bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of trifecta outcomes for laparoscopic partial nephrectomy between simple and complex renal masses: a retrospective cohort study
Authors: Mitra Arnab , Evangeline Sadanala Madhuri , George A. J. P. , Mukherjee Partho , Gowri Mahasampath , Kumar Santosh , Nirmal Thampi John 
Published: February 2025

Abstract

Background
Laparoscopic partial nephrectomy (LPN) remains technically challenging for complex renal masses, and there are limited data regarding its safety and efficacy. This study aims to compare the perioperative outcomes of LPN for complex renal masses with RENAL nephrometry score ≥ 7 vs. simple renal masses with RENAL score < 7, focusing on achieving the "Trifecta" outcome.

Materials and methods
We retrospectively analysed data from 170 patients who underwent LPN for malignant renal masses between 2017 and 2021. Patients were divided into Group A (score < 7) and Group B (score ≥ 7) based on RENAL score. Demographics, blood parameters, renal mass characteristics, surgical details, and pathology findings were compared. Perioperative outcomes were assessed based on Trifecta criteria: negative pathological surgical margin (PSM), warm ischemia time (WIT) ≤ 25 min, and no > grade 2 Clavien–Dindo complications.

Results
Group A and Group B comprised 88 (51.7%) and 82 (48.2%) patients, respectively. Trifecta outcomes were comparable between Group A (68.1%) vs. Group B (62.2%) (p = 0.5). There was no significant difference in patients with WIT ≤ 25 min (77.2% vs. 78%, p = 0.88) and negative PSM (92% vs. 86.5%, p = 0.19). The incidence of major complications was low overall but significantly higher for Group B (9.7%) vs. Group A (2.2%), p = 0.04. Perioperative glomerular filtration rate drop (17.2 vs.16.1, p = 0.66), estimated intraoperative Hb drop (2.1 vs. 2.09, p = 0.15) gm%, mean blood loss (180 vs. 221 ml, p = 0.9) and mean operation time (135 vs. 120 min, p = 0.64) did not significantly differ between Group A vs. Group B, respectively.

Conclusions
LPN is a safe approach for managing complex renal masses, yielding acceptable overall Trifecta outcomes when performed by experienced surgeons in high-volume centers. However, surgeons should be cognizant of the increased risk of positive surgical margins and postoperative complications in tumours with a RENAL score greater than or equal to 7.
The central role of trust and perceived risk in the acceptance of autonomous vehicles in an integrated UTAUT model
Authors: Kenesei Zsófia , Kökény László , Ásványi Katalin , Jászberényi Melinda 
Published: February 2025

Abstract
The adoption of autonomous vehicles (AVs) is crucial for the future of transport. Among their many benefits, one of the most important is increased safety. Yet a key barrier to consumer adoption is the perceived level of risk. In our research, we explore this controversy within the framework of the Unified Theory of Acceptance and Use of Technology (UTAUT) model including two key variables: trust and perceived risk. Based on a survey, we tested our hypotheses using structural equation modelling (SEM). Our results suggest that positive perceptions of technology attributes alone—performs well, no effort to use, supported—are not sufficient for acceptance; it is also essential that these attributes increase trust in AVs and thereby reduce perceived risk. If potential users have confidence in AVs and thus perceive a reduced risk, the perceived benefits of the technology can be significantly enhanced. We draw implications for theory and practice from our results, concentrating mainly on the potential to enhance trust in AVs.
De novo genome hybrid assembly and annotation of the endangered and euryhaline fish Aphanius iberus (Valenciennes, 1846) with identification of genes potentially involved in salinity adaptation
Authors: López-Solano Alfonso , Doadrio Ignacio , Nester Tessa Lynn , Perea Silvia 
Published: February 2025

Abstract

Background
The sequencing of non-model species has increased exponentially in recent years, largely due to the advent of novel sequencing technologies. In this study, we construct the Reference Genome of the Spanish toothcarp (Aphanius iberus (Valenciennes, 1846)), a renowned euryhaline fish species. This species is native to the marshes along the Mediterranean coast of Spain and has been threatened with extinction as a result of habitat modification caused by urbanization, agriculture, and its popularity among aquarium hobbyists since the mid-twentieth century. It is also one of the first Reference Genome for Euro-Asian species within the globally distributed order Cyprinodontiformes. Additionally, this effort aims to enhance our comprehension of the species' evolutionary ecology and history, particularly its remarkable adaptations that enable it to thrive in diverse and constantly changing inland aquatic environments.

Results
A hybrid assembly approach was employed, integrating PacBio long-read sequencing with Illumina short-read data. In addition to the assembly, an extensive functional annotation of the genome is provided by using AUGUSTUS, and two different approaches (InterProScan and Sma3s). The genome size (1.15 Gb) is consistent with that of the most closely related species, and its quality and completeness, as assessed with various methods, exceeded the suggested minimum thresholds, thus confirming the robustness of the assembly. When conducting an orthology analysis, it was observed that nearly all genes were grouped in orthogroups that included genes of genetically similar species. GO Term annotation revealed, among others, categories related with salinity regulation processes (ion transport, transmembrane transport, membrane related terms or calcium ion binding).

Conclusions
The integration of genomic data with predicted genes presents future research opportunities across multiple disciplines, such as physiology, reproduction, disease, and opens up new avenues for future studies in comparative genomic studies. Of particular interest is the investigation of genes potentially associated with salinity adaptation, as identified in this study. Overall, this study contributes to the growing database of Reference Genomes, provides valuable information that enhances the knowledge within the order Cyprinodontiformes, and aids in improving the conservation status of threatened species by facilitating a better understanding of their behavior in nature and optimizing resource allocation towards their preservation.
Transcriptomic, metabonomic and proteomic analyses reveal that terpenoids and flavonoids are required for Pinus koraiensis early defence against Bursaphelenchus xylophilus infection
Authors: Yu Lu , Wang Yanna , Wang Xiang , Han Shan , Wang Laifa , Wang Xizhuo 
Published: February 2025

Abstract
Pine wilt disease (PWD), caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, threatens Pinus seriously. Pinus koraiensis is one of the most important pine species in China and is the host for PWN. However, our understanding of the defence-regulating process following infection by B. xylophilus at the molecular level remains limited. To understand the mechanisms that P. koraiensis responds to B. xylophilus invasion, P. koraiensis was inoculated with B. xylophilus solutions and observed no obvious symptoms during the early stage; symptoms began to appear at 5 dpi. Therefore, we conducted comparative transcriptomic, metabonomic and proteomic analyses between P. koraiensis 5dpi and 0 dpi. In infected plants, 1574 genes were significantly up-regulated, including 17 terpenoid-, 41 phenylpropanoid- and 22 flavonoid-related genes. According to GO and KEGG enrichment analyses of significantly up-regulated genes, 86 GO terms and 16 KEGG pathways were significantly enriched. Most terms and pathways were associated with terpenoid-, phenylpropanoid-, flavonoid- and carbohydrate-related events. Similarly, the abundance of 36 and 30 metabolites, significantly increased in positive and negative polarity modes, respectively. Among them, naringenin and 3-methyl-2-oxovaleric acid exhibited significant toxic effects on B. xylophilus. According to functional analysis of significantly up-regulated metabolites, most terms were enriched in above pathways, in addition to alkaloid biosynthesis. Although the abundance of few proteins changed, response to stress term was significantly enriched in significant up-regulated proteins. Furthermore, plant receptor-like serine/threonine kinases, pectin methylation modulators, pinosylvin O-methyltransferase and arabinogalactan/proline-rich proteins were significantly up-regulated in the infected P. koraiensis compared to healthy plants. These proteins were not abundant in the healthy plant. Overall, these results indicate that P. koraiensis can actively response to PWN via various defense strategies, including events related to terpenoids, flavonoids, phenylpropanoids, lipids and alkaloids. Particularly, terpenoids and flavonoids are required for the early defence of P. koraiensis against B. xylophilus infection.
Aberrant expression of collagen type X in solid tumor stroma is associated with EMT, immunosuppressive and pro-metastatic pathways, bone marrow stromal cell signatures, and poor survival prognosis
Authors: Famili-Youth Elliot H. H. , Famili-Youth Aryana , Yang Dongfang , Siddique Ayesha , Wu Elizabeth Y. , Liu Wenguang , Resnick Murray B. , Chen Qian , Brodsky Alexander S. 
Published: February 2025

Abstract

Background
Collagen type X (ColXα1, encoded by COL10A1) is expressed specifically in the cartilage-to-bone transition, in bone marrow cells, and in osteoarthritic (OA) cartilage. We have previously shown that ColXα1 is expressed in breast tumor stroma, correlates with tumor-infiltrating lymphocytes, and predicts poor adjuvant therapy outcomes in ER+/HER2+ breast cancer. However, the underlying molecular mechanisms for these effects are unknown. In this study, we performed bioinformatic analysis of COL10A1-associated gene modules in breast and pancreatic cancer as well as in cells from bone marrow and OA cartilage. These findings provide important insights into the mechanisms of transcriptional and extracellular matrix changes which impact the local stromal microenvironment and tumor progression.

Methods
Immunohistochemistry was performed to examine collagen type X expression in solid tumors. WGCNA was used to generate COL10A1-associated gene networks in breast and pancreatic tumor cohorts using RNA-Seq data from The Cancer Genome Atlas. Computational analysis was employed to assess the impact of these gene networks on development and progression of cancer and OA. Data processing and statistical analysis was performed using R and various publicly-available computational tools.

Results
Expression of COL10A1 and its associated gene networks highlights inflammatory and immunosuppressive microenvironments, which identify aggressive breast and pancreatic tumors and contribute to metastatic potential in a sex-dependent manner. Both cancer types are enriched in stroma, and COL10A1 implicates bone marrow-derived fibroblasts as contributors to the epithelial-to-mesenchymal transition (EMT) in these tumors. Heightened expression of COL10A1 and its associated gene networks is correlated with poorer patient outcomes in both breast and pancreatic cancer. Common transcriptional changes and chondrogenic activity are shared between cancer and OA cartilage, suggesting that similar microenvironmental alterations may underlie both diseases.

Conclusions

COL10A1-associated gene networks may hold substantial value as regulators and biomarkers of aggressive tumor phenotypes with implications for therapy development and clinical outcomes. Identification of tumors which exhibit high expression of COL10A1 and its associated genes may reveal the presence of bone marrow-derived stromal microenvironments with heightened EMT capacity and metastatic potential. Our analysis may enable more effective risk assessment and more precise treatment of patients with breast and pancreatic cancer.
Evaluating the effectiveness of various teaching methods on dental plaque removal in children: a quasi-experimental study
Authors: Tusi Somayeh Khoramian , Momeni Zahra , Hamdollahpoor Hajar , Parviz Nastaran , Ghorbani Mahsa 
Published: February 2025

Abstract

Objective
Dental plaque is a major contributor to oral diseases, particularly in children, but its impact can be significantly mitigated through targeted oral health education. This study aimed to evaluate the effectiveness of various tooth-brushing instructional methods in reducing dental plaque in children.

Methods
A total of 120 children, aged 6 to 8, attending the pediatric department of Alborz Dental School, were randomly selected for the study. Participants were divided into four groups of 30 children each (15 boys and 15 girls). Each group received a different instructional method: (1) demonstration of tooth brushing on a dental model, (2) self-brushing in front of a mirror, (3) brushing another child’s teeth in front of a mirror, and (4) instruction via a standardized video. Dental plaque levels were measured using a disclosing agent before and after training, with a two-week follow-up to assess the impact of instruction. Senior students provided group-specific brushing training. Data were analyzed using SPSS-22 with ANOVA and t-tests, with significance set at p < 0.05.

Results
All four groups demonstrated significant reductions in plaque levels post-training and at the two-week follow-up compared to baseline, as measured by the O’Leary index. The group trained with dental models showed the most substantial plaque reduction (p < 0.001).

Conclusion
Instruction using dental models proved to be the most effective and sustainable method for reducing dental plaque in children, highlighting its potential for impactful and enduring oral hygiene education.
From eligibility to diagnosis: candidacy and the complex journey of cerebral palsy diagnosis within primary care
Authors: Baggaley Jessica , Seiboth Charlotte , Rapley Tim , Basu Anna 
Published: February 2025

Abstract

Background
Cerebral Palsy (CP) is an umbrella term for a group of permanent postural and movement conditions caused by non-progressive damage to the developing brain. Infants not identified with risk factors for CP around the time of birth are usually referred on from primary care after six months of age, essentially precluding early therapy. Candidacy, a seven-step dynamic theory, describes how individuals negotiate their eligibility for medical attention with themselves, others, and health services. This study aims to explore the CP diagnostic journey for community identified infants using the concept of candidacy.

Methods
Data was combined from two studies: an online survey of caregivers of children with CP about their earliest concerns and diagnosis journeys (n=255), and a series of interviews to support the development of a new tool to facilitate earlier identification of infants with emerging motor difficulties (11 parents, 11 health care professionals [HCPs]). A deductive thematic analysis was used with a semantic, critical realist approach. An initial analysis was framed by the Andersen Model of Total Patient delay, and then conceptualised using Candidacy.

Results
Participants had difficulties identifying whether their child needed medical attention, prompting online searches, and seeking advice from family and friends. HCP adjudications led to immediate or delayed referral, in which families continued their searches, reappearing at services until a referral was made. Once referred, families faced poor operating conditions, such as long waiting times. After learning the diagnosis criteria, participants began making requests for referral and navigated to private services if requests were denied. Participants felt that more information on infant development from a reliable source was needed to support new parents in raising their concerns to aid earlier identification.

Conclusion
Participants identified personal lack of infant development knowledge as being the limiting factor to earlier referral. Further research is needed to develop materials relevant for the UK and to understand General Practitioner perspectives regarding provision of such materials.
Histomorphometric and immunohistochemical assessment of treated dentin matrix delivered by platelet-rich fibrin for socket preservation in rabbit model
Authors: Sedek Eman M. , Khalil Nesma Mohamed , Abdul-Monem Mohamed M. 
Published: February 2025

Abstract

Objectives
This study aimed to test treated dentine matrix (TDM) with platelet-rich fibrin (PRF) for socket preservation, following tooth extraction compared to synthetic grafting material Nanobone (NB) with PRF.

Materials and methods

Study was conducted on New Zealand rabbits (n = 40). Bilateral first lower premolar extraction was performed, with one side left empty and the other side filled with (PRF) in one group (n = 20). In the other group (n = 20), one side was filled with TDM/PRF while the other side was filled with NB/ PRF. After one and three months, rabbits were euthanized, and the socket area was examined using haematoxylin and eosin (H&E) and Goldner Masson trichrome stains. One-way ANOVA and post-hoc tests were used for histomorphometric analysis. Immunohistochemical analysis of osteopontin was carried out.

Results
Histological analysis of NB/PRF and TDM/PRF groups showed a higher level of new bone formation in comparison to the control and PRF groups. Histomorphometric analysis revealed a significant increase in new bone formation in the TDM/PRF group compared to the NB/PRF group after one and three months (p = 0.042 and p < 0.001), respectively. There were no significant differences in the percentages of unmineralized bone between the TDM/PRF and NB/PRF groups at both intervals (p = 0.375 and 0.352, respectively). Regarding immunohistochemistry, NB/PRF showed the highest osteopontin immune expression followed by TDM/PRF. No significant differences were detected between both groups at both intervals (p = 0.234 & 0.607 respectively).

Conclusions
TDM/PRF showed the ability to form new bone in extraction sockets in rabbits.

Clinical relevance
TDM/PRF can be used as an alveolar bone grafting material for socket preservation.
Spatial interaction mapping of PD-1/PD-L1 in head and neck cancer reveals the role of macrophage-tumour barriers associated with immunotherapy response
Authors: Naei Vahid Yaghoubi , Tubelleza Rafael , Monkman James , Sadeghirad Habib , Donovan Meg L. , Blick Tony , Wicher Agata , Bodbin Sara , Viratham Amelie , Stad Robert , Basu Subham , Cooper Caroline , Barnett Catherine , O’Byrne Ken , Ladwa Rahul , Warkiani Majid Ebrahimi , Hughes Brett G. M. , Kulasinghe Arutha 
Published: February 2025

Abstract

Background
Mucosal head and neck squamous cell carcinoma (HNSCC) is often diagnosed at an advanced stage, where the prognosis is poor due to the high rates of recurrence and metastasis. With approximately one million new cases projected in 2024, worldwide mortality of HNSCC is estimated to reach 50% of detected cases the same year. Patients with early-stage tumours showed a 50–60% five-year survival rate in the US. Immune checkpoint inhibitors (ICIs) have shown promising results in prolonging survival in a subset of patients with recurrent or metastatic disease. However, challenges remain, particularly the limited efficacy of PD-1/PD-L1 blockade therapies. PD-L1 protein expression has been shown to be limited in its predictive power for ICI therapies. Emerging evidence shows that intricate characterisation of the tumour microenvironment (TME) is fundamental to understand interacting cells. This study aims to bridge the gap in understanding the tumor microenvironment by identifying distinct spatial patterns of PD-1/PD-L1 interactions and their association with immunotherapy responses in head and neck squamous cell carcinoma (HNSCC).

Methods
In this study, we sought to apply a more nuanced approach to understanding cellular interactions by mapping PD-1/PD-L1 interactions across whole-slide HNSCC tissue samples collected prior to ICI therapy. We used a combination of spatial proteomics (Akoya Biosciences) and an in situ proximity ligation assay (isPLA, Navinci Diagnostics) to visualise PD-1/PD-L1 interactions across cell types and cellular neighbourhoods within the tumour TME.

Results
Our findings indicate the existence of isPLA+ PD-1/PD-L1 interactions between macrophages/CD3 T cell-enriched neighbourhoods and tumour cells at the tumour-stroma boundaries in ICI-resistant tumours. The presence of these dense macrophage-tumour layers, which are either absent or dispersed in responders, indicates a barrier that may restrict immune cell infiltration and promote immune escape mechanisms. In contrast, responders had abundant B and T cell aggregates, predominantly around the tumour edges linked to enhanced immune responses to ICI therapy and better clinical outcomes.

Conclusion
This study highlights the utility of isPLA in detecting distinct tumour-immune interactions within the TME, offering new cellular interaction metrics for stratifying and optimising immunotherapy strategies.
Development of selective deconjugases for membrane-anchored LC3A/B in post-mitotic neurons
Authors: Choi Haneul , Park Sang-Won , Jang Deok-Jin , Lee Jin-A 
Published: February 2025

Abstract
Neuronal autophagy is essential for maintaining protein and organelle turnover, thereby safeguarding neuronal health. LC3, a central autophagy protein, exists in lipidated (LC3-II) and non-lipidated (LC3-I) forms, both critical for neurons due to their sensitivity to metabolic and proteostatic stress. To elucidate the specific roles of membrane-anchored LC3A/B in post-mitotic neurons, we engineered deconjugases with enhanced selectivity for lipidated LC3. By modifying LC3-interacting regions (LIRs) at the deconjugase termini, we significantly improved targeting specificity toward LC3A/B. Deconjugases with N-terminal LIR modifications reduced LC3A/B-associated autophagosomes, highlighting the importance of LIR positioning for specificity. Sequential N-terminal LIR arrangements further refined LC3A/B targeting without affecting GABARAP-associated autophagosomes. Moreover, reducing the hydrophobicity of the α3 helix to limit membrane residence time further improved selectivity. These targeted modifications demonstrate the potential of customized deconjugases to dissect and modulate specific autophagic pathways in neurons, paving the way for novel therapeutic strategies against neurodegenerative diseases associated with autophagy dysregulation.