bluuebunny/crossref_metadata_2025 huggingface dataset:
Micro-amplitude vibration-assisted scratching: a new method for one step and controllable fabrication of the microscale V-groove and nanoscale ripples
Authors: Wu Haoxiang , Huang Hu , Zhang Zhiyu , Yan Jiwang
Published: January 2025

Micro/nano hierarchical structures could endow materials with various surface functions. However, the multilayer and multiscale characteristics of micro/nano hierarchical structures bring difficulties for their one step and controllable fabrication. Accordingly, based on tip-based fabrication techniques, this study proposed a micro-amplitude vibration-assisted scratching method by introducing a periodic backward displacement into the conventional scratching process, which enabled the synchronous creation of the microscale V-groove and nanoscale ripples, i.e. a typical micro/nano hierarchical structure. The experiments and finite element modeling were employed to explore the formation process and mechanism of the micro/nano hierarchical structures. Being different from conventional cutting, this method was mainly based on the plow mechanism, and it could accurately replicate the shape of the indenter on the material surface. The microscale V-groove was formed due to the scratching action, and the nanoscale ripple was formed due to the extrusion action of the indenter on the microscale V-groove’s surface. Furthermore, the relationships between the processing parameters and the dimensions of the micro/nano hierarchical structures were established through experiments, and optimized processing parameters were determined to achieve regular micro/nano hierarchical structures. By this method, complex patterns constructed by various micro/nano hierarchical structures were fabricated on both flat and curved surfaces, achieving diverse surface structural colors.
Power quality enhancement in grid-connected PV systems with battery backup: A filterless control strategy
Authors: Tiwari Anurag
Published: January 2025

The present research paper presents a novel control strategy developed to maximize the utilization of grid-connected photovoltaic (PV) systems incorporated with battery backup. It is intended to provide enhanced power quality across a range of operating modes. The designed controller coordinates uninterrupted power transfer from PV modules to the grid, maintaining unity power factor (UPF) at the point of common coupling (PCC), and compensates for reactive power and current harmonics in the presence of PV generation. It also significantly improves the efficiency of using batteries in electric vehicle solutions, leading to system simplification. An MPPT (maximum power point tracking) controller is used to secure the optimal output from PV modules, which has been optimized with the P&O algorithm-based strategy. These approaches were extensively simulated in different operational modes to meet the IEEE standard requirement for THD of grid currents and load current under a wide range of nonlinear loads. In fixed-load conditions, total harmonic distortion (THD) values of 15.46%, 7.96%, and 3.84% were observed for load, inverter, and grid currents, respectively. In varying load conditions, THD values for inverter and grid currents were 10.88% and 7.41%, respectively, with a grid THD of 3.71%. In order to secure robust and efficient control, the proposed converter is used, and sinusoidal grid currents are achieved, indicating that this strategy works well in hybrid PV system-connected battery storage segments.
Britain’s World
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

Our participants reflected on the relationship between British power, national service as an institution, and their own part in it. Although they had differing views on whether their service contributed anything to the nation, they were united by a lack of questioning of the state’s basic right to demand military service, suggesting a degree of deference to the political system. Their sense of Britain’s world role was often vague, with a firm commitment to a notion of British power but lacking an explicit awareness of the Cold War context of their service. In same way, the nature of empire was equally unquestioned by the majority.
Style in Painting (1995)
Authors: Wollheim Richard
Published: January 2025

Wollheim describes his generative, psychologically realistic notion of individual style: one realized in the artist’s ‘practical capacities’, one that is ‘encapsulated in the artist’s body [ ... ] the hand, the arms’, that ‘puts within reach of a painter the fulfilment of his intentions’. He distinguishes the notion from the merely taxonomic, categorizing notion of general, historical, or universal style, which is not of genuine use in explanation. Painting must be understood as the mode of intentional action that it is. Wollheim stresses the importance of his distinction between ‘styledescription’ and ‘stylistic description’, an important difference which the taxonomic notion of style cannot capture. He concludes by observing that there are times of deviance from the normal ‘one style, one artist’ pattern: a painter may lose or depart from their individual style. Indeed, although style need not normally be consciously represented, the ‘time may arise in an artist’s life when he starts to represent his style internally [... if] this is a time of deep crisis, we have to be prepared for the possibility that these representations will be misrepresentations.’ The potential of introjection, crisis of identity and other maladies explored in depth psychology thus inevitably makes its appearance.
Imagination and Pictorial Understanding (1986)
Authors: Wollheim Richard
Published: January 2025

This is in reply to Anthony Savile, in the Joint Session of the Mind Association and the Aristotelian Society of 1986. Contrary to some theorists—Kendall Walton is the main figure in philosophy—‘we have a perfectly good explanation of how we perceive representations without invoking imagination.’ Wollheim’s famous view of pictorial representation involves a unitary ‘twofolded’ experience comprising the ‘configurational’ fold—seeing the arrangement of brush-strokes and the like—and the ‘recognitional’ fold—for example, seeing the figurative content. But even if ‘perception of representations is not necessarily imaginative, does it necessarily become imaginative when concepts and beliefs in excess of a certain limit are brought to bear upon it?’ Wollheim criticizes Savile’s answer; Wollheim’s alternative distinguishes the ‘internal spectator’ from the ‘external spectator’. Whereas the external spectator is the normal gallery-goer, the internal spectator is an imagined figure who is indeterminate in various respects but will possess ‘a repertoire of attitudes and responses to the represented scene’, and—crucially—‘is normally placed so that his field of vision is coincident with what can be seen in the picture’.
Selection and Landscape Evolution
Authors: Phillips Jonathan D
Published: January 2025

Darwinian natural selection is the best known, but only one, example of selection in nature. Variations occur, and some are more efficient, stable, durable, or better adapted than others and are therefore selected for—that is, they are more likely to occur, to be replicated, to have high functionality, and to persist or grow. This chapter discusses types of selection relevant to landscapes, including natural selection, ecosystem-level selection, biogeochemical selection, and environmental filtering. Various forms of abiotic selection are outlined, including gradient, resistance, and network selection. The local nature of selection is emphasized, and the barriers to ubiquitous, constant evolution toward increased efficiency explained. Three case studies of landscape evolution highlighting the role of different types of selection are given: estuarine marsh islands in North Carolina, the Brazilian Cerrado, and fluviokarst in central Kentucky.
Why Everything Is Connected to Everything Else
Authors: Phillips Jonathan D
Published: January 2025

In the landscape sciences, the principle that everything is connected to everything else is virtually axiomatic. Why are Earth systems so strongly interconnected? The crowded landscape concept suggests that components of environmental systems are bound to come in contact because there are so many of them and because of finite space and time for their existence. Connections persist due to connection selection—the preferential preservation of connections that are advantageous for survival and functioning. High connectivity may occasionally be detrimental (e.g., spread of diseases or contaminants), but it offers many advantages in terms of fluxes and distribution of mass, energy, and information; redundancy; and reduced vulnerability. A fully connected system is an optimal compromise between connectivity of individual components and overall complexity. An example shows how the lower Waccamaw River, South Carolina, absorbed impacts of three record floods in a four years owing to the advantages of high connectivity.
The Ethical Theory of W. D. Ross
Authors: Hooker Brad
Published: January 2025

This chapter focuses on the deontological pluralism of W. D. Ross. First, the structure of this ethical theory is explained and assessed, yielding a qualified endorsement. Then the focus moves on to the content of Ross’s prima facie duties. The chapter argues that Ross’s list of duties should be supplemented by agent-relative duties towards family and friends, moral permissions, and other moral rights. Furthermore, whereas Ross held that the duty to promote justice is an agent-neutral duty to bring about a match between virtue and happiness, this chapter argues that justice incorporates attention to agent-relative duties, to various rights, and to fairness, which is here explained in terms of sensitivity to relevant differences and insensitivity to irrelevant differences.
Ross and the Problem of Permissibility
Authors: Stratton-Lake Philip
Published: January 2025

Ross’s theory of prima facie duties captures well our moral intuitions about what we ought to do, and why. The shift from understanding basic principles in terms of prima facie duty rather than duty proper is very important, and his list of basic prima facie duties (fidelity, reparation, gratitude, maximizing the good and avoiding harm) is very plausible. But it does generate two problems relating to the permissible. The first is that it seems to leave us with no moral free space, as whenever the other four duties are absent, the good-maximizing duty kicks in. The result is that there is always something we are obligated to do. The second problem is that the theory leaves no space for the supererogatory. If there is always something we are obligated to do, then there is no space for the idea that some acts can be good if you do them, but not wrong if you don’t do them. It appears that whatever makes such actions good will also make them obligatory. I consider how Ross’s theory generates these unattractive consequences, and how the theory could be revised to avoid them.
On the Value of Intellectual and Aesthetic Activity: A Reply to Ross
Authors: Theunissen L Nandi
Published: January 2025

Is value personal in the sense that what is valuable is of value for someone, or is it impersonal in the sense that what is valuable, while it pertains to a subject, is of value simpliciter? Ross was a staunch proponent of the view that value is impersonal. The author is a proponent of the view that value is personal. This chapter asks which of them is right. The controversy is over the metaphysical structure. Since I have proverbial skin in the game, I will articulate a personal theory of value in terms I find plausible. Since I am personally exercised by a dispute that may appear scholastic to outsiders, I will make clear what turns on it for me. The controversy is over the metaphysical structure of non-instrumental value. But the abstract question is brought to bear on particular kinds of evaluative phenomena, and the phenomena arguably lend the dispute its liveliness and point. The battle is over forms of value that are properly thought ‘admirable’ or ‘commendable’ such as aesthetic and intellectual excellence. These values are marshalled as hard cases for the personal value theorist, so a lot turns on whether she can give a plausible account of them. I make the case that she can.
Couple-based lifestyle intervention for minority prostate cancer survivors: a randomized feasibility trial
Authors: Cho Dalnim , Li Yisheng , Basen-Engquist Karen , Acquati Chiara , Nguyen Nga T T , Ma Hilary , Pettaway Curtis A , McNeill Lorna H
Published: January 2025

Background

Black and Hispanic prostate cancer (PCa) survivors, who face a high burden of comorbid conditions and often engage in low levels of physical activity and healthy eating, remain significantly underrepresented in lifestyle intervention studies.

Purpose

Given the significance of spousal influence, we developed a culturally tailored lifestyle intervention for these survivors and their spouses and assessed its feasibility, acceptability, and impact on behavioral change.

Methods

Survivor-spouse couples were randomly assigned to an intervention group (n = 22), which received 12 health-coaching calls over 6 months, or a usual-care control group (n = 9). Assessments were conducted at baseline (T1), mid-intervention (T2, month 3), and post-intervention (T3, month 6).

Results

The mean attendance was 10.58 sessions, and the intervention received high acceptability scores. Assessment completion rates were 84% at T2 and 81% at T3 for survivors, and 77% at T2 and 81% at T3 for spouses. Intervention group survivors showed meaningful improvements in diet quality from T1 to T2 (+ 6.56) and a clinically important increase in moderate-to-vigorous physical activity (MVPA) from T1 to T3 (+ 17.5 min/day on average). Intervention group spouses also showed meaningful improvements in diet quality from T1 to T2 (+ 8.19) and from T1 to T3 (+ 6.34) and MVPA from T1 to T3 (+ 17.3 min/day on average). Control group participants showed improvements in MVPA.

Conclusions

This couple-based lifestyle intervention is feasible, highly accepted, and promising for improving healthy lifestyle behaviors among Black and Hispanic PCa survivors and their spouses. The results should be carefully interpreted and replicated in an adequately powered trial.
Cancer
Authors: James Nick
Published: January 2025

Cancer: A Very Short Introduction discusses the notion of cancer and how it affects people and the world as one of the biggest killers worldwide. It highlights that cancer is a problem that touches virtually everyone either directly or indirectly. Thus, cancer is a primary focus of many healthcare plans and government strategies. Paradoxically, with improving life expectancy, especially in low- and middle-income countries, cancer is becoming more common globally. This VSI provides an overview of the biology of the disease and its causes, including the growing role of evolutionary analysis in cancer research and trends in diagnosis and treatment, before detailing its subsequent economic consequences. It then looks into several issues, such as expensive drug development, new surgical and radiotherapy technologies, reduction of risk of developing cancer, and the use of complementary and alternative therapies.
Evolution and cancer
Authors: James Nick
Published: January 2025

This chapter, a new addition in the 2nd edition, provides an overview on the evolution of cancer. It points out that since one of the hallmarks of cancer is genomic instability, cancer cells will be more likely to generate new mutations. The advent of high-precision, relatively cheap DNA sequencing has allowed the field of cancer evolutionary biology to explode in recent years. The chapter then discusses evolutionary selection by treatment, which highlights the fact that different treatments in the same patients may produce different patterns of subsequent relapse. It elaborates on how obtaining DNA sequence data became key to understanding cancer behaviour and responses to treatment.
Cancer research
Authors: James Nick
Published: January 2025

This chapter elaborates on the extent and process of cancer research. It examines the differences between the rules for drugs and those for devices like radiotherapy and techniques such as surgery. Since drug treatments must meet different criteria, a new drug treatment requires testing in a series of clinical trials typically involving large numbers of patients. The chapter also discusses the process of comparing existing treatments, especially since requirements of trials differ in different countries. It mentions that new technologies, such as technical radiotherapeutic or surgical innovations, tend to be introduced via a marketing rather than a trials route, which will become increasingly problematical as healthcare budgets come under pressure.
The economics of cancer care
Authors: James Nick
Published: January 2025

This chapter explores the economics of cancer care. It explains that the changes in both medical technology and drug therapy are underpinned by extensive investment in new treatments by both drug and medical equipment manufacturers. While different systems have different pros and cons, a major difference can be seen between high-, middle-, and low-income countries. The chapter considers the interplay of factors in how healthcare systems operate and how the population behaves—which can substantially affect outcomes. It then looks into the likelihood that cancer incidence will rise as life expectancy improves with economic growth in low- and middle-income countries.
Alternative and complementary approaches to cancer care
Authors: James Nick
Published: January 2025

This chapter considers alternative and complementary approaches to cancer care. It explains that complementary medicines are aimed at running alongside conventional therapies as a form of support. Meanwhile, alternative medicines aim to replace the mainstream treatment with one that conventional medicine would regard as unproven at best and harmful at worst. Many patients will use both conventional and alternative or complementary treatments, since most people have only the sketchiest understanding of science and tend to view the claims of scientists and alternative practitioners as equally valid. The chapter also elaborates on various dietary approaches, which are also frequently adopted by patients alongside herbal remedies and herbal medicines. Vitamin and mineral preparations are also considered in this chapter.
AOP-networkFinder—a versatile tool for the reconstruction and visualization of Adverse Outcome Pathway networks from AOP-Wiki
Authors: Yarar Nurettin , Martens Marvin , Rognes Torbjørn , Lavender Jan , Dirven Hubert , Audouze Karine , Wojewodzic Marcin W
Published: January 2025

Motivation

The Adverse Outcome Pathways (AOP)-Wiki, a knowledge database for AOPs, requires an efficient way to present an overview of its content for the reconstruction of networks by experts in a given domain. We have developed the AOP-networkFinder, a user-friendly tool that retrieves AOPs of interest, allows network generation and cleaning, and finally visualizes networks built around the retrieved AOPs. Our tool constructs AOP networks by connecting AOPs that use the same Key Events (KEs) in a versatile but controlled manner. Genes related to these KEs are also displayed. The constructed networks can then be exported as images or to Cytoscape for further fine-tuning and statistical analysis.

Results

The AOP-networkFinder allows users to comprehensively identify relationships between KEs and visualize the overall structure of an AOP both quickly and easily. This is immensely beneficial to researchers who need to understand the complex interplay between different KEs and the overall pathway they are studying and helps them to build further networks of interest while logging relevant information about changes within the network. These efforts are in line with the Findable, Accessible, Interoperable, and Reusable principles, which are crucial attributes for any developed databases and tools for optimizing (re)use in a dynamically changing landscape of AOP-Wiki.

Availability and implementation

The AOP-networkFinder is an open-source application and is available online at aop-networkfinder.no, in the ‘Computational Toxicology at Norwegian Institute of Public Health’ Zenodo community at DOI 10.5281/zenodo.11068434, in the GitHub repository at github.com/folkehelseinstituttet/AOPnetworkFinder_v1, as well as in a Docker image at hub.docker.com/r/nurre123/aop_network_finder. The software is available under the GNU Affero General Public License (AGPL), v3.0. The tool uses the AOP-Wiki SPARQL endpoint to retrieve AOP data.
OrthoBrowser: gene family analysis and visualization
Authors: Hartwick Nolan T , Michael Todd P
Published: January 2025

Motivation

The analysis of gene families across diverse species is pivotal in elucidating evolutionary dynamics and functional genomic landscapes. Typical analysis approaches often require significant computational expertise and user time.

Results

We introduce OrthoBrowser, a static site generator that will index and serve phylogeny, gene trees, multiple sequence alignments, and novel multiple synteny alignments. This greatly enhances the usability of tools like OrthoFinder by making the detailed results much more visually accessible. This interface can scale reasonably up to hundreds of genomes, allows a user to filter this large dataset to a subset of samples they are interested in at that particular moment in time, or “zoom in” to only a subtree of the orthogroup. The multiple synteny alignment method uses a progressive hierarchical alignment approach in the protein space using orthogroup membership to establish orthology. Orthobrowser makes it easy for users to identify, interact with, explore, and share key information about their gene families of interest.

Availability and implementation

OrthoBrowser is pip installable and is available under MIT license at: https://gitlab.com/salk-tm/orthobrowser. Complete example OrthoBrowser results are available at: https://orthobrowserexamples.netlify.app/.
ESCARGOT: an AI agent leveraging large language models, dynamic graph of thoughts, and biomedical knowledge graphs for enhanced reasoning
Authors: Matsumoto Nicholas , Choi Hyunjun , Moran Jay , Hernandez Miguel E , Venkatesan Mythreye , Li Xi , Chang Jui-Hsuan , Wang Paul , Moore Jason H
Published: January 2025

Motivation

LLMs like GPT-4, despite their advancements, often produce hallucinations and struggle with integrating external knowledge effectively. While Retrieval-Augmented Generation (RAG) attempts to address this by incorporating external information, it faces significant challenges such as context length limitations and imprecise vector similarity search. ESCARGOT aims to overcome these issues by combining LLMs with a dynamic Graph of Thoughts and biomedical knowledge graphs, improving output reliability, and reducing hallucinations.

Result

ESCARGOT significantly outperforms industry-standard RAG methods, particularly in open-ended questions that demand high precision. ESCARGOT also offers greater transparency in its reasoning process, allowing for the vetting of both code and knowledge requests, in contrast to the black-box nature of LLM-only or RAG-based approaches.

Availability and implementation

ESCARGOT is available as a pip package and on GitHub at: https://github.com/EpistasisLab/ESCARGOT.
Species recovery as a half empty process: the case against ignoring social ecology for gray wolf recovery
Authors: vonHoldt Bridgett M , Blumstein Daniel T , Berger Joel , Carroll Carlos
Published: January 2025

The criteria used to assess recovery under the US Endangered Species Act (ESA) often fall short when considering social, group-living species. To illustrate this, we use recent insights on sociality in gray wolves to highlight how such definitional failures in implementing the ESA limit the efficacy of recovery efforts for species with complex societal arrays. The loss of conspecifics in social species has an enhanced impact on demographic viability that is not captured by estimates of population abundance. The reproductive skew in social species reduces effective population size and exacerbates threats to genetic health of populations. For group-living species such as wolves, it is critical that regulations consider sociality in recovery guidelines. Biological processes that include social behavior and group structure need to be more fully considered for the ESA to effectively reflect biological reality. Until regulations and policy include language that incorporates these considerations, the species we try to protect will lose.
BHSo4 Improving the quality of parastomal hernia care through a dedicated clinic
Authors: Warner-Levy John , Lockett Kylie , Goscimski Andrzej , Slade Dominic
Published: January 2025

Parastomal hernia (PSH) affects more than 50% of ostomates, but are frequently managed conservatively. The majority of colorectal surgeons do fewer than 3 PSH repairs annually and very few would declare a specialist interest in them.

In May 2022, we set up a dedicated monthly clinic for the assessment and management of PSH. Patients selected by our stomacare team are seen by two surgeons with a declared PSH interest. The purpose was to concentrate expertise and provide MDT decisions in clinic. From February 2023, 27 patients reported symptoms using the Measure Yourself Medical Outcome Profile (MYMOP2).

Since inception we have seen 78 new referrals (35 male, mean age 63), with the majority of stomas being end colostomies (50%). 50% had a tobacco use history with 18% being current smokers. 56% were obese (BMI > 30) with 24% being morbidly obese (BMI > 35). 45% (13% recurrent) presented with early, symptomatic, PSH (EHS grade 1), and 31% had concomitant midline hernias (EHS grades 2 & 4). MYMOP2 scores showed pain & discomfort as the most frequent symptom.

Over 2 years, 27% have been listed for surgery with 7 undergoing repair. 7% were discharged after initial assessment with 6% after one follow up. 50% have been managed conservatively and 3 died after referral. Since this clinic was set up no other surgeons are performing PSH repair with all new cases referred to it.

Dedicated PSH clinics concentrate expertise, provide excellent multidisciplinary team working and identify PSH symptoms early allowing consideration of effective early repair.
BHSeP13 Laparoscopic management of traumatic abdominal wall injury
Authors: Zanellato Artur , Ewing Anne , Skipwoth Richard , Damaskos Dimitrios
Published: January 2025

Background

Traumatic abdominal wall defects are consequence of either penetrating or blunt abdominal trauma, usually associated with multitrauma organs and the minimally invasive approach is still debateable. The authors present a case report of patients with traumatic injury of abdominal wall managed laparoscopically.

Case report

35 years old sustaining 2 stab wounds in the left interscapular area at level of 5th intercostal space (3 cm) and left flank at posterior axillar line (3 cm). He was brought to emergency department stable but with history of significant blood loss in the scene. Bloods Hb 101 otherwise unremarkable. CT scan demonstrated no internal organs injury. Wound was washed and closed in the emergency department and patient admitted for observation in the trauma unit. Later review by senior surgeon no signs of peritonism but proposed diagnostic laparoscopy for completion of thoraco-abdominal injury investigation and concerns of diaphragmatic injury. Intraoperative findings no visceral injury but large abdominal wall defect with omentum herniation. Omentum reduced and defect closed with 2-0 V-lock. Wound re-opened washed and external layer closure with loop PDS 0.

Conclusion

Penetrating thoraco-abdominal injuries should have laparoscopic exploration even though patient doesn't demonstrate signs of visceral injury due to the risk of abdominal wall and/or diaphragmatic unrecognized injuries that will be more difficult to correct at later stage and are a potential risk of complications such as incarceration.
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

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

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

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

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

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 < .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 < .0001) and related to a shorter follow-up (median 6.1 vs 10.3 years, P < .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

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

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

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

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

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

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.