors: Kuzichkin D. S. , Nichiporuk I. A. , Zhuravleva O. A. , Markin A. A. , Rykova M. P. , Zhuravleva T. V. , Sadova A. A. , Kutko O. V. , Shmarov V. A. , Ponomarev S. A.
Published: November 2022

Space flight factors are known to cause a malfunction in the human immune system and lead to damage to blood vessels. The hemostatic function of endothelium during space missions and its interaction with human immunity has not been determined so far. In this work, we investigated the markers of endothelial activation and damage (plasma concentrations of soluble thrombomodulin fraction (sTM), von Willebrand factor (vWF), highly sensitive C-reactive protein (hs-CRP)), as well as the level of D-dimer and compared them to the immunological parameters characterizing the state of human humoral and cellular immunity. The immune status of long-duration ISS crewmembers was assessed by whole-blood testing, and comprehensive postflight immune assessment included the analysis of leukocyte distribution. Flow cytometry was applied to determine the absolute counts and the percentage of lymphocyte subsets: B cells (CD19+), T cells (CD3+, CD3+CD4+, CD3+CD8+), NK cells (CD3−CD16+CD56+, CD11b+CD56+), and activated subsets (CD3+CD25+ and CD3+HLA-DR+). The in vitro basal cytokine production was investigated in whole blood cell culture. The cytokines IFN-gamma, IL-1-beta, IL-4, IL-6, IL-10, IL-18, and TNF-alpha were measured in plasma and the 24-h supernatants by a sensitive enzyme-linked immunosorbent assay. A significant increase in the plasma levels of vWF and hs-CRP and a decrease in the concentration of sTM after spaceflights were detected. Divergent changes in the parameters characterizing the state of the immune system were observed. We propose that the changes revealed may lead to an increase in the procoagulant activity of blood plasma, suppression of protein C activation and thrombin inhibition, as well as to an increase in the adhesive-aggregate potential of platelets, especially in case of changes in the rheological characteristics of blood flow during re-adaptation to ground conditions. We also speculate that the immune system might play an important role in vessel damage during long-duration missions.
Histone H2B.8 compacts flowering plant sperm through chromatin phase separation
Authors: Buttress Toby , He Shengbo , Wang Liang , Zhou Shaoli , Saalbach Gerhard , Vickers Martin , Li Guohong , Li Pilong , Feng Xiaoqi
Published: November 2022

Sperm chromatin is typically transformed by protamines into a compact and transcriptionally inactive state1,2. Sperm cells of flowering plants lack protamines, yet they have small, transcriptionally active nuclei with chromatin condensed through an unknown mechanism3,4. Here we show that a histone variant, H2B.8, mediates sperm chromatin and nuclear condensation in Arabidopsis thaliana. Loss of H2B.8 causes enlarged sperm nuclei with dispersed chromatin, whereas ectopic expression in somatic cells produces smaller nuclei with aggregated chromatin. This result demonstrates that H2B.8 is sufficient for chromatin condensation. H2B.8 aggregates transcriptionally inactive AT-rich chromatin into phase-separated condensates, which facilitates nuclear compaction without reducing transcription. Reciprocal crosses show that mutation of h2b.8 reduces male transmission, which suggests that H2B.8-mediated sperm compaction is important for fertility. Altogether, our results reveal a new mechanism of nuclear compaction through global aggregation of unexpressed chromatin. We propose that H2B.8 is an evolutionary innovation of flowering plants that achieves nuclear condensation compatible with active transcription.
Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells
Authors: Nguyenla Xammy , Wehri Eddie , Van Dis Erik , Biering Scott B. , Yamashiro Livia H. , Zhu Chi , Stroumza Julien , Dugast-Darzacq Claire , Graham Thomas G. W. , Wang Xuanting , Jockusch Steffen , Tao Chuanjuan , Chien Minchen , Xie Wei , Patel Dinshaw J. , Meyer Cindy , Garzia Aitor , Tuschl Thomas , Russo James J. , Ju Jingyue , Näär Anders M. , Stanley Sarah , Schaletzky Julia
Published: November 2022

SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with significant mortality and morbidity. At this time, the only FDA-approved therapeutic for COVID-19 is remdesivir, a broad-spectrum antiviral nucleoside analog. Efficacy is only moderate, and improved treatment strategies are urgently needed. To accomplish this goal, we devised a strategy to identify compounds that act synergistically with remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput screening in the presence of submaximal remdesivir concentrations, using a human lung epithelial cell line infected with a clinical isolate of SARS-CoV-2. This identified 20 approved drugs that act synergistically with remdesivir, many with favorable pharmacokinetic and safety profiles. Strongest effects were observed with established antivirals, Hepatitis C virus nonstructural protein 5A (HCV NS5A) inhibitors velpatasvir and elbasvir. Combination with their partner drugs sofosbuvir and grazoprevir further increased efficacy, increasing remdesivir’s apparent potency > 25-fold. We report that HCV NS5A inhibitors act on the SARS-CoV-2 exonuclease proofreader, providing a possible explanation for the synergy observed with nucleoside analog remdesivir. FDA-approved Hepatitis C therapeutics Epclusa® (velpatasvir/sofosbuvir) and Zepatier® (elbasvir/grazoprevir) could be further optimized to achieve potency and pharmacokinetic properties that support clinical evaluation in combination with remdesivir.
Seasonal variations of the airborne microbial assemblages of the Seoul subway, South Korea from 16S and ITS gene profiles with chemical analysis
Authors: Hassan Zohaib Ul , Cho Hana , Park Changwoo , Yim Yong-Hyeon , Kim Seil
Published: November 2022

In this study, we determined the seasonal airborne microbial diversity profiles at SMRT stations by sequencing the 16S rRNA and ITS. Particulate matter samples were collected from air purifiers installed in the platform area of the SMRT subway stations. Three stations that included the most crowded one were selected for the sampling. The sampling was done at each season during 2019. After extracting the total DNA from all seasonal samples, PCR was performed with Illumina overhang adapter primers for the V3–V4 region of the 16S rRNA gene and ITS2 region of the ITS gene. The amplified products were further purified, and sequencing libraries were made. Sequencing was carried with the Illumina Miseq Sequencing system (Illumina, USA) followed by in-depth diversity analyses. The elemental composition of the particulate matter samples collected from the different subway stations were obtained using a WD-XRF spectrometer. The SMRT microbiome showed extensive taxonomic diversity with the most common bacterial genera at the subway stations associated with the skin. Overall, the stations included in this study harbored different phylogenetic communities based onα- and β-diversity comparisons. Microbial assemblages also varied depending upon the season in which the samples were taken and the station. Major elements present at the subway stations were from aerosols generated between wheels and brake cushions and between the catenaries and the pantographs. This study shows that the microbial composition of the SMRT subway stations comes from a diverse combination of environmental and human sources, the season and the lifestyle of commuters.
Novel Venetin-1 nanoparticle from earthworm coelomic fluid as a promising agent for the treatment of non-small cell lung cancer
Authors: Rybicka Magda , Czaplewska Paulina , Rzymowska Jolanta , Sofińska-Chmiel Weronika , Wójcik-Mieszawska Sylwia , Lewtak Kinga , Węgrzyn Katarzyna , Jurczak Przemysław , Szpiech Agata , Nowak Jakub , Musiał Natalia , Fiołka Marta J.
Published: November 2022

The present research shows the antitumor activity of a protein-polysaccharide complex Venetin-1 obtained from the coelomic fluid of Dendrobaena veneta earthworms against A549 cancer cells. The investigations are a continuation of experiments on the antitumor activity of coelomic fluid obtained from this species. The Venetin-1 nanoparticle was obtained after thermal treatment of the coelomic fluid, separation from coelomocytes, filtration, and lyophilization. The preparation showed a selective effect on cancer cells, whereas normal cells were unaffected. Venetin-1 was effective against the lung cancer cells at doses of 31.3 and 62.5 µg/ml, and the results were imaged using light microscopy and scanning electron microscopy (SEM). The cells died mainly via the apoptosis pathway. Necrotic cells appeared sporadically in the microscopic view. SEM imaging revealed complete destruction of the A549 cells after the incubation with Venetin-1. The atomic force microscopy (AFM) analyses showed changes in the topography, peak force error images, and Young’s modulus (elasticity) of the A549 cells after the incubation with Venetin-1. The transmission electron cryomicroscopy (Cryo-TEM) analysis indicated a polymeric nature of the analyzed preparation. The samples of Venetin-1 showed a very homogeneous size profile with the microparticle size of approximately 58.23 nm. A significant decrease in Venetin-1 binding to sphingomyelin was observed. Venetin-1 lost its pore-forming activity or deactivation of the pore-forming activity occurred. This confirms the absence of hemolytic capacity of Venetin-1 towards red blood cells. The conducted analyses show the suitability of the obtained complex for biomedical research. The next step will consist in analyses of the effect of Venetin-1 on the immune system in mice.
ROOT parameters of sugarcane and soil compaction indicators under deep strip tillage and conventional tillage
Authors: de Lima Camila Cassante , De Maria Isabella Clerici , da Silva Guimarães Júnnyor Wellingthon , Figueiredo Getulio Coutinho , Dechen Sonia Carmela Falci , Bolonhezi Denizart
Published: November 2022

Soil tillage and agricultural traffic generate changes in soil physical attributes and affect the growth of the roots. This study evaluates the impact of system soil tillage on compaction and sugarcane root growth. The experiment was carried out on a Rhodic Kandiudox with two soil tillages (Deep Strip Tillage and Conventional Tillage) and two positions (beds or traffic lane and no traffic lane), totaling four treatments (DST-beds + no traffic lane, DST-traffic lane, CT-no traffic lane and CT-traffic lane). Soil penetration resistance (SPR), bulk density, dry mass, and root system lengths and volumes were evaluated. DST-beds presented lower values for SPR (1.45 MPa) compared to the other treatments (2.55 MPa). This lower SPR did not reflect significant increases in root growth in relation to the DST-traffic lane, meaning that the roots were not confined to the beds. The dry root mass for CT- traffic lane was 35% less than for DST- traffic lane, and CT-no traffic lane reduced of the root dry mass in the layers 0.0–0.2 and 0.2–0.4 m by 62% and 47%, respectively, compared to the DST-beds. Therefore, CT, although widely used, does not create adequate conditions for root development in the first sugarcane cycle, even in lanes with no traffic.
Clinical significance of prostate volume and testosterone reduction on lower urinary tract symptoms in patients with prostate cancer undergoing androgen deprivation therapy
Authors: Bang Woo Jin , Kim Hwanik , Oh Cheol Young , Jo Jung Ki , Cho Jin Seon , Shim Myungsun
Published: November 2022

To investigate the effect of both prostate volume and serum testosterone changes on lower urinary tract symptoms in patients with prostate cancer undergoing androgen deprivation therapy. A total of 167 patients who received androgen deprivation therapy for prostate cancer treatment from January 2010 to August 2020 were enrolled in this retrospective study. Changes in the International Prostate Symptom Score (IPSS) in the patient groups stratified by prostate volume and the amount of testosterone reduction were assessed every 4 weeks until 12 weeks after androgen deprivation therapy initiation. Longitudinal mixed models were used to assess the adjusted effects of prostate volume and testosterone reduction on IPSS change. All mean values of IPSS-total score (IPSS-total), voiding subscore (IPSS-vs), and storage subscore (IPSS-ss) significantly decreased from baseline to week 12 in both patients with small (< 33 mL) and large (≥ 33 mL) prostates. The mean values of IPSS-total, IPSS-vs, and IPSS-ss similarly decreased in patients with large prostate with a baseline IPSS-total of ≥ 13. However, in those with small prostate, IPSS-ss specifically remained unchanged, while IPSS-total and IPSS-vs significantly decreased. In addition, only in patients with small prostate (< 33 mL), patients with lesser testosterone reduction (< Δ400 ng/dL) showed greater improvement in IPSS-ss by 7.5% compared with those with greater testosterone reduction (≥ Δ400 ng/dL). In conclusion, although androgen deprivation therapy generally improves lower urinary tract symptoms, it may worsen specifically storage symptoms in patients with relatively small prostate and greater testosterone reduction. Our finding suggests that testosterone may influence lower urinary tract symptoms in these patients.
Identification of two QTLs, BPH41 and BPH42, and their respective gene candidates for brown planthopper resistance in rice
Authors: Tan Han Qi , Palyam Sreekanth , Gouda Jagadeesha , Kumar Prakash P. , Chellian Santhosh Kumar
Published: November 2022

The brown planthopper (BPH) is the leading cause of insect damage to rice plants and BPH infestations have caused profound losses in rice production since the 1970’s. There is an urgent need to discover new BPH resistance genes to ensure the successful production of rice. Here, a new BPH resistance source provided by SeedWorks International Pvt. Ltd., SWD10, was used for this purpose. QTL mapping using 232 F2 progenies and 216 polymorphic markers revealed two dominant BPH resistance QTLs, BPH41 and BPH42, located on chromosome 4. BPH resistance mechanism test revealed that antibiosis and antixenosis mechanisms both play a role in BPH resistance conferred by these two QTLs. The QTLs were delimited between markers SWRm_01617 and SWRm_01522 for BPH41, and SWRm_01695 and SWRm_00328 for BPH42. Additionally, using RNA-seq data of lines containing the resistant QTLs, we shortlisted four and three gene candidates for BPH41 and BPH42, respectively. Differential gene expression analysis of lines containing the QTLs suggested that SWD10 BPH resistance is contributed by the plant’s innate immunity and the candidate genes may be part of the rice innate immunity pathway. Currently, the newly identified QTLs are being utilized for breeding BPH resistant rice varieties and hybrids.
Detection of mitochondrial DNA mutations in circulating mitochondria-originated extracellular vesicles for potential diagnostic applications in pancreatic adenocarcinoma
Authors: Vikramdeo Kunwar Somesh , Anand Shashi , Khan Mohammad Aslam , Khushman Moh’d , Heslin Martin J. , Singh Seema , Singh Ajay Pratap , Dasgupta Santanu
Published: November 2022

There is a complete lack of highly sensitive and specific biomarkers for early pancreatic ductal adenocarcinoma (PDAC) diagnosis, limiting multi-modal therapeutic options. Mitochondrial DNA (mtDNA) is an excellent resource for biomarker discovery because of its high copy number and increased mutational frequency in cancer cells. We examined if mtDNA mutations can be detected in circulating extracellular vesicles (EVs) of PDAC patients and used for discerning between cancer and non-cancer subjects. A greater yield of circulating EVs (~ 1.4 fold;p = 0.002) was obtained in PDAC patients (n = 20) than non-cancer (NC) individuals (n = 10). PDAC-EVs contained a higher quantity of total DNA (~ 5.5 folds;p = 0.0001) than NC-EVs and had greater enrichment of mtDNA (~ 14.02-fold;p = 0.0001). PDAC-EVs also had higher levels of cardiolipin (a mitochondrial inner-membrane phospholipid), suggestive of their mitochondrial origin. All mtDNA mutations in PDAC-EVs were unique and frequency was remarkably higher. Most mtDNA mutations (41.5%) in PDAC-EVs were in the respiratory complex-I (RCI) (ND1-ND6), followed by the RCIII gene (CYTB; 11.2%). Among the non-coding genes, D-Loop andRNR2exhibited the most mutations (15.2% each). Altogether, our study establishes, for the first time, that mtDNA mutations can be detected in circulating EVs and potentially serve as a tool for reliable PDAC diagnosis.
Optimism bias and its relation to scenario valence, gender, sociality, and insecure attachment
Authors: Dricu Mihai , Moser Dominik A. , Aue Tatjana
Published: November 2022

Optimism bias refers to the tendency to display unjustified high/low expectations of future positive/negative events. This study asked 202 participants to estimate the likelihood of 96 different events. We investigated optimism biases for both oneself and the general population, and how these biases are influenced by gender, valence of the event, sociality of the event, as well as attachment anxiety and attachment avoidance. We found that sociality interacted with gender, with the difference in optimism bias for social vs. alone events being larger among women than among men. Attachment anxiety mainly reduced the optimism bias among men deliberating over future alone situations, while attachment avoidance primarily reduced optimism bias among female respondents deliberating over future social interactions. These results may have implications for the well-being and motivation of differently attached men and women and ultimately inspire psychotherapy interventions.
Fused Raman spectroscopic analysis of blood and saliva delivers high accuracy for head and neck cancer diagnostics
Authors: Koster Hanna J. , Guillen-Perez Antonio , Gomez-Diaz Juan Sebastian , Navas-Moreno Maria , Birkeland Andrew C. , Carney Randy P.
Published: November 2022

As a rapid, label-free, non-destructive analytical measurement requiring little to no sample preparation, Raman spectroscopy shows great promise for liquid biopsy cancer detection and diagnosis. We carried out Raman analysis and mass spectrometry of plasma and saliva from more than 50 subjects in a cohort of head and neck cancer patients and benign controls (e.g., patients with benign oral masses). Unsupervised data models were built to assess diagnostic performance. Raman spectra collected from either biofluid provided moderate performance to discriminate cancer samples. However, by fusing together the Raman spectra of plasma and saliva for each patient, subsequent analytical models delivered an impressive sensitivity, specificity, and accuracy of 96.3%, 85.7%, and 91.7%, respectively. We further confirmed that the metabolites driving the differences in Raman spectra for our models are among the same ones that drive mass spectrometry models, unifying the two techniques and validating the underlying ability of Raman to assess metabolite composition. This study bolsters the relevance of Raman to provide additive value by probing the unique chemical compositions across biofluid sources. Ultimately, we show that a simple data augmentation routine of fusing plasma and saliva spectra provided significantly higher clinical value than either biofluid alone, pushing forward the potential of clinical translation of Raman spectroscopy for liquid biopsy cancer diagnostics.
Exploration of a novel and efficient source for production of bacterial nanocellulose, bioprocess optimization and characterization
Authors: El-Naggar Noura El-Ahmady , El-Malkey Sahar E. , Abu-Saied M. A. , Mohammed A. B. Abeer
Published: November 2022

The demand for bacterial nanocellulose is expected to rise in the coming years due to its wide usability in many applications. Hence, there is a continuing need to screen soil samples from various sources to isolate a strain with a high capacity for bacterial nanocellulose production. Bacillus sp. strain SEE-12, which was isolated from a soil sample collected from Barhiem, Menoufia governorate, Egypt, displayed high BNC production under submerged fermentation. Bacillus sp. strain SEE-12 was identified as Bacillus tequilensis strain SEE-12. In static cultures, BNC was obtained as a layer grown in the air liquid interface of the fermentation medium. The response surface methodology was used to optimise the process parameters. The highest BNC production (22.8 g/L) was obtained using 5 g/L peptone, 5 g/L yeast extract, 50%, v/v Cantaloupe juice, 5 g/L Na2HPO4, 1.5 g/L citric acid, pH 5, medium volume of 100 mL/250 mL conical flask, inoculum size 5%, v/v, temperature 37 °C and incubation time 6 days. The BNC was purified and characterized by scanning electron microscopy (SEM), Energy-dispersive X-ray (EDX) spectroscopy, differential scanning calorimetry (DSC), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA) and transmission electron microscopy (TEM).
Association between thyroid cancer and cardiovascular disease risk: a nationwide observation study
Authors: Tsai Ming-Chieh , Hsieh Cheng-Tzu , Hsu Hsin-Yin , Yeh Tzu-Lin , Lee Wen-Chung , Chiang Chun-Ju , Hsiao Bo-Yu , Jhuang Jing-Rong , Tsai Wen-Hsuan , Cheng Shih-Ping , Chou Chao-Liang , Lee Chun-Chuan , Liu Sung-Chen , Tseng Po-Jung , Chien Kuo-Liong
Published: November 2022

Treatment with levothyroxine and radioiodine contribute alternative cardiovascular function in adults with thyroid cancer. The risks of long-term cardiovascular conditions among thyroid cancer patients is unknown. This study aimed to compare the incidence of coronary heart disease (CHD), ischemic stroke (IS), and atrial fibrillation (AF) among adults with thyroid cancer with that of the general population, especially when stratified by age (< 65 and ≥ 65 years old). This observational cohort study enrolled patients between January 1, 2011 and December 31, 2016 with a follow-up until December 31, 2018. This study analyzed the data of Taiwanese thyroid cancer patients registered on the National Taiwan Cancer Registry Database, with CHD and IS. SIR models were used to evaluate the association between thyroid cancer and CHD, IS, AF, and cardiovascular disease outcome, stratified by age and sex. SIR analyses were also conducted for both sexes, age groups (< 65, ≥ 65 years), and different follow-up years. After excluding 128 individuals (< 20 years or ≥ 85 years old) and with missing index data, 4274 eligible thyroid cancer patients without CHD history, 4343 patients without IS history, and 4247 patients without AF history were included for analysis. During the median follow-up of 3.5 (1.2) years among thyroid cancer patients, the observed number of new CHD events was 70; IS, 30; and AF, 20, respectively. The SIR was significantly higher for CHD (SIR, 1.57; 95% confidence interval [CI] 1.2–1.93) among thyroid cancer patients compared with the age- and sex-specific standardized population. However, the association between thyroid cancer and the risks of IS (SIR, 0.74; 95% CI 0.47–1), cardiovascular disease (SIR, 0.88; 95% CI 0.7–1.05), and atrial fibrillation (SIR, 0.74; 95% CI 0.42–1.06) were insignificant. Moreover, stratification by age < 65 or age ≥ 65 years old and by sex for CHD suggested that the diagnosis of thyroid cancer in the young may attenuate the CHD risk (SIR, 2.08; 95% CI 1.5–2.66), and the CVD risk was constant among both men (SIR, 1.63; 95% CI 1.03–2.24) and women (SIR, 1.53; 95% CI 1.06–1.99). The patients had persistent higher CHD risk for 5 years after cancer diagnosis. Thyroid cancer survivors have a substantial CHD risk, even at long-term follow-up, especially in those patients < 65 years old. Further research on the association between thyroid cancer and CHD risk is warranted.