bluuebunny/crossref_metadata_2025_split huggingface dataset:
MMP-2/9 inhibition modulates sharp wave abundance, inhibitory proteoglycan sulfation, and fear memory in juvenile zebrafish: relevance to affective disorders
Authors: Blanco I. , Deasy S. , Amontree Matthew , Gabriel M. , Caccavano A. , Vicini S. , Glasgow E. , Conant K 
Published: February 2025

AbstractSharp wave ripple (SWR) events, present in diverse species, spontaneously occur in the hippocampus during quiescent restfulness and slow-wave sleep. SWRs comprise a negative deflection, the sharp wave (SW) event with an often-superimposed ripple (R) and are the neural correlates of memory consolidation and recall. The Anterodorsolateral lobe (ADL) (zebrafish hippocampal homologue) exhibits SW and SWR events, and since SWs initiate SWRs, their abundance typically shows the same directionality. In previous work, we observed matrix metalloproteinase-9 (MMP-9)-dependent effects on depression-relevant behaviors, perineuronal net (PNN) levels, and SWR abundance in the adult rodent hippocampus. Here, we investigate MMP-2/9-dependent effects on biochemical, behavioral, and neurophysiological endpoints in juvenile zebrafish and zebrafish at the transition from the late juvenile period to early adulthood. With MMP-2/9 inhibition, juvenile zebrafish showed reduced SW amplitude and abundance together with increased fear memory retention and reduced sociability. Juvenile zebrafish also showed an increased percentage of longer-duration SW events. Except for a reduction in SW amplitude, these changes were not observed at the transition from late juvenile to early adulthood. These changes were accompanied by increased levels of chondroitin sulfate (CS) proteoglycan 4-O-sulfation, which modulates PNNs and excitatory-to-inhibitory (E/I) balance. Discontinuation of MMP-2/9 inhibition in juvenile zebrafish normalized deficits in ADL SW abundance and sociability. Together, these findings show that MMP-2/9 significantly influences E/I balance and learning and memory during the highly plastic juvenile period in zebrafish. Findings also have relevance to an emerging appreciation of PNN changes that may contribute to altered neuronal oscillations and mood or cognition.
Nonlinear breathers with crystalline symmetries
Authors: Schindler Frank , Bulchandani Vir B. , Benalcazar Wladimir A. 
Published: February 2025

Nonlinear lattice models can support “discrete breather” excitations that stay localized in space for all time. By contrast, the localized Wannier states of linear lattice models are dynamically unstable. Nevertheless, symmetric and exponentially localized Wannier states are a central tool in the classification of band structures with crystalline symmetries. Moreover, the quantized transport observed in nonlinear Thouless pumps relies on the fact that—at least in a specific model—discrete breathers recover Wannier states in the limit of vanishing nonlinearity. Motivated by these observations, we investigate the correspondence between nonlinear breathers and exponentially localized Wannier states for a family of discrete nonlinear Schrödinger equations with crystalline symmetries. We develop a formalism to analytically predict the breathers' spectrum, center of mass and symmetry data, and apply this to nonlinear generalizations of the Su-Schrieffer-Heeger chain and the breathing kagome lattice.

Published by the American Physical Society
2025
Multi-Fidelity Optimization of Turbulence in a Gas Turbine Combustor Simulator
Authors: Miklaszewski Jennifer , Folk Masha , Hamlington Peter 
Published: February 2025

Abstract
Combustor turbulence in a gas turbine engine greatly influences the efficiency of the downstream high pressure turbine stage. Here we use a multi-fidelity computational optimization methodology to modify the geometry of a non-reacting combustor simulator such that turbulence properties are optimized at the combustor-turbine interface. We modify the size, orientation, and positioning of the primary and dilution jets to minimize turbulence intensity at the combustor exit while demonstrating negligible or favorable changes to the pressure loss and mixing characteristics of the combustor. The optimization is performed using a machine learning surrogate-assisted genetic algorithm coupled with large eddy simulations (LES) and Reynolds-averaged Navier Stokes (RANS) simulations. The optimization is performed in three phases: (i) we develop a continuously-learning artificial neural network surrogate model, (ii) we perform a stochastic optimization with RANS simulations to narrow the parameter space, and (iii) we perform a stochastic optimization with a coarse-grid LES to identify the optimal solution. Using this approach, we are able to achieve a 5.35% reduction in turbulence intensity and a 0.42% reduction in pressure loss while maintaining good mixing uniformity at the combustor exit. These changes are enabled primarily by changing the aspect ratio and diameter of the primary zone and dilution jets, as well as the chute height and spacing of the primary zone jets. This successful demonstration of multi-fidelity optimization in the combustor simulator can be extended in the future to the design of improved gas turbine combustors.
Irregular and regular honeycomb lattice structures: Effective properties and design perspectives
Authors: Kumar Anil , Jain Atul , DasGupta Anirvan 
Published: February 2025

Abstract
A unified approach to determine the effective elastic properties of irregular and regular honeycomb lattice structures is presented. A micromechanics model of a lattice, based on the fundamental periodic element, is developed using Castigliano's second theorem to obtain a homogenized strain energy density function that yields all elastic properties of the lattice. The lattice geometry, comprising uniform slender beam elements, is specified by six lattice parameters for irregular lattices and four lattice parameters for regular lattices. These parameters generate Honeycomb (Hc) or Re-entrant Honeycomb (RHc) structures with different symmetry properties, which can cater to different design requirements. A comprehensive validation, including comparison with available analytical and full Finite Element (FE) results for different geometries and dimensions, confirms the accuracy of the proposed approach. The influence of the geometric parameters on the effective lattice properties is clearly revealed, which leads to some novel design insights. The existence of continuous and accidental L4 symmetry axis in tuned Hc and RHc lattices (including irregular ones) is brought out for the first time from this analysis. Interestingly, it is observed that high auxeticity coincides with low shear modulus, contrary to the existing postulate of high auxeticity implies high shear stiffness. It is also shown that auxeticity is a directional property in RHc lattice structures.
Hybrid Algorithm Approach for driving Distribution Static Compensator in Multiple Renewable Energy Systems
Authors: Suryawanshi Vidhyavati , Gupta Surbhi 
Published: February 2025

Abstract
There has been a recent drive towards integration of the renewable energy resources to the main grid to improve the environmental aspects in the energy generation sector. The integration brings about stability and quality issues that needs to be handled in order to achieve smooth operation at the load end. This involves issues likes voltage sags, swells, and harmonic distortions which are the key focused area in our research. The Distribution Static Compensators (DSTATCOMs) is being used in this paper for a four-machine system integrated with multiple renewable energy resources like solar, wind and fuel cell in order to enhance power quality issues at the loading end. The integration of sophisticated control mechanisms, such as neural networks (NNs) and metaheuristic algorithms like the BAT Optimization Algorithm (NN_BAT) was analyzed for performance of system dynamics under disturbances. The voltage sag and swell conditions were created in the different phases of 3 phase line. It was found that adaptive and predictive adjustments to the electrical network's dynamic conditions, ensured a THD% of 1.22 % and 1.72 % in line voltage and current respectively when voltage swell occurred. Also, when the system was subjected to sag in voltage the THD% was 1.29 % and 1.86 % for voltage and current respectively. It was found that hybrid strategy NN_BAT consistently performs better, achieving lower THD percentages in both voltage and current which indicates a more effective control in mitigating distortions and maintaining power quality.
The influences of the rotor waviness on the hydrodynamic characteristics of gas porous bearings with mixed CFD boundary conditions
Authors: Xia Peng , Liu Jiabao , Song Wenlong , Huang Zhongqiang , Yang Hao , Ma Wensheng , Guo Yanling 
Published: February 2025

Abstract
Manufacturing errors impacted the gas porous bearing's performance, particularly the waviness on the rotor surface that repeatedly squeezed the gas film during rotation. This study investigated the effects of waviness errors using a novel mixed computational fluid dynamics boundary condition that combined steady circumferential motion with transient radial motion. The mixed boundary condition was validated against numerical results. A transient CFD model was developed for gas porous bearings with rotor surface waviness. The transient squeezing effects from the rotating waviness significantly influenced both the hydrostatic and hydrodynamic performance of the bearing. By implementing periodic sinusoidal waviness, the effects of eccentricity, waviness amplitude, waviness number, rotor speed and supply pressure on the performances of the gas porous bearing were investigated.
Enhancement in Hydrodynamic Performance of a Quarter-Circular Breakwater Using a Porous Shield
Authors: Venkateswarlu Valliboina , Vijay K. G. , Sannasiraj Sannasi Annamalaisamy 
Published: February 2025

Abstract
The study evaluates the hydrodynamic performance of quarter-circular breakwaters (QCB) with various types of porous shields (say retrofits) under incident waves. The QCB with (i) vertical shield, (ii) seaside quarter-circular retrofit (QCR), (iii) shore side QCR, and (iv) partial rectangular retrofit (PRR) are proposed to enhance the performance of QCB. The effect of porous shields is analyzed using the quadratic pressure drop condition and dual boundary element method (DBEM) under the framework of linearized potential flow theory. Study results are validated with the available results reported by authors after some numerical modifications. The effect of shield porosity, and wave height on the reflection, transmission, energy loss, and vertical and horizontal forces on QCB and shield are reported as a function of relative water depth. A comparative study is performed among all the proposed breakwaters to identify an effective configuration against the incident waves. Around 39%, 30%, 31%, and 56% reduction of wave transmission is obtained for QCB with vertical shield, seaside, shoreside QCR, and PRR respectively, when compared with QCB alone for kh=1. The wave transmission KT=0.16 and energy loss KL=0.95 are obtained when kh=2 with the addition of the PRR for a QCB, which is observed as an effective porous shield against the incident waves when compared with the other types of shields. The 10%-20% retrofit porosity is recommended with clear spacing b/h=0.9 and the QCB radius of R2/h=0.7 for the effective distribution of the scattering coefficients against the incident waves.
Helping teaching assistants build confidence and community through reciprocal peer observations: a no-budget, low-barrier approach
Authors: Debets Cassandra , Hay Tristyn , Barker Megan K. 
Published: February 2025

ABSTRACT

Teaching assistants (TAs) are incredibly important in our teaching but are often under-supported in their roles—particularly in large courses, with large teams. Depending on instructor workload and TA contract hours, it can be challenging to support the professional development of these key members of the teaching team. To help our TAs develop their teaching and engage in a community of practice, we implemented a reciprocal peer observation. By observing each others’ tutorials in a structured way, we promoted a sense of community and collaborative learning among the TAs with only a small investment of time by instructors. We structured these peer visits using COPUS-TA, an observational tool that guides their tutorial visit and feedback conversations. From this process, our TAs increased their sense of confidence and community. This is a relatively simple approach to give TAs professional development and connection to their peers, embedded directly within a large-enrollment undergraduate course.
Passage-attenuated Powassan virus LI9P protects mice from lethal LI9 challenge and links envelope residue D308 to neurovirulence
Authors: Himmler Grace E. , Mladinich Megan C. , Conde Jonas N. , Gorbunova Elena E. , Lindner Marissa R. , Kim Hwan Keun , Mackow Erich R. 
Published: February 2025

ABSTRACT

Powassan virus (POWV) is an emergent tick-borne flavivirus that causes lethal encephalitic disease and chronic neurologic deficits in surviving patients. POWV-LI9 is a tick-derived isolate that causes neurovirulent disease and age-dependent lethality in mice. Serial passage of VeroE6 cells infected with LI9 resulted in eight amino acid changes in a POWV strain LI9P. LI9P fails to cause neurological sequelae, or lethality in C57BL/6 mice yet elicits neutralizing POWV antibody responses and protects mice from lethal LI9 challenge. Analysis revealed that LI9, but not LI9P, is present at high levels in the CNS, suggesting that LI9P is restricted from neuroinvasion or CNS replication. LI9 and LI9P are distinguished by a D308N envelope change within a domain associated with cell attachment. We evaluated the roles of Env-Domain III residue changes in LI9 virulence and LI9P attenuation using recombinant POWVs (recPOWVs) generated by reverse genetics. Remarkably, mutating D308N in LI9 completely abolished viral lethality and neuroinvasion in 50-week-old mice, reflecting the avirulent phenotype of LI9P. Analysis of the reciprocal N308D change in LI9P only partially restored neuroinvasion and lethality to the LI9P-N308D mutant, indicating that further LI9P residue changes contribute to LI9P attenuation. Consistent with differences in neuroinvasion, we found that rapid LI9P RNA synthesis and corresponding early IFN induction may contribute to LI9P clearance. Collectively, these findings define D308 as a determinant of POWV neuroinvasion and lethality, suggest potential mechanisms for restricted LI9P CNS entry, and reveal passage-attenuated LI9P as a candidate POWV vaccine platform.

IMPORTANCE
Powassan virus (POWV) infection causes a 10% lethal encephalitis, resulting in chronic neurological symptoms in half of survivors. POWV is transmitted in as short as 15 min following tick attachment, demonstrating the need for the development of POWV vaccines and therapeutics. Mechanisms of POWV neurovirulence remain to be defined to inform vaccine and therapeutic design. Cell culture passage has successfully been used to generate live-attenuated flavivirus vaccines. Accordingly, we serially passaged POWV LI9-infected VeroE6 cells and isolated an attenuated POWV strain, LI9P, that fails to cause neurologic sequelae or murine lethality. LI9P elicits neutralizing antibody responses, protects mice from a lethal WT POWV challenge, and is a potential POWV vaccine. Analysis of attenuating mutations in LI9P revealed that changing envelope residue D308N alone in LI9 prevents POWV neurovirulence and lethality in immunocompetent mice. Altogether, this study defines viral determinants of POWV pathogenesis and attenuating mutations that inform the development of live-attenuated POWV vaccines.
Essential genes encoded by the mating-type locus of the human fungal pathogen
Cryptococcus neoformans
Authors: Bian Zhuyun , Xu Ziyan , Peer Anushka , Choi Yeseul , Priest Shelby J. , Akritidou Konstantina , Dasgupta Ananya , Dahlmann Tim A. , Kück Ulrich , Nowrousian Minou , Sachs Matthew S. , Sun Sheng , Heitman Joseph 
Published: February 2025

ABSTRACT

Fungal sexual reproduction is controlled by the mating-type (
MAT
) locus. In contrast to a majority of species in the phylum Basidiomycota that have tetrapolar mating-type systems, the opportunistic human pathogen
Cryptococcus neoformans
employs a bipolar mating-type system, with two mating types (
a
and α) determined by a single
MAT
locus that is unusually large (~120 kb) and contains more than 20 genes. While several
MAT
genes are associated with mating and sexual development, others control conserved cellular processes (e.g., cargo transport and protein synthesis), of which five (
MYO2
,
PRT1
,
RPL22
,
RPL39
, and
RPO41
) have been hypothesized to be essential. In this study, through genetic analysis involving sporulation of heterozygous diploid deletion mutants, as well as in some cases construction and analyses of conditional expression alleles of these genes, we confirmed that with the exception of
MYO2
, both alleles of the other four
MAT
genes are indeed essential for cell viability. We further showed that while
MYO2
is not essential, its function is critical for infectious spore production, faithful cytokinesis, adaptation for growth at high temperature, and pathogenicity
in vivo
. Our results demonstrate the presence of essential genes in the
MAT
locus that are divergent between cells of opposite mating types. We discuss possible mechanisms to maintain functional alleles of these essential genes in a rapidly evolving genomic region in the context of fungal sexual reproduction and mating-type evolution.

IMPORTANCE

Sexual reproduction is essential for long-term evolutionary success. Fungal cell-type identity is governed by the
MAT
locus, which is typically rapidly evolving and highly divergent between different mating types. In this study, we show that the
a
and α alleles of four genes encoded in the
MAT
locus of the opportunistic human fungal pathogen
C. neoformans
are essential. We demonstrate that a fifth gene,
MYO2
, which had been predicted to be essential, is in fact dispensable for cell viability. However, a functional
MYO2
allele is important for cytokinesis and fungal pathogenicity. Our study highlights the need for careful genetic analyses in determining essential genes, which is complementary to high-throughput approaches. Additionally, the presence of essential genes in the
MAT
locus of
C. neoformans
provides insights into the function, maintenance, and evolution of these fast-evolving genomic regions.
Viral protease binds to nucleosomal DNA and cleaves nuclear cGAS that attenuates type I interferon
Authors: Wu Lei , Yan Ya , Yuan Ye , Zhao Zhenchao , Qu Weiyu , Huang Xiangyu , Wang Haiwei , Li Pingwei , Li Xin 
Published: February 2025

ABSTRACT

Nuclear cyclic GMP-AMP synthetase (cGAS) binds to nucleosome with high affinity to prevent its activation by self-DNA. Upon stimulation with double-stranded DNA, cGAS is activated and translocates from the nucleus to the cytoplasm, guided by its N-terminal domain. However, it remains unclear whether viruses can hijack cGAS translocation and regulate its activation. Here, we discovered that the protease 3C of picornavirus Seneca Valley virus (SVV) translocates from the cytoplasm to the nucleus upon viral infection and binds to nuclear DNA. Protease 3C specifically cleaves histone H2A while leaving other histone proteins unaffected. Additionally, DNA binding enhances the protease 3C’s ability to cleave nuclear cGAS, leading to its retention in the nucleus. This, in turn, suppresses the induction of type I interferon (IFN-I) following poly(dA:dT) stimulation. These findings reveal a novel mechanism by which a viral protease binds nuclear DNA, cleaves nuclear cGAS and histone H2A, and thereby mislocalizes cGAS, facilitating immune evasion.

IMPORTANCE
Cyclic GMP-AMP synthetase (cGAS) is robustly expressed in the nucleus and tightly tethered by chromatin to prevent its activation with self-DNA. During stimulation or infection, nuclear cGAS is activated and translocates from the nucleus to the cytoplasm. However, the viral strategies specifically targeting nuclear cGAS are completely unexplored. Here, we discovered that protease 3C of Seneca Valley virus translocates from the cytoplasm to the nucleus upon viral infection, binds to nuclear DNA, and specifically cleaves H2A. Furthermore, DNA binding to 3C enhances the cleavage of nuclear cGAS within its N-terminal domain. The hindrance of cGAS translocation from the nucleus to the cytoplasm results in the suppression of IFN-I induction and leads to immune evasion. This work uncovers a unique mechanism wherein a viral protease binds to nuclear DNA and cleaves nuclear cGAS and histone H2A, leading to viral evasion of cGAS-mediated immune restriction.
Toward the consensus of definitions for the phenomena of antifungal tolerance and persistence in filamentous fungi
Authors: Amich Jorge , Bromley Michael , Goldman Gustavo H. , Valero Clara 
Published: February 2025

ABSTRACT

Antifungal drug tolerance and persistence are being increasingly recognized in fungal pathogens. Accordingly, more and more research is being carried out to characterize and understand these phenomena. However, the terminology and methodology employed in the fungal community lack consensus, particularly for filamentous fungi, as they present further complexities when compared to single-celled microorganisms. Hence, with the aim to ensure consistency in the literature, in this Perspective article, we propose tailored definitions for tolerance and persistence in filamentous fungi and suggest methods to detect and investigate these phenomena in the laboratory.