bluuebunny/crossref_metadata_2025_split huggingface dataset:
SwrA extends DegU over an UP element to activate flagellar gene expression inBacillus subtilis
Authors: Mishra Ayushi , Hughes Anna C. , Amon Jeremy D. , Rudner David Z. , Wang Xindan , Kearns Daniel B. 
Published: August 2023

ABSTRACTSwrA activates flagellar gene expression inBacillus subtilisto increase the frequency of motile cells in liquid and elevate flagellar density to enable swarming over solid surfaces. Here we use ChIP-seq to show that SwrA interacts with many sites on the chromosome in a manner that depends on the response regulator DegU. We identify a DegU-specific inverted repeat DNA sequence and show that SwrA synergizes with phosphorylation to increase DegU DNA binding affinity. We further show that SwrA increases the size of the DegU footprint expanding the region bound by DegU towards the promoter. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription more that could be explained by deactivation. We conclude that SwrA/DegU forms a heteromeric complex that enables both remote binding and interaction between the activator and RNA polymerase in the context of an interceding UP element. We speculate that multimeric activators that resolve cis-element spatial conflicts are common in bacteria and likely act on flagellar biosynthesis loci and other long operons of other multi-subunit complexes.IMPORTANCEIn Bacteria, the sigma subunit of RNA polymerase recognizes specific DNA sequences called promoters that determine where gene transcription begins. Some promoters also have sequences immediately upstream called an UP element that is bound by the alpha subunit of RNA polymerase and is often necessary for transcription. Finally, promoters may be activated by transcription factors that bind DNA specific sequences and help recruit RNA polymerase to weak promoter elements. Here we show that the promoter for the 32 gene long flagellar operon inBacillus subtilisrequires an UP element and is activated by a heteromeric transcription factor of DegU and SwrA. Our evidence suggests that SwrA oligomerizes DegU over the DNA to allow RNA polymerase to interact with DegU and the UP element simultaneously. Heteromeric activator complexes are known but poorly-understood in bacteria and we speculate they may be needed to resolve spatial conflicts in the DNA sequence.
Disruption of Fuz in mouse embryos generates hypoplastic hindbrain development and reduced cranial nerve ganglia
Authors: Caiaffa Carlo Donato , Ambekar Yogeshwari S. , Singh Manmohan , Lin Ying Linda , Wlodarczyk Bogdan , Aglyamov Salavat R. , Scarcelli Giuliano , Larin Kirill V. , Finnell Richard 
Published: August 2023

ABSTRACTThe formation of the brain and spinal cord is initiated in the earliest stages of mammalian pregnancy in a highly organized process known as neurulation. Convergent and extension movements transforms a flat sheet of ectodermal cells into a narrow and elongated line of neuroepithelia, while a major source of Sonic Hedgehog signaling from the notochord induces the overlying neuroepithelial cells to form two apposed neural folds. Afterward, neural tube closure occurs by synchronized coordination of the surface ectoderm and adjacent neuroepithelial walls at specific axial regions known as neuropores. Environmental or genetic interferences can impair neurulation resulting in neural tube defects. TheFuzgene encodes a subunit of the CPLANE complex, which is a macromolecular planar polarity effector required for ciliogenesis. Ablation ofFuzin mouse embryos results in exencephaly and spina bifida, including dysmorphic craniofacial structures due to defective cilia formation and impaired Sonic Hedgehog signaling. In this work, we demonstrate that knockingFuzout during embryonic mouse development results in a hypoplastic hindbrain phenotype, displaying abnormal rhombomeres with reduced length and width. This phenotype is associated with persistent loss of ventral neuroepithelial stiffness, in a notochord adjacent area at the level of the rhombomere 5, preceding the development of exencephaly inFuzablated mutants. The formation of cranial and paravertebral ganglia is also impaired in these embryos, indicating thatFuzhas a critical function sustaining normal neural tube development and neuronal differentiation.SIGNIFICANCE STATEMENTNeural tube defects (NTDs) are a common cause of disability in children, representing the second most common congenital structural malformation in humans following only congenital cardiovascular malformations. NTDs affect approximately 1 to 2 pregnancies per 1000 births every year worldwide, when the mechanical forces folding the neural plate fails to close at specific neuropores located anteriorly (cranial) or posteriorly (caudal) along the neural tube, in a process known as neurulation, which happens throughout the third and fourth weeks of human pregnancy.
Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts
Authors: Maire Justin , Philip Gayle K. , Livingston Jadzia , Judd Louise M. , Blackall Linda L. , van Oppen Madeleine J. H. 
Published: August 2023

AbstractCorals rely on a wide range of microorganisms for their functioning, including intracellular dinoflagellates (Symbiodiniaceae) and bacteria. Marine heatwaves trigger the loss of Symbiodiniaceae from coral tissues - coral bleaching - often leading to death. While coral-bacteria interactions are widely studied, Symbiodiniaceae-bacteria interactions have remained largely uninvestigated. Here, we provide a genomic analysis of 49 bacteria, spanning 16 genera, that closely associate with six cultured Symbiodiniaceae species. We analyzed bacterial functional potential by focusing on potentially beneficial functions for the Symbiodiniaceae host, including B vitamin synthesis and antioxidant abilities, which may be crucial for Symbiodiniaceae heat tolerance and in turn coral resistance to thermal bleaching. These analyses suggest a wide potential for B vitamin synthesis and the scavenging of reactive oxygen species (through the production of carotenoids or antioxidant enzymes), and possibly the transfer of organic carbon to host cells. Single nucleotide polymorphism analysis between bacteria isolated from wild-type and heat-evolved Symbiodiniaceae cultures revealed that exposure to long-term elevated temperature has resulted in mutations in genes known to be involved in host-symbiont interactions, such as secretion systems. Climate change may therefore modify how Symbiodiniaceae and bacteria interact. This study provides an overview of the possible roles of Symbiodiniaceae-associated bacteria in Symbiodiniaceae functioning and heat tolerance, reinforcing the need for further studies of such interactions to fully understand coral biology and climate resilience.ImportanceSymbiotic microorganisms are crucial for the survival of corals and their resistance to coral bleaching in the face of climate change. However, the impact of microbe-microbe interactions on coral functioning is mostly unknown, but could be essential factors for coral adaption to future climates. Here, we investigated interactions between cultured dinoflagellates of the Symbiodiniaceae family, essential photosymbionts of corals, and associated bacteria. By assessing the genomic potential of 49 bacteria, we found that they are likely beneficial for Symbiodiniaceae, through the production of B vitamins and antioxidants. Additionally, bacterial genes involved in host-symbiont interactions, such as secretion systems, accumulated mutations following long-term exposure to heat, suggesting symbiotic interactions may change under climate change. This highlights the importance of microbe-microbe interactions in coral functioning.
Nonlinear Approximation for Mixed Convection Flow From a Vertical Plate With Exponentially Decaying Internal Heat Generation and Nonlinear Thermal Radiation
Authors: Jha Basant K. , Samaila Gabriel 
Published: August 2023

AbstractThis study considered dynamic features of mixed convection flow over a vertical plate influenced by nonlinear thermal radiation and exponentially decaying internal heat generation. The importance of the nonlinear density variation with temperature (NDT) and convective heating is also analyzed. The governing equations are transformed into ordinary differential equations using the similarity variables and solved in MAPLE 2022 by a Runge–Kutta Ferhlberg fourth-fifth order scheme. The results obtained show that, with an increase in the convection process, the internal heat generation convects more fluid away and consequently reduced the rate of heat flowing back into the plate. For a weak internal heat generation λx=0.5, the plate temperature is less than one (1) and the heat is observed to flow from the plate into the fluid on the surface of the right plate. Furthermore, for weak convection and nonlinear thermal radiation effects, the rate at which the heat flows into the plate increases with the convective heat transfer parameter increase. However, for a strong nonlinear thermal radiation effect, the rate at which the heat flows out of the plate increases. The flow feature is not only governed by the rate of internal heat generation but the generation as well reverses the heat flow from the plate since the temperature of the near the plate surface T is much higher than the environmental temperature Tf.
Effects of Variable Pressure Outlets for Array Jet Impingement Cooling With a Bidirectional Exit Air Scheme
Authors: Bonds Michael , Subbarama Iyer Ganesh , Ekkad Srinath V. 
Published: August 2023

Abstract
Array jet impingement in conjunction with other cooling methods such as effusion cooling is used in gas turbine combustion zones to provide optimized cooling in the form of double wall cooling around a combustion chamber. Utilizing a transient liquid crystal (TLC) technique an experimental investigation into the effects of pressure gradients and single versus multiple exits for array jet impingement crossflow is evaluated in the form of a detailed heat transfer analysis. In this study, four pressure gradients to bias mass flow ratios as (1:1), (2:1), (3:1), and (1:0), two jet array configurations either inline or staggered with jet to jet spacings (x/D = y/D) of 1.4, 1.9, and 2.2, three jet to target distances (z/D) ranging from 2 to 4, and three Reynolds number from 5000 to 15,000 are considered. In total, a test matrix of 72 different performance conditions was evaluated. Results are presented as local and area averaged Nusselt number plots along with local heat transfer coefficient contours. Overall, Nusselt number decreases with increased (z/D) and increased pressure gradient bias toward a single exit from (1:1) to (1:0). There is also slightly better performance from inline jet array configurations compared to staggered configurations.
Depletion Calculations for an Integral Small Molten Salt Reactor With Serpent
Authors: Wang Xiaolin , Nguyen T. Sinh , Wojtaszek Daniel 
Published: August 2023

Abstract
The molten salt reactor (MSR) concept is among the Generation IV designs considered feasible for providing clean, safe, sustainable, and economical energy supplies to the world's population. The depletion of fuel for a small modular fluoride molten salt reactor (sm-FMSR) with a closed fuel cycle based on the integral molten salt reactor concept has been investigated using Serpent. The Monte Carlo transport code Serpent has burnup capability and flow features that can be used to model fuel circulation and online fuel addition in an MSR. Three fueling schemes to control Serpent depletion cycles have been simulated and compared: step fueling (SF), continuous fueling with all fission products (FPs) accumulating in the reactor system (CFA), and continuous fueling with insoluble FPs separated from fuel (CFS). CFA and CFS require fewer depletion cycles that are longer in duration than the cycles required by SF, in order to maintain the effective multiplication factor (keff) within a working range over the seven years of the reactor fuel cycle. sm-FMSRs with SF and with CFA require similar quantities of “top-up” fuel, consume similar fuel (fissile) amounts, and result in similar fuel isotopic concentrations if keff is kept within a similar range. However, with separation of insoluble FPs from the circulating fuel, CFS gains a large reactivity worth due to the removal of FP poisons. This allows for reduction of fuel enrichment in both initial and total top-up fuel and leads to savings of a considerable fissile quantity in fueling MSR and in spent fuel. The Serpent depletion calculations require manual arithmetic calculations for adjustment of the Serpent built-in settings before the start of every calculation cycle for all three fueling schemes. Implementation of additional Serpent flow features in changing material volumes and flow constants would facilitate the simulation of the fuel depletion process and allow for more realistic simulations of fuel circulation.
Novel Payloads to Mitigate Maladaptive Inward Arterial Remodeling in Drug-Coated Balloon Therapy
Authors: Shazly Tarek , Uline Mark , Webb Clinton , Pederson Breanna , Eberth John F. , Kolachalama Vijaya B. 
Published: August 2023

Abstract
Drug-coated balloon therapy is a minimally invasive endovascular approach to treat obstructive arterial disease, with increasing utilization in the peripheral circulation due to improved outcomes as compared to alternative interventional modalities. Broader clinical use of drug-coated balloons is limited by an incomplete understanding of device- and patient-specific determinants of treatment efficacy, including late outcomes that are mediated by postinterventional maladaptive inward arterial remodeling. To address this knowledge gap, we propose a predictive mathematical model of pressure-mediated femoral artery remodeling following drug-coated balloon deployment, with account of drug-based modulation of resident vascular cell phenotype and common patient comorbidities, namely, hypertension and endothelial cell dysfunction. Our results elucidate how postinterventional arterial remodeling outcomes are altered by the delivery of a traditional anti-proliferative drug, as well as by codelivery with an anti-contractile drug. Our findings suggest that codelivery of anti-proliferative and anti-contractile drugs could improve patient outcomes following drug-coated balloon therapy, motivating further consideration of novel payloads in next-generation devices.
Exploring the Oxy-Fuel Combustion in Spark-Ignition Engines for Future Clean Powerplants
Authors: Serrano José Ramón , Díaz Jaime Martín , Gomez-Soriano Josep , Raggi Rodrigo 
Published: August 2023

Abstract
In the context of the CO2 challenge, oxy-fuel combustion in internal combustion engines (OFC-ICE) arises as a promising technology for carbon capture and almost zero-NOx solutions. Although the literature shows some experimental and theoretical works on OFC-ICE, there is a lack of systematic studies dealing with dilution strategies or where nonsynthetic exhaust gases recirculated (EGR) is used. Using a combination of zero-dimensional (0D)-one dimensional (1D) and computational fluid dynamics modeling and experimental measurements, dilution with oxygen (λ&gt;1) and real EGR in a single-cylinder spark-ignition OFC-ICE is here assessed, considering thermo-mechanical limitations and knocking. Results show that an EGR strategy is more appropriate than O2 dilution. A slightly poor mixture near stoichiometric conditions, with EGR rates around 70%, reduces NOx more than 99%, and CO and unburned hydrocarbons up to 90% with respect to the conventional internal combustion engines. It is concluded that OFC-ICE has a lower knocking propensity, thus allowing to increase the compression ratio to partially compensate for the expected efficiency diminution to about 4% points.
Enhancing sensitivity to leptonic CP violation using complementarity among DUNE, T2HK, and T2HKK
Authors: Agarwalla Sanjib Kumar , Das Sudipta , Giarnetti Alessio , Meloni Davide , Singh Masoom 
Published: August 2023

AbstractAfter the landmark discovery of non-zero$$\theta _{13}$$θ13by the modern reactor experiments, unprecedented precision on neutrino mass-mixing parameters has been achieved over the past decade. This has set the stage for the discovery of leptonic CP violation (LCPV) at high confidence level in the next-generation long-baseline neutrino oscillation experiments. In this work, we explore in detail the possible complementarity among the on-axis DUNE and off-axis T2HK experiments to enhance the sensitivity to LCPV suppressing the$$\theta _{23}-\delta _{\textrm{CP}}$$θ23-δCPdegeneracy. We find that none of these experiments individually can achieve the milestone of 3$$\sigma $$σLCPV for at least 75% choices of$$\delta _{\textrm{CP}}$$δCPin its entire range of$$[-180^{\circ }, 180^{\circ }]$$[-180∘,180∘], with their nominal exposures and systematic uncertainties. However, their combination can attain the same for all values of$$\theta _{23}$$θ23with only half of their nominal exposures. We observe that the proposed T2HKK setup in combination with DUNE can further increase the CP coverage to more than 80% with only half of their nominal exposures. We study in detail how the coverage in$$\delta _{\textrm{CP}}$$δCPfor$$\ge $$≥3$$\sigma $$σLCPV depends on the choice of$$\theta _{23}$$θ23, exposure, optimal runtime in neutrino and antineutrino modes, and systematic uncertainties in these experiments in isolation and combination. We find that with an improved systematic uncertainty of 2.7% in appearance mode, the standalone T2HK setup can provide a CP coverage of around 75% for all values of$$\theta _{23}$$θ23. We also discuss the pivotal role of intrinsic, extrinsic, and total CP asymmetries in the appearance channel and extrinsic CP asymmetries in the disappearance channel while analyzing our results.
On Human-like Biases in Convolutional Neural Networks for the Perception of Slant from Texture
Authors: Wang Yuanhao , Zhang Qian , Aubuchon Celine , Kemp Jovan , Domini Fulvio , Tompkin James 
Published: August 2023

Depth estimation is fundamental to 3D perception, and humans are known to have biased estimates of depth. This study investigates whether convolutional neural networks (CNNs) can be biased when predicting the sign of curvature and depth of surfaces of textured surfaces under different viewing conditions (field of view) and surface parameters (slant and texture irregularity). This hypothesis is drawn from the idea that texture gradients described by local neighborhoods—a cue identified in human vision literature—are also representable within convolutional neural networks. To this end, we trained both unsupervised and supervised CNN models on the renderings of slanted surfaces with random Polka dot patterns and analyzed their internal latent representations. The results show that the unsupervised models have similar prediction biases as humans across all experiments, while supervised CNN models do not exhibit similar biases. The latent spaces of the unsupervised models can be linearly separated into axes representing field of view and optical slant. For supervised models, this ability varies substantially with model architecture and the kind of supervision (continuous slant vs. sign of slant). Even though this study says nothing of any shared mechanism, these findings suggest that unsupervised CNN models can share similar predictions to the human visual system. Code: github.com/brownvc/Slant-CNN-Biases.
Hugo Grotius’s De iure belli ac pacis: A Report on the Worldwide Census of the 1650 Edition
Authors: Cleary Matthew , Corredera Edward Jones , Dufour Pablo Nicolas , Nathan Jonathan , Salerno Emanuele , Somos Mark 
Published: August 2023

Abstract
This note studies the 1650 edition of Hugo Grotius’s De iure belli ac pacis. Using online and card catalogues, we have located eighty-nine copies, thirty-seven of which we examined in person, with an additional six fully digitised copies online. We hope that this research note on the preliminary results will generate greater interest in this unduly neglected edition. The note shows how, despite the connection established in the history of seventeenth-century politics that emphasized the ties between Grotius and the Peace of Westphalia, the reception of Grotius’s 1650 edition bore no relation to the debates at Osnabrück and Münster. However, this is an influential edition, cherished by collectors and authors. According to our findings, it would be reproduced in a number of later reprints.
‘Holding Fast to the Heritage of Freedom’: the Grotian Moment(s) of the Universal Declaration of Human Rights and the Early United Nations (1941–1949)
Authors: Quiroga-Villamarín Daniel R. 
Published: August 2023

Abstract
As our contemporary international order seems to come apart at its seams in the trenches of Eastern Europe, many observers have sought solace in the promises made by the historical crucible in which this order was forged. It was, after all, in the aftermath of a previous global conflagration that a planetary constellation of statespeople attempted to create an architecture that would save ‘succeeding generations from the scourge of war’ under the aegis of the ‘United Nations Organization’ (uno). In hindsight, it is easy to look at the years that led to the creation of this international institution—and the proclamation of the Universal Declaration of Human Rights (udhr) of 1948, one of its central pillars—as a decisive ‘Grotian moment,’ insofar as it promised a new age for international ordering. And yet, the historical record shows that those contemporary to the making of the uno and the udhr were less certain about the ‘Grotianness’ of the moment they were living. In this sense, I argue that the plural legacies of the years 1941–1948 have been contested and disputed from the outset. In this contribution I think with, and perhaps against, the notion of ‘Grotian moments’ to interrogate how a narrative of the udhr as a watershed period for secularized individual rights came to eclipse another account of the udhr, which highlighted the centrality of collective welfare for the post-war settlement.
Sexual Orientation and the Criminalisation of Private Consensual Sexual Acts Between Adults of the Same Gender
Authors: Ssenyonjo Manisuli 
Published: August 2023

Abstract
As of September 2023, consensual same-sex sexual acts between adults (for both men and women) in private were criminalised in a total of 67 United Nations (UN) member States. Most of these States were in Africa, a continent of more than 1.4 billion people, where more than 30 out of Africa Union’s 55 States criminalised consensual same-sex sexual acts between adults in private. The justification advanced in favour of criminalisation is that non-heterosexual sexual acts do not conform to the moral, cultural or religious views of a section of society. In some States, consensual same-sex sexual acts between adults in private were punishable by a maximum penalty of death or long prison sentences. The African Charter on Human and Peoples’ Rights (the Charter) and several protocols adopted under the Charter do not prohibit explicitly discrimination based on real or perceived sexual orientation, gender identity and sexual characteristics. Thus, sexual orientation has remained on the margins of the African regional human rights system and has also remained largely outside the consideration of the African Commission (and the African Court) on Human and Peoples’ Rights, the limited jurisprudence is mainly between negative and retrogressive. This article examines the criminalisation of private, consensual same-sex relations, sexual or affective, between adult persons of the same gender or sex in Africa with particular reference to Uganda’s Anti-Homosexuality Act 2023 and its impact on human rights including respect for life, privacy, human dignity, integrity, liberty and security of the person, equality and non-discrimination, health, as well as freedom of association, expression and peaceful assembly.