bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allogenic MSC infusion in kidney transplantation recipients promotes within 4 hours distinct B cell and T cell phenotypes
Authors: Hendriks Sanne H. , Heidt Sebastiaan , Reinders Marlies E.J. , Koning Frits , van Kooten Cees 
Published: October 2024

BackgroundInfusion of mesenchymal stromal cells (MSCs) has been proposed as immune-modulatory therapy in solid organ transplantation. The use of allogenic MSCs could improve standardization and allow for direct availability of the product.MethodThe nonrandomized phase Ib Neptune clinical trial provided safety and feasibility data on the use of allogenic bone-marrow-derived MSCs, infused in 10 patients at week 25 and 26 post kidney transplantation. Here, we performed detailed analysis on the peripheral blood immune cell composition of these patients up to 52 weeks post transplantation. We used a 40 marker antibody panel with mass cytometry to assess potential effects of MSC therapy on the immune system.ResultsWe showed minor changes in major immune lineages at week 27, 34 and 52 post kidney transplantation after MSC infusion at week 25 and week 26, confirming previous data with regular flow cytometry. However, in a direct comparison between pre- and post MSC infusion, as soon as 4 hours after MSC infusion, we observed a significant increase in cell numbers of B cell and T cell subsets that shared a unique expression of CD11b, CD11c, CD38, CD39, and Ki-67.ConclusionExploring these CD11b+CD11c+CD38+CD39+Ki-67+ B cells and T cells in the context of MSC infusion after kidney transplantation may be a promising avenue to better understand the immunological effects of MSC therapy.
Multi-omics analyses were combined to construct ubiquitination-related features in colon adenocarcinoma and identify ASNS as a novel biomarker
Authors: Wang Zhaohui , Zhang Wenbing , Yin Xin , Wu Qinqing , Zhang Yongwei , Qian Yeben , Bao Qian , Liu Fubao 
Published: October 2024

BackgroundAs one of the malignant tumors with the highest incidence and fatality in the world, colon adenocarcinoma (COAD) has a very complex pathogenic mechanism, which has not yet been fully elucidated. Ubiquitin can regulate cell proliferation, cell cycle, apoptosis, DNA damage repair, and other processes by changing the activity of substrate proteins or causing ubiquitin-proteasome degradation. These are the key links in the pathogenesis of COAD, and ubiquitin plays an important role in the occurrence and development of COAD.MethodsWe integrated transcriptomics, single-cell and clinical omics, and TCGA and GEO databases of COAD patient data. Cox and Lasso regression was employed to assess ubiquitination genes in COAD for generating ubiquitination-related features. The aim was to evaluate the prognostic value of these features for tumors and their impact on the immune microenvironment. At the same time, the expression level of model genes was further analyzed using single-cell data. Finally, the expression and function of ASNS, a key gene for this trait, were detected in vitro.ResultsIn our study, based on identifiable changes in the expression of marker genes, this feature can be used to classify patients with COAD. Kaplan-Meier survival analysis indicated that those with elevated risk scores in each cohort experienced inferior outcomes. There is good validation in both the training queue and the validation queue. The results of the immune infiltration analysis showed that the immune infiltration rate was significantly increased in the high-risk group. After the knockdown of ASNS, an important gene in the signature, the activity and migration capacity of SW620 and RKO cell lines and colony formation capacity were dramatically reduced in cell tests.ConclusionWe screened ubiquitination-related genes and constructed ubiquitination-related features, which can be used as reliable prognostic indicators of COAD. ASNS was identified as a possible biomarker for COAD.
Monocyte-derived Galectin-9 and PD-L1 differentially impair adaptive and innate immune response in chronic HBV infection and their expression remain unaltered after antiviral therapy
Authors: Dey Debangana , Biswas Satabdi , Pal Sourina , Nandi Sarthak , Khatun Najma , Jha Rambha , Chakraborty Bidhan Chandra , Baidya Ayana , Ghosh Ranajoy , Banerjee Soma , Ahammed SK Mahiuddin , Chowdhury Abhijit , Datta Simanti 
Published: October 2024

IntroductionPatients with chronic HBV infection (CHI) exhibit defective anti-viral immune-response whose underlying causes still remain unclear. Monocytes act as immune sentinels for pathogens and can regulate immunity via interaction with other immune-cells, apart from differentiating into macrophages. Immune-checkpoint molecules (ICMs) expressed by immune-cells, including monocytes are known to negatively regulate immune-responses. Here, we evaluated the expression of ICMs, namely, Gal-9, PD-L1, and CTLA-4 on monocytes in different phases of CHI, identified the viral and the host factors causing their aberrant expression and investigated their impact during interaction of monocytes with T-cells, B-cells and NK-cells and also on monocyte to macrophage differentiation. Influence of Tenofovir therapy on the expression of monocytic ICMs was also studied.MethodsCollection of blood and liver-tissue samples from HBV infected patients and controls, flow-cytometry, cell sorting, cell culture and immune-fluorescence were performed for this study.ResultsGal-9+ and PD-L1+-monocytes were significantly increased in HBeAg-positive as well as HBeAg-negative chronic hepatitis B (CHB) patients than healthy controls (HC). In immune-tolerant (IT) subjects, only Gal-9+-monocytes and in inactive carriers (IC), PD-L1+-monocytes were higher than HC while CTLA-4+-monocytes remained comparable among groups. High serum Hepatitis B surface antigen (HBsAg) concentration in CHB as well as IT and TNF-α in CHB triggered monocytic Gal-9-expression whereas, PD-L1 was induced by elevated TNF-α and IL-4 in CHB and IL-1β in CHB and IC. Purified monocytes from CHB and IT having high Gal-9 expression led to expansion of CD4+CD25+FOXP3+-Tregs, CD19+IL-10+-Bregs and CD19+CD27-CD21–atypical memory B-cells and these monocytes also preferentially differentiated into M2-macrophages. These phenomena were reversed by anti-Gal-9-antibody. Parallelly, PD-L1+-monocytes in CHB and IC reduced IL-2/IFN-γ and IL-6 production by HBV-specific T- and B-cells respectively, which were restored by anti-PD-L1-antibody. Both Gal-9+- and PD-L1+-monocytes caused decline in IFN-γ+-NK-cells but enhanced IL-10-expressing HBV-specific-T-cells and NK-cells. Increased intrahepatic CD14+Gal-9+ and CD14+PD-L1+-monocytes were noted in CHB patients than HC. One-year tenofovir therapy failed to reduce monocytic Gal-9 and PD-L1 along with the levels of HBsAg, TNF-α, IL-1β and IL-4.ConclusionsMonocytic Gal-9 and PD-L1, expressed heterogeneously in different phases of CHI, exert diverse inhibitory effects on immune-responses and their therapeutic targeting could boost anti-HBV immunity.
Varying photosynthetic quotients strongly influence net kelp primary production and seasonal differences increase under warming
Authors: Franke Kiara , Kroth Frederike , Karsten Ulf , Bartsch Inka , Iñiguez Concepción , Graiff Angelika 
Published: October 2024

Reliable net primary production (NPP) estimations of kelp forests are important to evaluate their C-fixation potential. Photosynthetic oxygen measurements can be converted to C-fixation using photosynthetic quotients (PQs). Although there is a known high variability in PQs, the extent and the consequences for NPP is understudied in kelp species. Thus, the present study aimed (i) to quantify the variability of PQs, (ii) to model NPP and (iii) to assess the impact of warming on both. The kelp, Laminaria hyperborea, was studied near the island of Helgoland (North Sea, Germany) along a depth gradient (2, 4, 6 m below mean low water spring tide) across all four seasons. Blade discs were cultivated during at least 6 days per season under simulated ambient photosynthetic photon flux density (PPFD) and temperature conditions and, in parallel, in a warming scenario (+ 4°C). PQs were calculated from parallel oxygen production and 14C-fixation measurements at saturating PPFD at the end of the incubation period. Seasonal PQs varied between 1.7 and 4.4, with highest values in summer due to increased oxygen production. The warming scenario stimulated C-fixation in most seasons, lowering the PQ in comparison to ambient temperature conditions, while collection depth had no significant effect on PQs. The seasonal PQs were used to model daily NPP rates for kelp standing stock at 4 m depth. These daily NPP rates were compared between temperature treatments and with daily NPP rates based on fixed PQs. The warming scenario had a stimulating effect on daily NPP rates in the high-light season spring. In the low-light season autumn, warming resulted in negative daily NPP rates, as the high respiration rates could not be compensated by gross photosynthesis. Overall, annual NPP rate under warming conditions (347 g C m–2 yr–1) was 14% higher than the annual NPP rate under ambient conditions (303 g C m–2 yr–1). Modelling daily NPP with fixed PQs, which neglects the seasonal variation of the PQs, led to a high overestimation of up to 255%. We, therefore, recommend modelling NPP rates not with a fixed PQ, but with seasonal PQs determined under different temperature scenarios in order to obtain reliable future predictions.
Ultrasound assessment of insular development in adequate-for-gestational-age fetuses and fetuses with early-onset fetal growth restriction using 3D-ICRV technology
Authors: Xue Jinfeng , Xue Jinluan , Ru Yanhui , Zhang Ge , Yin Hong , Liu Dequan 
Published: October 2024

ObjectiveThis study aimed to evaluate the growth trajectory of the insula in adequate-for-gestational-age (AGA) and early-onset fetal growth restriction (FGR) fetuses and analyze the difference between the two groups using three-dimensional inversion crytal and realistic vue technique (3D-ICRV).MethodsSingleton pregnant women, with a gestational age ranging from 20 to 32+6 weeks, who underwent routine examinations at Shandong Maternal and Child Care Hospital between March 2023 and December 2023 were included. The participants were divided into two groups: the FGR and AGA fetuses. Three-dimensional volumes were obtained using transabdominal ultrasound in the transverse section of the fetal hypothalamus based on different gestational ages. 3D-ICRV rendering technology was used for 3D imaging of the fetal insula. Volumes with a clear display of the insula were selected. We observed the morphology of the insula, and measured the area and circumference of the insula. By evaluating the growth trajectory of the insula in AGA and FGR fetuses, differences in insular development between the two groups were compared.ResultsOverall, 203 participants were included in this study, with 164 and 39 in the AGA and FGR groups, respectively. The 3D volumes were successfully acquired, and the area and circumference of the insula were measured using 3D-ICRV imaging technology. We found that as gestational age increased, the area and circumference of the insula gradually increased and showed positive correlations with the gestational age, with no significant changes in morphology. The growth rate of insular area and insular circumference in the FGR group is slower than that in the AGA group (insular area: 0.15 vs 0.19 cm2 / week, insular circumference: 0.25 vs 0.28 cm / week). The area and circumference of the insula in the FGR group were significantly different from those in the AGA group (insular area: p = 0.003, insular circumference: p = 0.004).ConclusionThe measured values of the insula using 3D-ICRV identify the differences in insular development between the FGR and AGA fetuses. The findings of this study have important implications for the prenatal evaluation of cortical development and maturity in FGR fetuses and further clinical consultation and management.
Analysis of corneal surface shape following overnight orthokeratology with different optical zone diameters
Authors: Chen Minfeng , Zhang Ronghan , Zhu Chengwei , Peng Lulu , Zhao Sijun , Mao Xinjie 
Published: October 2024

PurposeThis study analyzed the corneal surface shape following overnight orthokeratology with different optical zone diameters.MethodsA total of 82 eyes belonging to 41 myopic children who completed 1 month of the orthokeratology (ortho-k) lens wear at the Eye Hospital of Wenzhou Medical University from January 2022 to January 2023 were retrospectively analyzed. According to the size of the base curve (BC) of ortho-k lens, patients were divided into BC 5.0 and BC 6.0 groups. The changes in decentration distance and corneal refraction of the two groups after the ortho-k lens wear were analyzed. Independent sample t-tests were used to compare these two outcome measures between the two groups.ResultsThe decentration distance of BC 5.0 group (0.37 ± 0.19 mm) was significantly lower than that of BC 6.0 group (0.49 ± 0.25 mm, t = −2.330, p = 0.022). In the BC 5.0 group, the direction of decentration was superonasal in 3 cases, inferonasal in 2 cases, inferotemporal in 21 cases, and superotemporal in 6 cases. In the BC 6.0 group, the direction of decentration was superonasal in 2 cases, inferonasal in 2 cases, inferotemporal in 27 cases, and superotemporal in 19 cases. The optical zone area (8.19 ± 2.96 mm2) and reverse curve zone area (30.05 ± 6.74 mm2) in the BC 5.0 group were significantly lower than in the BC 6.0 group (10.42 ± 2.03 mm2, t = −4.043, p &lt; 0.001; 38.21 ± 4.77 mm2, t = −6.422, p &lt; 0.001). The change in the rate of refraction in the horizontal direction in BC 5.0 group were significant higher than in BC 6.0 group.ConclusionBase curve 5.0 mm ortho-k lens is better positioned than BC 6.0 mm lens. A small BC ortho-k forms a smaller optical zone and reverse curve area, which might get a greater aiameter of alignment curve to facilitate positioning better than the traditional BC lens. In addition, a small BC lens increases positive refraction in the peripheral area, resulting in a greater negative pressure than the traditional BC lens.
Profiling cytokines in peritoneal effluent through a targeted multiplex cytokine panel provides novel insight into the localized proinflammatory processes in patients undergoing peritoneal dialysis
Authors: Okulewicz Patrycja , Wojciuk Bartosz , Wojciechowska-Koszko Iwona , Domański Leszek , Gołembiewska Edyta 
Published: October 2024

ObjectivesThe number of relevant markers indicating local intraperitoneal inflammation in patients undergoing peritoneal dialysis (PD) is limited. Therefore, this study aimed to evaluate the compatibility of peritoneal effluent (PE) for proteomic analysis and assess its potential utility in immunoprofiling studies.MethodsThis pilot study included six PD patients from the Peritoneal Dialysis Center, Department of Nephrology, Transplantology, and Internal Medicine in Szczecin, Poland. All patients were clinically stable, with no signs of infections or malignancy at the time of study. PE samples were collected during routine surveillance visits at the Peritoneal Dialysis Center. Proteomic analysis of the samples was conducted using the Olink® (Olink Proteomics AB, Uppsala, Sweden) Target 48 Cytokine panel.ResultsPE samples were successfully analyzed, with 28 out of 45 proteins found within the limit of quantitation (LOQ) and 32 out of 45 proteins detected above the limit of detection (LOD). No significant interference from the matrix was observed in the assay. Biomarkers associated with low-grade inflammation showed varied levels, and the observed patterns were comparable across all patients.ConclusionThis study suggests that utilizing a cytokine panel with relative quantification is a promising method for PE immunoprofiling.
Trends and hotspots in the field of diabetic retinopathy imaging research from 2000–2023
Authors: Zhang Qing , Zhang Ping , Chen Naimei , Zhu Zhentao , Li Wangting , Wang Qiang 
Published: October 2024

BackgroundDiabetic retinopathy (DR) poses a major threat to diabetic patients’ vision and is a critical public health issue. Imaging applications for DR have grown since the 21st century, aiding diagnosis, grading, and screening. This study uses bibliometric analysis to assess the field’s advancements and key areas of interest.MethodsThis study performed a bibliometric analysis of DR imaging articles collected from the Web of Science Core Collection database between January 1st, 2000, and December 31st, 2023. The literature information was then analyzed through CiteSpace.ResultsThe United States and China led in the number of publications, with 719 and 609, respectively. The University of London topped the institution list with 139 papers. Tien Yin Wong was the most prolific researcher. Invest. Ophthalmol. Vis. Sci. published the most articles (105). Notable burst keywords were “deep learning,” “artificial intelligence,” et al.ConclusionThe United States is at the forefront of DR research, with the University of London as the top institution and Invest. Ophthalmol. Vis. Sci. as the most published journal. Tien Yin Wong is the most influential researcher. Hotspots like “deep learning,” and “artificial intelligence,” have seen a significant rise, indicating artificial intelligence’s growing role in DR imaging.
Comparative metagenomic study unveils new insights on bacterial communities in two pine-feeding Ips beetles (Coleoptera: Curculionidae: Scolytinae)
Authors: Khara Arunabha , Chakraborty Amrita , Modlinger Roman , Synek Jiří , Roy Amit 
Published: October 2024

BackgroundClimate change has recently boosted the severity and frequency of pine bark beetle attacks. The bacterial community associated with these beetles acts as “hidden players,” enhancing their ability to infest and thrive on defense-rich pine trees. There is limited understanding of the environmental acquisition of these hidden players and their life stage-specific association with different pine-feeding bark beetles. There is inadequate knowledge on novel bacterial introduction to pine trees after the beetle infestation. Hence, we conducted the first comparative bacterial metabarcoding study revealing the bacterial communities in the pine trees before and after beetle feeding and in different life stages of two dominant pine-feeding bark beetles, namely Ips sexdentatus and Ips acuminatus. We also evaluated the bacterial association between wild and lab-bred beetles to measure the deviation due to inhabiting a controlled environment.ResultsSignificant differences in bacterial amplicon sequence variance (ASVs) abundance existed among different life stages within and between the pine beetles. However, Pseudomonas, Serratia, Pseudoxanthomonas, Taibaiella, and Acinetobacter served as core bacteria. Interestingly, I. sexdentatus larvae correspond to significantly higher bacterial diversity and community richness and evenness compared to other developmental stages, while I. acuminatus adults displayed higher bacterial richness with no significant variation in the diversity and evenness between the life stages. Both wild and lab-bred I. sexdentatus beetles showed a prevalence of the bacterial family Pseudomonadaceae. In addition, wild I. sexdentatus showed dominance of Yersiniaceae, whereas Erwiniaceae was abundant in lab-bred beetles. Alternatively, Acidobacteriaceae, Corynebacteriaceae, and Microbacteriaceae were highly abundant bacterial families in lab-bred, whereas Chitinophagaceae and Microbacteriaceae were highly abundant in wild I. accuminatus. We validated the relative abundances of selected bacterial taxa estimated by metagenomic sequencing with quantitative PCR.ConclusionOur study sheds new insights into bacterial associations in pine beetles under the influence of various drivers such as environment, host, and life stages. We documented that lab-breeding considerably influences beetle bacterial community assembly. Furthermore, beetle feeding alters bacteriome at the microhabitat level. Nevertheless, our study revisited pine-feeding bark beetle symbiosis under the influence of different drivers and revealed intriguing insight into bacterial community assembly, facilitating future functional studies.
Pathotype determination of sorghum anthracnose (Colletotrichum sublineola) isolates from Ethiopia using sorghum differentials
Authors: Mekonen Moges , Tesfaye Kassahun , Mengiste Tesfaye , Chala Alemayehu , Nida Habte , Mekonnen Tilahun , Abreha Kibrom B. , Geleta Mulatu 
Published: October 2024

IntroductionSorghum anthracnose, caused by Colletotrichum sublineola, is the most destructive disease of sorghum, which causes up to 80% grain yield loss in susceptible varieties. The use of resistance varieties is an effective, durable, and eco-friendly strategy for anthracnose control. Knowledge of the phenotypic and genetic variation in C. sublineola is vital for designing appropriate anthracnose management strategies.MethodsThe present study examined the morphology and virulence of 25 C. sublineola isolates recovered from various sorghum-producing regions of Ethiopia against 18 known sorghum anthracnose differentials, 6 Ethiopian sorghum landraces, and a variety of Bonsa.ResultsAnalysis of variance (ANOVA) revealed significant differences among sorghum genotypes, C. sublineola isolates, and their interactions. There was a significant difference between the isolates in virulence, with each isolate exhibiting virulence in 8–72% of the sorghum genotypes tested. Among the 25 tested isolates, the top four most virulent isolates were from Pawe, suggesting that this area is suitable for pathogen diversity studies and host plant resistance screening. The sorghum genotypes IS_18760, Brandes, and Bonsa showed resistance to all tested isolates. Consequently, they may provide potential sources of resistance genes for sorghum breeding programs to develop cultivars resistant to different C. sublineola pathotypes. However, the resistant check SC748-5 was susceptible to isolates NK73_F37, while another resistant check SC112-14 was susceptible to isolates PW123_F47 and PW122_F47. Cluster analysis grouped 22 isolates into seven clusters based on their morphological characters, whereas 24 pathotypes were identified among 25 isolates that were tested on 25 sorghum genotypes.DiscussionHence, this study revealed high variation in C. sublineola in Ethiopia suggesting the need for broad-spectrum resistance to control the disease. Sorghum genotypes resistant to various C. sublineola isolates were identified in this study, which can be used in sorghum breeding programs aiming to develop resistant cultivars to anthracnose. Highly virulent C. sublineola isolates were also identified which could be used in sorghum germplasm resistance screening. The report is the first to show the existence of C. sublineola pathotypes in Ethiopia.