bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis and preclinical evaluation of a 89Zr-labelled human single chain antibody for non-invasive detection of hepatic myofibroblasts in acute liver injury
Authors: Pringle Toni A. , Ramon-Gil Erik , Leslie Jack , Oakley Fiona , Wright Matthew C. , Knight James C. , Luli Saimir 
Published: January 2024

AbstractSynaptophysin is expressed on fibrogenic hepatic myofibroblasts. C1–3 is a single chain human antibody (scAb) that binds specifically to synaptophysin on hepatic myofibroblasts, providing a targeting vector for novel in vivo imaging agents of chronic liver disease. C1–3 and a negative control scAb, CSBD9, were radiolabelled with zirconium-89 via desferrioxamine chelation to enable non-invasive molecular imaging with positron emission tomography (PET). DFO-scAb conjugates were characterised by gel electrophoresis (SDS-PAGE) and MALDI-TOF spectrometry, and 89Zr-labelled with high radiolabelling efficiency (99%). [89Zr]Zr-DFO-C1–3 exhibited high in vitro stability (> 99%) in mouse and human sera over 3 days at 25 and 37 °C. Activated hepatic myofibroblasts incubated with [89Zr]Zr-DFO-C1–3 displayed significantly higher internalised activity (59.46%, P = 0.001) compared to the [89Zr]Zr-DFO-CSBD9 control, indicating synaptophysin-mediated uptake and high binding specificity of [89Zr]Zr-DFO-C1–3. Mice with CCl4-induced acute liver damage exhibited significantly higher liver uptake of [89Zr]Zr-DFO-C1–3, compared to controls, confirmed by both Cerenkov imaging and ex vivo gamma counting (4.41 ± 0.19%ID/g, P < 0.0001). CCl4-induced liver damage and the number of hepatic myofibroblasts was confirmed by αSMA staining of liver sections. These findings indicate that [89Zr]Zr-DFO-C1–3 has promising utility as a PET imaging agent for non-invasive detection of hepatic myofibroblasts following acute liver injury.
NMGMDA: a computational model for predicting potential microbe–drug associations based on minimize matrix nuclear norm and graph attention network
Authors: Liang Mingmin , Liu Xianzhi , Chen Qijia , Zeng Bin , Wang Lei 
Published: January 2024

AbstractThe prediction of potential microbe–drug associations is of great value for drug research and development, especially, methods, based on deep learning, have been achieved significant improvement in bio-medicine. In this manuscript, we proposed a novel computational model named NMGMDA based on the nuclear norm minimization and graph attention network to infer latent microbe–drug associations. Firstly, we created a heterogeneous microbe–drug network in NMGMDA by fusing the drug and microbe similarities with the established drug–microbe associations. After this, by using GAT and NNM to calculate the predict scores. Lastly, we created a fivefold cross validation framework to assess the new model NMGMDA's progressiveness. According to the simulation results, NMGMDA outperforms some of the most advanced methods, with a reliable AUC of 0.9946 on both MDAD and aBioflm databases. Furthermore, case studies on Ciprofloxacin, Moxifoxacin, HIV-1 and Mycobacterium tuberculosis were carried out in order to assess the effectiveness of NMGMDA even more. The experimental results demonstrated that, following the removal of known correlations from the database, 16 and 14 medications as well as 19 and 17 microbes in the top 20 predictions were validated by pertinent literature. This demonstrates the potential of our new model, NMGMDA, to reach acceptable prediction performance.
Genomic epidemiology and evolutionary analysis during XBB.1.16-predominant periods of SARS-CoV-2 omicron variant in Bangkok, Thailand: December 2022–August 2023
Authors: Puenpa Jiratchaya , Chansaenroj Jira , Suwannakarn Kamol , Poovorawan Yong 
Published: January 2024

AbstractThe growing occurrence of novel recombinants, such as XBB.1.16, has emerged and become predominant, raising concerns about the impact of genomic recombination on the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study investigated the molecular epidemiological trends and evolution of the Omicron XBB.1.16 epidemic in Bangkok between December 2022 and August 2023. Partial spike and complete genome sequencing of SARS-CoV-2 samples collected from collaborating hospitals were performed. The analysis of 491 partial spike sequences identified 15 distinct lineages, with XBB.1.16 dominating the lineages beginning in March 2023. Phylogenetic analysis revealed at least four distinct XBB.1.16 lineages, suggesting multiple independent introductions into Bangkok. The estimated emergence of XBB.1.16 occurred approximately in January 2022, with an evolutionary rate of 0.79 × 10–3 substitutions per site per year. Monitoring the genomic epidemiology and evolution of XBB.1.16 is vital for the early detection of new strains or emerging variants, which may guide vaccine design and the inclusion of new vaccine strains.
Nano carbon-modified air purification filters for removal and detection of particulate matters from ambient air
Authors: Attia Yasser A. , Ezet Abd Elhakim , Saeed Samar , Galmed Ahmed H. 
Published: January 2024

AbstractParticulate matters (PMs) pose significant risks to human health and the environment, necessitating research to enhance air purification filters and reduce harmful emissions. This study focuses on the preparation of carbon nanomaterials, including graphitic carbon nitride nanosheets (g-C3N4 NSs), reduced graphene oxide (r-GO), and carbon nanotubes (CNT), for modifying filters in air particle monitoring devices. The objective is to investigate the impact of these nanomaterials on enhancing PM adsorption efficiency. Quantitative and qualitative analyses of the modified filters’ adsorption efficiency towards PMs are performed using spectroscopic techniques such as Energy-Dispersive X-ray Spectroscopy (EDX), Inductively Coupled Plasma (ICP), and Laser-Induced Breakdown Spectroscopy (LIBS). The results reveal that CNT-modified filters exhibit superior adsorption efficiency compared to the control, g-C3N4, and r-GO-modified filters. The exceptional performance of CNTs is attributed to their large specific surface area and pore volume. Additionally, LIBS demonstrates its capability to detect heavy metals like Cd, which remain undetected by EDX and ICP. The technique proves sensitive for heavy metal monitoring. This novel approach is expected to garner significant attention and contribute to the development of improved air purification technologies.
Hyponatremia after COVID-19 is frequent in the first year and increases re-admissions
Authors: Biagetti Betina , Sánchez-Montalvá Adrián , Puig-Perez Albert , Campos-Varela Isabel , Pilia María Florencia , Anderssen-Nordahl Emilie , González-Sans Didac , Miarons Marta , Simó Rafael 
Published: January 2024

AbstractHyponatremia on admission has been related to worse outcomes in patients with COVID-19 infection. However, little is known about the frequency and the associated risk factors of hyponatremia after COVID-19 discharge. We performed an observational 24-month follow-up study of patients admitted during the first COVID-19 wave. Kaplan–Meier curves and Cox proportional hazard models were used to assess the main variables in predicting hyponatremia on follow-up (HYPO-FU). A total of 161 out of 683 (24.4%) developed HYPO-FU. The group with HYPO-FU comprised of more men [(62.3%) vs. (49.2%); p < 0.01], older [65.6 ± 18.2 vs. 60.3 ± 17.0; p < 0.01] and more frequently re-admitted [(16.2%) vs. (3.8%); p < 0.01). The rate of HYPO-FU was higher in the first year 23.6 per 100 individuals per year. After Cox regression analysis, the independent risk factors of HYPO-FU were diabetes [OR 2.12, IC 95% (1.48–3.04)], hypertension [OR 2.18, IC 95% (1.53–3.12)], heart failure [OR 3.34, IC 95% (1.72–6.48)] and invasive ventilation support requirement [OR: 2.38, IC 95% (1.63–3.50)]. To conclude, HYPO-FU was frequent in the first year after COVID-19 infection, and the risk was higher in older men with comorbidities, increasing rehospitalisation. Further studies aimed at evaluating the beneficial effects of correcting hyponatremia in these patients are warranted.
Nanocarrier-mediated probiotic delivery: a systematic meta-analysis assessing the biological effects
Authors: Pandey Ramendra Pati , Gunjan  , Himanshu  , Mukherjee Riya , Chang Chung-Ming 
Published: January 2024

AbstractProbiotics have gained a significant attention as a promising way to improve gut health and overall well-being. The increasing recognition of the potential health advantages associated with functional food products, leading to a specific emphasis on co-encapsulating probiotic bacteria and bioactive compounds within a unified matrix. To further explore this concept, a meta-analysis was performed to assess the effects of probiotics encapsulated in nanoparticles. A comprehensive meta-analysis was conducted, encompassing 10 papers published from 2017 to 2022, focusing on the encapsulation of probiotics within nanoparticles and their viability in various gastrointestinal conditions. The selection of these papers was based on their direct relevance to the research topic. Random-effect models were used to aggregate study-specific risk estimates. In the majority of studies, it was observed that nano-encapsulated nanoparticles showed improved viability over time compared to their free state counterparts. At various time intervals, the odds ratios (OR) with 95% confidence intervals (CI) were estimated using fixed and random effect models. At 0 min, the OR (95%CI) was 2.79 (2.79; 2.80) and 2.38 (2.14; 2.64) for. At 30 and 60 min observation was at similar rate of 2.23 (2.23; 2.24) and 2.05 (1.73; 2.43). However, at 90 min it was 1.39 (1.39; 1.39) and 1.66 (1.29; 2.14) and at 120 min 2.41 (2.41; 2.42) and 2.03 (1.63; 2.52). Overall evaluation of encapsulation revealed an improvement in probiotic bacterial viability in simulated the gastrointestinal environments.
Optimizing strategy for the discovery of compositionally-biased or low-complexity regions in proteins
Authors: Harrison Paul M. 
Published: January 2024

AbstractProteins can contain tracts dominated by a subset of amino acids and that have a functional significance. These are often termed ‘low-complexity regions’ (LCRs) or ‘compositionally-biased regions’ (CBRs). However, a wide spectrum of compositional bias is possible, and program parameters used to annotate these regions are often arbitrarily chosen. Also, investigators are sometimes interested in longer regions, or sometimes very short ones. Here, two programs for annotating LCRs/CBRs, namely SEG and fLPS, are investigated in detail across the whole expanse of their parameter spaces. In doing so, boundary behaviours are resolved that are used to derive an optimized systematic strategy for annotating LCRs/CBRs. Sets of parameters that progressively annotate or ‘cover’ more of protein sequence space and are optimized for a given target length have been derived. This progressive annotation can be applied to discern the biological relevance of CBRs, e.g., in parsing domains for experimental constructs and in generating hypotheses. It is also useful for picking out candidate regions of interest of a given target length and bias signature, and for assessing the parameter dependence of annotations. This latter application is demonstrated for a set of human intrinsically-disordered proteins associated with cancer.
Seroincidence of SARS-CoV-2 infection prior to and during the rollout of vaccines in a community-based prospective cohort of U.S. adults
Authors: Nash Denis , Srivastava Avantika , Shen Yanhan , Penrose Kate , Kulkarni Sarah G. , Zimba Rebecca , You William , Berry Amanda , Mirzayi Chloe , Maroko Andrew , Parcesepe Angela M. , Grov Christian , Robertson McKaylee M. 
Published: January 2024

AbstractThis study used repeat serologic testing to estimate infection rates and risk factors in two overlapping cohorts of SARS-CoV-2 N protein seronegative U.S. adults. One mostly unvaccinated sub-cohort was tracked from April 2020 to March 2021 (pre-vaccine/wild-type era, n = 3421), and the other, mostly vaccinated cohort, from March 2021 to June 2022 (vaccine/variant era, n = 2735). Vaccine uptake was 0.53% and 91.3% in the pre-vaccine and vaccine/variant cohorts, respectively. Corresponding seroconversion rates were 9.6 and 25.7 per 100 person-years. In both cohorts, sociodemographic and epidemiologic risk factors for infection were similar, though new risk factors emerged in the vaccine/variant era, such as having a child in the household. Despite higher incidence rates in the vaccine/variant cohort, vaccine boosters, masking, and social distancing were associated with substantially reduced infection risk, even through major variant surges.
Bioprospecting of endophytic fungi from medicinal plant Anisomeles indica L. for their diverse role in agricultural and industrial sectors
Authors: Toppo Prabha , Jangir Pooja , Mehra Namita , Kapoor Rupam , Mathur Piyush 
Published: January 2024

AbstractEndophytes are microorganisms that inhabit various plant parts and cause no damage to the host plants. During the last few years, a number of novel endophytic fungi have been isolated and identified from medicinal plants and were found to be utilized as bio-stimulants and bio fertilizers. In lieu of this, the present study aims to isolate and identify endophytic fungi associated with the leaves of Anisomeles indica L. an important medicinal plant of the Terai-Duars region of West Bengal. A total of ten endophytic fungi were isolated from the leaves of A. indica and five were identified using ITS1/ITS4 sequencing based on their ability for plant growth promotion, secondary metabolite production, and extracellular enzyme production. Endophytic fungal isolates were identified as Colletotrichum yulongense Ai1, Colletotrichum cobbittiense Ai2, Colletotrichum alienum Ai2.1, Colletotrichum cobbittiense Ai3, and Fusarium equiseti. Five isolates tested positive for their plant growth promotion potential, while isolates Ai4. Ai1, Ai2, and Ai2.1 showed significant production of secondary metabolites viz. alkaloids, phenolics, flavonoids, saponins, etc. Isolate Ai2 showed maximum total phenolic concentration (25.98 mg g−1), while isolate Ai4 showed maximum total flavonoid concentration (20.10 mg g−1). Significant results were observed for the production of extracellular enzymes such as cellulases, amylases, laccases, lipases, etc. The isolates significantly influenced the seed germination percentage of tomato seedlings and augmented their growth and development under in vitro assay. The present work comprehensively tested these isolates and ascertained their huge application for the commercial utilization of these isolates both in the agricultural and industrial sectors.
Effects of various types of organo-mica on the physical properties of polyimide nanocomposites
Authors: Jeon Hara , Na Changyub , Kwac Lee Ku , Kim Hong Gun , Chang Jin-Hae 
Published: January 2024

AbstractPoly(amic acid) (PAA) was synthesized using dianhydride 4,4’-oxydiphthalic anhydride and diamine 3,3'-dihydroxybenzidine, and polyimide (PI) hybrid films were synthesized by dispersing organo-mica in PAA through a solution intercalation method. Hexadimethrine-mica (HM-Mica), 1,2-dimethylhexadecylimidazolium-mica (MI-Mica), and didodecyldiphenylammonium-mica (DP-Mica), which were obtained via the organic modification of pristine mica, were used as the organo-micas for the PI hybrid films. The organo-mica content was varied from 0.5 to 3.0 wt% with respect to the PI matrix. The thermomechanical properties, morphology, and optical transparency of the resultant PI hybrid films were measured and compared. Dispersion of even small amounts of organo-mica effectively improved the physical properties of the PI hybrids, and maximum enhancements in physical properties were observed at a specific critical content. Electron microscopy of the hybrid films revealed that the organo-mica uniformly dispersed throughout the polymer matrix at the nanoscale level when added at low contents but aggregated in the matrix when added at levels above the critical content. Structural changes in the organo-mica closely influenced the changes in the physical properties of the hybrid films. All PI hybrid films with various organo-mica contents showed similar optical properties, but that prepared with MI-Mica demonstrated the best thermomechanical properties. All synthesized PI hybrid films were transparent regardless of the type and content of organo-mica used.
Investigation of the Suzuki–Miyaura cross-coupling reaction on a palladium H-beta zeolite with DFT calculations
Authors: Boekfa Bundet , Maihom Thana , Ehara Masahiro , Limtrakul Jumras 
Published: January 2024

AbstractMetal or metal cluster-doped zeolites catalyse a wide variety of reactions. In this work, a coupling reaction between bromobenzene and phenylboronic acid to yield biphenyl with the Pd–H-Beta zeolite catalyst was investigated with density functional theory (DFT) calculations. Utilizing a model system with tetrahedral Pd4 clusters within the H-Beta zeolite, it was demonstrated that the catalyst exhibited notable reactivity by effectively reducing the activation energy barrier for the reaction. Our investigation revealed that the zeolite framework facilitated electron transfer to the Pd cluster, thereby increasing the reaction activity. The coupling reaction was shown to be exothermic and comprise three main steps: oxidative addition of bromobenzene (C6H5Br), transmetallation with phenylboronic acid (C6H5B(OH)2), and reductive elimination of biphenyl (C12H10). Specifically, in the transmetallation step, which was the rate-determining step, the C–B bond breaking in phenylboronic acid (C6H5B(OH)2) and the phenylboronate anion (C6H5B(OH)3–) were compared under neutral and basic conditions, respectively. This comprehensive study clarifies the mechanism for the reaction with the modified Pd zeolite catalyst and highlights the essential role of the zeolite framework.
Comparison of mortality rates in patients with carbapenem-resistant Enterobacterales bacteremia according to carbapenemase production: a multicenter propensity-score matched study
Authors: Baek Moon Seong , Kim Jong Ho , Park Joung Ha , Kim Tae Wan , Jung Hae In , Kwon Young Suk 
Published: January 2024

AbstractThe spread of carbapenem-resistant Enterobacterales (CRE) poses a public health threat worldwide. We aimed to compare the mortality rates between the carbapenemase-producing (CP) and non-CP CRE bacteremia. We conducted a retrospective cohort study in patients with CRE bacteremia after propensity score (PS) matching. We performed a Kaplan–Meier curve analysis to identify the cumulative hazard for 30-day mortality. There were 318 patients with CRE between January 1, 2018, and December 31, 2022. There were 252 patients with CP-CRE and 66 with non-CP-RE, respectively. Before PS matching, the 30-day mortality rates were 40.9% in the non-CP-CRE group and 53.2% in the CP-CRE group (p = 0.097). In patients in the intensive care unit (ICU), the mortality rates were 49.0% in the non-CP-CRE group and 57.1% in the CP-CRE group (p = 0.340). After PS matching, the hazard ratio (HR) for mortality in the CP-CRE group was 1.49 (95% confidence interval [CI] 0.74–3.03), p = 0.266). In ICU patients, the HR of CP-CRE was 1.11 (95% CI 0.36–3.39, p = 0.860). The Kaplan–Meier curve for 30-day mortality showed no difference in cumulative hazard. After PS matching, there was no difference in 30-day mortality between patients with CP-CRE and non-CP-CRE bacteremia.
Development and validation of a novel lysosome-related LncRNA signature for predicting prognosis and the immune landscape features in colon cancer
Authors: Li Fengming , Wang Wenyi , Lai Guanbiao , Lan Shiqian , Lv Liyan , Wang Shengjie , Liu Xinli , Zheng Juqin 
Published: January 2024

AbstractLysosomes are essential components for managing tumor microenvironment and regulating tumor growth. Moreover, recent studies have also demonstrated that long non-coding RNAs could be used as a clinical biomarker for diagnosis and treatment of colorectal cancer. However, the influence of lysosome-related lncRNA (LRLs) on the progression of colon cancer is still unclear. This study aimed to identify a prognostic LRL signature in colon cancer and elucidated potential biological function. Herein, 10 differential expressed lysosome-related genes were obtained by the TCGA database and ultimately 4 prognostic LRLs for conducting a risk model were identified by the co-expression, univariate cox, least absolute shrinkage and selection operator analyses. Kaplan–Meier analysis, principal-component analysis, functional enrichment annotation, and nomogram were used to verify the risk model. Besides, the association between the prognostic model and immune infiltration, chemotherapeutic drugs sensitivity were also discussed in this study. This risk model based on the LRLs may be promising for potential clinical prognosis and immunotherapeutic responses related indicator in colon cancer patients.
Utilizing molecular docking and cell validation to explore the potential mechanisms of lupenone attenuating the inflammatory response via NF‐κB pathway
Authors: Wang Xiangpei , Liu Mei , Li Xiaofen , Zhang Mei , Xu Feng , Liu Hongyun , Wu Hongmei 
Published: January 2024

AbstractDiabetic nephropathy (DN), a common microvascular complicating disease of diabetes. Lupenone, a pentacyclic triterpenoid, has anti-inflammatory effects and can prevent type 2 diabetes mellitus and treat renal damage, however, the effects and mechanisms of lupenone in DN remain unclear. Thereby,the MTT method was used to investigate the antiproliferative effect of lupenoneon the cell line rat glomerular mesangial cells (HBZY-1). Molecular docking was used to investigate the combination of lupenone and MCP-1, IL-1β, TNF-α, IKKβ, IκBα, and NF-κB p65 proteins. The expression of mRNA of the pro-inflammatory cytokines (MCP-1, IL-1β and TNF-α) and the NF-κB signalling pathway in HBZY-1 cells were assessed by RT-PCR. The protein expressions of pro-inflammatory cytokines and NF-κB pathway were got by Western blot. Result showed that lupenone inhibited the proliferative activity of HBZY-1 cells at non-cytotoxic concentrations. Molecular docking results showed that lupenone combined well with the target proteins. Moreover, lupenone could significantly reduced the mRNA and protein expressions for pro-inflammatory cytokines and IKKβ, p-p65 and p-IκBα. Lupenone may play an anti-inflammatory role in DN treatment by inhibiting the NF-κB signalling pathway. These results provided a new understanding of the pharmacological mechanisms of lupenone in treatment of DN.