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PubMed2026

Artificial Intelligence for Colorectal Surgeons-Part II: Research Applications, Challenges in Adoption, and Practical Resources.

BACKGROUND: This is part II of a 2-part series examining artificial intelligence in colorectal surgery. Part I established foundational concepts and clinical applications. Implementation, however, requires understanding research methodologies, available resources, and the specific challenges currently limiting widespread adoption. These topics are the focus of part II. OBJECTIVE: To examine artificial intelligence's transformation of surgical research, provide practical implementation resources, address adoption challenges, and explore future directions in colorectal surgery. METHODS: Comprehensive literature review focusing on artificial intelligence research methodology, implementation barriers, educational resources, and emerging technologies relevant to colorectal surgeons. RESULTS: Artificial intelligence streamlines clinical trial design through predictive modeling and natural language processing, reducing enrollment challenges that contribute to failed or inadequate trial accrual. Machine learning enables heterogeneity analysis within clinical trials, identifying treatment-responsive subgroups. Foundation models unlock analysis of unstructured electronic health record data at scale. Professional societies and universities offer specialized artificial intelligence education programs, with open-access data sets facilitating research participation. However, implementation faces multifaceted challenges: technical infrastructure demands, with real-time processing requiring dedicated graphics processing unit clusters; regulatory frameworks struggling with continuously evolving algorithms; undefined liability distribution for artificial intelligence-assisted decisions; algorithmic bias risking health care disparities; and the "black box" problem limiting clinical trust. Economic barriers include substantial initial costs without clear reimbursement pathways. Future directions include multimodal artificial intelligence integrating imaging, genomics, and histopathology; cognitive robotic systems with real-time decision support; digital twin technology for patient-specific surgical simulation; and global surgical artificial intelligence networks enabling distributed learning across institutions. CONCLUSIONS: Although artificial intelligence offers transformative potential for colorectal surgery research and practice, successful implementation requires addressing technical, regulatory, ethical, and economic challenges. The surgeon's evolving role demands both traditional expertise and computational fluency. Future advances in multimodal integration, autonomous systems, and global collaboration will fundamentally reshape surgical practice but will require thoughtful implementation prioritizing patient benefit and clinical value.

Humans↗
PubMed2025

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.

The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. In future publications, these data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.

Journal Article↗
PubMed2025

Exploring endothelial cell environments across organs in spatially resolved omics data.

Endothelial cells are ubiquitously present in the human body and line the luminal surface of blood and lymphatic vessels. The oxygen-dependence of cells impacts their proximity to blood vessels, and consequently, to endothelial cells depending on their functional properties and priorities. This paper presents cell-to-nearest-endothelial-cell distance distributions for various cell types using 399 spatially resolved omics datasets from 14 studies comprising 12 tissue types with a total of 47,349,496 cells. Additionally, we developed an open-source web-based interactive tool, Cell Distance Explorer, that allows researchers to interactively visualize cell graphs and linkages in 2D and 3D datasets. Finally, we present a hierarchical neighborhood analysis focused on the endothelial cell neighborhoods in small and large intestine datasets. This paper provides an open-access resource (datasets, tools, and analyses) to characterize and compare cell distances and cell neighborhoods in spatially resolved omics data.

Journal Article↗
PubMed2025

A Systematic Review of Spatial Epidemiological Modeling Approaches Applied During the COVID-19 Pandemic.

BACKGROUND: A wide range of epidemiological modeling approaches have been applied to the SARS-CoV-2 pandemic, which presents an opportunity to assess common approaches applied to specific research questions. Spatial models interrogate how heterogeneities and host movement dynamics influence local and regional patterns of disease, issues that were of great interest for understanding and controlling SARS-CoV-2. OBJECTIVE: Here we present a systematic review of spatial epidemiological modeling approaches of SARS-CoV-2. We describe common themes and highlight unique strategies, providing a foundation for researchers to devise spatial models most appropriate for future pathogens and epidemics. Our review also categorizes the research questions that were addressed with spatial models, highlights parameter estimation techniques, and describes the cyber infrastructure used for model development. METHODS: We conducted a systematic review using Web of Science and a standardized set of keywords, followed by thorough examination of abstracts and full texts to determine which studies met our inclusion criteria. To guide our description and comparisons of models, we developed a Geography, Population, Movement (GPM) framework that conceptualizes the interactions between three distinct subcomponents of any spatial model. The geographic model represents the physical arena in which the model is implemented, the intra-population model describes the transmission and disease processes that occur within distinct spatial units of the geography, and the movement model describes the algorithms that dictate how hosts move among spatial units within the geography. RESULTS: The search identified a total of 193 articles, of which 109 were included in our review. The most abundant intra-population modeling methods were agent-based (47.7%) and compartmental modeling (29.4%) approaches. Movement models ranged in complexity, with the most complex models implementing commuter movement among many points of interest in the geographic arena, which were sometimes parameterized by fine-scale mobility data. Geographic models ranged from describing microcosms, such as single classrooms, all the way up to multi-country models. Of the 63.3% of models studies that specified the programming language used, we detected ten different languages, with Matlab and Python being the most frequent, although only 30.6% of studies provided open-access code for their models. We also described eight specialized software systems that were used to construct agent-based or compartment models of COVID-19. CONCLUSIONS: Our review identified and characterized a variety of spatial modeling strategies and software that were usefully employed to address many relevant epidemiological questions for COVID-19. Future research is needed to quantitatively assess which modeling approaches are most appropriate in specific situations, to answer specific questions, or to apply to certain disease systems. Moreover, future cyberinfrastructure could help to modularize and standardize modeling approaches, which would increase transparency and reproducibility, and which would facilitate a detailed examination of which model attributes relate to model performance in a variety of contexts.

COVID-19↗
PubMed1980

Endoscopic studies of dyspepsia in a general practice.

In an urban general practice serving 7800 patients, all patients presenting over five and a half years with dyspepsia lasting more than two weeks were investigated by fibreoptic endoscopy and cholecystography, and many by barium meal. Of the 393 patients with dyspepsia, 346 completed the investigation: 180 had specific disease of the oesophagus, stomach, duodenum, or gall bladder, including six with carcinoma. Al further 67 had mucosal disease, and only 99 patients had no abnormality. After the first year the number of patients presenting annually and the percentage of patients with specific lesions remained constant. The annual incidence for patients with dyspepsia was about 1% and for patients with specific lesions 0.4%, suggesting that each year those who became symptom free (either spontaneously or because of treatment) were balanced by a similar number who developed symptoms. In contrast to the conclusions of other workers that an "open-access" endoscopy service could not be justified because the number of patients with specific lesins fell during their survey, we suggest that such endoscopy services are indeed worth while for providing an accurate diagnosis of dyspepsia.

Cholecystography↗
PubMed1975

Access by general practitioners to physiotherapy department of a district general hospital.

There has been much opposition, voiced most notably in the Tunbridge Report, to general-practitioner access to hospital rehabilitation services. Co-operation between general practitioners, physiotherapists, and the consultant with responsibility for the physiotherapy department at a general district hospital has provided an efficient open-access service. This service has been welcomed by the general practitioners because it supplies prompt treatment for their patients and by the physiotherapists because it enables them to minimise disability by treating musculoskeletal problems at an early stage.

Family Practice↗
PubMed2026

Antibiotic-impregnated bone graft to prevent infection after total hip arthroplasty (ABOGRAFT): protocol for a randomised, double-blind, placebo-controlled trial.

INTRODUCTION: Studies have shown promising results using bone graft as a carrier for local administration of antibiotics to reduce the risk of prosthetic joint infection (PJI). The objective of this clinical trial is to determine if tobramycin and vancomycin-impregnated bone graft is safe and effective in reducing the rate of PJI after total hip arthroplasty (THA). METHODS AND ANALYSIS: This study is an international, randomised, double-blinded, placebo-controlled clinical drug trial. Patients scheduled for THA (n=1100) requiring bone grafting (excluding revisions due to an ongoing infection) are randomised in a 1:1 ratio to prophylactic treatment with tobramycin and vancomycin or placebo-impregnated bone graft.The primary outcome is the time to reoperation due to infection or diagnosis of PJI, expressed as a relative risk difference between the two groups. A risk reduction of at least 50% is considered clinically relevant. Secondary outcomes are time to and reason for reoperation and implant revision, type of micro-organism and antibiotic susceptibility pattern within 2 and 5 years after surgery. Safety outcomes are the number of adverse events and revision rate due to aseptic loosening. The primary analysis will be performed using proportional hazard models. ETHICS AND DISSEMINATION: The study has been approved under the Clinical Trial Regulation No 536/2014 (EU CT; 2024-510921-25-00). Results will be published in open-access peer-reviewed journals and disseminated to patient organisations and the media, and de-identified individual participant data will be curated and shared on reasonable request in accordance with the Findability, Accessibility, Interoperability and Reuse principles, subject to the laws and regulations governing data protection in each participating country. TRIAL REGISTRATION NUMBER: NCT05169229.

Humans↗
PubMed2025

Pharmacoproteomics in the development of personalised medicine in Age-related Macular Degeneration (PHARPRO-AMD) study protocol.

INTRODUCTION: Age-related macular degeneration (AMD) is the leading cause of irreversible vision loss among people over 55 years of age globally, being neovascular AMD (nAMD) its most aggressive form. Its treatment consists of the use of drugs that block vascular endothelial growth factor (anti-VEGF). Proteomics may allow the identification of differentially expressed proteins between responders and non-responders to each anti-VEGF drug. Thus, the objective of Pharmacoproteomics in the development of personalised medicine in Age-related Macular Degeneration (PHARPRO-AMD) is to find new proteomic biomarkers, predictive of response to antiangiogenic treatment in patients with nAMD. METHODS AND ANALYSIS: PHARPRO-AMD is a nationwide, multicentre, prospective, observational study. Treatment-naïve patients with nAMD starting anti-VEGF therapy will be enrolled and followed up for 2 years. During this period, clinical variables will be gathered to classify treatment response. In addition, blood, tear and vitreous and aqueous humour samples will be collected and will undergo a ZenoSWATH proteomic analysis. Relevant biomarkers identified and response classification will be used to perform a multivariate logistic regression and construct receiver operating characteristic curves. RESULTS: The study is expected to identify a panel of proteomic biomarkers predictive of anti-VEGF treatment response. Integrating data from invasive and non-invasive biological samples may enhance clinical applicability. Once validated, these biomarkers could support the design of future clinical trials on biomarker-guided therapies, helping to optimise treatment regimens and improve visual outcomes. CONCLUSIONS: The PHARPRO-AMD study aims to provide proof-of-concept for biomarker-guided anti-VEGF therapy in nAMD, potentially improving vision outcomes. A notable limitation is the exclusion of patients with visual acuity above 73 Early Treatment of Diabetic Retinopathy Study letters, a criterion chosen to reduce potential ceiling effects and improve response assessment accuracy. ETHICS AND DISSEMINATION: Approved by the Galician Network of Ethics Committees, with nationwide validity. Anonymised data will be deposited in open-access repositories and published in peer-reviewed journals. TRIAL REGISTRATION NUMBER: Spanish Clinical Studies Registry (REec) (0033-2024-OBS).

Humans↗
PubMed2026

The ASH HematOmics Program supports integrative analysis of genomic and clinical data in hematologic diseases.

The increasing availability of genomic and transcriptomic sequencing has uncovered diverse genomic alterations and distinct gene expression profiles driving hematologic diseases, yet a data integration and sharing platform dedicated to hematology remains lacking. We developed the American Society of Hematology (ASH) HematOmics Program (ASHOP; ashop.hematology.org), a resource for exploring somatic alterations and gene fusions, transcriptomic results, and clinical data from 5960 patients spanning B-cell precursor and T-cell acute lymphoblastic leukemia, acute myeloid leukemia, myelodysplastic syndromes, and chronic lymphocytic leukemia. Users can explore genomic alteration landscapes and comutation patterns via lollipop and matrix plots and analyze significantly altered genes in user-defined subcohorts. Transcriptomes can be explored through interactive uniform manifold approximation and projections, clustering, differential expression, and pathway enrichment. Genomic, transcriptomic features, and clinical outcomes can be correlated in a user-driven manner or combined to precisely define study cohorts. We illustrate the following 4 use cases of ASHOP: (1) stratification of DUX4-rearranged B-cell leukemias into Early/Multipotent and Committed subgroups with distinct outcomes, (2) characterization of HOXA/HOXB expression patterns in acute myeloid leukemias, (3) correlating mutational burden with mismatch repair deficiency and mutational signatures, and (4) investigation of TP53 alteration landscape. ASHOP is an open-access resource to inform genomic and transcriptomic data interpretation for hematologic malignancies and will expand to support additional diseases and data modalities from the ASH community.

Humans↗
PubMed2025

Competition and cooperation: The plasticity of bacterial interactions across environments.

Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is whether species engage in cooperative or competitive interactions. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By computationally simulating thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This modeling approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions in response to the availability of environmental resources.

Microbial Interactions↗
PubMed1989

Endoscopic findings and diagnoses in unselected dyspeptic patients at a primary health care center.

This study reports the findings on endoscopy and the final diagnoses of 172 consecutive patients with dyspepsia from a primary health care center. The purpose of our study was to carry out a thorough gastroenterologic investigation of all patients consulting their general practitioner and reporting dyspepsia during 1 full year, from a population within a defined geographic area. The examinations included patient history, physical examination, laboratory tests, esophagogastroduodenoscopy (EGD), and sigmoidoscopy. All the examinations, including the EGDs, were done at the primary care center. A final diagnosis was settled after a minimum of 6 months. Six per cent had esophagitis, 13% had peptic ulcer disease, 1% had gastric cancer, and 1% had irritable bowel disease. Completely normal endoscopies were seen in 19%. No patient had villous atrophy. Sixty-four per cent had non-ulcer dyspepsia, and 26% had inflammatory bowel syndrome, with great overlapping. It is concluded that open-access endoscopy is a valuable service to primary care, the result of which greatly enhances the diagnostic accuracy in dyspeptic patients entering primary care.

Adult↗
PubMed1990

The predictive value of history in dyspepsia.

Symptomatic patients referred to an open-access upper gastrointestinal endoscopy completed a detailed, self-administered questionnaire aimed at assessing the predictive value of history in dyspepsia. Nine hundred and thirty patients were suitable for analysis. Of these, 29% were found to have organic dyspepsia. A substantial overlap of symptoms and demographic data was found among the various endoscopic diagnoses. Discriminating variables were identified by stepwise logistic regression analysis and included in predictive score models. Pain relieved by antacids, age above 40 years, previous peptic ulcer disease, male sex, symptoms provoked by berries, and night pain relieved by antacids and food were found to predict organic dyspepsia with a sensitivity and specificity of approximately 70%, when applied on the observed material. Similar probabilities were found for score models of peptic ulcer and esophagitis. In general, the low prevalence of organic diseases resulted in low positive and high negative predictive values. Accordingly, the main impact of the predictive models may be to reduce the number of negative endoscopies rather than to predict a precise diagnosis. Independent of disease category and age, 41% of the subjects expressed a fear of malignancy, emphasizing the value of reassurance from a negative endoscopy.

Adult↗
PubMed1990

The benefit of colonoscopy.

In a prospective study involving 833 consecutive outpatient and open-access colonoscopies, attempts were made to characterize the benefit of colonoscopy in terms of both predicted and unpredicted findings and therapeutic procedures. The endoscopist therefore predicted the endoscopic findings before the endoscopy. The results were compared for the different indications for colonoscopy. The overall agreement between the predictions and the colonoscopic findings was 61%. Clinically significant abnormalities were found in about half the examinations. The most frequent abnormal findings were benign polyps (24%), inflammatory bowel disease (17%), and malignancy (5%). In about half the patients with a malignancy the indication for colonoscopy was rectal bleeding, and half of the malignancies were not predicted. The greatest benefit of colonoscopy was found in patients referred because of overt rectal bleeding or occult faecal blood, and abnormal barium enema or endoscopy findings. The importance of complete colonoscopy in connection with operation for colorectal carcinoma is emphasized.

Colonic Polyps↗
PubMed1975

Community electrocardiography.

The report of the Joint Working Party on General Medical Services (1973) considered in detail the provision of electrocardiographic services for general practitioners. These are based either on primary health care teams using their own apparatus, or on hospitals offering open-access to their cardiac departments.In this survey I attempted to compare the proportions of general practitioners using their own electrocardiographs with those using hospital-based apparatus, and with those without direct access to any electrocardiograph facilities, and to evaluate the use made of such services, when available.

Electrocardiography↗
PubMedDate not supplied

Computerized health information networks: house calls of the future?

The Cleveland Free-Net is the nation's first free open-access computer system providing health information to the public. An online survey was developed for the family medicine clinic housed within the Free-Net to study the characteristics of the users of the system and the reason they selected the Free-Net as a source of health information. Three areas were addressed: 1) user demographics; 2) content analysis of questions; and 3) reasons Free-Net was used instead of the person's own health care provider. An analysis of the initial system done in 1985 revealed that early users of the system were known to be predominantly white male professionals, generally in the 25-35 age range. In comparison to that profile, more of the users in this study were women, but the majority of users continued to be white male professionals. Questions asked can be classified in six categories: diagnosis, symptoms, treatment, medications, laboratory tests, and prevention. The main categories of medical concerns were cardiovascular, gastrointestinal, obstetrical, and gynecologic problems. Users tended to use the Free-Net for health information rather than their physician because the traditional means was not always appropriate for the life-style of this population.

Adult↗
PubMed1986

Upper gastrointestinal endoscopy--a view from general practice.

An open-access upper gastrointestinal endoscopy service for general practitioners is described. Between July 1981 and May 1985, 391 endoscopies were performed on 354 patients. In contrast to the results of other studies, demand for endoscopy and the pick-up rate for major lesions has remained steady, and the number of requests for barium meals has fallen by almost a quarter. Major lesions - cancer, gastric and duodenal ulcers and severe oesophagitis - were found in 33% of patients. Oesophagitis accounted for 28% of positive endoscopies and 18% of positive endoscopies in patients with barium negative dyspepsia. With scarce resources there may, however, be a case for ;selective' access to upper gastrointestinal endoscopy in the future.

Adult↗
PubMed1974

An appointment system in a teaching practice.

Some patients have difficulty in achieving an appointment to see a doctor in a university teaching practice. Only five per cent of patients indicated serious difficulty. Patients who discriminate in favour of seeing a particular doctor have greater difficulty. It is suggested also that some patients have the same difficulty if they are making an appointment to see a particular doctor.Clearly there is a need to explore the problem further to determine the nature of the difficulties which patients experience. It might then be expected that improvements can be made which will help patients to achieve appointments more easily. At the same time it has to be recognised that there may be some patients who will continue to have difficulty in achieving an appointment however much they are helped. Such patients may need access to community health care services in a manner entirely different from the appointment system.Most patients prefer to see their general practitioner by appointment. Both open-access surgeries and appointment systems cause difficulties for patients. The former is associated with the difficulty of long waiting periods and the second with difficulties in achieving an appointment. As some form of appointment system is likely to be continued, particularly for group practices and health centres, it is probably timely to audit patients' experience of achieving appointments.University teaching practices present general practitioners with unusual additional stresses on an appointment system. The full-time teacher's day is divided between service to patients and teaching or research. Any reduction in the availability of a particular doctor in a group may result in patients having difficulty in making an appointment. This argument could equally apply to any group of practitioners who have commitments other than to general medical services.

Appointments and Schedules↗
PubMed1984

Breast cancer: views of general practitioners on its detection and treatment.

A considerable proportion of women with breast cancer in this country present for treatment in late stages of the disease; Britain's primary health-care system means that in most cases the possible diagnosis of breast cancer is first made in general practice. This offers ample opportunity for early diagnosis and a better understanding about the way the general practitioners perceive the problems associated with the disease. With that specific aim, the present article reports on a survey conducted simultaneously in Oxford and in Edinburgh. Results show that general practitioners in the survey are deeply concerned about breast cancer and see a definite role for themselves in its early detection and long-term management. They also see a need for more health education that includes the encourgement of breast self-examination programmes. Most are in favour of open-access breast clinics for women and, in general, they feel positive about self-education programmes.

Adult↗