bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applying In Situ Ionic Crosslinking in Bioprinting Using Algae Cells
Authors: Rahman Taieba Tuba , Wood Nathan , Rahman Al Mazedur , Pei Zhijian , Qin Hongmin 
Published: December 2023

Abstract
Bioprinting using algae cells has many potential applications including tissue engineering, environmental engineering, contaminant removal from water, and establishing space habitats. In extrusion-based bioprinting, bioink needs to be crosslinked after being extruded from the nozzle for printed constructs to first achieve and then maintain adequate shape fidelity. Crosslinking methods used in reported studies on algae-contained bioinks include both photo-crosslinking and ionic crosslinking. This paper reports a preliminary study where the coaxial nozzle-based in situ ionic crosslinking method was used in bioprinting of algae cells without additional crosslinking of printed samples for the first time. In comparison with photo-crosslinking, in situ ionic crosslinking can minimize bioink preparation time and complexity, eliminate cells’ exposure to ultraviolet radiation, and reduce the number of post-printing steps. In this preliminary study, the bioink was an alginate solution containing algae (Chlorella vulgaris) cells, and the crosslinking solution was a calcium chloride solution. The coaxial nozzle had two nozzles: inner and outer nozzles. In printing, the bioink was delivered through the outer nozzle while the crosslinking solution was delivered through the inner nozzle. The shape of the printed samples was a square block with dimensions of 30 × 30 × 10 mm. It was observed that, 9 days after printing, the algae cells grew within the printed samples, and the samples could keep their shapes relatively well. Many knowledge gaps exist regarding the effects of input variables in bioprinting of algae cells using this method. This paper discusses future research directions to fill these knowledge gaps.
Numerical Investigation of Nanofluid as a Coolant in a Prismatic Battery for Thermal Management Systems
Authors: Venkateswarlu B. , Kim Sung Chul , Joo Sang Woo , Chavan Santosh 
Published: December 2023

Abstract
This study delves into the realm of numerical investigation of the heat transfer performance of nanofluids as coolants for prismatic batteries. Nanofluids are being employed in battery cooling systems to enhance overall thermal management and ensure the safe operation of batteries, particularly in situations involving high heat generation. In this study, different types of nanofluids were used along with a base fluid of ethylene glycol–water (EG–water 50%). The energy equations consider the effects of viscous dissipation and heat generation. The model generates a set of nonlinear partial differential equations, which can be transformed into ordinary differential equations (ODEs) using appropriate similarity variables. These ODEs are then solved numerically by employing the Runge–Kutta–Fehlberg method along with the shooting method to obtain solutions. The simulations in both 2D and 3D showcase the results for various parameters pertaining to thermal and velocity fields, heat transfer rate, and drag force. The findings reveal that heat generation leads to a staggering increase in temperature of 78.22%. However, using aluminum nanoparticles (NPs) as opposed to copper nanoparticles quickly reduced the battery’s maximum temperature by 9.31%. The exceptional heat generation strengths of CuO–EG and Al2O3–EG nanofluids also resulted in a significant increase in their heat transfer rates of around 40.42% and 42.13%, respectively. Additionally, the aluminum NPs exhibited a more rapid heat transfer rate of 4.06% when compared to the copper nanoparticles. This research contributes to the development of improved cooling strategies for prismatic battery applications, ultimately paving the way for enhanced battery performance, an extended lifespan, and improved safety in a wide range of industries and electric vehicles.
If You Build It, Will They Understand? Considerations for Creating Shared Understanding Through Design Artifacts
Authors: Krishkakumar Sandeep , Letting Cynthia , Soria Zurita Nicolas F. , Menold Jessica 
Published: December 2023

Abstract
Design representations play a pivotal role in the design process. In particular, design representations enable the formation of a shared understanding between team members, enhancing team performance. This paper explores the relationship between design representation modality (low-fidelity prototypes and sketches) and shared understanding among designers during communicative acts between design dyads. A mixed-methods study with 44 participants was conducted to investigate if representation modality affects shared understanding and identifies the factors that shape shared understanding during communication. Quantitative results suggest that low-fidelity prototypes and sketches did not significantly differ in terms of the shared understanding they facilitated within dyads. Qualitative analysis identified four factors at the representation- and actor-level that influence how shared understanding is built between individuals during design communication. This research extends our understanding of the utility of design representations given the needs of communicative contexts; specifically, this work demonstrates that designers must understand the perspectives of listeners during communication to create representations that accurately represent the information that a listener seeks to gain.
An Improved Fractional Moment Maximum Entropy Method With Polynomial Fitting
Authors: Li Gang , Wang Yixuan , Zeng Yan , He Wanxin 
Published: December 2023

Abstract
The moment method is commonly used in reliability analysis, in which the maximum entropy method (MEM) and polynomial fitting (PF) have been widely used due to their advantages in accuracy and efficiency, respectively. In this paper, we propose a novel reliability analysis method by combining MEM and PF. The probability density function is preliminarily estimated using the fractional moment maximum entropy method (FM-MEM), based on which PF is then used to further improve the accuracy. The proposed method can avoid the phenomenon of the negative probability density and function oscillations in PF effectively. Moreover, the order of the exponential polynomial in the FM-MEM is adaptively selected in the preliminary solution calculation process. An iterative process for the number of exponential polynomial terms is also proposed, using the integral of the moment error function and the integrals of the local and global negative probability density as the convergence criteria. Four numerical examples and one engineering example are tested, and the results are compared with those of the Monte Carlo simulation and the classical FM-MEM results, respectively, demonstrating the good performance of the proposed method.
The respiratory enzyme complex Rnf is vital for metabolic adaptation and virulence in
Fusobacterium nucleatum
Authors: Britton Timmie A. , Wu Chenggang , Chen Yi-Wei , Franklin Dana , Chen Yimin , Camacho Martha I. , Luong Truc T. , Das Asis , Ton-That Hung 
Published: December 2023

ABSTRACT

The Gram-negative oral pathobiont
Fusobacterium nucleatum
can traverse to extra-oral sites such as placenta and colon, promoting adverse pregnancy outcomes and colorectal cancer, respectively. How this anaerobe sustains many metabolically changing environments enabling its virulence potential remains unclear. Informed by our genome-wide transposon mutagenesis, we report here that the highly conserved

R
hodobacter

n
itrogen-
f
ixation (Rnf) complex, encoded by the
rnfCDGEAB
gene cluster, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of the Rnf complex via non-polar, in-frame deletion of
rnfC
(Δ
rnfC
) abrogates polymicrobial interaction (or coaggregation) associated with adhesin RadD and biofilm formation. The defect in coaggregation is not due to reduced cell surface of RadD, but rather an increased level of extracellular lysine, which binds RadD and inhibits coaggregation. Indeed, removal of extracellular lysine via washing Δ
rnfC
cells restores coaggregation, while addition of lysine inhibits this process. These phenotypes mirror that of a mutant (Δ
kamA
) that fails to metabolize extracellular lysine. Strikingly, the Δ
rnfC
mutant is defective in ATP production, cell growth, cell morphology, and expression of the enzyme MegL that produces hydrogen sulfide (H
2
S) from cysteine. Targeted metabolic profiling demonstrated that catabolism of many amino acids, including histidine and lysine, is altered in Δ
rnfC
cells, thereby reducing production of ATP and metabolites including H
2
S and butyrate. Most importantly, we show that the Δ
rnfC
mutant is severely attenuated in a mouse model of preterm birth. The indispensable function of Rnf complex in fusobacterial pathogenesis via modulation of bacterial metabolism makes it an attractive target for developing therapeutic intervention.

IMPORTANCE

This paper illuminates the significant question of how the oral commensal
Fusobacterium nucleatum
adapts to the metabolically changing environments of several extra-oral sites such as placenta and colon to promote various diseases as an opportunistic pathogen. We demonstrate here that the highly conserved

R
hodobacter

n
itrogen-
f
ixation complex, commonly known as Rnf complex, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of this Rnf complex causes global defects in polymicrobial interaction, biofilm formation, cell growth and morphology, hydrogen sulfide production, and ATP synthesis. Targeted metabolomic profiling demonstrates that the loss of this respiratory enzyme significantly diminishes catabolism of numerous amino acids, which negatively impacts fusobacterial virulence as tested in a preterm birth model in mice.
Epstein-Barr virus induces germinal center light zone chromatin architecture and promotes survival through enhancer looping at the
BCL2A1
locus
Authors: Dai Joanne , SoRelle Elliott D. , Heckenberg Emma , Song Lingyun , Cable Jana M. , Crawford Gregory E. , Luftig Micah A. 
Published: December 2023

ABSTRACT

Epstein-Barr virus (EBV) is a ubiquitous human virus that promotes B-cell activation and maturation through expression of latency proteins and non-coding RNAs. In this study, we provide evidence that EBV mimics the molecular phenotype of germinal center (GC) B cells. EBV infection of primary human B cells promotes their rapid proliferation and GC dark zone (DZ)-like gene expression profile. Following this transient hyperproliferative period, the activation of NF-κB target genes, including
Bcl2a1
(BFL-1), simulates the transition from the DZ to the T-cell supported light zone (LZ). We previously characterized the regulatory landscape of EBV
+
B cells at the
Bcl2a1
locus defining a key role for the viral EBV nuclear antigen (EBNA) 3A protein in promoting three-dimensional chromatin architecture correlated with BFL-1 expression. Here, we define the global chromatin accessibility of tonsillar B cells and find that naïve and memory B cells have highly similar accessibility profiles that differ substantially from those of DZ and LZ B cells. Notably, multiple regions within the
Bcl2a1
locus are significantly more accessible in DZ and LZ versus naïve and memory subsets. However, we found that BFL-1 upregulation from DZ to LZ correlates with a significant increase in three-dimensional (3-D) chromatin association between accessible upstream enhancer regions and the BFL-1 transcriptional start site. These elements were critical for BFL-1 expression in lymphoblastoid cell lines (LCLs). Moreover, increased BFL-1 expression in LCLs protected against extrinsic apoptosis. Collectively, these results suggest a conserved mechanism underlying BFL-1 upregulation that promotes survival of both LZ and EBV
+
immortalized B cells.

IMPORTANCE

Epstein-Barr virus has evolved with its human host leading to an intimate relationship where infection of antibody-producing B cells mimics the process by which these cells normally recognize foreign antigens and become activated. Virtually everyone in the world is infected by adulthood and controls this virus pushing it into life-long latency. However, immune-suppressed individuals are at high risk for EBV+ cancers. Here, we isolated B cells from tonsils and compare the underlying molecular genetic differences between these cells and those infected with EBV. We find similar regulatory mechanism for expression of an important cellular protein that enables B cells to survive in lymphoid tissue. These findings link an underlying relationship at the molecular level between EBV-infected B cells in vitro with normally activated B cells
in vivo
. Our studies also characterize the role of a key viral control mechanism for B cell survival involved in long-term infection.
Strategies for high cell density cultivation of
Akkermansia muciniphila
and its potential metabolism
Authors: Wu Haiting , Qi Shuhua , Yang Ruixiong , Pan Qihua , Lu Yinghua , Yao Chuanyi , He Ning , Huang Song , Ling Xueping 
Published: December 2023

ABSTRACT

Akkermansia muciniphila
(
A. muciniphila
) has sparked widespread interest as a potential probiotic bacterium with many physiological functions that colonizes the human intestinal tract. The development of its
in vitro
culture is a promising and urgent research direction. Therefore, culture conditions were first optimized, and a significant improvement of cell density of
A. muciniphila
was achieved in a shake flask with 15.0 g/L of glucose, 37.0 g/L of tryptone, and an initial pH of 7.8. A high OD
600
(optical density at 600 nm) value of 13.03 (1.03 × 10
10
CFU/mL) was reached in a 5-L bioreactor by stage pH controlling, which is the highest reported value by use of a sole carbon source (glucose). Analysis of cell characteristics and protein expression showed that the optimized culture did not affect cellular morphology and the expression of the special outer membrane functional protein (Amuc_1100), while remarkably improving cell hydrophobicity, which is beneficial for bacterial colonization of the gut. The pattern of supernatant metabolites indicated that the optimized medium may promote cell reproduction by inducing cells to produce dethiobiotin and strengthen the metabolic pathway of glycerol 3-phosphate by shifting more glyceraldehyde 3-phosphate dehydrogenase toward secretion at the cell surface, thereby improving cell surface hydrophobicity and adhesion to mucin. This study accomplished the high cell density culture of
A. muciniphila
without affecting its biological function, which also provides a more conducive fermentation strategy to enhance cell adhesion and facilitates its colonization in the gut.

IMPORTANCE

Currently, there is significant interest in
Akkermansia muciniphila
as a promising next-generation probiotic, making it a hot topic in scientific research. However, to achieve efficient industrial production, there is an urgent need to develop an
in vitro
culture method to achieve high biomass using low-cost carbon sources such as glucose. This study aims to explore the high-density fermentation strategy of
A. muciniphila
by optimizing the culture process. This study also employs techniques such as LC-MS and RNA-Seq to explain the possible regulatory mechanism of high-density cell growth and increased cell surface hydrophobicity facilitating cell colonization of the gut
in vitro
culture. Overall, this research sheds light on the potential of
A. muciniphila
as a probiotic and provides valuable insights for future industrial production.
Development and application of a nomogram model for the prediction of carbapenem-resistant
Klebsiella pneumoniae
infection in neuro-ICU patients
Authors: Lu Guangyu , Zhang Jingyue , Shi Tian , Liu Yuting , Gao Xianru , Zeng Qingping , Ding Jiali , Chen Juan , Yang Kai , Ma Qiang , Liu Xiaoguang , Ren Chuanli , Yu Hailong , Li Yuping 
Published: December 2023

ABSTRACT

This study aimed to develop and validate a simple-to-use nomogram model to assess the risk of infection caused by carbapenem-resistant
Klebsiella pneumoniae
(CRKP) in neurocritically ill patients. The clinical data of 544 patients with CRKP infection admitted to a neurointensive care unit (neuro-ICU) were retrospectively analyzed. The demographic data, laboratory test results, and clinical characteristics of patients in the neuro-ICU were collected. Subsequently, multivariate regression analysis was used to construct a nomogram to predict the risk of CRKP infection in these patients. The calibration ability, clinical effectiveness, and discriminative ability of the nomogram were evaluated. The incidence of CRKP infection was estimated to be 6.43%, and a majority of bacterial isolates causing the infection were found in sputum (74.3%). Multivariate regression analysis showed that the number of antibiotics of ≥2 [odds ratio (OR): 9.08, 95% confidence interval (CI): 2.78–29.71], undergoing surgery (OR: 3.84, 95% CI: 1.09–13.54), and long neuro-ICU stay (OR: 1.08, 95% CI: 1.01–1.14) were associated with CRKP infection in neurocritically ill patients. The nomogram model demonstrated good calibration and discrimination in both the training and validation sets, with area under the curve values of 0.860 and 0.907, respectively. This study developed and validated a nomogram that combines three easily accessed variables during clinical practice to predict the risk of nosocomial CRKP infection in neuro-ICU patients. The tool demonstrated a good predictive performance and discrimination, which might serve as a useful tool to facilitate early detection and reduction of the CRKP infection risk in neurocritically ill patients.

IMPORTANCE
Patients in neuro-ICU are at a high risk of developing nosocomial CRKP infection owing to complex conditions, critical illness, and frequent invasive procedures. However, studies focused on constructing prediction models for assessing the risk of CRKP infection in neurocritically ill patients are lacking at present. Therefore, this study aims to establish a simple-to-use nomogram for predicting the risk of CRKP infection in patients admitted to the neuro-ICU. Three easily accessed variables were included in the model, including the number of antibiotics used, surgery, and the length of neuro-ICU stay. This nomogram might serve as a useful tool to facilitate early detection and reduction of the CRKP infection risk of neurocritically ill patients.
Evaluation of mycobacteria infection prevalence and optimization of the identification process in North Sardinia, Italy
Authors: Chen Xiang , Sechi Leonardo Antonio , Molicotti Paola 
Published: December 2023

ABSTRACT

Mycobacterium tuberculosis
(MTB) and non-tuberculous mycobacteria (NTM) are the most common pathogens of mycobacterial infection, and their prevalence varies around the world. This study aimed to estimate the prevalence of mycobacterial infection and drug resistance in North Sardinia, Italy and to optimize the process of mycobacteria identification. From January 2020 to April 2023, samples from 1,836 suspected individuals in North Sardinia were analyzed. Conventional methods (microscopy smear and culture) and molecular methods (polymerase chain reaction, DNA probe, and mass spectrum) were used in MTB and NTM identification. Among 1,836 suspected individuals, 89 were MTB-positive and 44 were NTM-positive. Bronchial aspiration and bronchoalveolar lavage performed well as substitute specimens for sputum in MTB detection. For drug resistance, 71.91% of MTB and 83.33% of NTM were resistant to at least one antibiotic. The average turn-around time of MTB, slowly growing mycobacteria, and rapidly growing mycobacteria was 7.12, 48.87, and 11.27 days, respectively. Overall, our results show that the prevalence of mycobacterial infection in North Sardinia is relatively optimistic. However, the high proportion of drug resistance detected in the isolates is alarming. The implementation of advanced techniques could help optimize the process of mycobacteria identification.

IMPORTANCE
Mycobacterial infection is a major threat to public health worldwide. Accurate identification of infected species and drug resistance detection are critical factors in treatment. We focused on shortening the turn-around time of identifying mycobacteria species and antibiotic resistance tests.
Identification of Melittin-Like Proteins with a Molecular Weight of 67 kDa that Interact with Na+/K+-ATPase
Authors: Varfolomeeva L. A. , Klimanova E. A. , Sidorenko S. V. , Fedorov D. A. , Lopina O. D. 
Published: December 2023

Abstract
Melittin, a peptide from bee venom, was found to be able to interact with many proteins, including calmodulin target proteins and ion-transporting P-type ATPases. It is assumed that melittin mimics a protein module involved in protein-protein interactions within cells. Previously, a Na+/K+-ATPase containing the α1 isoform of the catalytic subunit was found to co-precipitate with a protein with a molecular weight of about 70 kDa that interacts with antibodies against melittin by cross immunoprecipitation. In the presence of a specific Na+/K+-ATPase inhibitor (ouabain), the amount of protein with a molecular weight of 70 kDa interacting with Na+/K+-ATPase increases. In order to identify melittin-like protein from murine kidney homogenate, a fraction of melittin-like proteins with a molecular weight of approximately 70 kDa was obtained using affinity chromatography with immobilized antibodies specific to melittin. By mass spectrometry analysis, the obtained protein fraction was found to contain three molecular chaperones of Hsp70 superfamily: mitochondrial mtHsp70 (mortalin), Hsp73, Grp78 (BiP) of endoplasmic reticulum. These data suggest that chaperones from the HSP-70 superfamily contain a melittin-like module.
Hydrogenation of Acetylene over Pd–Ag/Sibunit Catalysts: Effect of the Deposition Sequence of Active Component Precursors
Authors: Yurpalova D. V. , Afonasenko T. N. , Trenikhin M. V. , Leont’eva N. N. , Arbuzov A. B. , Temerev V. L. , Shlyapin D. A. 
Published: December 2023

Abstract
The study investigates interactions between palladium and silver in Pd–Ag bimetallic catalysts supported on a mesoporous carbon material Sibunit and, in particular, the dependence of these interactions on the deposition sequence of the metal precursors. Using XRD and TEM results, it was shown that impregnating the support with an aqueous solution that contained nitrate salts of both metals, followed by hydrogen treatment at 500°C, generates uniformly sized Pd0.6Ag0.4 particles (dav = 5.6 nm). These particles exhibit high selectivity (79%) in the reaction of acetylene hydrogenation to ethylene. The catalysts synthesized by sequential impregnation of the support with solutions of Pd and Ag nitrates interleaved with heat treatment in H2 exhibited a lower selectivity (68–73%) due to the formation of particles non-uniform both in composition and size (about 4 to 60 nm). The IR spectroscopy data suggest this effect is presumably associated with the removal of O-containing functional groups from the carbon surface during the reduction of the supported precursor. Given that O-groups act as anchoring sites for the precursors of active components and suppress the ability of Sibunit to reduce metals from their salt solutions, the subsequent deposition of the second metal salt causes a non-uniform distribution of this metal on the surface and the generation of larger particles.