bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Experiential Learning Opportunity in Norway: Computation for Bioengineering and Mechanical Engineering Students
Authors: Clarin Julia , Vargas Ana I. , Jennings Turner , Salinas Samuel D. , Amini Reza , Tjiptowidjojo Yustianto , Yelle Benjamin , Jacobsen Mojgan Y. , Eide Trine , Udberg-Helle Cecilie , Olsen Torjer A. , Crossen Jonathan , Prot Victorien , Skallerud Bjørn , Amini Rouzbeh 
Published: February 2024

Abstract
The global learning initiative at Northeastern University is focused on fostering intercultural communication skills. The Dialogue of Civilization (DOC) program serves as a mechanism to achieve such a goal by offering faculty-led international experiences. In this paper, we have presented a detailed account of a DOC program that took place in Norway. The primary objective of the program was to teach mechanical engineering and bio-engineering students computational skills while stimulating critical thinking about the cultural and social aspects of technology and engineering in Norway. The program focused on two courses: a technical course and a special topics course. The technical course introduced students to finite element analysis, with practical applications and site visits in Norway to enhance experiential learning. In the special topics course, the interplay between modern technologies, like green energy, state policies, and the rights and traditions of the indigenous Sámi people was explored. The course highlighted both the progressive social policies in Norway and the historical discrimination against the Sámi. Student feedback was positive and experiential learning components such as guest lectures and site visits were particularly appreciated. Additional surveys showed that students' self-confidence was higher following the DOC program. In addition, female-identifying students had higher confidence in their future success after completion of this program as compared to their male-identifying counterparts. Our paper is expected to serve as a resource for educators seeking to integrate technical education with intercultural experiences and discussions on social and cultural impacts in engineering.
The BIORES-21 Survey: Insights Into Remote and Online Education in Biomechanics and Mechanobiology
Authors: Mukherjee Debanjan , Lai Victor , Huang Zhongping , Singh Anita 
Published: February 2024

Abstract
The COVID-19 pandemic necessitated mainstream adoption of online and remote learning approaches, which were highly advantageous yet challenging in many ways. The online modality, while teaching biomedical engineering-related topics in the areas of biomechanics, mechanobiology, and biomedical sciences, further added to the complexity faced by the faculty and students. Both the benefits and the challenges have not been explored systematically by juxtaposing experiences and reflections of both the faculty and students. Motivated by this need, we designed and conducted a systematic survey named BIORES-21, targeted toward the broader bio-engineering community. Survey responses and our inferences from survey findings cumulatively offer insight into the role of employed teaching/learning technology and challenges associated with student engagement. Survey data also provided insights on what worked and what did not, potential avenues to address some underlying challenges, and key beneficial aspects such as integration of technology and their role in improving remote teaching/learning experiences. Overall, the data presented summarize the key benefits and challenges of online learning that emerged from the experiences during the pandemic, which is valuable for the continuation of online learning techniques as in-person education operations resumed broadly across institutions, and some form of online learning seems likely to sustain and grow in the near future.
Computational Pulsatile Flow and Efficiency Analysis of Biocompatible Microfluidic Artificial Lungs for Different Fiber Configurations
Authors: Asiltürk Ahmet Yusuf , Atalık Kunt 
Published: February 2024

Abstract
Average-sized microfluidic artificial lungs consisting of rows and columns of fiber bundles with different column to row aspect ratios (AR) are numerically analyzed for flow characteristics, maximum gas transfer performance, minimum pressure drop, and proper wall shear stress (WSS) values in terms of biocompatibility. The flow is fully laminar and assumed to be incompressible and Newtonian. The transport analysis is performed using a combined convection-diffusion model, and the numerical simulations are carried out with the finite element method. The inlet volumetric flow is modeled as a sinusoidal wave function to simulate the cardiac cycle and its effect on the device performance. The model is first validated with experimental studies in steady-state condition and compared with existing correlations for transient conditions. Then, the validated model is used for a parametric study in both steady and pulsatile flow conditions. The results show that increasing the aspect ratio in fiber configuration leads to converging gas transfer, higher pressure drop, and higher WSS. While determining the optimum configuration, the acceptable shear stress levels play a decisive role to ensure biocompatibility. Also, it is observed that the steady analysis underestimates the gas transfer for higher aspect ratios.
Operational Strategies of Two-Spool Micro Gas Turbine With Alternative Fuels: A Performance Assessment
Authors: Gaitanis Aggelos , Tiwari Ravi Nath , De Paepe Ward , Ferrari Mario Luigi , Contino Francesco , Breuhaus Peter 
Published: February 2024

Abstract
Micro gas turbines (mGT) have not yet succeeded in conquering the small-scale combined heat and power (CHP) market. One reason is that their electrical efficiency is not high enough to maintain a cost-effective operation. A two-shaft intercooled mGT has the potential to meet the current market demand. This technology maintains a high electrical efficiency even at part-load and coupled with its fuel-flexible combustion chamber, it is an ideal candidate for CHP concepts in a renewable future. In this paper, performance analysis on two-spool mGT is carried out with various fuel blends. Attention is given to the low-pressure and high-pressure compressors and the variation of surge margin by adding hydrogen and syngas. Two control strategies for the mGT are adopted. In the first scenario, the two shafts have equal rotational speeds while in the second, the speeds are controlled independently. As the engine is operated at equal speeds, the maximum performance with 100 vol. % of syngas is observed at 85% of the nominal load while 100 vol. % of hydrogen shows maximum efficiency at a load of 63.7%. At electric power lower than 60% and for high amounts of syngas in natural gas, the low-pressure compressor (LPC) operates closely to surge line. In the second scenario, the efficiency increases as the load decreases and the LPC runs in an efficient and safe operating region. Additionally, the amount of nitrogen in syngas affects the part-load performance of the two-spool mGT.
Multi-Fidelity Design of Porous Microstructures for Thermofluidic Applications
Authors: Eweis-Labolle Jonathan Tammer , Zhao Chuanning , Won Yoonjin , Bostanabad Ramin 
Published: February 2024

Abstract
As modern electronic devices are increasingly miniaturized and integrated, their performance relies more heavily on effective thermal management. In this regard, two-phase cooling methods which capitalize on thin-film evaporation atop structured porous surfaces are emerging as potential solutions. In such porous structures, the optimum heat dissipation capacity relies on two competing objectives that depend on mass and heat transfer. Optimizing these objectives for effective thermal management is challenging due to the simulation costs and the high dimensionality of the design space which is often a voxelated microstructure representation that must also be manufacturable. We address these challenges by developing a data-driven framework for designing optimal porous microstructures for cooling applications. In our framework, we leverage spectral density functions to encode the design space via a handful of interpretable variables and, in turn, efficiently search it. We develop physics-based formulas to simulate the thermofluidic properties and assess the feasibility of candidate designs based on offline image-based analyses. To decrease the reliance on expensive simulations, we generate multi-fidelity data and build emulators to find Pareto-optimal designs. We apply our approach to a canonical problem on evaporator wick design and obtain fin-like topologies in the optimal microstructures which are also characteristics often observed in industrial applications.
Understanding Thermo-Fluidic Characteristics of a Triangular Solar Air Heater Having W-Shaped Rib-Turbulators: A 3D Computational Fluid Dynamics Study
Authors: Mahanand Yadaba , Senapati Jnana Ranjan 
Published: February 2024

Abstract
A solar air heater duct with W-shaped rib-turbulators on the collector plate disrupts the flow that enhances the heat transfer from the hot surface due to turbulence in the flow. In this analysis, a three-dimensional fluid domain of the W-shaped ribbed triangular solar air heater duct is numerically simulated to analyze the impact of roughness and flow parameters on thermo-fluidic performance; also, the turbulence behavior near the rib surfaces is presented. Roughness variables like non-dimensional pitch and non-dimensional height varied from 6.23 to 17.85 and 0.04 to 0.053, respectively. In contrast, the flow parameter, like the Reynolds number, is kept in the range of 4×103 to 18×103. A maximal performance evaluation criterion of 1.51 is attained for the W-shape ribs with a non-dimensional pitch of 7.14 and a non-dimensional height of 0.047 at a Reynolds number of 15×103. For the W-shaped rib-turbulators with a non-dimensional pitch of 7.14 and a non-dimensional height of 0.047 at a Reynolds number of 15×103, the maximum heat transfer is found to be 1.826 times that of a smooth duct. Accordingly, in the parametric range, the maximum friction penalty is 2.63 times that of a smooth duct. Some useful correlations are established considering the computational data.
Activation of CzcS/CzcR during zinc excess regulates copper tolerance and pyochelin biosynthesis of
Pseudomonas aeruginosa
Authors: Li Ting , Cao Huiluo , Duan Cheng , Chen Shuzhen , Xu Zeling 
Published: February 2024

ABSTRACT

Zinc is an important transition metal that is essential for numerous physiological processes while excessive zinc is cytotoxic.
Pseudomonas aeruginosa
is a ubiquitous opportunistic human pathogen equipped with an exquisite zinc homeostatic system, and the two-component system CzcS/CzcR plays a key role in zinc detoxification. Although an increasing number of studies have shown the versatility of CzcS/CzcR, its physiological functions are still not fully understood. In this study, transcriptome analysis was performed, which revealed that CzcS/CzcR is silenced in the absence of the zinc signal but modulates global gene expression when the pathogen encounters zinc excess. CzcR was demonstrated to positively regulate the copper tolerance gene
ptrA
and negatively regulate the pyochelin biosynthesis regulatory gene
pchR
through direct binding to their promoters. Remarkably, the upregulation of
ptrA
and downregulation of
pchR
were shown to rescue the impaired capacity of copper tolerance and prevent pyochelin overproduction, respectively, caused by zinc excess. This study not only advances our understanding of the regulatory spectrum of CzcS/CzcR but also provides new insights into stress adaptation mediated by two-component systems in bacteria to balance the cellular processes that are disturbed by their signals.

IMPORTANCE

CzcS/CzcR is a two-component system that has been found to modulate zinc homeostasis, quorum sensing, and antibiotic resistance in
Pseudomonas aeruginosa
. To fully understand the physiological functions of CzcS/CzcR, we performed a comparative transcriptome analysis in this study and discovered that CzcS/CzcR controls global gene expression when it is activated during zinc excess. In particular, we demonstrated that CzcS/CzcR is critical for maintaining copper tolerance and iron homeostasis, which are disrupted during zinc excess, by inducing the expression of the copper tolerance gene
ptrA
and repressing the pyochelin biosynthesis genes through
pchR
. This study revealed the global regulatory functions of CzcS/CzcR and described a new and intricate adaptive mechanism in response to zinc excess in
P. aeruginosa
. The findings of this study have important implications for novel anti-infective interventions by incorporating metal-based drugs.
A pleiotropic role of sialidase in the pathogenicity of
Porphyromonas gingivalis
Authors: Pham Christopher , Guo Shuaiqi , Han Xiao , Coleman Laurynn , Sze Ching Wooen , Wang Huizhi , Liu Jun , Li Chunhao 
Published: February 2024

ABSTRACT

As one of the keystone pathogens of periodontitis, the oral bacterium
Porphyromonas gingivalis
produces an array of virulence factors, including a recently identified sialidase (PG0352). Our previous report involving loss-of-function studies indicated that PG0352 plays an important role in the pathophysiology of
P. gingivalis
. However, this report had not been corroborated by gain-of-function studies or substantiated in different
P. gingivalis
strains. To fill these gaps, herein we first confirm the role of PG0352 in cell surface structures (e.g., capsule) and serum resistance using
P. gingivalis
W83 strain through genetic complementation and then recapitulate these studies using
P. gingivalis
ATCC33277 strain. We further investigate the role of PG0352 and its counterpart (PGN1608) in ATCC33277 in cell growth, biofilm formation, neutrophil killing, cell invasion, and
P. gingivalis
-induced inflammation. Our results indicate that PG0352 and PGN1608 are implicated in
P. gingivalis
cell surface structures, hydrophobicity, biofilm formation, resistance to complement and neutrophil killing, and host immune responses. Possible molecular mechanisms involved are also discussed. In summary, this report underscores the importance of sialidases in the pathophysiology of
P. gingivalis
and opens an avenue to elucidate their underlying molecular mechanisms.
Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control
Salmonella enterica
Authors: Acton Luke , Pye Hannah V. , Thilliez Gaëtan , Kolenda Rafał , Matthews Michaela , Turner A. Keith , Yasir Muhammad , Holden Emma , Al-Khanaq Haider , Webber Mark , Adriaenssens Evelien M. , Kingsley Robert A. 
Published: February 2024

ABSTRACT

The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen
Salmonella enterica
. To determine phage host range, a diverse collection of
Enterobacteriaceae
and
Salmonella enterica
was used and genes involved in infection by six SPLA phages were identified using
Salmonella
Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide (LPS), cellulose, and BtuB. Lipopolysaccharide was identified as a susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with
S
. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b which suggested that emergence of LPS mutations in culture with SPLA1a represented collateral sensitivity to SPLA5b. We show that bacteria-phage co-culture with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to single phage co-culture. Identification of host susceptibility and resistance genes and understanding infection dynamics are critical steps in the rationale design of phage cocktails against specific bacterial pathogens.

IMPORTANCE

As antibiotic resistance continues to emerge in bacterial pathogens, bacterial viruses (phage) represent a potential alternative or adjunct to antibiotics. One challenge for their implementation is the predisposition of bacteria to rapidly acquire resistance to phages. We describe a functional genomics approach to identify mechanisms of susceptibility and resistance for newly isolated phages that infect and lyse
Salmonella enterica
and use this information to identify phage combinations that exploit collateral sensitivity, thus increasing efficacy. Collateral sensitivity is a phenomenon where resistance to one class of antibiotics increases sensitivity to a second class of antibiotics. We report a functional genomics approach to rationally design a phage combination with a collateral sensitivity dynamic which resulted in increased efficacy. Considering such evolutionary trade-offs has the potential to manipulate the outcome of phage therapy in favor of resolving infection without selecting for escape mutants and is applicable to other virus-host interactions.
A novel high-throughput microwell outgrowth assay for HIV-infected cells
Authors: Fenton Anthony D. , Archin Nancie , Turner Anne-Marie , Joseph Sarah , Moeser Matthew , Margolis David M. , Browne Edward P. 
Published: February 2024

ABSTRACT

Although antiretroviral therapy (ART) is effective at suppressing HIV replication, a viral reservoir persists that can reseed infection if ART is interrupted. Curing HIV will require elimination or containment of this reservoir, but the size of the HIV reservoir is highly variable between individuals. To evaluate the size of the HIV reservoir, several assays have been developed, including PCR-based assays for viral DNA, the intact proviral DNA assay, and the quantitative viral outgrowth assay (QVOA). QVOA is the gold standard assay for measuring inducible replication-competent proviruses, but this assay is technically challenging and time-consuming. To begin progress toward a more rapid and less laborious tool for quantifying cells infected with replication-competent HIV, we developed the Microwell Outgrowth Assay, in which infected CD4 T cells are co-cultured with an HIV-detecting reporter cell line in a polydimethylsiloxane (PDMS)/polystyrene array of nanoliter-sized wells. Transmission of HIV from infected cells to the reporter cell line induces fluorescent reporter protein expression that is detected by automated scanning across the array. Using this approach, we were able to detect HIV-infected cells from ART-naïve people with HIV (PWH) and from PWH on ART with large reservoirs. Furthermore, we demonstrate that infected cells can be recovered from individual rafts and used to analyze the diversity of viral sequences. Although additional development and optimization will be required for quantifying the reservoir in PWH with small latent reservoirs, this assay may be a useful prototype for microwell assays of infected cells.

IMPORTANCE
Measuring the size of the HIV reservoir in people with HIV (PWH) will be important for determining the impact of HIV cure strategies. However, measuring this reservoir is challenging. We report a new method for quantifying HIV-infected cells that involves culturing cells from PWH in an array of microwells with a cell line that detects HIV infection. We show that this approach can detect rare HIV-infected cells and derive detailed virus sequence information for each infected cell.
Activation of protein kinase receptor (PKR) plays a pro-viral role in mammarenavirus-infected cells
Authors: Witwit Haydar , Khafaji Roaa , Salaniwal Arul , Kim Arthur S. , Cubitt Beatrice , Jackson Nathaniel , Ye Chengjin , Weiss Susan R. , Martinez-Sobrido Luis , de la Torre Juan Carlos 
Published: February 2024

ABSTRACT

Many viruses, including mammarenaviruses, have evolved mechanisms to counteract different components of the host cell innate immunity, which is required to facilitate robust virus multiplication. The double-stranded RNA (dsRNA) sensor protein kinase receptor (PKR) pathway plays a critical role in the cell anti-viral response. Whether PKR can restrict the multiplication of the Old World mammarenavirus lymphocytic choriomeningitis virus (LCMV) and the mechanisms by which LCMV may counteract the anti-viral functions of PKR have not yet been investigated. Here we present evidence that LCMV infection results in very limited levels of PKR activation, but LCMV multiplication is enhanced in the absence of PKR. In contrast, infection with a recombinant LCMV with a mutation affecting the 3′−5′ exonuclease (ExoN) activity of the viral nucleoprotein resulted in robust PKR activation in the absence of detectable levels of dsRNA, which was associated with severely restricted virus multiplication that was alleviated in the absence of PKR. However, pharmacological inhibition of PKR activation resulted in reduced levels of LCMV multiplication. These findings uncovered a complex role of the PKR pathway in LCMV-infected cells involving both pro- and anti-viral activities.

IMPORTANCE
As with many other viruses, the prototypic Old World mammarenavirus LCMV can interfere with the host cell innate immune response to infection, which includes the dsRNA sensor PKR pathway. A detailed understanding of LCMV-PKR interactions can provide novel insights about mammarenavirus-host cell interactions and facilitate the development of effective anti-viral strategies against human pathogenic mammarenaviruses. In the present work, we present evidence that LCMV multiplication is enhanced in PKR-deficient cells, but pharmacological inhibition of PKR activation unexpectedly resulted in severely restricted propagation of LCMV. Likewise, we document a robust PKR activation in LCMV-infected cells in the absence of detectable levels of dsRNA. Our findings have revealed a complex role of the PKR pathway during LCMV infection and uncovered the activation of PKR as a druggable target for the development of anti-viral drugs against human pathogenic mammarenaviruses.