bluuebunny/crossref_metadata_2025 huggingface dataset:
Ukrainian Refugees, Race, and International Law's Choice Between Order and Justice
Authors: Jackson Sow Marissa
Published: October 2022

The resurgence of racist rhetoric and policies concerning people fleeing the war in Ukraine serves as a reminder that the ostensible goals of the 1951 Convention Relating to the Status of Refugees and 1967 Protocol are regularly eschewed by states making decisions about how to allocate grants of asylum. This Essay makes the claim that racial tiering of protection-seekers demonstrates that states use international refugee law to negotiate their national whiteness contracts and to secure racially hegemonic geopolitical ordering.
Remembering Nyota Inyoka: Queering Narratives of Dance, Archive, and Biography
Authors: Chatterjee Sandra , Cramer Franz Anton , Haitzinger Nicole
Published: October 2022

In this article, the three co-authors collaboratively address practices of queering in relation to the Parisian choreographer of color Nyota Inyoka (1896–1971), whose biography and identity remain mysterious even after extensive research. Writing from three different research perspectives and relating to three different aspects of her life and work, the co-authors analyze Nyota Inyoka and practices of Queering the Archive, her staging of Shiva as a performance of (culturally) “queer possibility,” and the act of remembering Nyota Inyoka in a contemporary context in terms of queering ethnicity and “cultural belonging.” Juxtaposing and interweaving notions and practices of queering and créolité/creolizing over the course of the article, the co-authors attempt to respect Nyota Inyoka's “right to opacity” (Glissant [1996] 2020, 45) and remember her on her own terms.
Queering the Skeleton in Dance's Closet
Authors: Ross Janice
Published: October 2022

This article explores the role a human skeleton played in the queering and shaping of dance modernism. In the early decades of the twentieth century, an important intervention propelling dance toward a modernist aesthetic while disrupting the regulatory norms of gender construction, began in a women's college gymnasium via a skeleton. Two impulses generate this archival-based inquiry: one that traces the history and symbolic formulations of nationalism, race, and gender that followed skeletons into the university as they anchored conceptualizations of the modernist dancing body; and another that locates the intervention of a queer body in dance through this skeleton.
Communication strategy use of EFL learners in videoconferencing, virtual world and face-to-face environments
Authors: Cirit-Işıklıgil Nazlı Ceren , Sadler Randall W. , Arıca-Akkök Elif
Published: October 2022

This study investigates the communication strategy (CS) use of English as a foreign language (EFL) learners in videoconferencing (VC), virtual world (VW), and face-to-face environments. The study was conducted with 30 senior Turkish undergraduate EFL students. The data were collected via video and audio recordings of three opinion-exchange tasks, a background and post-task questionnaire, and an interview that includes a retrospective think-aloud protocol. The participants worked in groups of five to complete the opinion-exchange tasks in each of the three environments. The findings indicated that the participants made use of a wide range of CSs, and although some of the CSs differed, mostly the same types were employed in all the environments. However, the results revealed that the frequency of CSs showed variance among environments, with the highest number in the VC environment and the lowest in the VW. It was possible to establish a connection between the differences in the frequency and the types of strategy use with the distinctive features of the environments, the proficiency level of the participants, and the type of the tasks that was utilized. Additively, 10 new strategy types were discovered.
City Size and Public Service Access: Evidence from Brazil and Indonesia
Authors: Post Alison E. , Kuipers Nicholas
Published: October 2022

Most global population growth over the next two decades is projected to occur in small- and medium-sized cities in low- and middle-income countries. Expectations derived from the literature on fiscal federalism suggest that this is a cause for concern, as larger cities are thought to deliver public goods more effectively than smaller ones owing to economics of scale. Drawing on detailed cross-sectional data from Brazil and Indonesia, we show that smaller municipalities tend to possess more basic public health clinics and schools per capita, scattered throughout their territory, than larger cities. We theorize that the greater prevalence of such facilities in small cities reflects a relative lack of non-state alternatives, fewer concerns regarding “urban” problems faced in larger cities, and politicians’ greater ability to secure and claim credit for such facilities. We illustrate the logic of this argument in case studies of otherwise-similar cities of different sizes in Brazil, and with shadow cases from Indonesia. Our analysis underscores how jurisdiction size and non-state service provision can affect government services.
Attitudes Toward Civil Liberties and Rights Among Politically Charged Online Groups
Authors: Fasce Angelo , Avendaño Diego
Published: October 2022

Abstract. Civil liberties and rights such as freedom of expression, press, thought, religion, association, lifestyle, and equality against the law are being subjected to controversies in Western countries. We developed two hypotheses aimed at explaining divergent attitudes toward civil liberties among politically charged online communities on each side of the political spectrum. A study using a cross-sectional sample of social media users ( N = 902) suggests that, as expected by our hypotheses, support for civil liberties tend to be higher among online groups of rightists – with economic conservatism being the only direct positive predictor and left-wing authoritarianism being a strong negative predictor. These results are discussed in relation to polarization over civil liberties and perceived power imbalances between online groups.
Recovery and genome reconstruction of novel magnetotactic Elusimicrobiota from bog soil
Authors: Uzun Maria , Koziaeva Veronika , Dziuba Marina , Alekseeva Lolita , Krutkina Maria , Sukhacheva Marina , Baslerov Roman , Grouzdev Denis
Published: October 2022

Studying the minor part of the uncultivated microbial majority (“rare biosphere”) is difficult even with modern culture-independent techniques. The enormity of microbial diversity creates particular challenges for investigating low-abundance microbial populations in soils. Strategies for selective sample enrichment to reduce community complexity can aid in studying the rare biosphere. Magnetotactic bacteria, apart from being a minor part of the microbial community, are also found in poorly studied bacterial phyla and certainly belong to a rare biosphere. The presence of intracellular magnetic crystals within magnetotactic bacteria allows for their significant enrichment using magnetic separation techniques for studies using a metagenomic approach. This work investigated the microbial diversity of a black bog soil and its magnetically enriched fraction. The poorly studied phylum representatives in the magnetic fraction were enriched compared to the original soil community. Two new magnetotactic species, Candidatus Liberimonas magnetica DUR002 and Candidatus Obscuribacterium magneticum DUR003, belonging to different classes of the relatively little-studied phylum Elusimicrobiota, were proposed. Their genomes contain clusters of magnetosome genes that differ from the previously described ones by the absence of genes encoding magnetochrome-containing proteins and the presence of unique Elusimicrobiota-specific genes, termed mae. The predicted obligately fermentative metabolism in DUR002 and lack of flagellar motility in the magnetotactic Elusimicrobiota broadens our understanding of the lifestyles of magnetotactic bacteria and raises new questions about the evolutionary advantages of magnetotaxis. The findings presented here increase our understanding of magnetotactic bacteria, soil microbial communities, and the rare biosphere.
Mutated lncRNA increase the risk of type 2 diabetes by promoting β cell dysfunction and insulin resistance
Authors: Guo Wan-Hui , Guo Qi , Liu Ya-Lin , Yan Dan-Dan , Jin Li , Zhang Rong , Yan Jing , Luo Xiang-Hang , Yang Mi
Published: October 2022

Islet β cell dysfunction and insulin resistance are the main pathogenesis of type 2 diabetes (T2D), but the mechanism remains unclear. Here we identify a rs3819316 C > T mutation in lncRNA Reg1cp mainly expressed in islets associated with an increased risk of T2D. Analyses in 16,113 Chinese adults reveal that Mut-Reg1cp individuals had higher incidence of T2D and presented impaired insulin secretion as well as increased insulin resistance. Mice with islet β cell specific Mut-Reg1cp knock-in have more severe β cell dysfunction and insulin resistance. Mass spectrometry assay of proteins after RNA pulldown demonstrate that Mut-Reg1cp directly binds to polypyrimidine tract binding protein 1 (PTBP1), further immunofluorescence staining, western blot analysis, qPCR analysis and glucose stimulated insulin secretion test reveal that Mut-Reg1cp disrupts the stabilization of insulin mRNA by inhibiting the phosphorylation of PTBP1 in β cells. Furthermore, islet derived exosomes transfer Mut-Reg1cp into peripheral tissue, which then promote insulin resistance by inhibiting AdipoR1 translation and adiponectin signaling. Our findings identify a novel mutation in lncRNA involved in the pathogenesis of T2D, and reveal a new mechanism for the development of T2D.
Cryo-EM structure of an ATTRwt amyloid fibril from systemic non-hereditary transthyretin amyloidosis
Authors: Steinebrei Maximilian , Gottwald Juliane , Baur Julian , Röcken Christoph , Hegenbart Ute , Schönland Stefan , Schmidt Matthias
Published: October 2022

Wild type transthyretin-derived amyloid (ATTRwt) is the major component of non-hereditary transthyretin amyloidosis. Its accumulation in the heart of elderly patients is life threatening. A variety of genetic variants of transthyretin can lead to hereditary transthyretin amyloidosis, which shows different clinical symptoms, like age of onset and pattern of organ involvement. However, in the case of non-hereditary transthyretin amyloidosis ATTRwt fibril deposits are located primarily in heart tissue. In this structural study we analyzed ATTRwt amyloid fibrils from the heart of a patient with non-hereditary transthyretin amyloidosis. We present a 2.78 Å reconstructed density map of these ATTRwt fibrils using cryo electron microscopy and compare it with previously published V30M variants of ATTR fibrils extracted from heart and eye of different patients. All structures show a remarkably similar spearhead like shape in their cross section, formed by the same N- and C-terminal fragments of transthyretin with some minor differences. This demonstrates common features for ATTR fibrils despite differences in mutations and patients.
Impacts of shared mobility on vehicle lifetimes and on the carbon footprint of electric vehicles
Authors: Morfeldt Johannes , Johansson Daniel J. A.
Published: October 2022

Shared cars will likely have larger annual vehicle driving distances than individually owned cars. This may accelerate passenger car retirement. Here we develop a semi-empirical lifetime-driving intensity model using statistics on Swedish vehicle retirement. This semi-empirical model is integrated with a carbon footprint model, which considers future decarbonization pathways. In this work, we show that the carbon footprint depends on the cumulative driving distance, which depends on both driving intensity and calendar aging. Higher driving intensities generally result in lower carbon footprints due to increased cumulative driving distance over the vehicle’s lifetime. Shared cars could decrease the carbon footprint by about 41% in 2050, if one shared vehicle replaces ten individually owned vehicles. However, potential empty travel by autonomous shared vehicles—the additional distance traveled to pick up passengers—may cause carbon footprints to increase. Hence, vehicle durability and empty travel should be considered when designing low-carbon car sharing systems.
Sea level extremes and compounding marine heatwaves in coastal Indonesia
Authors: Han Weiqing , Zhang Lei , Meehl Gerald A. , Kido Shoichiro , Tozuka Tomoki , Li Yuanlong , McPhaden Michael J. , Hu Aixue , Cazenave Anny , Rosenbloom Nan , Strand Gary , West B. Jason , Xing Wen
Published: October 2022

Low-lying island nations like Indonesia are vulnerable to sea level Height EXtremes (HEXs). When compounded by marine heatwaves, HEXs have larger ecological and societal impact. Here we combine observations with model simulations, to investigate the HEXs and Compound Height-Heat Extremes (CHHEXs) along the Indian Ocean coast of Indonesia in recent decades. We find that anthropogenic sea level rise combined with decadal climate variability causes increased occurrence of HEXs during 2010–2017. Both HEXs and CHHEXs are driven by equatorial westerly and longshore northwesterly wind anomalies. For most HEXs, which occur during December-March, downwelling favorable northwest monsoon winds are enhanced but enhanced vertical mixing limits surface warming. For most CHHEXs, wind anomalies associated with a negative Indian Ocean Dipole (IOD) and co-occurring La Niña weaken the southeasterlies and cooling from coastal upwelling during May-June and November-December. Our findings emphasize the important interplay between anthropogenic warming and climate variability in affecting regional extremes.
Transient inhibition of p53 enhances prime editing and cytosine base-editing efficiencies in human pluripotent stem cells
Authors: Li Mu , Zhong Aaron , Wu Youjun , Sidharta Mega , Beaury Michael , Zhao Xiaolan , Studer Lorenz , Zhou Ting
Published: October 2022

Precise gene editing in human pluripotent stem cells (hPSCs) holds great promise for studying and potentially treating human diseases. Both prime editing and base editing avoid introducing double strand breaks, but low editing efficiencies make those techniques still an arduous process in hPSCs. Here we report that co-delivering of p53DD, a dominant negative fragment of p53, can greatly enhance prime editing and cytosine base editing efficiencies in generating precise mutations in hPSCs. We further apply PE3 in combination with p53DD to efficiently create multiple isogenic hPSC lines, including lines carrying GBA or LRRK2 mutations associated with Parkinson disease and a LMNA mutation linked to Hutchinson-Gilford progeria syndrome. We also correct GBA and LMNA mutations in the patient-specific iPSCs. Our data show that p53DD improves PE3 efficiency without compromising the genome-wide safety, making it feasible for safe and routine generation of isogenic hPSC lines for disease modeling.
Molecular insights into DNA recognition and methylation by non-canonical type I restriction-modification systems
Authors: Zhu Jingpeng , Gao Yina , Wang Yong , Zhan Qi , Feng Han , Luo Xiu , Li Peipei , Liu Songqing , Hou Hai , Gao Pu
Published: October 2022

Type I restriction-modification systems help establish the prokaryotic DNA methylation landscape and provide protection against invasive DNA. In addition to classical m6A modifications, non-canonical type I enzymes catalyze both m6A and m4C using alternative DNA-modification subunits M1 and M2. Here, we report the crystal structures of the non-canonical PacII_M1M2S methyltransferase bound to target DNA and reaction product S-adenosylhomocysteine in a closed clamp-like conformation. Target DNA binds tightly within the central tunnel of the M1M2S complex and forms extensive contacts with all three protein subunits. Unexpectedly, while the target cytosine properly inserts into M2’s pocket, the target adenine (either unmethylated or methylated) is anchored outside M1’s pocket. A unique asymmetric catalysis is established where PacII_M1M2S has precisely coordinated the relative conformations of different subunits and evolved specific amino acids within M2/M1. This work provides insights into mechanisms of m6A/m4C catalysis and guidance for designing tools based on type I restriction-modification enzymes.
Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control
Authors: Nadler Franziska , Lavdovskaia Elena , Krempler Angelique , Cruz-Zaragoza Luis Daniel , Dennerlein Sven , Richter-Dennerlein Ricarda
Published: October 2022

Translation termination requires release factors that read a STOP codon in the decoding center and subsequently facilitate the hydrolysis of the nascent peptide chain from the peptidyl tRNA within the ribosome. In human mitochondria eleven open reading frames terminate in the standard UAA or UAG STOP codon, which can be recognized by mtRF1a, the proposed major mitochondrial release factor. However, two transcripts encoding for COX1 and ND6 terminate in the non-conventional AGA or AGG codon, respectively. How translation termination is achieved in these two cases is not known. We address this long-standing open question by showing that the non-canonical release factor mtRF1 is a specialized release factor that triggers COX1 translation termination, while mtRF1a terminates the majority of other mitochondrial translation events including the non-canonical ND6. Loss of mtRF1 leads to isolated COX deficiency and activates the mitochondrial ribosome-associated quality control accompanied by the degradation of COX1 mRNA to prevent an overload of the ribosome rescue system. Taken together, these results establish the role of mtRF1 in mitochondrial translation, which had been a mystery for decades, and lead to a comprehensive picture of translation termination in human mitochondria.
Synthesized spatiotemporal mode-locking and photonic flywheel in multimode mesoresonators
Authors: Nie Mingming , Jia Kunpeng , Xie Yijun , Zhu Shining , Xie Zhenda , Huang Shu-Wei
Published: October 2022

Dissipative Kerr soliton (DKS) frequency combs—also known as microcombs—have arguably created a new field in cavity nonlinear photonics, with a strong cross-fertilization between theoretical, experimental, and technological research. Spatiotemporal mode-locking (STML) not only adds new degrees of freedom to ultrafast laser technology, but also provides new insights for implementing analogue computers and heuristic optimizers with photonics. Here, we combine the principles of DKS and STML to demonstrate the STML DKS by developing an unexplored ultrahigh-quality-factor Fabry–Pérot (FP) mesoresonator based on graded index multimode fiber (GRIN-MMF). Complementing the two-step pumping scheme with a cavity stress tuning method, we can selectively excite either the eigenmode DKS or the STML DKS. Furthermore, we demonstrate an ultralow noise microcomb that enhances the photonic flywheel performance in both the fundamental comb linewidth and DKS timing jitter. The demonstrated fundamental comb linewidth of 400 mHz and DKS timing jitter of 500 attosecond (averaging times up to 25 μs) represent improvements of 25× and 2.5×, respectively, from the state-of-the-art. Our results show the potential of GRIN-MMF FP mesoresonators as an ideal testbed for high-dimensional nonlinear cavity dynamics and photonic flywheel with ultrahigh coherence and ultralow timing jitter.
Endothelial alpha globin is a nitrite reductase
Authors: Keller T. C. Stevenson , Lechauve Christophe , Keller Alexander S. , Broseghini-Filho Gilson Brás , Butcher Joshua T. , Askew Page Henry R. , Islam Aditi , Tan Zhe Yin , DeLalio Leon J. , Brooks Steven , Sharma Poonam , Hong Kwangseok , Xu Wenhao , Padilha Alessandra Simão , Ruddiman Claire A. , Best Angela K. , Macal Edgar , Kim-Shapiro Daniel B. , Christ George , Yan Zhen , Cortese-Krott Miriam M. , Ricart Karina , Patel Rakesh , Bender Timothy P. , Sonkusare Swapnil K. , Weiss Mitchell J. , Ackerman Hans , Columbus Linda , Isakson Brant E.
Published: October 2022

Resistance artery vasodilation in response to hypoxia is essential for matching tissue oxygen and demand. In hypoxia, erythrocytic hemoglobin tetramers produce nitric oxide through nitrite reduction. We hypothesized that the alpha subunit of hemoglobin expressed in endothelium also facilitates nitrite reduction proximal to smooth muscle. Here, we create two mouse strains to test this: an endothelial-specific alpha globin knockout (EC Hba1Δ/Δ) and another with an alpha globin allele mutated to prevent alpha globin’s inhibitory interaction with endothelial nitric oxide synthase (Hba1WT/Δ36–39). The EC Hba1Δ/Δ mice had significantly decreased exercise capacity and intracellular nitrite consumption in hypoxic conditions, an effect absent in Hba1WT/Δ36–39 mice. Hypoxia-induced vasodilation is significantly decreased in arteries from EC Hba1Δ/Δ, but not Hba1WT/Δ36–39 mice. Hypoxia also does not lower blood pressure in EC Hba1Δ/Δ mice. We conclude the presence of alpha globin in resistance artery endothelium acts as a nitrite reductase providing local nitric oxide in response to hypoxia.
Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps
Authors: Ye Xinhai , Yang Yi , Zhao Can , Xiao Shan , Sun Yu H. , He Chun , Xiong Shijiao , Zhao Xianxin , Zhang Bo , Lin Haiwei , Shi Jiamin , Mei Yang , Xu Hongxing , Fang Qi , Wu Fei , Li Dunsong , Ye Gongyin
Published: October 2022

Parasitoid wasps are rapidly developing as a model for evolutionary biology. Here we present chromosomal genomes of two Anastatus wasps, A. japonicus and A. fulloi, and leverage these genomes to study two fundamental questions—genome size evolution and venom evolution. Anastatus shows a much larger genome than is known among other wasps, with unexpectedly recent bursts of LTR retrotransposons. Importantly, several genomic innovations, including Piwi gene family expansion, ubiquitous Piwi expression profiles, as well as transposable element-piRNA coevolution, have likely emerged for transposable element silencing to maintain genomic stability. Additionally, we show that the co-option evolution arose by expression shifts in the venom gland plays a dominant role in venom turnover. We also highlight the potential importance of non-venom genes that are coexpressed with venom genes during venom evolution. Our findings greatly advance the current understanding of genome size evolution and venom evolution, and these genomic resources will facilitate comparative genomics studies of insects in the future.
Targeting vasoactive intestinal peptide-mediated signaling enhances response to immune checkpoint therapy in pancreatic ductal adenocarcinoma
Authors: Ravindranathan Sruthi , Passang Tenzin , Li Jian-Ming , Wang Shuhua , Dhamsania Rohan , Ware Michael Brandon , Zaidi Mohammad Y. , Zhu Jingru , Cardenas Maria , Liu Yuan , Gumber Sanjeev , Robinson Brian , Sen-Majumdar Anish , Zhang Hanwen , Chandrakasan Shanmuganathan , Kissick Haydn , Frey Alan B. , Thomas Susan N. , El-Rayes Bassel F. , Lesinski Gregory B. , Waller Edmund K.
Published: October 2022

A paucity of effector T cells within tumors renders pancreatic ductal adenocarcinoma (PDAC) resistant to immune checkpoint therapies. While several under-development approaches target immune-suppressive cells in the tumor microenvironment, there is less focus on improving T cell function. Here we show that inhibiting vasoactive intestinal peptide receptor (VIP-R) signaling enhances anti-tumor immunity in murine PDAC models. In silico data mining and immunohistochemistry analysis of primary tumors indicate overexpression of the neuropeptide vasoactive intestinal peptide (VIP) in human PDAC tumors. Elevated VIP levels are also present in PDAC patient plasma and supernatants of cultured PDAC cells. Furthermore, T cells up-regulate VIP receptors after activation, identifying the VIP signaling pathway as a potential target to enhance T cell function. In mouse PDAC models, VIP-R antagonist peptides synergize with anti-PD-1 antibody treatment in improving T cell recruitment into the tumors, activation of tumor-antigen-specific T cells, and inhibition of T cell exhaustion. In contrast to the limited single-agent activity of anti-PD1 antibodies or VIP-R antagonist peptides, combining both therapies eliminate tumors in up to 40% of animals. Furthermore, tumor-free mice resist tumor re-challenge, indicating anti-cancer immunological memory generation. VIP-R signaling thus represents a tumor-protective immune-modulatory pathway that is targetable in PDAC.
Modeling intercellular communication in tissues using spatial graphs of cells
Authors: Fischer David S. , Schaar Anna C. , Theis Fabian J.
Published: October 2022

Models of intercellular communication in tissues are based on molecular profiles of dissociated cells, are limited to receptor–ligand signaling and ignore spatial proximity in situ. We present node-centric expression modeling, a method based on graph neural networks that estimates the effects of niche composition on gene expression in an unbiased manner from spatial molecular profiling data. We recover signatures of molecular processes known to underlie cell communication.
Mapping neurotransmitter systems to the structural and functional organization of the human neocortex
Authors: Hansen Justine Y. , Shafiei Golia , Markello Ross D. , Smart Kelly , Cox Sylvia M. L. , Nørgaard Martin , Beliveau Vincent , Wu Yanjun , Gallezot Jean-Dominique , Aumont Étienne , Servaes Stijn , Scala Stephanie G. , DuBois Jonathan M. , Wainstein Gabriel , Bezgin Gleb , Funck Thomas , Schmitz Taylor W. , Spreng R. Nathan , Galovic Marian , Koepp Matthias J. , Duncan John S. , Coles Jonathan P. , Fryer Tim D. , Aigbirhio Franklin I. , McGinnity Colm J. , Hammers Alexander , Soucy Jean-Paul , Baillet Sylvain , Guimond Synthia , Hietala Jarmo , Bedard Marc-André , Leyton Marco , Kobayashi Eliane , Rosa-Neto Pedro , Ganz Melanie , Knudsen Gitte M. , Palomero-Gallagher Nicola , Shine James M. , Carson Richard E. , Tuominen Lauri , Dagher Alain , Misic Bratislav
Published: October 2022

Neurotransmitter receptors support the propagation of signals in the human brain. How receptor systems are situated within macro-scale neuroanatomy and how they shape emergent function remain poorly understood, and there exists no comprehensive atlas of receptors. Here we collate positron emission tomography data from more than 1,200 healthy individuals to construct a whole-brain three-dimensional normative atlas of 19 receptors and transporters across nine different neurotransmitter systems. We found that receptor profiles align with structural connectivity and mediate function, including neurophysiological oscillatory dynamics and resting-state hemodynamic functional connectivity. Using the Neurosynth cognitive atlas, we uncovered a topographic gradient of overlapping receptor distributions that separates extrinsic and intrinsic psychological processes. Finally, we found both expected and novel associations between receptor distributions and cortical abnormality patterns across 13 disorders. We replicated all findings in an independently collected autoradiography dataset. This work demonstrates how chemoarchitecture shapes brain structure and function, providing a new direction for studying multi-scale brain organization.
Using CFD simulations to investigate the shear stress in hydrodynamic cavitation reactors coupled with experimental validation using colony count measurements
Authors: Polgár Máté , Agarwal Charu , Gogate Parag , Németh Gábor , Csóka Levente
Published: October 2022

The current work investigates the shear stress distribution in hydrodynamic cavitation reactors with two different geometries using CFD simulations. Venturi type (positive geometry) and bore (negative geometry) were used to induce cavitation. Experimental validation of the predictions from simulations was also conducted by calculating the reduction rate in the colony count of Legionella pneumophila, a pathogenic bacterial strain. Both the numerical and experimental studies revealed the significant influence of the shape of the cavitation-inducing geometry on the flow characteristics and the distribution of shear stress. The simulation data indicated high shear stress formation in the positive geometry as a venturi, with the cavitation ranges for the two reactors being far apart from each other. The experimental study also confirmed that the flow conditions in the venturi-type reactor were more favourable compared to the bore geometry, resulting in a bacterial reduction efficiency as high as 99.98%. It was clearly demonstrated that the geometry of the cavitating device plays a crucial role in deciding the shear stress and its efficacy for the desired applications as per the predictions of the simulation model validated by the experimental results.
Effects of different virtual reality technology driven dual-tasking paradigms on posture and saccadic eye movements in healthy older adults
Authors: Imaoka Yu , Flury Andri , Hauri Laura , de Bruin Eling D.
Published: October 2022

Postural sway and eye movements are potential biomarkers for dementia screening. Assessing the two movements comprehensively could improve the understanding of complicated syndrome for more accurate screening. The purpose of this research is to evaluate the effects of comprehensive assessment in healthy older adults (OA), using a novel concurrent comprehensive assessment system consisting of stabilometer and virtual reality headset. 20 healthy OA (70.4 ± 4.9 years) were recruited. Using a cross-sectional study design, this study investigated the effects of various dual-tasking paradigms with integrated tasks of visuospatial memory (VM), spatial orientation (SO), and visual challenge on posture and saccades. Dual-task paradigms with VM and SO affected the saccadic eye movements significantly. Two highly intensive tests of anti-saccade with VM task and pro-saccade with SO task also influenced postural sway significantly. Strong associations were seen between postural sway and eye movements for the conditions where the two movements theoretically shared common neural pathways in the brain, and vice versa. This study suggests that assessing posture and saccades with the integrated tasks comprehensively and simultaneously could be useful to explain different functions of the brain. The results warrant a cross-sectional study in OA with and without dementia to explore differences between these groups.
Ramp-shaped neural tuning supports graded population-level representation of the object-to-scene continuum
Authors: Park Jeongho , Josephs Emilie , Konkle Talia
Published: October 2022

We can easily perceive the spatial scale depicted in a picture, regardless of whether it is a small space (e.g., a close-up view of a chair) or a much larger space (e.g., an entire class room). How does the human visual system encode this continuous dimension? Here, we investigated the underlying neural coding of depicted spatial scale, by examining the voxel tuning and topographic organization of brain responses. We created naturalistic yet carefully-controlled stimuli by constructing virtual indoor environments, and rendered a series of snapshots to smoothly sample between a close-up view of the central object and far-scale view of the full environment (object-to-scene continuum). Human brain responses were measured to each position using functional magnetic resonance imaging. We did not find evidence for a smooth topographic mapping for the object-to-scene continuum on the cortex. Instead, we observed large swaths of cortex with opposing ramp-shaped profiles, with highest responses to one end of the object-to-scene continuum or the other, and a small region showing a weak tuning to intermediate scale views. However, when we considered the population code of the entire ventral occipito-temporal cortex, we found smooth and linear representation of the object-to-scene continuum. Our results together suggest that depicted spatial scale information is encoded parametrically in large-scale population codes across the entire ventral occipito-temporal cortex.
Dynamic analysis and optimal control considering cross transmission and variation of information
Authors: Kang Sida , Hou Xilin , Hu Yuhan , Liu Hongyu
Published: October 2022

Cross-transmission of information has a profound influence on the progress of science and technology and the discipline integration in the field of education. In this work, knowledge gained from the viral recombination and variation in COVID-19 transmission is applied to information transmission. Virus recombination and virus variation are similar to the crossing and information fusion phenomena in information transmission. An S2I4MR model with information crossing and variation is constructed. Then, the local and global asymptotic stabilities of the information-free equilibrium and information-existence equilibrium are analyzed. Additionally, the basic reproduction number $$R_0$$

R
0

of the model is calculated. As such, an optimal control strategy is hereby proposed to promote the cross-transmission of information and generate variant information. The numerical simulations support the results of the theoretical analysis and the sensitivity of the system towards certain control parameters. In particular, the results show that strengthening information crossing promotes the generation of variant information. Furthermore, encouraging information exchange and enhancing education improve the generation of information crossing and information variation.
An aphid inspired metaheuristic optimization algorithm and its application to engineering
Authors: Liu Renyun , Zhou Ning , Yao Yifei , Yu Fanhua
Published: October 2022

The biologically inspired metaheuristic algorithm obtains the optimal solution by simulating the living habits or behavior characteristics of creatures in nature. It has been widely used in many fields. A new bio-inspired algorithm, Aphids Optimization Algorithm (AOA), is proposed in this paper. This algorithm simulates the foraging process of aphids with wings, including the generation of winged aphids, flight mood, and attack mood. Concurrently, the corresponding optimization models are presented according to the above phases. At the phase of the flight mood, according to the comprehensive influence of energy and the airflow, the individuals adaptively choose the flight mode to migrate; at the phase of attack mood, individuals use their sense of smell and vision to locate food sources for movement. Experiments on benchmark test functions and two classical engineering design problems, indicate that the desired AOA is more efficient than other metaheuristic algorithms.
Natural cycles in South Pacific Gyre strength and the Southern Annular Mode
Authors: Hitt Nicholas T. , Sinclair Daniel J. , Neil Helen L. , Fallon Stewart J. , Komugabe-Dixson Aimée , Fernandez Denise , Sutton Philip J. , Hellstrom John C.
Published: October 2022

The South Pacific Gyre (SPG) plays a vital role in regulating Southern Hemisphere climate and ecosystems. The SPG has been intensifying since the twentieth century due to changes in large scale wind forcing. These changes result from variability in the Southern Annular Mode (SAM), causing warming along the eastern SPG which affects local ecosystems. However, our understanding of SPG variability on timescales greater than several decades is poor due to limited observations. Marine sediment cores are traditionally used to determine if recent ocean trends are anomalous, but rarely capture centennial variability in the southwest Pacific and limit our understanding of SPG variability. Here we capture centennial SPG dynamics using a novel high-resolution paleocirculation archive: radiocarbon reservoir ages (R) and local reservoir corrections (∆R) in SPG deep-sea black corals. We find black coral R and ∆R correlates with SAM reconstructions over 0–1000 cal BP and 2000–3000 cal BP. We propose this correlation indicates varying transport of well-ventilated subtropical waters resulting from SPG and SAM interactions. We reconstruct several ‘spin up’ cycles reminiscent of the recent gyre intensification, which has been attributed to anthropogenic causes. This implies gyre strength and SAM show natural co-variability on anthropogenic timescales which should factor into future climate projections.
Automation of generative adversarial network-based synthetic data-augmentation for maximizing the diagnostic performance with paranasal imaging
Authors: Kong Hyoun-Joong , Kim Jin Youp , Moon Hye-Min , Park Hae Chan , Kim Jeong-Whun , Lim Ruth , Woo Jonghye , Fakhri Georges El , Kim Dae Woo , Kim Sungwan
Published: October 2022

Thus far, there have been no reported specific rules for systematically determining the appropriate augmented sample size to optimize model performance when conducting data augmentation. In this paper, we report on the feasibility of synthetic data augmentation using generative adversarial networks (GAN) by proposing an automation pipeline to find the optimal multiple of data augmentation to achieve the best deep learning-based diagnostic performance in a limited dataset. We used Waters’ view radiographs for patients diagnosed with chronic sinusitis to demonstrate the method developed herein. We demonstrate that our approach produces significantly better diagnostic performance parameters than models trained using conventional data augmentation. The deep learning method proposed in this study could be implemented to assist radiologists in improving their diagnosis. Researchers and industry workers could overcome the lack of training data by employing our proposed automation pipeline approach in GAN-based synthetic data augmentation. This is anticipated to provide new means to overcome the shortage of graphic data for algorithm training.
An in silico comparative transcriptome analysis identifying hub lncRNAs and mRNAs in brain metastatic small cell lung cancer (SCLC)
Authors: Mikaeili Namini Arsham , Jahangir Motahareh , Mohseni Maryam , Kolahi Ali Asghar , Hassanian-Moghaddam Hossein , Mazloumi Zeinab , Motallebi Marzieh , Sheikhpour Mojgan , Movafagh Abolfazl
Published: October 2022

Small cell lung cancer (SCLC) is a particularly lethal subtype of lung cancer. Metastatic lung tumours lead to most deaths from lung cancer. Predicting and preventing tumour metastasis is crucially essential for patient survivability. Hence, in the current study, we focused on a comprehensive analysis of lung cancer patients' differentially expressed genes (DEGs) on brain metastasis cell lines. DEGs are analysed through KEGG and GO databases for the most critical biological processes and pathways for enriched DEGs. Additionally, we performed protein–protein interaction (PPI), GeneMANIA, and Kaplan–Meier survival analyses on our DEGs. This article focused on mRNA and lncRNA DEGs for LC patients with brain metastasis and underlying molecular mechanisms. The expression data was gathered from the Gene Expression Omnibus database (GSE161968). We demonstrate that 30 distinct genes are up-expressed in brain metastatic SCLC patients, and 31 genes are down-expressed. All our analyses show that these genes are involved in metastatic SCLC. PPI analysis revealed two hub genes (CAT and APP). The results of this article present three lncRNAs, Including XLOC_l2_000941, LOC100507481, and XLOC_l2_007062, also notable mRNAs, have a close relation with brain metastasis in lung cancer and may have a role in the epithelial-mesenchymal transition (EMT) in tumour cells.
Utilization of ex vivo tissue model to study skin regeneration following microneedle stimuli
Authors: Liu Xue , Barresi Rebecca , Kaminer Michael , Qian Kun , Thillou Fabienne , Bataillon Michel , Liao I-Chien , Zheng Qian , Bouez Charbel
Published: October 2022

Microneedling is a popular skin resurfacing and rejuvenation procedure. In order to develop better adjunct products for consumers, there is a scientific need to establish greater understanding of the mechanism in which microneedling stimulates regeneration within skin. The purpose of this study is to develop a physiologically relevant ex vivo tissue model which closely mimics the actual microneedling procedure to elucidate its mechanism of action. In this study, human ex vivo skin was subjected to microneedling treatment and cultured for 6 days. Histological analysis demonstrated that the ex vivo skin was able to heal from microneedling injury throughout the culture period. Microneedling treatment stimulated proliferation and barrier renewal of the skin. The procedure also increased the levels of inflammatory cytokines and angiogenic growth factors in a dynamic and time dependent fashion. The tissue demonstrated hallmark signs of epidermal regeneration through morphological and molecular changes after the treatment. This is one of the first works to date that utilizes microneedled ex vivo skin to demonstrate its regenerative behavior. Our model recapitulates the main features of the microneedling treatment and enables the evaluation of future cosmetic active ingredients used in conjunction with microneedling.
Genesis of fecal floatation is causally linked to gut microbial colonization in mice
Authors: Aalam Syed Mohammed Musheer , Crasta Daphne Norma , Roy Pooja , Miller A. Lee , Gamb Scott I. , Johnson Stephen , Till Lisa M. , Chen Jun , Kashyap Purna , Kannan Nagarajan
Published: October 2022

The origin of fecal floatation phenomenon remains poorly understood. Following our serendipitous discovery of differences in buoyancy of feces from germ-free and conventional mice, we characterized microbial and physical properties of feces from germ-free and gut-colonized (conventional and conventionalized) mice. The gut-colonization associated differences were assessed in feces using DNA, bacterial-PCR, scanning electron microscopy, FACS, thermogravimetry and pycnometry. Based on the differences in buoyancy of feces, we developed levô in fimo test (LIFT) to distinguish sinking feces (sinkers) of germ-free mice from floating feces (floaters) of gut-colonized mice. By simultaneous tracking of microbiota densities and gut colonization kinetics in fecal transplanted mice, we provide first direct evidence of causal relationship between gut microbial colonization and fecal floatation. Rare discordance in LIFT and microbiota density indicated that enrichment of gasogenic gut colonizers may be necessary for fecal floatation. Finally, fecal metagenomics analysis of ‘floaters’ from conventional and syngeneic fecal transplanted mice identified colonization of > 10 gasogenic bacterial species including highly prevalent B. ovatus, an anaerobic commensal bacteria linked with flatulence and intestinal bowel diseases. The findings reported here will improve our understanding of food microbial biotransformation and gut microbial regulators of fecal floatation in human health and disease.
Long-term hospitalisations in survivors of paediatric solid tumours in France
Authors: Bejarano-Quisoboni Daniel , Pelletier-Fleury Nathalie , Allodji Rodrigue S. , Fresneau Brice , Boussac Majorie , Pacquement Hélène , Doz François , Berchery Delphine , Pluchart Claire , Bondiau Piere-Yves , Nys Julie , Jackson Angela , Demoor-Goldschmidt Charlotte , Dumas Agnes , Thomas-Teinturier Cécile , Schwartz Boris , Journy Neige , Rubino Carole , Vu-Bezin Giao , Valteau-Couanet Dominique , El-Fayech Chiraz , Dufour Christelle , Haddy Nadia , de Vathaire Florent
Published: October 2022

The late effects of treatments for childhood cancers may lead to severe and multiple health conditions requiring hospitalisation. We aimed to estimate the hospitalisation rate among childhood cancer survivors (CCS) in France, to compare them with the general population and to investigate the associated factors. We matched total of 5439 5-year solid CCS diagnosed before the age of 21 between 1945 and 2000 by sex, birth year and region of residence to 386,073 individuals of the French general population. After linkage with the national hospital discharge database, we estimated the relative hospitalisation rate (RHR), the absolute excess risks (AERs) and the relative bed-day ratio (RBDR) during 2006–2018. We used generalised linear models to estimate associations between hospitalisation and survivor characteristics. Overall, the RHR was 2.49 (95% confidence interval [CI] 2.46–2.52) and the RBDR was 3.49 (95% CI 3.46–3.51). We found that neoplasm-related hospitalisations had the highest AER (105.8 per 1000 person-years), followed by genitourinary system diseases (34.4 per 1000 person-years) and cardiovascular diseases (19.2 per 1000 person-years). In adjusted analysis, CCS treated with chemotherapy (risk ratio [RR] 1.62, 95% CI 1.53–1.70), radiotherapy (RR 2.11, 95% CI 1.99–2.24) or both (RR 2.59, 95% CI 2.46–2.73) had a higher risk of hospitalisation than the ones who had not received any of these treatments. CCS treated during the past decades by chemotherapy and/or radiotherapy now had a higher hospitalisation risk for all main categories of diagnosis than the general population. Prevention strategies and medical surveillance programmes may promote a long-term decrease in the hospitalisation rate among CSS.
Expression of membrane Hsp90 is a molecular signature of T cell activation
Authors: Scarneo Scott A. , Smith Aaron P. , Favret Jacob , O’Connell Robert , Pickeral Joy , Yang Kelly W. , Ferrari Guido , Loiselle David R. , Hughes Philip F. , Kulkarni Manjusha M. , Gargesha Madhusudhana , Scott Bryan , Roy Debashish , Haynes Barton F. , Kwiek Jesse J. , Haystead Timothy A. J.
Published: October 2022

Heat shock protein 90 (Hsp90) maintains cellular proteostasis during stress and has been under investigation as a therapeutic target in cancer for over two decades. We and others have identified a membrane expressed form of Hsp90 (mHsp90) that previously appeared to be restricted to rapidly proliferating cells exhibiting a metastatic phenotype. Here, we used HS-131, a fluor-tethered mHsp90 inhibitor, to quantify the effect of T cell activation on the expression of mHsp90 in human and mouse T cells. In cell-based assays, stimulation of human T cells induced a 20-fold increase in mHsp90 expression at the plasma membrane, suggesting trafficking of mHsp90 is regulated by TCR and inflammatory mediated signaling. Following injection of HS-131 in mouse models of human rheumatoid arthritis and inflammatory bowel disease, we detected localization of the probe at sites of active disease, consistent with immune cell invasion. Moreover, despite rapid hepatobiliary clearance, HS-131 demonstrated efficacy in reducing the mean clinical score in the CIA arthritis model. Our results suggest mHsp90 expression on T cells is a molecular marker of T cell activation and potentially a therapeutic target for chronic diseases such as rheumatoid arthritis.
Sars-Cov2 world pandemic recurrent waves controlled by variants evolution and vaccination campaign
Authors: Campi Gaetano , Perali Andrea , Marcelli Augusto , Bianconi Antonio
Published: October 2022

While understanding the time evolution of Covid-19 pandemic is needed to plan economics and tune sanitary policies, a quantitative information of the recurrent epidemic waves is elusive. This work describes a statistical physics study of the subsequent waves in the epidemic spreading of Covid-19 and disclose the frequency components of the epidemic waves pattern over two years in United States, United Kingdom and Japan. These countries have been taken as representative cases of different containment policies such as "Mitigation" (USA and UK) and "Zero Covid" (Japan) policies. The supercritical phases in spreading have been identified by intervals with RIC-index > 0. We have used the wavelet transform of infection and fatality waves to get the spectral analysis showing a dominant component around 130 days. Data of the world dynamic clearly indicates also the crossover to a different phase due to the enforcement of vaccination campaign. In Japan and United Kingdom, we observed the emergence in the infection waves of a long period component (~ 170 days) during vaccination campaign. These results indicate slowing down of the epidemic spreading dynamics due to the vaccination campaign. Finally, we find an intrinsic difference between infection and fatality waves pointing to a non-trivial variation of the lethality due to different gene variants.