bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary Mismatch and Lifestyle‐Related Diseases: A Study of a 6‐Month Intensive Lifestyle Intervention
Authors: MacDonald Christopher Scott , Bennekou Mia Aagaard , Nielsen Sabrina Mai , Junker Anders Ellekær , Biering‐Sørensen Tor , Langberg Henning , Christensen Robin , Lieberman Daniel E. , Zachariae Claus , Pallisgaard Jannik Langtved 
Published: December 2024

ABSTRACTChronic medical conditions caused by the inadequate adaptation of the body to modern lifestyles, such as physical inactivity and unhealthy diets, are on the rise. This study assessed whether a comprehensive lifestyle intervention, including high volumes of supervised exercise, could improve health outcomes. Eight volunteers with lifestyle‐related diseases received a 6‐month lifestyle intervention consisting of 8000–10 000 steps/day, 6 moderate‐intensity endurance and 3 resistance training sessions per week, a 5‐week long hike, and dietary advice. This was followed by 7 months of limited remote supervision, ending 13 months from baseline. The participants (3 females, 5 males; mean age 42.9 years) had conditions including type 2 diabetes (T2D), depression/stress, and metabolic syndrome (MS). After 6 months, body weight decreased significantly by 23 kg (95% CI; −33.7 to −12.2), with a minor non‐significant decrease in lean body mass of 1.96 kg (95% CI; −4.34 to 0.27). Maximal oxygen consumption (VO2max) increased by 18.5 mL/O2/kg/min. (95% CI; 13.8–23.1) and systolic and diastolic blood pressures decreased by 33 (95% CI; −39 to −26) and 18 mmHg (95% CI; −23 to −14), respectively. Three of the 4 participants with T2D had normalized glycated hemoglobin (HbA1c) levels, and all showed improved 2‐h oral glucose tolerance (OGTT) without pharmacological treatment. Participants with T2D continued to lower HbA1c during the 7‐month follow‐up period. This 6‐month lifestyle intervention restored metabolic health and improved cardiovascular health in 8 participants with lifestyle‐related diseases while reducing the need for pharmacological treatments. These findings suggest that comprehensive lifestyle changes can reverse several medical conditions caused by evolutionary mismatch.
Genetic dissection of ear‐related trait divergence between maize and teosinte
Authors: Wu Shenshen , Zhang Han , Fang Zhengfu , Li Zichao , Yang Ning , Yang Fang 
Published: December 2024

SUMMARYMaize has undergone remarkable domestication and shows striking differences in architecture and ear morphology compared to its wild progenitor, called teosinte. However, our understanding of the genetic mechanisms underlying the ear morphology differences between teosinte and cultivated maize is still limited. In this study, we explored the genetic basis of ear‐related traits at both early and mature stages by analyzing a population derived from a cross between Mo17 and a teosinte line, mexicana. We identified 31 quantitative trait loci (QTLs) associated with four IM‐related and four ear‐related traits, with 27 QTLs subjected to selection during the domestication process. Several key genes related to ear development were found under selection, including KN1 and RA1. Analysis of gene expression in the IM of developing ears from the population revealed the prominent roles of cis‐variants in gene regulation. We also identified a large number of trans‐eQTLs responsible for gene expression variation, and enrichment analysis on a trans‐eQTL hotspot revealed the possible involvement of the sulfur metabolic pathway in controlling ear traits. Integrating the expression and phenotypic mapping data, we pinpointed several candidate genes potentially influencing ear development. Our findings advance the understanding of the genetic basis driving ear trait variation during maize domestication.
A removal lemma for ordered hypergraphs
Authors: Towsner Henry 
Published: December 2024

AbstractWe prove a removal lemma for induced ordered hypergraphs, simultaneously generalizing Alon–Ben‐Eliezer–Fischer's removal lemma for ordered graphs and the induced hypergraph removal lemma. That is, we show that if an ordered hypergraph has few induced copies of a small ordered hypergraph then there is a small modification so that has no induced copies of . (Note that we do not need to modify the ordering .) We give our proof in the setting of an ultraproduct (i.e., a Keisler graded probability space), where we can give an abstract formulation of hypergraph removal in terms of sequences of ‐algebras. We then show that ordered hypergraphs can be viewed as hypergraphs where we view the intervals as an additional notion of a “very structured” set. Along the way we give an explicit construction of the bijection between the ultraproduct limit object and the corresponding hyerpgraphon.
A Visual Representation of Engineering Catalogs Using Variational Autoencoders
Authors: Sridhara Saketh , Suresh Krishnan 
Published: December 2024

Abstract
Catalogs have been used for over a century for designing engineering systems. While catalogs are excellent repositories of engineering information, they are difficult to navigate and visualize, specifically to spot clusters, gaps, substitutes, and outliers. Inspired by Ashby charts for material selection, we propose here a visual representation of engineering catalogs using neural networks. In particular, we employ variational autoencoders (VAEs) to project catalog data onto a lower-dimensional latent space. The latent space can then be visualized to explore the underlying structure of the catalog. Specifically, catalog creators can identify gaps and outliers in their data, while end-users can compare catalogs from competitors and easily find substitutes. Contours can be superimposed on the latent space to enable selection based on user-defined attributes; these contours are generalizations of design indices associated with Ashby charts. Various examples of catalogs ranging from materials and bearings, to motors and batteries are illustrated using the proposed method. By using these examples, we (1) study the impact of the latent space dimension on the representational error, (2) illustrate how designers can easily choose alternate configurations based on their design requirements, and (3) identify gaps in catalog offerings, providing a stimulus for new product development.
The gene
MAB_2362
is responsible for intrinsic resistance to various drugs and virulence in
Mycobacterium abscessus
by regulating cell division
Authors: Ju Yanan , Li Lijie , Zhang Jingran , Yusuf Buhari , Zeng Sanshan , Fang Cuiting , Tian Xirong , Han Xingli , Ding Jie , Zhang Han , Ma Wanli , Wang Shuai , Chen Xinwen , Zhang Tianyu 
Published: December 2024

ABSTRACT

Mycobacterium abscessus
exhibits intrinsic resistance to most antibiotics, hence leading to infections that are difficult to treat. To address this issue, the identification of new molecular targets is essential for the development or repositioning of therapeutic agents. This study demonstrated that the
MAB_2362
-knockout strain, Mab
Δ2362
, became significantly susceptible to a range of antibiotics, not only
in vitro
but also exhibited susceptibility to rifabutin, bedaquiline, and linezolid
in vivo
. While the bacterial burden of the wild-type
M. abscessus
(Mab
Wt
) increased by over 1 log
10
CFU/lung in a murine infection model 16 days post-infection, that of Mab
Δ2362
strain decreased by more than 1 log
10
CFU/lung, which suggests that the disruption leads to attenuation. Bioinformatics analysis revealed that MAB_2362 shares the highest similarity (41.35%) with SteA, a protein known to influence cell division in
Corynebacterium glutamicum
, suggesting that MAB_2362 might be involved in cell division. Mab
Δ2362
cells exhibited a median length of 2.62 µm, which was substantially longer than the 1.44 µm recorded for Mab
Wt
cells. Additionally, multiple cell division septa were observed in 42% of Mab
Δ2362
cells, whereas none were seen in Mab
Wt
cells. An ethidium bromide uptake assay further suggested a higher cell envelope permeability in Mab
Δ2362
compared to Mab
Wt
. Collectively, these findings underscore the role of
MAB_2362
in intrinsic resistance and virulence of
M. abscessus
possibly through the regulation of cell division. Thus, MAB_2362 emerges as a promising candidate for targeted interventions in the pursuit of novel antimicrobials against
M. abscessus
.
Development and application of a quadruple RT-qPCR assay for the simultaneous detection of NoV GI, NoV GII, and HAV in bivalve shellfish
Authors: Wang Yan , Wang Jinfeng , Wei Maolin , Liu Libing , Wang Jianchang , Xu Xiangdong 
Published: December 2024

ABSTRACT

To achieve rapid and simultaneous detection of NoV GI, NoV GII, and HAV, a quadruple real-time fluorescence quantitative PCR (RT-qPCR) assay was developed using MS2 bacteriophage as a process control virus. The quadruple RT-qPCR assay effectively detected NoV GI, NoV GII, HAV, and MS2 RNA with detection limits of 10
2
copies/μL, 10
3
copies/μL, 10
2
copies/μL, and 10
3
copies/μL, respectively, within 1 hour 50 minutes. The quadruple RT-qPCR assay could specifically detect NoV GI, NoV GII, HAV, and MS2 without cross-reactions with other common pathogens, demonstrating good reproducibility with intra-assay and inter-assay coefficients of variation all below 2.11%. In this study, 337 bivalve shellfish samples collected from various regions of Hebei Province were pretreated using the proteinase K-PEG 8000 precipitation-chloroform method, and viral nucleic acids were enriched and extracted from a volume of viral solution that was doubled. The developed quadruple RT-qPCR assay was used to detect NoV GI, NoV GII, and HAV in bivalve shellfish samples, and the positive rates were 19.88% (67/337), 20.47% (69/337), and 4.75% (16/337), respectively. In addition, mixed infections of NoV GI and NoV GII (10.68%, 36/337) and NoV GI and HAV (0.89%, 3/337) were observed. In all, 200 bivalve shellfish samples were randomly selected for the assay, and it was found that the total, positive, negative coincidence rates, and Kappa values of the quadruple RT-qPCR assay were 98.3%, 99.1%, 98.2%, and 0.945, respectively, compared with the single RT-qPCR assay. These results show that the developed quadruple RT-qPCR assay has comparable performance to the single RT-qPCR assay.

IMPORTANCE
Food-borne diseases caused by viral contamination have become a growing concern, and bivalve shellfish is a crucial source of infection, with many outbreaks of non-bacterial acute gastroenteritis associated with raw food or the use of undercooked shellfish such as oysters. As food contamination problems caused by NoV and HAV become more severe, it is important to study and establish a sensitive and efficient assay to simultaneously detect NoV and HAV by applying the MS2 process control virus for the protection of bivalve shellfish food safety and the monitoring of the above food-borne viral contamination. In addition, bivalve shellfish samples contain a large number of PCR inhibitors such as polysaccharides, lipids, and proteins, so optimization of the virus enrichment and extraction method is essential and is expected to provide a research basis for subsequent related experiments.
An adenoviral vector encoding an inflammation-inducible antagonist, HMGB1 Box A, as a novel therapeutic approach to inflammatory diseases
Authors: Shirey Kari Ann , Joseph John , Coughlan Lynda , Nijhuis Haye , Varley Alan W. , Blanco Jorge C. G. , Vogel Stefanie N. 
Published: December 2024

ABSTRACT

Influenza, as well as other respiratory viruses, can trigger local and systemic inflammation resulting in an overall “cytokine storm” that produces serious outcomes such as acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). We hypothesized that gene therapy platforms could be useful in these cases if the production of an anti-inflammatory protein reflects the intensity and duration of the inflammatory condition. The recombinant protein would be produced and released only in the presence of the inciting stimulus, avoiding immunosuppression or other unwanted side effects that may occur when treating infectious diseases with anti-inflammatory drugs. To test this hypothesis, we developed AdV.C3-Tat/HIV-Box A, an inflammation-inducible cassette that remains innocuous in the absence of inflammation but releases HMGB1 Box A, an antagonist of high mobility group box 1 (HMGB1), in response to inflammatory stimuli such as lipopolysaccharide (LPS) or influenza virus infection. We report here that this novel inflammation-inducible HMGB1 Box A construct in a non-replicative adenovirus (AdV) vector mitigates lung and systemic inflammation therapeutically in response to influenza infection. We anticipate that this strategy will apply to the treatment of multiple diseases in which HMGB1-mediated signaling is a central driver of inflammation.

IMPORTANCE

Many inflammatory diseases are mediated by the action of a host-derived protein, HMGB1, on Toll-like receptor 4 (TLR4) to elicit an inflammatory response. We have engineered a non-replicative AdV vector that produces HMGB1 Box A, an antagonist of HMGB1-induced inflammation, under the control of an endogenous complement component C3 (C3) promoter sequence, that is inducible by LPS and influenza
in vitro
and
ex vivo
in macrophages (Mϕ) and protects mice and cotton rats therapeutically against infection with mouse-adapted and human non-adapted influenza strains, respectively,
in vivo
. We anticipate that this novel strategy will apply to the treatment of multiple infectious and non-infectious diseases in which HMGB1-mediated TLR4 signaling is a central driver of inflammation.
Comparative evaluation of sensititre YeastOne and VITEK2 antifungal susceptibility tests with CLSI broth microdilution method of clinical
Cryptococcus
isolates in Taiwan
Authors: Weng Tzu-Ping , Wang Shin-Wei , Lo Shih-Ting , Su Shu-Li , Hsieh Ming-I , Tsai Pei-Jane , Tsai Pei-Fang , Wu Chi-Jung , Lee Nan-Yao , Ko Wen-Chien , Chen Po-Lin 
Published: December 2024

ABSTRACT

Commercial antifungal susceptibility tests were available for clinical yeast isolates. However, the updated Sensititre YeastOne (SYO) version YO10C excluded
Cryptococcus
species for susceptibility testing. Uncorrelation of antifungal susceptibility patterns by SYO and therapeutic outcomes had been recently reported. We compared the performance of current commercial susceptibility tests with the standard CLSI broth microdilution (BMD) method for clinical
Cryptococcus
isolates. Forty-seven clinical
Cryptococcus
isolates were included from 1 January 2012 to 30 June 2023, among which 44 isolates were
Cryptococcus neoformans
while 3 were
Cryptococcus gattii
. The performance of SYO version YO10C and VITEK2 YS09 was compared with the CLSI BMD method and correlated with MLST analysis and ERG11 mutation detection. Non-wild-type (non-WT) strains to amphotericin B (AMB) were observed in 11 isolates with the CLSI BMD method and 8 with SYO among 44
C
.
neoformans
isolates, but only 1 isolate was classified as non-WT by both methods. Additionally, all
C. neoformans
isolates were susceptible to AMB with their MIC ≤1 µg/mL according to the clinical breakpoint defined by EUCAST. Non-WT to FLC were observed in 5
C
.
neoformans
isolates with SYO, but they were classified as WT by CLSI BMD and VITEK2. The essential agreements between SYO and CLSI BMD were >90% to most antifungal agents except ITC in
C. neoformans
isolates (64%) and AMB in
C. gattii
group (67%). Between SYO and CLSI BMD, the major error (ME) rates were 11% (
n
= 5) to FLC, 5% (
n
= 2) to ITC, and 2% (
n
= 1) to 5FC in
C. neoformans
isolates, and the very major error to 5FC was found in one
C. gattii
isolate. ERG11 mutation with identical I199V was detected in 89% (
n
= 39)
C. neoformans
isolates, and 97% (
n
= 38) of them belonged to sequence type (ST) 5. The ERG11 mutation or cryptococcal ST was not associated with a decrease of antifungal susceptibilities. ME of FLC by SYO version YO10C compared to the CLSI BMD method reached up to 11% of
C. neoformans
isolates. The results of FLC MIC by SYO should be interpreted cautiously and correlated with therapeutic response, and further verification with the CLSI BMD method or VITEK2 is required.

IMPORTANCE

The study pointed out the major errors of fluconazole susceptibility results in clinical
Cryptococcus neoformans
isolates between the commercial Sensititre YeastOne Susceptibility Plate version YO10C and the standard CLSI broth microdilution method. The results should be interpreted carefully with clinical correlation, and a different method of antifungal susceptibility testing should be considered if a discrepancy of susceptibility results is suspected.
A novel sustained-release agent based on disulfide-induced recombinant collagen hydrogels for the prevention and treatment of
Schistosoma
infections
Authors: Wang Jie , Song Lijun , Xing Yuntian , Dai Yang , Hu Jinyuan , Qu Guoli , Xu Yongliang , Yin Xuren , Hang Derong , Zhang Jianfeng , Xiong Chunrong , Shi Liang , Xu Fei 
Published: December 2024

ABSTRACT

Schistosomiasis is commonly managed using the praziquantel, but it is only effective against adult worms and duration of action is short. Liver fibrosis will worsen if eggs are still present after stopping treatment. Therefore, this study aimed to develop a sustained drug release system for effectively preventing and treating schistosomiasis. A disulfide bond-induced three-dimensional (3D) recombinant collagen hydrogel was developed for sustained praziquantel release. Three collagen sequences were developed based on the sequence for
Scl2
of
S. pyogene
, with different substitutions of residues for cysteine (S-VCL-S1, S-VCL-S2, and S-VCL-S3). Their properties were tested. Mice were infected with
Schistosoma japonicum
cercariae and treated either with praziquantel collagen hydrogel or niclosamide collagen hydrogel. The worm-killing effect was examined. The application of hydrogel-niclosamide on the skin for 24 h effectively prevented
Schistosome
cercariae from infecting mice and showed 70.95% and 81.73% reduction in the number of eggs and worms, respectively. The combined use of niclosamide and anti-cercariae cream showed 100% protection after 24 h. The hydrogel-praziquantel also showed a 100% reduction of worms and eggs after 24 h of subcutaneous injection. The subcutaneous injection of praziquantel after 28 days of infection showed 95.19% and 80.12% reduction of worm and egg counts, respectively, and the development of larvae was significantly slowed down. Liver analysis showed no infection after 7 days of treatment. These results suggest developing a novel type of sustained-release agent against schistosomiasis based on the recombinant collagen hydrogel that provides a potential new treatment for schistosomiasis.

IMPORTANCE
This study introduces an new way for treating schistosomiasis: a special collagen hydrogel that gradually releases medication to treat schistosomiasis effectively. This innovation provides a promising way to treat schistosomiasis. It represents a significant step forward in the fight against this disease and offers hope for more effective and safer treatments in the future.
Model-based Toolchain for Core Flight System (cFS) Embedded Systems
Authors: Valente Hugo , de Miguel Miguel , Pérez-Muñoz Ángel , Alonso Alejandro , Zamorano Juan , de la Puente Juan 
Published: December 2024

The space domain is experiencing a paradigm shift with the rise of micro and nanosatellites. Historically, launching a satellite required a big financial risk only sustained by governments or big companies. Nowadays, with the miniaturization of satellites, there has been a significant reduction in costs and, as a consequence, a greater opportunity for universities and smaller businesses to launch satellites into space.
Companies are taking advantage of this reduction in launch and manufacturing costs to gain a competitive edge by adopting what is known as “Agile Space”, which emphasizes rapid iterations. To facilitate this high development pace, specialized toolchains and frameworks are designed for satellite software development.
In this article, we provide a solution to reduce the development time of embedded software systems by ensuring consistency between the design and the implementation. We have integrated the core Flight System (cFS), a message-oriented framework developed by NASA based on a publish-subscribe architecture, with TASTE, a toolset from the European Space Agency. This integration combines modeling capabilities and automatic code generation, reducing error-prone repetitive tasks. It ensures consistency across different development stages allowing the end-user to focus on the implementation-specific details. To demonstrate the feasibility and advantages of this model-based toolchain, we present a case study of the UPMSat-2 microsatellite. This study demonstrates how this approach can be used to successfully support the development of embedded software systems.
Two-Dimensional Siloxene: A Promising Silicon-Based Material with Buffered Volume Change As Anode for Lithium Ion Batteries
Authors: Zhang Xiaoxiao , Xin Le , Qiu Dantong , Qu Huainan , Liu Miao , Ding Tianyao , Zheng Dong , Qu Deyang 
Published: December 2024

Silicon has emerged as a potential anode material for lithium-ion batteries due to its high theoretical capacity of 3579 mAh g−1 (Li3.75Si). However, the alloy reaction with a high lithium content presents challenges, such as significant volumetric expansion and an unstable solid electrolyte interphase layer, which are detrimental to the electrodes and lead to rapid capacity fade [1]. Siloxene, a silicon compound with a layered structure, has attracted attention in lithium-ion battery applications due to its small volume change and moderate capacity [2, 3]. This material is obtained through the topotactic deintercalation of Ca2+ from layered CaSi2 [4]. Microscopically, the layered structure of siloxene consists of Si6 rings interconnected with or without oxygen to form planes, with Si–OH/Si–H bonds on the surface of these planes [5]. Macroscopically, siloxene exhibits a morphology of stacked layered sheets. Our research explored how the layered morphology of siloxene changes during the lithiation/delithiation process. Figure 1 showed that the siloxene sheets bulge together during lithiation and revert to separate sheets after delithiation. The buffered volume change of the layered siloxene material contributed to significantly better cycling performance compared to chunky SiO and spherical Si/C materials. Additionally, the cycling performance of siloxene was further improved when it was blended with graphite materials.
[1] Kim, N., Kim, Y., Sung, J., & Cho, J. (2023). Issues impeding the commercialization of laboratory innovations for energy-dense Si-containing lithium-ion batteries. Nature Energy, 8(9), 921-933.
[2] Loaiza, L. C., Monconduit, L., & Seznec, V. (2020). Si and Ge‐based anode materials for Li‐, Na‐, and K‐ion batteries: a perspective from structure to electrochemical mechanism. Small, 16(5), 1905260.
[3] Loaiza, L. C., Dupré, N., Davoisne, C., Madec, L., Monconduit, L., & Seznec, V. (2021). Complex lithiation mechanism of siloxene and germanane: two promising battery electrode materials. Journal of The Electrochemical Society, 168(1), 010510.
[4] Yamanaka, S., Matsuura, H., & Ishikawa, M. (1996). New deintercalation reaction of calcium from calcium disilicide. Synthesis of layered polysilane. Materials Research Bulletin, 31(3), 307-316.
[5] Weiss, A., Beil, G. & Meyer, H. (1980). The Topochemical Reaction of CaSi2 to a Two-Dimensional Subsiliceous Acid Si6H3(OH)3 (= Kautskys’ Siloxene). Zeitschrift für Naturforschung B, 35(1), 25-30.

Figure 1