bluuebunny/crossref_metadata_2025_split huggingface dataset:
BHSeP25 Complex incisional hernia: a case discussion involving prevention, treatment and its complication
Authors: Setoue Debora , Rezende Pietro , Torres Priscila , Brito Ana , Murakami Abel , Birolini Cláudio , Utiyama Edivaldo 
Published: January 2025

Abstract

Objective
To report a challenger case which surgical approach involves relevant strategies to prevent and treat complications of complex incisional hernias. In extraordinary circumstances, in this case report, it will be shown strategies to lead with chronic sinus and its postoperative complications.

Methods
This case report refers to a patient, masculine, 74 years old, with a history of complex perineal infection, needing a colostomy—which was realized in another hospital. During his hospitalization, he evolved with evisceration. In the surgical procedure to correct the evisceration, the team deemed it was necessary to put a pre aponeurotic mesh and a pre peritoneal mesh. In this hospital, the patient presented in the outpatient consult with an ostomy, a parastomal hernia and a chronic sinus. In this case report, we address possible preventions, better treatments and how to deal with complications.

Conclusion
Cases like this illustrate the abstruse related to the treatment of complex hernias associated with the presence of chronic sinus and its possible evolutions.
Estimation of the postoperative fatality window in colorectal cancer surgery
Authors: Rutegård Martin , Matthiessen Peter , Rutegård Jörgen , Haapamäki Markku M , Svensson Johan 
Published: January 2025

Abstract

Background
Postoperative death measured 30 days after surgery is a conventional quality metric, whereas intervals up to 90 days are increasingly used, although data-driven time windows have scarcely been investigated.

Methods
The Swedish Colorectal Cancer Registry was used to identify all patients subjected resection for colorectal cancer between 2007 and 2020. All patients were followed up until 180 days after surgery. A join-point statistical hazard model was used to model a declining hazard to a transition point, followed by a stable death rate. This method was subsequently applied to describe postoperative deaths for the entire cohort and subgroups according to tumour location (colon and rectum).

Results
Some 56 096 patients electively operated on for colorectal cancer during the study interval were included, with a 30-day and 90-day fatality of 805 (1.43%) and 1458 (2.60%) patients respectively. The derived postoperative fatality window, after which the death rate transitioned to a stable rate, was 23.8 (95% c.i. 21.5 to 28.2) days after surgery. There was no significant difference in the time window between rectal cancer (22.9 days; 95% c.i. 15.1 to 28.4) and colon cancer (27.3 days; 95% c.i. 21.4 to 31.8) patients (P = 0.455). However, postoperative fatality time windows were extended in patients aged at least 80 years and with American Society of Anesthesiologists’ grade III or IV.

Conclusion
The traditional postoperative time window of 30 days was confirmed to be an appropriate metric in elective colorectal cancer surgery when evaluated with a hazards-based statistical framework. Importantly, this time window is influenced by older age and advanced co-morbidity, which could prompt increased vigilance for these patient groups.
Conceptions of participation in child protection care assessments—A discourse analysis of independent experts accounts
Authors: Jørgensen Tone , Aasheim Greve Rakel , Evans McGinn Polly , Christiansen Øivin 
Published: January 2025

Abstract
Although there is a growing knowledge base on children’s participation in child welfare, little research has examined the child’s position as a participant in child protection assessments undertaken by independent experts. Independent experts are commonly used in child protection care proceedings to assess families and contribute to a sound basis for care order decisions. Their reports are highly influential in the child welfare decision-making process. Based on twelve qualitative interviews with independent experts, we explore accounts of their practices of involving children in their investigation. Using a discursive approach, we analyse how the experts use various interpretative repertoires about children’s participation to reason about the position of themselves and the child as participants in the care assessment. Our analysis demonstrates four distinct positions in their discursive constructions of children’s participation. These are the protector position, the investigator position, the facilitator position, and the non-therapist position, each with a distinct interpretation repertoire. The article discusses these in relation to the specific practice context that independent expert care assessments are a part of. Further, we argue for an increased awareness of how conceptualizations of participation simultaneously contribute to what positions become available for children as participants in an independent expert care assessment.
BuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis
Authors: Kumari Naina , Kumar Samir , Roy Anupama , Saini Princy , Jaiswal Sarika , Iquebal Mir Asif , Angadi Ulavappa B , Kumar Dinesh 
Published: January 2025

Abstract
Amidst the global challenge of extreme poverty, the livestock sector can significantly contribute to global sustainable development goals by enhancing resilience, smallholder productivity, and market participation. The Indian livestock sector is one of the largest in the world with a total livestock population of 535.82 million, ∼10.7% of the world’s livestock population. Buffalo (Bubalus bubalis) holds significant importance in India and other Asian countries, notably contributing to their economies by surpassing cattle in milk production and providing various valuable products. The limited availability of genomic and transcriptomic resources for buffaloes hinders the efforts to enhance their traits for increased milk and meat production. To address this gap, this study adopted the state-of-the-art bioinformatics tools to analyse 2429 transcriptomes representing 438 BioSamples from 23 BioProjects obtained from a public domain database, representing 76 different types of tissues and cell types from all major organ systems in buffalo species (river and swamp). The outcome of this exhaustive genomic data led to the development of a relational buffalo expression database based on a three-tier architecture named as BuffExDb (http://46.202.167.198/buffex/). The user-friendliness and flexibilities in retrieval of tissue-specific genes (TSGs) and their functional annotation are the major characteristics of BuffExDb. This is the first of its kind that offers an effortlessly navigable and filterable database, enabling users to examine and visualize the expression levels of each tissue across multiple samples, simultaneously. It also provides the Tau score parameter for the identification of TSGs along with their essential roles in tissue development, maintenance, and function as observed through the enrichment test for gene ontologies. The exhaustive outcome of this work would pave the way for the biological, functional, and evolutionary studies for easy access. This prior information based on tissue-specific mechanisms can be used for future genomic research, especially in association studies in endeavour of enhanced buffalo breeding and conservation programmes.
Database URL: http://46.202.167.198/buffex/
The impact of advanced medical therapies on time to resection and colorectal cancer outcomes in ulcerative colitis patients undergoing colectomy
Authors: Visser Eva , Luberto Antonio , Heuthorst Lianne , Hompes Roel , Vermeire Séverine , D’Haens Geert R , Bemelman Willem A , D’Hoore André , Bislenghi Gabriele , Buskens Christianne J 
Published: January 2025

Abstract

Background
We aimed to evaluate the impact of advanced medical therapies (biologicals and small molecules) on time to colectomy and oncological outcomes in ulcerative colitis (UC).

Methods
This cohort study included UC patients who underwent colectomy between 2003 and 2022 at 2 referral centers in Belgium and the Netherlands. Exposure was the use of advanced medical therapies. Primary outcomes were time to colectomy and colorectal cancer (CRC) rate, compared between 4 periods: P1 (2003-2007), P2 (2008-2012), P3 (2013-2017), and P4 (2018-2022). Secondary outcomes were oncological outcomes, including incidental cancers found unexpectedly in resection specimens or during endoscopic follow-up for medication switch.

Results
Among 716 patients, the usage of advanced therapies increased from 36.8% in P1 to 89.7% in P4 (P &lt; .0001). Median time to colectomy remained comparable (P1: 7.1 years [interquartile ranges (IQR), 2.8-12.9] vs P4: 7.2 years [IQR, 2.7-14.6]; P = not significant). Colectomy and colorectal cancer was diagnosed in 72 (10.1%) patients, with no significant change over time (P = .44). Proportion of CRC was lower in patients treated with advanced therapies (4.7% vs 23.6%, P &lt; .0001) and related to a shorter follow-up (median 6.1 vs 10.3 years, P &lt; .0001). Advanced therapy patients had higher incidental cancer rates (37.5% vs 8.3%, P = .002), which was associated with reduced CRC-related survival (HR for CRC-related death: 3.3, 95% CI 1.17-9.4; P = .02).

Conclusion
Despite increased usage of advanced medical therapies, time to resection and CRC rates have remained unchanged in UC patients undergoing colectomy over the past 2 decades. Advanced therapy patients had higher incidental cancers rates, associated with decreased CRC survival. Awareness of timely colectomy is crucial for this group.
Variant cardiac transthyretin amyloidosis presenting as hypertrophic cardiomyopathy with left ventricular outflow tract obstruction: a case report
Authors: Höller Viktoria , Santner Viktoria , Schmid Johannes , Zirlik Andreas , Verheyen Nicolas 
Published: January 2025

Abstract

Background
Left ventricular outflow tract obstruction (LVOTO) is common in hypertrophic cardiomyopathy (HCM) but has not been reported in hereditary transthyretin amyloidosis (ATTRv).

Case summary
Here, we describe a 67-year-old male patient with a hypertrophic phenotype who was initially diagnosed with LVOTO attributed to HCM. Echocardiographic features included a hyperdynamic left ventricular ejection fraction, severe septal hypertrophy, and elongated residual mitral leaflets permitting their systolic anterior motion. The patient was childless, and family history was negative for any cardiovascular disease. Significant coronary artery disease was diagnosed. In cardiac magnetic resonance imaging, the concurrent presence of different late enhancement patterns initially prevented an unequivocal diagnosis. Due to progressive neuropathy, genetic testing for ATTRv was performed and identified a pathogenic variant in the TTR gene. Cardiac involvement was confirmed by amyloid scintigraphy with a Perugini score of 3, and treatment with ribonucleic acid silencing therapy was commenced.

Discussion
The present case illustrates that LVOTO can occur in patients with ATTRv. While cardiac imaging pointed towards sarcomeric HCM, the coexisting red flags initiated re-evaluation of the diagnosis suggesting cardiac amyloidosis as a potential cause. The presence of non-cardiac red flags of transthyretin amyloidosis (ATTR) should initiate specific diagnostic work-up even if ATTR is unlikely based on cardiac imaging.
Mechanical thrombectomy of a clot-in-transit followed by low-dose systemic lysis: a case report of pulmonary embolism and progressive right heart failure
Authors: Loebig Stephanie , Weyand Sebastian , Metzger Alexander , Seizer Peter 
Published: January 2025

Abstract

Background
Acute pulmonary embolism (PE) is a life-threatening situation. While anticoagulation should be initiated without any delay in all patients with an intermediate or high clinical probability of PE, individual acute phase treatment in patients with intermediate or intermediate-high-risk PE still can be optimized.

Case summary
An 82-year-old female patient was referred to our emergency department after experiencing syncope and acute onset of shortness of breath. Computed tomography (CT) of the chest showed central and extensive peripheral PE. Echocardiography additionally revealed a massive and highly mobile clot-in-transit located in the right atrium (RA). Given the size and mobility of the clot-in-transit, we chose to perform an off-label mechanical thrombectomy. Due to repeated PE with progressive right ventricular (RV) failure and high peripheral thrombus burden, we decided to perform low-dose systemic lysis. After 24 h, she showed significant clinical improvement and was discharged later with recovered RV function and dimensions.

Discussion
In that case, acute PE was complicated by the presence of a large clot-in-transit in the RA. Initially, there was no indication for mechanical thrombectomy or systemic lysis for the patient’s intermediate to high-risk PE. The risk of embolization of the very large clot-in-transit prompted us to remove the mobile thrombus mechanically. When the repeated PE resulted in an increase in afterload and progressive right heart failure, we decided to perform low-dose systemic lysis. The off-label use of the FlowTriever® prevented the impending embolization of the 14 cm long thrombus from the RA into the pulmonary circulation. In this case, lysis also appears to make sense, particularly given the high peripheral thrombus burden.
Umbrella reviews: a methodological guide
Authors: Fernandez Ritin Santiago , Sharifnia Amir Masoud , Khalil Hanan 
Published: January 2025

Abstract
Archie Cochrane’s call for organized summaries of randomized controlled trials highlighted the need for systematic reviews and meta-analyses, which have since evolved to include diverse methodologies. Umbrella reviews have emerged as a high-level synthesis method, aggregating data from multiple systematic reviews and offering comprehensive insights. Their integration of advanced methodologies and interdisciplinary approaches underscores their importance in shaping evidence-based practice and policy-making globally. This methods corner paper examines the significance of umbrella reviews as a methodological advancement in evidence synthesis, detailing the various types of umbrella reviews and the key steps involved in conducting them.
Multiple regulators constrain the abundance of Caenorhabditis elegans DLK-1 in ciliated sensory neurons
Authors: Sun Yue , Zhou Junxiang , Debnath Arunima , Xie Bokun , Wang Zhiping , Jin Yishi 
Published: January 2025

Abstract
The conserved MAP3K DLKs are widely known for their functions in synapse formation, axonal regeneration and degeneration, and neuronal survival, notably under traumatic injury and chronic disease conditions. In contrast, their roles in other neuronal compartments are much less explored. Through an unbiased forward genetic screening in C. elegans for altered patterns of GFP-tagged DLK-1 expressed from the endogenous locus, we have recently uncovered a mechanism by which the abundance of DLK-1 is tightly regulated by intraflagellar transport in ciliated sensory neurons. Here, we report additional mutants identified from the genetic screen. Most mutants exhibit increased accumulation of GFP::DLK-1 in sensory endings, and the levels of misaccumulated GFP::DLK-1 are exacerbated by loss of function in cebp-1, the b-Zip transcription factor acting downstream of DLK-1. We identify several new mutations in genes encoding proteins functioning in intraflagellar transport and cilia assembly, in components of BBSome, MAPK-15, and DYF-5 kinases. We report a novel mutation in the chaperone HSP90 that causes misaccumulation of GFP::DLK-1 and up-regulation of CEBP-1 selectively in ciliated sensory neurons. We also find that the guanylate cyclase ODR-1 constrains GFP::DLK-1 abundance throughout cilia and dendrites of AWC neurons. Moreover, in odr-1 mutants, AWC cilia display distorted morphology, which is ameliorated by loss of function in dlk-1 or cebp-1. These data expand the landscape of DLK-1 signaling in ciliated sensory neurons and underscore a high degree of cell- and neurite- specific regulation.
Convergent Evolution and Predictability of Gene Copy Numbers Associated with Diets in Mammals
Authors: Wilhoit Kayla , Yamanouchi Shun , Chen Bo-Jyun , Yamasaki Yo Y , Ishikawa Asano , Inoue Jun , Iwasaki Wataru , Kitano Jun 
Published: January 2025

Abstract
Convergent evolution, the evolution of the same or similar phenotypes in phylogenetically independent lineages, is a widespread phenomenon in nature. If the genetic basis for convergent evolution is predictable to some extent, it may be possible to infer organismic phenotypes and the capability of organisms to utilize new ecological resources based on genome sequence data. While repeated amino acid changes have been studied in association with convergent evolution, relatively little is known about the potential contribution of repeated gene copy number changes. In this study, we explore whether gene copy number changes of particular gene families are linked to diet shifts in mammals and assess whether trophic ecology can be inferred from the copy numbers of a specific set of gene families. Using 86 mammalian genome sequences, we identified 24 gene families with a trend toward higher copy numbers in herbivores, carnivores, and omnivores, even after phylogenetic corrections. We were able to confirm previous findings on genes such as amylase, olfactory receptors, and xenobiotic metabolism genes, and identify novel gene families whose copy numbers correlate with dietary patterns. For example, omnivores exhibited higher copy numbers of genes encoding regulators of translation. We also established a discriminant function based on the copy numbers of 13 gene families that can help predict trophic ecology to some extent. These findings highlight a possible association between convergent evolution and repeated copy number changes in specific gene families, suggesting the potential to develop a method for predicting animal ecology from genome sequence data.
Efficient analytical partial derivatives of modal phase velocity with respect to layer parameters
Authors: Das Prabir , Naskar Tarun 
Published: January 2025

SUMMARY
Multichannel analysis of surface wave (MASW) is a non-destructive technique to characterize the sub-surface using the dispersive nature of Rayleigh waves. Field dispersion curves are inverted to predict the shear wave velocity structure of the ground and pavement profile. Adjusting the dynamic properties of the initially assumed soil profile necessitates information regarding the dominant sensitive layers. Therefore, a swift and accurate computation of the Jacobian of phase velocity is essential to generate an appropriate shear wave velocity profile and accelerate the inversion process. This is especially crucial for the 2-D MASW survey, which requires hundreds of 1-D inversions to create a high resolution 2-D profile. Available numerical methods are computationally expensive and often suffer from instabilities for highly sensitive layers. The existing analytical methods involve mathematical complexities and require rigorous treatment. Furthermore, they are time-consuming and often found to be marginally faster than the numerical methods. Based on the fast delta matrix algorithm, the paper presents a new efficient analytical formulation of the Jacobian matrix of modal phase velocities concerning the layer parameters. The proposed algorithm leverages the simpler and fewer matrix elements of the fast delta matrix, thus significantly reducing the number of mathematical operations required. Additionally, it reduces the algorithm's cost by factorizing non-zero elements, thereby markedly reducing the computational time. Five different types of synthetic earth models are adopted from the published literature to validate the accuracy and efficacy of the newly developed algorithm. The presented work will significantly benefit the practicing engineers and geophysicists in processing field MASW test data.
A Role for Leucine-Rich α2-Glycoprotein in Leukocyte Trafficking and Mucosal Inflammation in Inflammatory Bowel Disease
Authors: Mishima Takashi , Fujimoto Minoru , Urushima Hayato , Funajima Eiji , Suzuki Yuji , Ohkawara Tomoharu , Murata Okinori , Serada Satoshi , Naka Tetsuji 
Published: January 2025

Abstract

Background
Leucine-rich α2-glycoprotein (LRG) has been identified as a disease activity marker that reflects pathology of inflammatory diseases including inflammatory bowel disease (IBD). Whereas LRG was reported to modulate transforming growth factor beta-1 (TGF-β) signaling, the role of LRG in inflammatory diseases has not been fully clarified. Here we investigated the role of LRG in IBD.

Methods
First, we investigated the difference of pathologies between wild-type (WT) mice and LRG-deficient (LRG−/−) mice in dextran sodium sulfate (DSS)-induced experimental colitis. Next, we analyzed the role of LRG in colonic inflammation by using in vitro assay.

Results
Prompt LRG upregulation was detected on the colonic epithelial cells on day 1 post 3% DSS treatment. Body weight loss after DSS treatment was significantly less severe in LRG−/− mice than in WT mice. Histological examination disclosed that leukocyte infiltration in colonic tissue was attenuated in LRG−/− mice compared with WT mice on day 3. Interestingly, the expression of endoglin, one of adhesion molecules in vascular endothelial cells, was markedly elevated in WT mice on day 1 post-DSS treatment, but was not in LRG−/− mice. Anti-TGF-β antibody treatment in mice with DSS colitis revealed that TGF-β is critical for endoglin upregulation in endothelial cells. Importantly, recombinant LRG when added to the culture media enhanced TGF-β1-induced endoglin expression in endothelial cells and increased adherence of monocytes to endothelial cells.

Conclusions
Our data suggest that LRG accelerates the progression of colonic inflammation at least in part by enhancing leukocyte trafficking through the upregulation of TGF-β1-induced endoglin expression in vascular endothelial cells.
More or the same? Radical, disruptive, discontinuous, and breakthrough innovation
Authors: Verhoeven Dennis , Kovacs Adrian , Marullo Cristina , Di Minin Alberto , Van Looy Bart 
Published: January 2025

Abstract
This paper addresses the conceptual ambiguity in the literature on exceptional innovations, labeled “radical,” “disruptive,” “breakthrough,” or “discontinuous.” A bibliometric analysis of 4407 articles shows that different labels are used by papers with shared theoretical foundations and thematic orientation. An in-depth analysis of 60 seminal contributions shows that definitions are (I) not always provided, (II) inconsistent within labels, and (III) not distinctive across labels. This complicates the exploration of the literature and the comparison of results. Definitions, when provided, agree on the existence of two underlying dimensions—novelty and impact—but disagree on how the labels relate to these dimensions. To advance conceptual clarity, we propose a typology of innovation trajectories that treats novelty and impact as distinct concepts and clarifies how and when novelty relates to impact.