bluuebunny/crossref_metadata_2025_split huggingface dataset:
The adult shell matrix protein repertoire of the marine snail Crepidula is dominated by conserved genes that are also expressed in larvae
Authors: Lopez-Anido Rebecca N. , Batzel Grant O. , Ramirez Gabriela , Wang Yiqun , Neal Stephanie , Lesoway Maryna P. , Goodheart Jessica A. , Lyons Deirdre C. 
Published: September 2024

AbstractMollusca is a morphologically diverse phylum, exhibiting an immense variety of calcium carbonate structures. Proteomic studies of adult shells often report high levels of rapidly-evolving, ‘novel’ shell matrix proteins (SMPs), which are hypothesized to drive shell diversification. However, relatively little is known about the phylogenetic distribution of SMPs, or about the function of individual SMPs in shell construction. To understand how SMPs contribute to shell diversification a thorough characterization of SMPs is required. Here, we build tools and a foundational understanding of SMPs in the marine gastropod species Crepidula fornicata and Crepidula atrasolea because they are genetically-enabled mollusc model organisms. First, we established a staging system of shell development in C. atrasolea for the first time. Next, we leveraged previous findings in C. fornicata combined with phylogenomic analyses of 95 metazoan species to determine the evolutionary lineage of its adult SMP repertoire. We found that 55% of C. fornicata’s SMPs belong to molluscan orthogroups, with 27% restricted to Gastropoda, and only 5% restricted at the species level. The low percentage of species-restricted SMPs underscores the importance of broad-taxon sampling and orthology inference approaches when determining homology of SMPs. From our transcriptome analysis, we found that the majority of C. fornicata SMPs that were found conserved in C. atrasolea were expressed in both larval and adult stages. We then selected a subset of SMPs of varying evolutionary ages for spatial-temporal analysis using in situ hybridization chain reaction (HCR) during larval shell development in C. atrasolea. Out of the 18 SMPs analyzed, 12 were detected in the larval shell field. These results suggest overlapping larval vs. adult SMP repertoires. Using multiplexed HCR, we observed five SMP expression patterns and three distinct cell populations within the shell field. These patterns support the idea that modular expression of SMPs could facilitate divergence of shell morphological characteristics. Collectively, these data establish an evolutionary and developmental framework in Crepidula that enables future comparisons of molluscan biomineralization to reveal mechanisms of shell diversification.
The evolution of tenascins
Authors: Adams Josephine C. , Tucker Richard P. 
Published: September 2024

Abstract
Background
The evolution of extracellular matrix is tightly linked to the evolution of organogenesis in metazoans. Tenascins are extracellular matrix glycoproteins of chordates that participate in integrin-signaling and morphogenetic events. Single tenascins are encoded by invertebrate chordates, and multiple tenascin paralogs are found in vertebrates (designated tenascin-C, tenascin-R, tenascin-W and tenascin-X) yet, overall, the evolution of this family has remained unclear.

Results
This study examines the genomes of hemichordates, cephalochordates, tunicates, agnathans, cartilaginous fishes, lobe-finned fishes, ray-finned fishes and representative tetrapods to identify predicted tenascin proteins. We comprehensively assess their evolutionary relationships by sequence conservation, molecular phylogeny and examination of conservation of synteny of the encoding genes. The resulting new evolutionary model posits the origin of tenascin in an ancestral chordate, with tenascin-C-like and tenascin-R-like paralogs emerging after a whole genome duplication event in an ancestral vertebrate. Tenascin-X appeared following a second round of whole genome duplication in an ancestral gnathostome, most likely from duplication of the gene encoding the tenascin-R homolog. The fourth gene, encoding tenascin-W (also known as tenascin-N), apparently arose from a local duplication of tenascin-R.

Conclusions
The diversity of tenascin paralogs observed in agnathans and gnathostomes has evolved through selective retention of novel genes that arose from a combination of whole genome and local duplication events. The evolutionary appearance of specific tenascin paralogs coincides with the appearance of vertebrate-specific cell and tissue types where the paralogs are abundantly expressed, such as the endocranium and facial skeleton (tenascin-C), an expanded central nervous system (tenascin-R), and bone (tenascin-W).
Evaluation of 1021Bp, a close relative of Pseudomonas eucalypticola, for potential of plant growth promotion, fungal pathogen suppression and boxwood blight control
Authors: Kong Ping , Hong Chuanxue 
Published: September 2024

Abstract
Background
Pseudomonas eucalypticola, a new species of the P. fluorescens group that generates most Pseudomonas-based biocontrol agents, has not been found in any plants other than Eucalyptus dunnii leaves. Except for antagonism to the growth of a few fungi, its features in plant growth promotion and disease control have not been evaluated. Here, we identified a similar species of P. eucalypticola, 1021Bp, from endophyte cultures of healthy leaves of English boxwood (Buxus sempervirens ‘Suffruticosa’) and investigated its antifungal activity, plant growth promotion traits, and potential for boxwood blight control.

Results
Colorimetric or plate assays showed the properties of 1021Bp in nitrogen fixation, phosphate solubilization, and production of indole-3-acetic acid (IAA) and siderophores, as well as the growth suppression of all five plant fungal pathogens, including causal agents of widespread plant diseases, gray mold, and anthracnose. Boxwood plant leaves received 87.4% and 65.8% protection from infection when sprayed with cell-free cultural supernatant (CFS) but not the resuspended bacterial cells at 108–9/mL of 1021Bp at one and seven days before inoculation (dbi) with boxwood blight pathogen, Calonectria pseudonaviculata, at 5 × 104 spores/mL. They also received similarly high protection with the 1021Bp cell culture without separation of cells and CFS at 14 dbi (67.5%), suggesting a key role of 1021Bp metabolites in disease control.

Conclusions
Given the features of plant growth and health and its similarity to P. eucalypticola with the P. fluorescens lineage, 1021Bp has great potential to be developed as a safe and environmentally friendly biofungicide and biofertilizer. However, its metabolites are the major contributors to 1021Bp activity for plant growth and health. Application with the bacterial cells alone, especially with nonionic surfactants, may result in poor performance unless survival conditions are present.
A novel injectable boron doped-mesoporous nano bioactive glass loaded-alginate composite hydrogel as a pulpotomy filling biomaterial for dentin regeneration
Authors: Naga Marwa S. , Helal Hala M. , Kamoun Elbadawy A. , Moaty Maha Abdel , Omar Samia S. Abdel Rehim , Ghareeb Ahmed Z. , El-Fakharany Esmail M. , El Din Mona Mohy 
Published: September 2024

Abstract
Background
Different materials have been used as wound dressings after vital pulp therapies. Some of them have limitations such as delayed setting, difficult administration, slight degree of cytotoxicity, crown discoloration and high cost. Therefore, to overcome these disadvantages, composite scaffolds have been used in regenerative dentistry. This study aims to construct and characterize the physicochemical behavior of a novel injectable alginate hydrogel loaded with different bioactive glass nanoparticles in various concentrations as a regenerative pulpotomy filling material.

Methods
Alginate hydrogels were prepared by dissolving alginate powder in alcoholic distilled water containing mesoporous bioactive glass nanoparticles (MBG NPs) or boron-doped MBG NPs (BMBG NPs) at 10 and 20 wt% concentrations. The mixture was stirred and incubated overnight in a water bath at 50 0 C to ensure complete solubility. A sterile dual-syringe system was used to mix the alginate solution with 20 wt% calcium chloride solution, forming the hydrogel upon extrusion. Then, constructed hydrogel specimens from all groups were characterized by FTIR, SEM, water uptake percentage (WA%), bioactivity and ion release, and cytotoxicity. Statistical analysis was done using One-Way ANOVA test for comparisons between groups, followed by multiple pairwise comparisons using Bonferroni adjusted significance level (p < 0.05).

Results
Alginate/BMBG loaded groups exhibited remarkable increase in porosity and pore size diameter [IIB1 (168), IIB2 (183) (µm)]. Similarly, WA% increased (~ 800%) which was statistically significant (p < 0.05). Alginate/BMBG loaded groups exhibited the strongest bioactive capability displaying prominent clusters of hydroxyapatite precipitates on hydrogel surfaces. Ca/P ratio of precipitates in IIA2 and IIB1 (1.6) were like Ca/P ratio for stoichiometric pure hydroxyapatite (1.67). MTT assay data revealed that the cell viability % of human gingival fibroblast cells have declined with increasing the concentration of both powders and hydrogel extracts in all groups after 24 and 48 h but still higher than the accepted cell viability % of (˃70%).

Conclusions
The outstanding laboratory performance of the injectable alginate/BMBGNPs (20 wt%) composite hydrogel suggested it as promising candidate for pulpotomy filling material potentially enhancing dentin regeneration in clinical applications.
Characterization of giant endocrine cells in the fundic stomach of African catfish (Clarias gariepinus) demonstrated by histochemical, immunohistochemical and ultrastructure microscopy methods suggesting their role in immunity
Authors: Abd-El-Hafeez Hanan H. , Alnasser Sulaiman Mohammed , Baker Zyad M. , Aref Mohamed , Alsafy Mohamed A.M. , El-Gendy Samir A.A. , Zahran Eman , A. Hams Mohamed M. , Alghamdi Ali H. , Khalifa Mahmoud Osman , Kamal Basma M. , Alghamdi Fawzyah A. , Soliman Soha A. , Massoud Diaa 
Published: September 2024

AbstractEndocrine cells in the fundic stomach of Clarias gariepinus were characterized in this work using transmission electron microscopy, immunohistochemistry, and histochemistry. Performic acid mixed with alcian blue pH2.5 and silver stain were among the histochemical stains used for endocrine cells. Endocrine cells can be found in the epithelium, lamina propria, submucosa, muscular layer, serosa, and the area between the stomach glands. Endocrine cells with one or more nuclei were found. Endocrine cells were studied using CD3, CD21, and CD68 in an immunohistochemistry analysis. The expression of the lymphocyte marker CD3 by endocrine cells is remarkable. In addition, they had a strong immunological response to CD21 and CD68, which are characteristics of phagocytic cells. Granules of varied sizes and electron densities are packed densely into the cytoplasm of the cells, as seen by transmission electron microscopy. We propose that endocrine cells play a crucial role in immune defense. The role of endocrine cells in the gut’s immune system is an area that needs further investigation.
Cell therapy using ex vivo reprogrammed macrophages enhances antitumor immune responses in melanoma
Authors: Noonepalle Satish kumar Reddy , Gracia-Hernandez Maria , Aghdam Nima , Berrigan Michael , Coulibaly Hawa , Li Xintang , Zevallos-Delgado Christian , Pletcher Andrew , Weselman Bryan , Palmer Erica , Knox Tessa , Sotomayor Eduardo , Chiappinelli Katherine B. , Wardrop Duncan , Horvath Anelia , Shook Brett A. , Lee Norman , Dritschilo Anatoly , Fernandes Rohan , Musunuri Karthik , Shibata Maho , Villagra Alejandro 
Published: September 2024

Abstract
Background
Macrophage-based cell therapies have shown modest success in clinical trials, which can be attributed to their phenotypic plasticity, where transplanted macrophages get reprogrammed towards a pro-tumor phenotype. In most tumor types, including melanoma, the balance between antitumor M1-like and tumor-promoting M2-like macrophages is critical in defining the local immune response with a higher M1/M2 ratio favoring antitumor immunity. Therefore, designing novel strategies to increase the M1/M2 ratio in the TME has high clinical significance and benefits macrophage-based cell therapies.

Methods
In this study, we reprogrammed antitumor and proinflammatory macrophages ex-vivo with HDAC6 inhibitors (HDAC6i). We administered the reprogrammed macrophages intratumorally as an adoptive cell therapy (ACT) in the syngeneic SM1 murine melanoma model and patient-derived xenograft bearing NSG-SGM3 humanized mouse models. We phenotyped the tumor-infiltrated immune cells by flow cytometry and histological analysis of tumor sections for macrophage markers. We performed bulk RNA-seq profiling of murine bone marrow-derived macrophages treated with vehicle or HDAC6i and single-cell RNA-seq profiling of SM1 tumor-infiltrated immune cells to determine the effect of intratumor macrophage ACT on the tumor microenvironment (TME). We further analyzed the single-cell data to identify key cell-cell interactions and trajectory analysis to determine the fate of tumor-associated macrophages post-ACT.

Results
Macrophage ACT resulted in diminished tumor growth in both mouse models. We also demonstrated that HDAC6 inhibition in macrophages suppressed the polarization toward tumor-promoting phenotype by attenuating STAT3-mediated M2 reprogramming. Two weeks post-transplantation, ACT macrophages were viable, and inhibition of HDAC6 rendered intratumor transplanted M1 macrophages resistant to repolarization towards protumor M2 phenotype in-vivo. Further characterization of tumors by flow cytometry, single-cell transcriptomics, and single-cell secretome analyses revealed a significant enrichment of antitumor M1-like macrophages, resulting in increased M1/M2 ratio and infiltration of CD8 effector T-cells. Computational analysis of single-cell RNA-seq data for cell-cell interactions and trajectory analyses indicated activation of monocytes and T-cells in the TME.

Conclusions
In summary, for the first time, we demonstrated the potential of reprogramming macrophages ex-vivo with HDAC6 inhibitors as a viable macrophage cell therapy to treat solid tumors.
Survival of the fastest? A descriptive analysis of severely injured trauma patients primarily admitted or secondarily transferred to major trauma centers in a Danish inclusive trauma system
Authors: Møller Thea Palsgaard , Jensen Josefine Tangen , Medici Roar Borregaard , Rudolph Søren Steemann , Andersen Lars Bredevang , Roed Jakob , Blomberg Stig Nikolaj Fasmer , Christensen Helle Collatz , Edwards Mark 
Published: September 2024

Abstract
Background
Trauma systems are crucial for enhancing survival and quality of life for trauma patients. Understanding trauma triage and patient outcomes is essential for optimizing resource allocation and trauma care.

Aims
The aim was to explore prehospital trauma triage in Region Zealand, Denmark. Specifically, characteristics for patients who were either primarily admitted or secondarily transferred to major trauma centers were described.

Methods
A retrospective descriptive study of severely injured trauma patients was conducted from January 2017 to December 2021.

Results
The study comprised 744 patients including 55.6% primary and 44.4% secondary patients. Overall, men accounted for 70.2% of patients, and 66.1% were aged 18–65 years. The secondary patients included more women—34.2% versus 26.3% and a higher proportion of Injury Severity Score of ≥ 15—59.6% versus 47.8%, compared to primary patients. 30-day survival was higher for secondary patients—92.7% versus 87%. Medical dispatchers assessed urgency as Emergency level A for 98.1% of primary patients and 86.3% for secondary patients. Physician-staffed prehospital units attended primary patients first more frequently—17.1% versus 3.5%. Response times were similar, but time at scene was longer for primary patients whereas time from injury to arrival at a major trauma center was longer for secondary patients.

Conclusions
Secondary trauma patients had higher Injury Severity Scores and better survival rates. They were considered less urgent by medical dispatchers and less frequently assessed by physician-staffed units. Prospective quality data are needed for further investigation of optimal triage and continuous quality improvement in trauma care.
Intensive care unit caseload and workload and their association with outcomes in critically unwell patients: a large registry-based cohort analysis
Authors: Zajic Paul , Engelbrecht Teresa , Graf Alexandra , Metnitz Barbara , Moreno Rui , Posch Martin , Rhodes Andrew , Metnitz Philipp 
Published: September 2024

Abstract
Background
Too high or too low patient volumes and work amounts may overwhelm health care professionals and obstruct processes or lead to inadequate personnel routine and process flow. We sought to evaluate, whether an association between current caseload, current workload, and outcomes exists in intensive care units (ICU).

Methods
Retrospective cohort analysis of data from an Austrian ICU registry. Data on patients aged ≥ 18 years admitted to 144 Austrian ICUs between 2013 and 2022 were included. A Cox proportional hazards model with ICU mortality as the outcome of interest adjusted with patients’ respective SAPS 3, current ICU caseload (measured by ICU occupancy rates), and current ICU workload (measured by median TISS-28 per ICU) as time-dependent covariables was constructed. Subgroup analyses were performed for types of ICUs, hospital care level, and pre-COVID or intra-COVID period.

Results
415 584 patient admissions to 144 ICUs were analysed. Compared to ICU caseloads of 76 to 100%, there was no significant relationship between overuse of ICU capacity and risk of death [HR (95% CI) 1.06 (0.99–1.15), p = 0.110 for > 100%], but for lower utilisation [1.09 (1.02–1.16), p = 0.008 for ≤ 50% and 1.10 (1.05–1.15), p < 0.0001 for 51–75%]. Exceptions were significant associations for caseloads > 100% between 2020 and 2022 [1.18 (1.06–1.30), p = 0.001], i.e., the intra-COVID period. Compared to the reference category of median TISS-28 21–30, lower [0.88 (0.78–0.99), p = 0.049 for ≤ 20], but not higher workloads were significantly associated with risk of death. High workload may be associated with higher mortality in local hospitals [1.09 (1.01–1.19), p = 0.035 for 31–40, 1.28 (1.02–1.60), p = 0.033 for > 40].

Conclusions
In a system with comparably high intensive care resources and mandatory staffing levels, patients’ survival chances are generally not affected by high intensive care unit caseload and workload. However, extraordinary circumstances, such as the COVID-19 pandemic, may lead to higher risk of death, if planned capacities are exceeded. High workload in ICUs in smaller hospitals with lower staffing levels may be associated with increased risk of death.
Transcriptional silencing in Saccharomyces cerevisiae: known unknowns
Authors: Dhillon Namrita , Kamakaka Rohinton T. 
Published: September 2024

AbstractTranscriptional silencing in Saccharomyces cerevisiae is a persistent and highly stable form of gene repression. It involves DNA silencers and repressor proteins that bind nucleosomes. The silenced state is influenced by numerous factors including the concentration of repressors, nature of activators, architecture of regulatory elements, modifying enzymes and the dynamics of chromatin.Silencers function to increase the residence time of repressor Sir proteins at silenced domains while clustering of silenced domains enables increased concentrations of repressors and helps facilitate long-range interactions. The presence of an accessible NDR at the regulatory regions of silenced genes, the cycling of chromatin configurations at regulatory sites, the mobility of Sir proteins, and the non-uniform distribution of the Sir proteins across the silenced domain, all result in silenced chromatin that only stably silences weak promoters and enhancers via changes in transcription burst duration and frequency.These data collectively suggest that silencing is probabilistic and the robustness of silencing is achieved through sub-optimization of many different nodes of action such that a stable expression state is generated and maintained even though individual constituents are in constant flux.
Prevalence of cardiovascular events in a population-based registry of patients with systemic lupus erythematosus
Authors: Joyce Daniel P. , Berger Jeffrey S. , Guttmann Allison , Hasan Ghadeer , Buyon Jill P. , Belmont H. Michael , Salmon Jane , Askanase Anca , Bathon Joan , Geraldino-Pardilla Laura , Ali Yousaf , Ginzler Ellen M. , Putterman Chaim , Gordon Caroline , Helmick Charles G. , Barbour Kamil E. , Gold Heather T. , Parton Hilary , Izmirly Peter M. 
Published: September 2024

Abstract
Background
The Manhattan Lupus Surveillance Program (MLSP), a population-based retrospective registry of patients with systemic lupus erythematosus (SLE), was used to investigate the prevalence of cardiovascular disease events (CVE) and compare rates among sex, age and race/ethnicity to population-based controls.

Methods
Patients with prevalent SLE in 2007 aged ≥ 20 years in the MLSP were included. CVE required documentation of a myocardial infarction or cerebrovascular accident. We calculated crude risk ratios and adjusted risk ratios (ARR) controlling for sex, age group, race and ethnicity, and years since diagnosis. Data from the 2009–2010 National Health and Nutrition Examination Survey (NHANES) and the 2013–2014 NYC Health and Nutrition Examination Survey (NYC HANES) were used to calculate expected CVE prevalence by multiplying NHANES and NYC HANES estimates by strata-specific counts of patients with SLE. Crude prevalence ratios (PRs) using national and NYC estimates and age standardized prevalence ratios (ASPRs) using national estimates were calculated.

Results
CVE occurred in 13.9% of 1,285 MLSP patients with SLE, and risk was increased among men (ARR:1.7, 95%CI:1.2–2.5) and older adults (age > 60 ARR:2.5, 95%CI:1.7–3.8). Compared with non-Hispanic Asian patients, CVE risk was elevated among Hispanic/Latino (ARR:3.1, 95%CI:1.4-7.0) and non-Hispanic Black (ARR:3.5, 95%CI1.6-7.9) patients as well as those identified as non-Hispanic and in another or multiple racial groups (ARR:4.2, 95%CI:1.1–15.8). Overall, CVE prevalence was higher among patients with SLE than nationally (ASPR:3.1, 95%CI:3.0-3.1) but did not differ by sex. Compared with national race and ethnicity-stratified estimates, CVE among patients with SLE was highest among Hispanics/Latinos (ASPR:4.3, 95%CI:4.2–4.4). CVE was also elevated among SLE registry patients compared with all NYC residents. Comparisons with age-stratified national estimates revealed PRs of 6.4 (95%CI:6.2–6.5) among patients aged 20–49 years and 2.2 (95%CI:2.1–2.2) among those ≥ 50 years. Male (11.3, 95%CI:10.5–12.1), Hispanic/Latino (10.9, 95%CI:10.5–11.4) and non-Hispanic Black (6.2, 95%CI:6.0-6.4) SLE patients aged 20–49 had the highest CVE prevalence ratios.

Conclusions
These population-based estimates of CVE in a diverse registry of patients with SLE revealed increased rates among younger male, Hispanic/Latino and non-Hispanic Black patients. These findings reinforce the need to appropriately screen for CVD among all SLE patients but particularly among these high-risk patients.