bluuebunny/crossref_metadata_2025 huggingface dataset:
POST DISASTER HOUSING RECONSTRUCTION (PDHR) IN IBAJI AND LOKOJA, KOGI STATE-NIGERIA
Authors: Richard Jimoh , Adejo Adaji , James Rotimi , Luqman Oyewobi
Published: July 2024

The post-disaster housing reconstruction is a process distinct from the construction of housing when situations are normal, because reactive measures are put in place after disasters have occurred. It has been established that most of the time, emergency relief efforts are usually seen as being successful but the same cannot be said of post disaster housing reconstruction projects because they often fail to meet the set objectives. Hence, the study assessed post disaster housing reconstruction (PDHR) in Ibaji and Lokoja Local Government Areas of Kogi State, Nigeria. This was done through the self-administration of structured questionnaires to 56 professionals directly or indirectly involved on the reconstruction projects. Findings indicated that market and environment related factors have the most significant effects on resources availability during post disaster housing reconstruction. While the main challenges confronting post disaster housing reconstruction are inconsistencies in post disaster housing policy as well as insufficient capacity of the construction industry in the study area. However, PDHR has not achieved the desired objectives owing to challenges stymieing its effective implementation. Home owner-driven model therefore should be adopted for PDHR. The study is significant in that the PDHR challenges identified when measures are put in place to manage them, all the stakeholder beginning with victims will have a sustainable housing, government agencies will be up to date with robust approach to solving reconstruction issues and donors will have value for their money.
INVESTIGATION ON THE FLEXURAL STRENGTH OF PALM KERNEL SHELL CONCRETE FOR STRUCTURAL APPLICATIONS
Authors: I.T. Yusuf , Y.O. Babatunde , A. Abdullah
Published: July 2024

An increase in the cost of conventional aggregate and the resulting environmental ecological imbalance has propelled research in the use of organic and industrial wastes as alternatives. The use of palm kernel shell concrete (PKSC) for structural applications such as beams is yet to be explored, mainly as a result of fewer research in the flexural strength of PKSC. This study investigates the flexural strength of palm kernel shell concrete (PKSC) for structural applications such as beams. Standard 150 x 150 x 150mm cube size and 100 x 100 x 500mm prisms of PKSC samples were casted at 1:1:2 mix ratio at water cement ratio of 0.5, and tested at age of 7, 14, 21 and 28 days according to BS EN 12390 â€“ 3 (2002) and BS EN 12390 - 5 (2000). Method of batch by volume was adopted. At 28 days, the results show that the PKSC beam can support a load of 3981N with a deflection and flexural strength of 0.947mm and 2.883N/mm2 respectively. Also, the theoretical values of flexural strength and deflection compares well with the experimental values. A power equation in the form y = axn relating flexural strength with compressive strength produced a R2 value of 0.94 and relative predictive error of 0.028, the latter compares well with ACI 363 (1992) minimum value of 0.026 for power equations.
ASSESSMENT OF SURFACE WATER QUALITY OF ERO DAM FOR IRRIGATION PURPOSE
Authors: Omofunmi Olorunwa Eric , Fasiku Folasade Atinuade , Ogunleye Kayode Samuel
Published: July 2024

The physicochemical parameters of surface water surface of Ero Dam for irrigation were assessed. Water samples were selected from three locations (upstream, downstream and control). Tested parameters for water samples are pH, electrical conductivity (EC), total dissolved solids (TDS), calcium (Ca2+), magnesium (Mg2+), sodium (Na+), potassium (K+), chloride (Cl-), carbonate (C03-), bicarbonate (HC03-), boron (B), sulphate (S042-), nitrate (NO3-N) and phosphate (PO4-P). The samples were determined in accordance with the American Public Health Association standards. Data were analysed using descriptive statistics. Evaluation of surface water quality of Ero Dam was carried out using different irrigation indices methods such as sodium adsorption ratio (SAR), residual sodium carbonate (RSC), sodium percentage (Na %), potential salinity (PS), The Soluble sodium percentageÂ  (SSP), Kelly ratio (KR), magnesium adsorption ratio (MAR) and permeability index (PI) and compared with standard limits. The findings indicated that the concentrations of the Ca2+,Â  Mg2+, Na+, K+, Cl-, C03-, HC03-, B, S042-, NO3-N and PO4-P were within the acceptance limits for irrigation purposes except K+ that above the limits specified. Results indicated that majority, 87.5% of irrigation indices fall under excellent or suitable and classified as salinity (C1) and SAR (S1) which was known as (CISI). Hence, there are none degree of restriction in the application Ero Dam water quality for irrigation. Therefore, the results were concluded, that the study area surface water quality was suitable for irrigation.
PROBLEMS AND CHALLENGES OF SOLID WASTE MANAGEMENT: A CASE STUDY IN SOUTH JOHOR, MALAYSIA
Authors: Salim Mohd. Razman , Othman Fadil , Marzuky Sabarinah
Published: July 2024

Many urban areas in Malaysia are experiencing waste management problems due to the enhancement of urbanization and industrialization. These are further escalated by urban growth, changing consumption habits as well as social lifestyles. This new growth has been accompanied with an ever increasing rural-urban migration which culminates in the proliferation of squatter areas due to the scarcity of land and resources. The increase has given rise to collection and disposal problems which could pose as a potential environmental pollution and health risk to the general public through disease transmission. In this paper, the impact of solid waste management to the environment will be evaluated. It is also aim at introducing to the public the awareness of the health and safety risks caused by solid waste.
Entre a Interlocução de Pesquisas e Pesquisadores(As): O Compromisso dos Periódicos em Fomentar Redes de Pesquisas
Authors: Yume Nagasaki Jéssica
Published: July 2024

O objetivo desta carta editorial é debater o compromisso dos periódicos em fomentar redes de pesquisas dos textos publicados. Embora seja uma missão hercúlea- pois a comunicação não se perfaz apenas de maneira individualizada mas busca atingir a comunidade científica como um todo- a proposta é pensar na edição para além de textos individualizados, entendendo o diálogo que se estabelece entre eles de maneira orgânica,que contemplam pesquisas e pesquisadores(as) nacionais e internacionais. Em uma edição de 20 textos publicados, com 49 autores(as), advindos de todas as regiões do Brasil e em âmbito internacional de países como Portugal, Espanha, França, Reino Unido, Alemanha e Argentina, as pesquisas se entrecruzam trazendo um olhar diferenciado sobre cada tema e contexto social. Tais quesitos são trabalhados na edição por meio da construção do sumário e da carta editorial, em que são os primeiros documentos publicados e que organizam a forma de leitura dos artigos, não os limitando, mas pensando como textos submetidos em momentos distintos e com processo de construção científica e editorial individual são capazes de se comunicar, trazendo abordagens inovadoras sobre discussões semelhantes. Nesta perspectiva, um dos resultados é o que se atribui ao conceito de rede de pesquisa, qual seja: um mecanismo que impulsiona a criação do conhecimento e estabelece o intercâmbio de informações. Como o periódico científico está à disposição da comunidade acadêmica, estabelecendo estruturas e mecanismos que atendam a publicação científica de qualidade, cabe aos pesquisadores(as) se utilizar desta configuração para fortalecer suas redes de pesquisas.
PALAVRAS-CHAVE: Periódicos Científicos; Redes de Pesquisas; Intercâmbio de informações; Diálogo entre pesquisadores(as).
Parabolic isometries of the fine curve graph of the torus
Authors: Guihéneuf Pierre‐Antoine , Militon Emmanuel
Published: July 2024

In this article, we finish the classification of actions of torus homeomorphisms on the fine curve graph initiated by Bowden, Hensel, Mann, Militon, and Webb. This is made by proving that if , then acts elliptically on if and only if has bounded deviations in some direction . The proof involves some kind of slow rotation sets for torus homeomorphisms.
Fibroblast growth factor homologous factors: canonical and non‐canonical mechanisms of action
Authors: Goldfarb Mitchell
Published: July 2024

Since their discovery nearly 30 years ago, fibroblast growth factor homologous factors (FHFs) are now known to control the functionality of excitable tissues through a range of mechanisms. Nervous and cardiac system dysfunctions are caused by loss‐ or gain‐of‐function mutations in FHF genes. The best understood ‘canonical’ targets for FHF action are voltage‐gated sodium channels, and recent studies have expanded the repertoire of ways that FHFs modulate sodium channel gating. Additional ‘non‐canonical’ functions of FHFs in excitable and non‐excitable cells, including cancer cells, have been reported over the past dozen years. This review summarizes and evaluates reported canonical and non‐canonical FHF functions.

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Long-Life Na3V2(PO4)3||Graphite Energy Storage Device Enabled via Regulating the Area Density of Anode
Authors: Pi Yuqiang , Yang Caisheng , He Jiangting , Du Chengyue , Chen Jingjing , Xiong Meiqi
Published: July 2024

The regular graphite can only provide the negligible capacity for Na-ion intercalation, due to the narrow layer spacing and unstable thermodynamic factor. In this study, an energy storage device is created using the prelithiated graphite and Na3V2(PO4)3&NaClO4-based electrolyte, achieving an initial energy density of 317 W h kg−1 and a long lifespan of 1000 cycles with a 71.3% energy retention under the current rate of 1 C. Additionally, the prelithiated graphite anode could be recognized as an artificial Li metal with a strong skeleton, which reduces the volume changes and provides the growth substrate for Na-ion storage by the plating/stripping behavior. When the Li is depleted by participating in the reconstruction of SEI and the occurrence of complex side reactions, the battery system would die as a result. Therefore, the amounts of excess Li have a significant impact on the electrochemical performance of this device. That is to say that regulating the area density of anode enables a long-life Na3V2(PO4)3||graphite energy storage device.
Stability of Plane Parallel Flow Revisited for Particle–Fluid Suspensions
Authors: Ru C. Q.
Published: July 2024

An alternative model is proposed for hydrodynamic stability of plane parallel flow of an incompressible Newtonian fluid with suspended solid particles. For heavy particle-laden dusty gases with negligible particle volume fraction, the effective complex-form mean velocity in the modified Orr–Sommerfeld equation derived by the present model is showed to be essentially identical to the well-known Saffman's classical results. In the limit cases of small or large Stokes number of particles, simple formulas are derived for the effective Reynolds number ratio of the particle-laden suspension to the clear fluid without particles under otherwise identical conditions. The derived formula for particles of finite particle-to-fluid density ratio and small Stokes number is verified by comparing predicted results with known data, although a comparison of the derived formula with known results for particles of finite density ratio and large Stokes number cannot be made here due to the lack of available data. It is hoped that the present work could offer a conceptually novel and relatively simplified model for hydrodynamics of solid particle–fluid suspensions.
Reconstruction and Generation of Porous Metamaterial Units Via Variational Graph Autoencoder and Large Language Model
Authors: Naghavi Khanghah Kiarash , Wang Zihan , Xu Hongyi
Published: July 2024

In this paper, we propose and compare two novel deep generative model-based approaches for the design representation, reconstruction, and generation of porous metamaterials characterized by complex and fully connected solid and pore networks. A highly diverse porous metamaterial database is curated, with each sample represented by solid and pore phase graphs and a voxel image. All metamaterial samples adhere to the requirement of complete connectivity in both pore and solid phases. The first approach employs a dual decoder variational graph autoencoder to generate both solid phase and pore phase graphs. The second approach employs a variational graph autoencoder for reconstructing/generating the nodes in the solid phase and pore phase graphs and a transformer-based large language model (LLM) for reconstructing/generating the connections, i.e., the edges among the nodes. A comparative study was conducted, and we found that both approaches achieved high accuracy in reconstructing node features, while the LLM exhibited superior performance in reconstructing edge features. Reconstruction accuracy is also validated by voxel-to-voxel comparison between the reconstructions and the original images in the test set. Additionally, discussions on the advantages and limitations of using LLMs in metamaterial design generation, along with the rationale behind their utilization, are provided.
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

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

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.
Microstructure, mechanical, and tribological properties of transition metal (Nb, V, W) nitride coating on AISI-1045 steel by cathodic cage plasma deposition
Authors: Filho E. A. M. , Naeem M. , Díaz-Guillén J. C. , Sousa E. M. , Costa T. H. C. , Iqbal Javed , Sousa R. R. M.
Published: July 2024

AISI-1045 steel is a medium-carbon, medium-strength steel that usually requires surface engineering to be usable in industrial applications. Using the cathodic cage plasma deposition technique, transition metal (Nb, V, W) nitride coating is deposited on this steel using cathodic cage lids of these metals. The hardness of untreated steel (1.8 GPa) is upgraded to 11.2, 12.2, and 9.7 GPa for niobium nitride, vanadium nitride, and tungsten nitride coating, respectively. The elastic modulus, the ratio of hardness-elastic modulus (H/E, H2/E, and H3/E2), and the plasticity factor depict the improvement in mechanical and elastic properties. The sample treated with a niobium cage lid exhibits the Nb4N5 phase, the vanadium cage lid shows the VN phase (along with the Fe4N phase), and the tungsten cage lid consists of W2N3, WFeN2, and Fe4N phases. Among these coatings, the thickness of niobium nitride coating is maximum (1.87 μm), and a low deposition rate is obtained for tungsten nitride coating (0.83 μm). In addition to this coating, a nitrogen diffusion zone (∼60 μm) is also formed beneath the coating, which creates a hardness gradient between the coating and the substrate. The ball-on-disc wear tester shows that niobium nitride coating deposition reduces the wear rate from 19.5 × 10−3 to 8.8 × 10−3 mm3/N m and exhibits excellent wear performance.
Integrating Resistance Training Into Secondary School Physical Education Lessons: Effects of a 6-Week Intervention on Athletic Motor Skill Competencies
Authors: Murray James A. , Esformes Joseph I. , Byrne Paul J. , Moody Jeremy A.
Published: July 2024

Purpose: The purpose of this study was to examine the effects of resistance training (RT) in physical education lessons on athletic motor skill competencies in secondary school children. Method: Seventy-eight males were randomized into experimental year groups or a control group. Experimental groups participated in RT during physical education lessons for a 6-week half-term. The control group continued with their games-based curriculum. Countermovement jump (CMJ) height, seated medicine ball throw (SMBT) distance, and RT skills battery scores were measured preintervention and postintervention. Results: All experimental groups significantly improved SMBT distance and RT skills quotient (P < .05). All intervention year groups also significantly improved CMJ height (P < .05), except for year 9. Although the control group did not show improvements in CMJ height and RT skills quotient, there was a significant improvement in SMBT distance (P < .05). The year 7 and 8 males exhibited greater improvements in CMJ height and SMBT distance (d = 0.21–0.79) than in year 9 (d = 0.00–0.40). Conclusion: Results of the study indicated that a 6-week half-term RT intervention in physical education lessons can improve athletic motor skill competencies (P < .05, d = 0.21–2.51) in male youths.
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

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

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

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

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

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

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

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

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.
Ultrahigh-temperature metamorphism revealed by felsic granulite xenoliths in southern Tibet
Authors: Sun Wen-Rui , Wang Rui , Zhong Xin , Glorie Stijn , Zhang Liang-Liang
Published: July 2024

The Himalayan-Tibetan orogen experienced extensive thermal disturbance during the Indian-Asian collision, yet evidence for ultrahigh-temperature metamorphism (UHTM, >900 °C) remains scant. We report a UHTM event in the Lhasa Block, identified from felsic granulite xenoliths in Sangsang near the Tangra Yum Co Rift (TYR) of southern Tibet. These xenoliths exhibit a mineral assemblage of garnet + rutile + quartz + K-feldspar + plagioclase ± kyanite. Elemental mapping indicates garnet underwent high-temperature chemical homogenization. Employing Raman elastic geothermobarometry, Ti-in-quartz, and Zr-in-rutile geothermometers, we deduced pressure-temperature (P-T) conditions of 12–16 kbar and 870–975 °C, suggesting conditions were in the ultrahigh-temperature (UHT) range. The predicted P-T range is the most reliable estimation for Sangsang xenoliths to date, although the actual P-T conditions were likely higher due to viscous reset and chemical diffusion. An in situ garnet Lu-Hf date (ca. 26 ± 8 Ma) suggests that the UHT event occurred during the early Miocene, and in situ rutile U-Pb dates (ca. 12–11 Ma) indicate that the UHT conditions persisted until at least the timing of xenolith exhumation. Combined with the geological records in the Himalayan-Tibetan orogen, we suggest that the mantle upwelling contributed most to heating the Tibetan crust in the TYR and ultimately induced UHTM. Our study serves as an example of the UHTM formation mechanism within the active orogenic system.
Metastatic presentation of dermatofibrosarcoma protuberans as massive lower gastrointestinal bleed
Authors: Babu Basil , Jayant Divij , Behera Arunanshu , Kothari Anand
Published: July 2024

Dermatofibrosarcoma protuberans (DFSP) is an aggressive tumour with multiple local recurrences and rare metastatic potential. Fibrosarcomatous transformation occurs in a few cases of DFSP which makes them more aggressive in terms of recurrence and metastasis. Here we report the case of a woman in her late 30s who presented with massive lower gastrointestinal (GI) bleeding with a history of multiple surgeries for DFSP on her anterior abdominal wall. The bleeding source was identified to be a mass lesion in the jejunum, which was excised. The patient recovered well and the histopathology revealed fibrosarcoma of the jejunum. Follow-up investigations showed multiple lung nodules, ascites and abdominal lymph nodes suggesting progressive disease. She is currently receiving chemotherapy and progressing well 3 months postoperatively. Patients with fibrosarcomatous changes within DFSP must be followed up closely as it is associated with increased metastatic potential.
Potential dopaminergic deficit in patients with geriatric psychiatric disorders as revealed by DAT-SPECT: a cross-sectional study
Authors: Takenoshita Shintaro , Terada Seishi , Kojima Katsuhide , Nishikawa Naoto , Miki Tomoko , Yokota Osamu , Fujiwara Masaki , Takaki Manabu
Published: July 2024

Background

It has been reported that patients with geriatric psychiatric disorders include many cases of the prodromal stages of neurodegenerative diseases. Abnormal123I-2β-carbomethoxy-3β-(4-iodophenyl)-N-(3-fluoropropyl) nortropane dopamine transporter single-photon emission computed tomography (DAT-SPECT) reveals a nigrostriatal dopaminergic deficit and is considered useful to detect dementia with Lewy bodies and Parkinson’s disease as well as progressive supranuclear palsy and corticobasal degeneration. We aimed to determine the proportion of cases that are abnormal on DAT-SPECT in patients with geriatric psychiatric disorders and to identify their clinical profile.

Methods

The design is a cross-sectional study. Clinical findings of 61 inpatients aged 60 years or older who underwent DAT-SPECT and had been diagnosed with psychiatric disorders, but not neurodegenerative disease or dementia were analysed.

Results

36 of 61 (59%) had abnormal results on DAT-SPECT. 54 of 61 patients who had DAT-SPECT (89%) had undergone123I-metaiodobenzylguanidine myocardial scintigraphy (123I-MIBG scintigraphy); 12 of the 54 patients (22.2%) had abnormal findings on123I-MIBG scintigraphy. There were no cases that were normal on DAT-SPECT and abnormal on123I-MIBG scintigraphy. DAT-SPECT abnormalities were more frequent in patients with late-onset (55 years and older) psychiatric disorders (69.0%) and depressive disorder (75.7%), especially late-onset depressive disorder (79.3%).

Conclusion

Patients with geriatric psychiatric disorders include many cases showing abnormalities on DAT-SPECT. It is suggested that these cases are at high risk of developing neurodegenerative diseases characterised by a dopaminergic deficit. It is possible that patients with geriatric psychiatric disorders with abnormal findings on DAT-SPECT tend to show abnormalities on DAT-SPECT first rather than on123I-MIBG scintigraphy.
Economic burden of chronic obstructive pulmonary disease and post-tuberculosis sequelae in low- and middle-income countries: a database compiled from a systematic review and meta-analysis
Authors: Lin Yuling , Walker Alexandra , Batta Marguerite , Ottilie-Kovelman Sierra , Duchenko Anna , Brugger Curdin , Keiser Olivia , Wallis Robert S , Reither Klaus , Tediosi Fabrizio , Antillon Marina
Published: July 2024

Background

Chronic obstructive pulmonary disease (COPD) and tuberculosis (TB) impose a substantial economic burden globally. This systematic review summarised the evidence on the costs of COPD, including post-TB diseases in low- and middle-income countries.

Methods

A systematic review was conducted and studies published between 1 January 2013 and 28 March 2022 (the date of the search) were identified using various electronic databases without language restrictions. Titles, abstracts and full texts were screened in duplicate and data were extracted and verified by reviewers. Eligible studies were categorised as cost analysis and/or economic burden studies, and costs were converted to 2021 United State dollar. Meta-analysis was conducted on the costs of hospitalisations, medication and outpatient visits.

Results

128 cost studies and 65 economic burden studies were included in this review. The data collected are presented in the Cost Database of COPD and Post-TB (CD-CPTB). The majority of studies were from Asia, Eastern Europe and Latin America, with a few from other middle-income countries. There were extremely limited data on the costs of post-TB sequelae and only a few studies were from Africa (n=6) and low-income (n=5) countries. The direct medical costs of COPD ranged from $26 per hospitalisation in India to $2694 per year per patient with severe disease in Mexico, while the costs of acute exacerbation of COPD ranged from $137 to $4207 per exacerbation with both the minimum and maximum costs occurring in Turkey. The costs were lower in lower middle-income countries compared with upper middle-income countries. Finally, considerable economic burden was attributable to smoking and air pollution.

Conclusion

The review and the CD-CPTB database give a thorough snapshot of the current evidence of the costs and economic burden of COPD and post-TB diseases. Future research is needed to investigate the economic impact after TB treatment and should be prioritised in Africa and low-income countries where there has been a lack of data collection.

Protocol registration number

CRD42022326609.