bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeneous Transfer Learning of Electrohydrodynamic Printing Under Zero-Gravity Toward In-Space Manufacturing
Authors: Wolf Rayne , Jiang Liangkui , Alharbi Khawlah , Zhang Pengyu , Wang Chao , Qin Hantang 
Published: July 2024

Abstract
As we continue to commercialize space and mature in-space manufacturing (ISM) processes, there is a strong need to transfer the knowledge we learn from experiments on the ground to zero-gravity environments. Physics-motivated manufacturing processes, like additive manufacturing, experience a shift in fabrication parameters due to the absence of gravity and the change of environments. Thus, we found traditional machine learning methods are not capable of addressing this domain shift and present a transfer learning scheme as a solution in this paper. We tested a kernel ridge regression model built for heterogeneous transfer learning (KRR-HeITL) on data from the electrohydrodynamic inkjet printing (EHD printing) process. EHD printing is a process that uses electrical force to control material flows, thus achieving the fabrication of electronics without requiring gravity. Our team has successfully conducted three rounds of parabolic flights to validate this technology for ISM. We trained on multiple datasets built from on-ground experiments and tested using zero-gravity printing data obtained from parabolic flight tests. Measurements of the Taylor cone both on-ground and in zero-gravity were taken and exploited as a part of the training data. We found that our method obtains good interpolation accuracy (MAPE 3.85%) compared to traditional machine learning methods (MAPE 16.84%) for predicting the printed line width. We concluded that the KRR-HeITL method is well suited for zero-gravity domain shifts of EHD printing parameters. This study paves the way for future predictions of ISM parameters when there are only on-ground experiments or very limited zero-gravity datasets for a given process.
Mean Squared Error May Lead You Astray When Optimizing Your Inverse Design Methods
Authors: Habibi Milad , Bernard Shai , Wang Jun , Fuge Mark 
Published: July 2024

Abstract
When performing time-intensive optimization tasks, such as those in topology or shape optimization, researchers have turned to machine-learned inverse design (ID) methods—i.e., predicting the optimized geometry from input conditions—to replace or warm start traditional optimizers. Such methods are often optimized to reduce the mean squared error (MSE) or binary cross entropy between the output and a training dataset of optimized designs. While convenient, we show that this choice may be myopic. Specifically, we compare two methods of optimizing the hyperparameters of easily reproducible machine learning models including random forest, k-nearest neighbors, and deconvolutional neural network model for predicting the three optimal topology problems. We show that under both direct inverse design and when warm starting further topology optimization, using MSE metrics to tune hyperparameters produces less performance models than directly evaluating the objective function, though both produce designs that are almost one order of magnitude better than using the common uniform initialization. We also illustrate how warm starting impacts both the convergence time, the type of solutions obtained during optimization, and the final designs. Overall, our initial results portend that researchers may need to revisit common choices for evaluating ID methods that subtly tradeoff factors in how an ID method will actually be used. We hope our open-source dataset and evaluation environment will spur additional research in those directions.
Archaeal mevalonate pathway in the uncultured bacterium
Candidatus
Promineifilum breve belonging to the phylum Chloroflexota
Authors: Kanno Kosuke , Kuriki Riko , Yasuno Yoko , Shinada Tetsuro , Ito Tomokazu , Hemmi Hisashi 
Published: July 2024

ABSTRACT

The archaeal mevalonate pathway is a recently discovered modified version of the eukaryotic mevalonate pathway. This pathway is widely conserved in archaea, except for some archaeal lineages possessing the eukaryotic or other modified mevalonate pathways. Although the pathway seems almost exclusive to the domain Archaea, the whole set of homologous genes of the pathway is found in the metagenome-assembled genome sequence of an uncultivated bacterium,
Candidatus
Promineifilum breve, of the phylum Chloroflexota. To prove the existence of the archaea-specific pathway in the domain Bacteria, we confirmed the activities of the enzymes specific to the pathway, phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, because only these two enzymes are absent in closely related Chloroflexota bacteria that possess a different type of modified mevalonate pathway. The activity of anhydromevalonate phosphate decarboxylase was evaluated by carotenoid production
via
the archaeal mevalonate pathway reconstituted in
Escherichia coli
cells, whereas that of phosphomevalonate dehydratase was confirmed by an
in vitro
assay using the recombinant enzyme after purification and iron-sulfur cluster reconstruction. Phylogenetic analyses of some mevalonate pathway-related enzymes suggest an evolutionary route for the archaeal mevalonate pathway in
Candidatus
P. breve, which probably involves horizontal gene transfer events.

IMPORTANCE
The recent discovery of various modified mevalonate pathways in microorganisms, such as archaea and Chloroflexota bacteria, has shed light on the complexity of the evolution of metabolic pathways, including those involved in primary metabolism. The fact that the archaeal mevalonate pathway, which is almost exclusive to the domain Archaea, exists in a Chloroflexota bacterium provides valuable insights into the molecular evolution of the mevalonate pathways and associated enzymes. Putative genes probably involved in the archaeal mevalonate pathway have also been found in the metagenome-assembled genomes of Chloroflexota bacteria. Such genes can contribute to metabolic engineering for the bioproduction of valuable isoprenoids because the archaeal mevalonate pathway is known to be an energy-saving metabolic pathway that consumes less ATP than other mevalonate pathways do.
Salmonella
Typhimurium alters galactitol metabolism under ciprofloxacin treatment to balance resistance and virulence
Authors: Chen Qiwei , Yu Yongfeng , Xu Yongchang , Quan Heng , Liu Donghui , Li Caiyu , Liu Mengyao , Gong Xiaowei 
Published: July 2024

ABSTRACT

Ciprofloxacin-resistant
Salmonella
Typhimurium (
S.
Typhimurium) causes a significant health burden worldwide. A wealth of studies has been published on the contributions of different mechanisms to ciprofloxacin resistance in
Salmonella
spp. But we still lack a deep understanding of the physiological responses and genetic changes that underlie ciprofloxacin exposure. This study aims to know how phenotypic and genotypic characteristics are impacted by ciprofloxacin exposure, from ciprofloxacin-susceptible to ciprofloxacin-resistant strains
in vitro
. Here, we investigated the multistep evolution of resistance in replicate populations of
S.
Typhimurium during 24 days of continuously increasing ciprofloxacin exposure and assessed how ciprofloxacin impacts physiology and genetics. Numerous studies have demonstrated that RamA is a global transcriptional regulator that prominently perturbs the transcriptional landscape of
S.
Typhimurium, resulting in a ciprofloxacin-resistant phenotype appearing first; the quinolone resistance-determining region mutation site can only be detected later. Comparing the microbial physiological changes and RNA sequencing (RNA-Seq) results of ancestral and selectable mutant strains, the selectable mutant strains had some fitness costs, such as decreased virulence, an increase of biofilm-forming ability, a change of “collateral” sensitivity to other drugs, and inability to utilize galactitol. Importantly, in the ciprofloxacin induced, RamA directly binds and activates the
gatR
gene responsible for the utilization of galactitol, but RamA deletion strains could not activate
gatR
. The elevated levels of RamA, which inhibit the galactitol metabolic pathway through the activation of
gatR
, can lead to a reduction in the growth rate, adhesion, and colonization resistance of
S
. Typhimurium. This finding is supported by studies conducted in M9 medium as well as
in vivo
infection models.

IMPORTANCE

Treatment of antibiotic resistance can significantly benefit from a deeper understanding of the interactions between drugs and genetics. The physiological responses and genetic mechanisms in antibiotic-exposed bacteria are not well understood. Traditional resistance studies, often retrospective, fail to capture the entire resistance development process and typically exhibit unpredictable dynamics. To explore how clinical isolates of
S.
Typhimurium respond to ciprofloxacin, we analyzed their adaptive responses. We found that
S.
Typhimurium RamA-mediated regulation disrupts microbial metabolism under ciprofloxacin exposure, affecting genes in the galactitol metabolic pathways. This disruption facilitates adaptive responses to drug therapy and enhances the efficiency of intracellular survival. A more comprehensive and integrated understanding of these physiological and genetic changes is crucial for improving treatment outcomes.
Dissecting structure and function of the monovalent cation/H
+
antiporters Mdm38 and Ylh47 in
Saccharomyces cerevisiae
Authors: Tsujii Masaru , Tanudjaja Ellen , Zhang Haoyu , Shimizukawa Haruto , Konishi Ayumi , Furuta Tadaomi , Ishimaru Yasuhiro , Uozumi Nobuyuki 
Published: July 2024

ABSTRACT

Saccharomyces cerevisiae
Mdm38 and Ylh47 are homologs of the Ca
2+
/H
+
antiporter Letm1, a candidate gene for seizures associated with Wolf-Hirschhorn syndrome in humans. Mdm38 is important for K
+
/H
+
exchange across the inner mitochondrial membrane and contributes to membrane potential formation and mitochondrial protein translation. Ylh47 also localizes to the inner mitochondrial membrane. However, knowledge of the structures and detailed transport activities of Mdm38 and Ylh47 is limited. In this study, we conducted characterization of the ion transport activities and related structural properties of Mdm38 and Ylh47. Growth tests using Na
+
/H
+
antiporter-deficient
Escherichia coli
strain TO114 showed that Mdm38 and Ylh47 had Na
+
efflux activity. Measurement of transport activity across
E. coli
-inverted membranes showed that Mdm38 and Ylh47 had K
+
/H
+
, Na
+
/H
+
, and Li
+
/H
+
antiport activity, but unlike Letm1, they lacked Ca
2+
/H
+
antiport activity. Deletion of the ribosome-binding domain resulted in decreased Na
+
efflux activity in Mdm38. Structural models of Mdm38 and Ylh47 identified a highly conserved glutamic acid in the pore-forming membrane-spanning region. Replacement of this glutamic acid with alanine, a non-polar amino acid, significantly impaired the ability of Mdm38 and Ylh47 to complement the salt sensitivity of
E. coli
TO114. These findings not only provide important insights into the structure and function of the Letm1-Mdm38-Ylh47 antiporter family but by revealing their distinctive properties also shed light on the physiological roles of these transporters in yeast and animals.

IMPORTANCE

The inner membrane of mitochondria contains numerous ion transporters, including those facilitating H
+
transport by the electron transport chain and ATP synthase to maintain membrane potential. Letm1 in the inner membrane of mitochondria in animals functions as a Ca
2+
/H
+
antiporter. However, this study reveals that homologous antiporters in mitochondria of yeast, Mdm38 and Ylh47, do not transport Ca
2+
but instead are selective for K
+
and Na
+
. Additionally, the identification of conserved amino acids crucial for antiporter activity further expanded our understanding of the structure and function of the Letm1-Mdm38-Ylh47 antiporter family.
The frequency and function of nucleoprotein-specific CD8
+
T cells are critical for heterosubtypic immunity against influenza virus infection
Authors: Amoah Samuel , Cao Weiping , Sayedahmed Ekramy E. , Wang Yuanyuan , Kumar Amrita , Mishina Margarita , Eddins Devon J. , Wang Wen-Chien , Burroughs Mark , Sheth Mili , Lee Justin , Shieh Wun-Ju , Ray Sean D. , Bohannon Caitlin D. , Ranjan Priya , Sharma Suresh D. , Hoehner Jessica , Arthur Robert A. , Gangappa Shivaprakash , Wakamatsu Nobuko , Johnston H. Richard , Pohl Jan , Mittal Suresh K. , Sambhara Suryaprakash 
Published: July 2024

ABSTRACT

Cytotoxic T lymphocytes (CTLs) mediate host defense against viral and intracellular bacterial infections and tumors. However, the magnitude of CTL response and their function needed to confer heterosubtypic immunity against influenza virus infection are unknown. We addressed the role of CD8
+
T cells in the absence of any cross-reactive antibody responses to influenza viral proteins using an adenoviral vector expressing a 9mer amino acid sequence recognized by CD8
+
T cells. Our results indicate that both CD8
+
T cell frequency and function are crucial for heterosubtypic immunity. Low morbidity, lower viral lung titers, low to minimal lung pathology, and better survival upon heterosubtypic virus challenge correlated with the increased frequency of NP-specific CTLs. NP-CD8
+
T cells induced by differential infection doses displayed distinct RNA transcriptome profiles and functional properties. CD8
+
T cells induced by a high dose of influenza virus secreted significantly higher levels of IFN-γ and exhibited higher levels of cytotoxic function. The mice that received NP-CD8
+
T cells from the high-dose virus recipients through adoptive transfer had lower viral titers following viral challenge than those induced by the low dose of virus, suggesting differential cellular programming by antigen dose. Enhanced NP-CD8
+
T-cell functions induced by a higher dose of influenza virus strongly correlated with the increased expression of cellular and metabolic genes, indicating a shift to a more glycolytic metabolic phenotype. These findings have implications for developing effective T cell vaccines against infectious diseases and cancer.

IMPORTANCE
Cytotoxic T lymphocytes (CTLs) are an important component of the adaptive immune system that clears virus-infected cells or tumor cells. Hence, developing next-generation vaccines that induce or recall CTL responses against cancer and infectious diseases is crucial. However, it is not clear if the frequency, function, or both are essential in conferring protection, as in the case of influenza. In this study, we demonstrate that both CTL frequency and function are crucial for providing heterosubtypic immunity to influenza by utilizing an Ad-viral vector expressing a CD8 epitope only to rule out the role of antibodies, single-cell RNA-seq analysis, as well as adoptive transfer experiments. Our findings have implications for developing T cell vaccines against infectious diseases and cancer.
Unraveling the assembly mechanism of SADS-CoV virus nucleocapsid protein: insights from RNA binding, dimerization, and epitope diversity profiling
Authors: Zhang Ying , Wu Fang , Han Yongyue , Wu Yuzhe , Huang Liqiu , Huang Yuanwei , Yan Di , Jiang Xiwen , Ma Jingyun , Xu Wei 
Published: July 2024

ABSTRACT

The swine acute diarrhea syndrome coronavirus (SADS-CoV) has caused significant disruptions in porcine breeding and raised concerns about potential human infection. The nucleocapsid (N) protein of SADS-CoV plays a vital role in viral assembly and replication, but its structure and functions remain poorly understood. This study utilized biochemistry, X-ray crystallography, and immunization techniques to investigate the N protein’s structure and function in SADS-CoV. Our findings revealed distinct domains within the N protein, including an RNA-binding domain, two disordered domains, and a dimerization domain. Through biochemical assays, we confirmed that the N-terminal domain functions as an RNA-binding domain, and the C-terminal domain is involved in dimerization, with the crystal structure analysis providing visual evidence of dimer formation. Immunization experiments demonstrated that the disordered domain 2 elicited a significant antibody response. These identified domains and their interactions are crucial for viral assembly. This comprehensive understanding of the N protein in SADS-CoV enhances our knowledge of its assembly and replication mechanisms, enabling the development of targeted interventions and therapeutic strategies.

IMPORTANCE
SADS-CoV is a porcine coronavirus that originated from a bat HKU2-related coronavirus. It causes devastating swine diseases and poses a high risk of spillover to humans. The coronavirus N protein, as the most abundant viral protein in infected cells, likely plays a key role in viral assembly and replication. However, the structure and function of this protein remain unclear. Therefore, this study employed a combination of biochemistry and X-ray crystallography to uncover distinct structural domains in the N protein, including RNA-binding domains, two disordered domains, and dimerization domains. Additionally, we made the novel discovery that the disordered domain elicited a significant antibody response. These findings provide new insights into the structure and functions of the SADS-CoV N protein, which have important implications for future studies on SADS-CoV diagnosis, as well as the development of vaccines and anti-viral drugs.
Host range of naturally and artificially evolved symbiotic bacteria for a specific host insect
Authors: Sugiyama Ryuga , Moriyama Minoru , Koga Ryuichi , Fukatsu Takema 
Published: July 2024

ABSTRACT

Diverse insects are intimately associated with specific symbiotic bacteria, where host and symbiont are integrated into an almost inseparable biological entity. These symbiotic bacteria usually exhibit host specificity, uncultivability, reduced genome size, and other peculiar traits relevant to their symbiotic lifestyle. How host-symbiont specificity is established at the very beginning of symbiosis is of interest but poorly understood. To gain insight into the evolutionary issue, we adopted an experimental approach using the recently developed evolutionary model of symbiosis between the stinkbug
Plautia stali
and
Escherichia coli
. Based on the laboratory evolution of
P. stali-E. coli
mutualism, we selected Δ
cyaA
mutant of
E. coli
as an artificial symbiont of
P. stali
that has established mutualism by a single mutation. In addition, we selected a natural cultivable symbiont of
P. stali
of relatively recent evolutionary origin. These artificial and natural symbiotic bacteria of
P. stali
were experimentally inoculated to symbiont-deprived newborn nymphs of diverse stinkbug species. Strikingly, the mutualistic
E. coli
was unable to establish infection and support growth and survival of all the stinkbug species except for
P. stali
, uncovering that host specificity can be established at a very early stage of symbiotic evolution. Meanwhile, the natural symbiont was able to establish infection and support growth and survival of several stinkbug species in addition to
P. stali
, unveiling that a broader host range of the symbiont has evolved in nature. Based on these findings, we discuss what factors are relevant to the establishment of host specificity in the evolution of symbiosis.

IMPORTANCE

How does host-symbiont specificity emerge at the very beginning of symbiosis? This question is difficult to address because it is generally difficult to directly observe the onset of symbiosis. However, recent development of experimental evolutionary approaches to symbiosis has brought about a breakthrough. Here we tackled this evolutionary issue using a symbiotic
Escherichia coli
created in laboratory and a natural
Pantoea
symbiont, which are both mutualistic to the stinkbug
Plautia stali
. We experimentally replaced essential symbiotic bacteria of diverse stinkbugs with the artificial and natural symbionts of
P. stali
and evaluated whether the symbiotic bacteria, which evolved for a specific host, can establish infection and support the growth and survival of heterospecific hosts. Strikingly, the artificial symbiont showed strict host specificity to
P. stali
, whereas the natural symbiont was capable of symbiosis with diverse stinkbugs, which provide insight into how host-symbiont specificity can be established at early evolutionary stages of symbiosis.
Structural characteristics of BtKY72 RBD bound to bat ACE2 reveal multiple key residues affecting ACE2 usage of sarbecoviruses
Authors: Su Chao , He Juanhua , Wang Liang , Hu Yu , Cao Jian , Bai Bin , Qi Jianxun , Gao George Fu , Yang Mengsu , Wang Qihui 
Published: July 2024

ABSTRACT

Two different sarbecoviruses, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2, have caused serious challenges to public health. Certain sarbecoviruses utilize angiotensin-converting enzyme 2 (ACE2) as their cellular receptor, whereas some do not, speculatively due to the two deletions in their receptor-binding domain (RBD). However, it remains unclear whether sarbecoviruses with one deletion in the RBD can still bind to ACE2. Here, we showed that two phylogenetically related sarbecoviruses with one deletion, BtKY72 and BM48-31, displayed a different ACE2-usage range. The cryo-electron microscopy structure of BtKY72 RBD bound to bat ACE2 identified a key residue important for the interaction between RBD and ACE2. In addition, we demonstrated that the mutations involving four types of core residues enabled the sarbecoviruses with deletion(s) to bind to human ACE2 (hACE2) and broadened the ACE2 usage of SARS-CoV-2. Our findings help predict the potential hACE2-binding ability to emerge sarbecoviruses and develop pan-sarbecovirus therapeutic agents.

IMPORTANCE
Many sarbecoviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), possess the ability to bind to receptor angiotensin-converting enzyme 2 (ACE2) through their receptor-binding domain (RBD). However, certain sarbecoviruses with deletion(s) in the RBD lack this capability. In this study, we investigated two closely related short-deletion sarbecoviruses, BtKY72 and BM48-31, and revealed that BtKY72 exhibited a broader ACE2-binding spectrum compared to BM48-31. Structural analysis of the BtKY72 RBD-bat ACE2 complex identifies a critical residue at position 493 contributing to these differences. Furthermore, we demonstrated that the mutations involving four core residues in the RBD enabled the sarbecoviruses with deletion(s) to bind to human ACE2 and expanded the ACE2 usage spectra of SARS-CoV-2. These findings offer crucial insights for accurately predicting the potential threat of newly emerging sarbecoviruses to human health.
Complete genome sequence of
Alloalcanivorax xenomutans
HF10, an alkane-degrading bacterium under hypersaline conditions
Authors: Zheng Jie , Yu Bo 
Published: July 2024

ABSTRACT

We report the complete genome sequence of
Alloalcanivorax xenomutans
HF10, an alkane-degrading strain isolated from the sediments of ocean in Xiamen, China, with a high salt tolerance potential of more than 10%. Its genome is composed of a 4.76-Mb chromosome.