Category: Nevin Manimala

Nucleic Acids Res. 2026 Jun 27:gkag420. doi: 10.1093/nar/gkag420. Online ahead of print.

ABSTRACT

Computational methods are central to the life sciences. The rapid growth and diversification of software tools and databases make it difficult to find, compare, and reuse methods for a given task. bio.tools is a community-driven registry designed to improve the visibility of research software and allow researchers to simplify access to the software ecosystem through structured, interoperable, and accessible metadata. Tools are annotated using the EDAM ontology and additional controlled vocabularies, enabling users to search and filter by scientific topics, operations, input/output data types, and data formats. bio.tools supports interactive exploration via rich tool landing pages and provides programmatic access through a documented API for search, retrieval, and registry statistics. The registry has expanded to almost 33,000 annotated tools through the combined contributions of thousands of community members and semi-automated literature mining that keep the registry up to date. Recent improvements to the registry include machine-assisted scoring to prioritise curator review, and consolidation of both its standards stack and software architecture. bio.tools has also become a foundational upstream metadata source that is reused by other services in the ELIXIR Research Software Ecosystem and beyond, to support synchronisation, cross-linking, and additional downstream services. bio.tools is freely available at https://bio.tools.

PMID:42363751 | DOI:10.1093/nar/gkag420

J Psychosoc Oncol. 2026 Jun 27:1-16. doi: 10.1080/07347332.2026.2692942. Online ahead of print.

ABSTRACT

OBJECTIVE: This study sought to understand the differences in how young adults with various cancer predisposition syndromes (CPS) feel toward disclosing their diagnosis to romantic partners.

METHODS: Young adults with a CPS completed a cross-sectional survey. Data analysis of 158 responses was performed via SPSS v 27.0 descriptive statistics. One-way ANOVA analyses, and post-hoc pairwise comparisons examining CPS, gender, and sexual orientation were performed.

RESULTS: Individuals with Lynch syndrome favored disclosing later in a relationship compared to those with Li-Fraumeni syndrome (LFS) (p = 0.050). Individuals who identified as bisexual preferred disclosing more information about their CPS than those who identified as heterosexual (p = 0.035).

CONCLUSIONS: Individuals with various CPS experience a myriad of feelings and attitudes surrounding dating and disclosure. This information can lead to better sensitivity and awareness of this topic by healthcare providers, ultimately improving the level of care given to these individuals.

PMID:42363725 | DOI:10.1080/07347332.2026.2692942

Biopreserv Biobank. 2026 Jun 27:19475535261448800. doi: 10.1177/19475535261448800. Online ahead of print.

ABSTRACT

BACKGROUND: The Kids Eye Biobank collects biospecimens, images, and clinical data from pediatric ophthalmology patients for future research use. A broad informed consent model is used; participants have opt-in choices, which include the creation of cell lines/organoids, use of whole genome sequencing (WGS) data, sharing resources with industry, and receiving future communications. This study aimed to characterize participant consent preferences and investigate associations between participant characteristics and their consent preferences.

METHODS: Participant demographics, diagnosis, and consent preferences were abstracted from the Kids Eye Biobank’s records. Variables were analyzed using descriptive statistics and chi-square test. Patient engagement methods were used throughout the study.

RESULTS: Between January 2020 and April 2025, 391 patients were approached and 342 (87%) enrolled. Of the enrolled participants, 265 (78%) had a substitute decision-maker, and 205 (60%) were diagnosed with a malignant neoplasm affecting the eye. Demographic data were available for 273 (80%) participants; 50% were boys/men, 48% identified as belonging to a visible racial minority, and 67% reported a religious affiliation. Participants with malignant neoplasms opted in more to the use of WGS data and to the sharing of WGS data and cell lines/organoids with industry (p < 0.05). Participants belonging to a visible racial minority opted in less to the generation of cell lines/organoids (p < 0.05) and to receiving communications about future research (p = 0.002) compared with White participants.

CONCLUSION: Informed consent preferences may be influenced by participant diagnosis and/or race. These findings may help the Kids Eye Biobank tailor its communication strategies and diversify its participant population.

PMID:42363713 | DOI:10.1177/19475535261448800

J Adolesc Young Adult Oncol. 2026 Jun 27:21565333261464968. doi: 10.1177/21565333261464968. Online ahead of print.

ABSTRACT

PURPOSE: Adolescents and young adults (AYAs) with cancer are at risk for treatment-related infertility, yet gaps in fertility preservation (FP) counseling persist. While patient-level barriers are well described, provider-level factors remain understudied. We evaluated oncology providers’ perceived versus demonstrated knowledge of FP guidelines and identified barriers to oncofertility care.

METHODS: We conducted a cross-sectional survey of oncology providers at a single academic medical center caring for postpubertal AYA patients receiving gonadotoxic therapy. The survey assessed demographics, prior FP training, counseling and referral practices, and perceived barriers. Participants self-rated their FP knowledge and completed guideline-based clinical vignettes to assess demonstrated knowledge, enabling direct comparison of perceived versus demonstrated knowledge.

RESULTS: Providers reported limited formal oncofertility training, with most rating prior education as fair or poor. Knowledge varied across FP strategies, with high familiarity for ovarian suppression and sperm cryopreservation and lower familiarity for ovarian transposition and male-directed surgical techniques. A trend toward discordance between perceived and demonstrated knowledge was observed but was not statistically significant. Awareness of institutional FP resources and referral pathways was limited. Providers most frequently cited patient-level barriers, including treatment urgency and cost, although provider- and system-level barriers were also reported.

DISCUSSION: Oncology providers may overestimate oncofertility knowledge, contributing to inconsistent counseling and missed opportunities for FP. This pattern, combined with gaps in training and awareness of institutional protocols, highlights the need for competency-based education, clearer institutional communication, and improved referral systems. Objective assessments may better identify knowledge gaps and guide targeted interventions to support guideline-concordant FP care.

PMID:42363674 | DOI:10.1177/21565333261464968

Pain Res Manag. 2026;2026(1):e1671698. doi: 10.1155/prm/1671698.

ABSTRACT

BACKGROUND: Intravenous lidocaine infusion is increasingly used in chronic pain services; however, real-world data regarding durability of analgesic benefit and safety in routine practice remain limited.

OBJECTIVE: To evaluate patient-reported analgesic outcomes, duration of benefit and safety profile of intravenous lidocaine infusion in a tertiary chronic pain service.

METHODS: A retrospective service evaluation was conducted at Leicester General Hospital, pain management department, including all adult patients who received intravenous lidocaine infusion between October 2024 and March 2025. Lidocaine was administered at 3 mg/kg over 1 h under monitored day-case conditions. Patients were contacted by structured telephone follow-up to assess Numerical Rating Scale (NRS) pain scores, duration of benefit, adverse effects and satisfaction. Descriptive statistics were used to summarise outcomes.

RESULTS: Of 136 treated patients, 112 completed follow-up (82.4%). Mean baseline NRS decreased from 8.0 to 4.5 during the early posttreatment period, representing an absolute reduction of 3.5 points. More than 60% of patients reported clinically meaningful improvement, while sustained pain relief beyond 3 months was reported by 29% of patients. Adverse effects occurred in 17% of cases and were mild and self-limiting, with no serious adverse events observed. Overall satisfaction with treatment was high, with 85% of patients indicating that they would recommend intravenous lidocaine infusion for chronic pain management. Among these, 47% were receiving the infusion for the first time.

CONCLUSION: In this real-world cohort, intravenous lidocaine infusion was associated with short- to medium-term patient-reported pain improvement and a favourable safety profile. While a subset experienced sustained benefit beyond 3 months, most patients reported shorter duration relief. Prospective controlled studies using validated outcome measures are required to define long-term efficacy and optimal patient selection.

PMID:42363661 | DOI:10.1155/prm/1671698

Vet Dermatol. 2026 Jun 26. doi: 10.1111/vde.70098. Online ahead of print.

ABSTRACT

BACKGROUND: Fluorescent light energy (FLE; Phovia, Vetoquinol) is a photobiomodulation therapy that promotes healing and reduces inflammation. Cutaneous epitheliotropic lymphoma (CTCL) is a neoplastic skin disease with limited treatment options. Although FLE is not considered genotoxic, its use in neoplastic conditions is off-label.

HYPOTHESIS: To assess the safety and clinical effect of FLE as an adjunctive treatment for canine CTCL.

ANIMALS: Eight client-owned dogs were diagnosed with CTCL via biopsy analysis and immunohistochemical analysis.

MATERIALS AND METHODS: Each dog had one CTCL lesion treated with FLE with a lesion serving as a vehicle-control. Treatments were administered weekly for 6 weeks, followed by 3 months follow-up. Focal nodular lesions were assessed weekly using Response Evaluation Criteria of Solid Tumours (RECIST), while diffuse lesions were evaluated using the Canine Epitheliotropic Lymphoma Extent and Severity Index (CELESI). Owner-perceived efficacy and quality of life were assessed using the Owner Global Assessment of Treatment Efficacy (OGATE) and a quality-of-life (QoL) survey.

RESULTS: No statistically significant differences in estimated marginal means were observed between sites at any time point (p > 0.05). Within-subject analyses suggested more favourable lesion progression at FLE-treated sites, and 75% of RECIST-evaluated FLE lesions maintained stable disease. Diffuse FLE-treated lesions demonstrated clinical severity reductions of ≤ 35.3%. Over 66% of owners rated treatment response as ‘fair’ to ‘excellent’ on the OGATE. One dog was withdrawn at Week 3 as a consequence of unrelated worsening.

CONCLUSIONS AND CLINICAL RELEVANCE: FLE appears to be a safe adjunctive therapy for canine CTCL, although statistically significant treatment effects were not demonstrated.

PMID:42363651 | DOI:10.1111/vde.70098

J Intern Med. 2026 Jun 26. doi: 10.1111/joim.70130. Online ahead of print.

ABSTRACT

BACKGROUND: Existing models for predicting postoperative acute kidney injury (AKI) after non-cardiac surgery are often complex and insufficiently validated for broad clinical use. We developed and externally validated a simple yet accurate model for predicting both overall and critical AKI that can be readily applied in routine practice.

METHODS: The severity index model for AKI (SIM-AKI) was developed using data from 191,938 patients undergoing non-cardiac surgery at a tertiary hospital and externally validated using three independent datasets from other tertiary hospitals (n = 118,047; 86,092; 3727). Variables were selected using least absolute shrinkage and selection operator regression with 10-fold cross-validation, and predictor stability was assessed using backward elimination across 100 bootstrap resamples before multinomial logistic regression modeling. Model performance was evaluated using the C-statistic for discrimination, calibration plots, Brier scores, and decision curve analysis (DCA) for clinical utility.

RESULTS: The SIM-AKI model incorporated age, sex, diabetes mellitus, American Society of Anesthesiologists classification, cancer surgery, emergency status, major abdominal surgery, anemia, hypoalbuminemia, estimated glomerular filtration rate, intraoperative transfusion, and operation time. For overall AKI, C-statistics were 0.801 (95% CI 0.796-0.806) in development and 0.754, 0.742, and 0.759 in validation cohorts. For critical AKI, C-statistics were 0.838 (95% CI 0.826-0.850) in development and 0.796, 0.805, and 0.767 in validation cohorts, demonstrating good calibration and clinical benefit in DCA. The SIM-AKI compared favorably with existing AKI prediction models in discrimination.

CONCLUSION: SIM-AKI may serve as a reliable perioperative tool for predicting the risk of both overall and critical postoperative AKI in patients undergoing non-cardiac surgery.

PMID:42363648 | DOI:10.1111/joim.70130

Histopathology. 2026 Jun 26. doi: 10.1111/his.70202. Online ahead of print.

ABSTRACT

This systematic review with meta-analysis aims to analyse the existing literature on clinicopathological features of sporadic gastric hyperplastic polyps (GHP), with special emphasis on risk factors associated with neoplastic transformation, as well as available immunohistochemical and molecular data relevant to GHP carcinogenesis. We searched two electronic databases and included studies reporting the presence of dysplasia and adenocarcinoma arising in GHP. Meta-analysis of odds ratios (ORs) was performed using random-effects models. We included 58 studies, 11 of which were included in quantitative synthesis. The overall rate of neoplastic transformation in GHP was 6.0% and progression to adenocarcinoma was observed in 1.5%. Statistically significant risk factors for neoplastic transformation were age ≥65 years (OR 2.60; 95% confidence interval [CI] [1.88-3.59]), size ≥20 mm (OR 4.63; 95% CI [1.82; 11.77]) with increasing size thresholds, as well as intestinal metaplasia (OR 3.65; 95% CI [1.68; 7.97]). Although the evidence is limited, the available data suggest that GHP located in the cardia or arising in a dysplastic background gastric mucosa may represent higher-risk subsets. Immunohistochemical subtyping of dysplasia showed a progressive shift from a predominantly gastric phenotype in non-neoplastic GHP to a hybrid (gastric-intestinal) phenotype in dysplasia and adenocarcinoma. TP53 alterations and chromosomal instability were the most frequently reported molecular events. GHP present a significant neoplastic potential, particularly in the presence of additional clinicopathological risk factors. Lesion size, patient age and – above all – the status of the surrounding gastric mucosa should guide endoscopic management, pathological interpretation and surveillance strategies.

PMID:42363644 | DOI:10.1111/his.70202

Psychol Health Med. 2026 Jun 26:1-13. doi: 10.1080/13548506.2026.2694730. Online ahead of print.

ABSTRACT

Sickle Cell Disorder (SCD) is a complex, multi-system blood condition affecting 7.78 million people, with 80% of global cases in sub-Saharan Africa, especially Nigeria. The condition is associated with physical health complications and increased risk of emotional difficulties, highlighting the need for scalable psychosocial interventions for adolescents with SCD in Nigeria. This pilot study assessed the effect of Bibliotherapy as a low-intensity, scalable intervention for adolescents with SCD. The non-randomised pilot-controlled trial involved 42 adolescents with SCD recruited from a Sickle Cell Centre and a Haematology Clinic. Participants were stratified by gender, age and baseline Rosenberg Self-Esteem (RSE) scores, and dyad-matched into Intervention and Control groups to reduce baseline differences. The treatment arm received weekly, virtual, group-based, manualised Bibliotherapy over five weeks, based on selected texts from a memoir by a Nigerian psychiatrist who lived with SCD. Pre-specified primary outcome was the RSE score; secondary outcomes were Hope, Depressive symptoms and Satisfaction with the intervention. The control group received no intervention beyond routine psychoeducation. Participants were aged 13-19 years (M = 16.1, SD = 1.96), with 59.5% females. Controlling for baseline scores, age and gender, the intervention showed a statistically significant effect on self-esteem scores with medium effect size {F (1,37) = 4.84, p = 0.03, Partial Eta Squared = 0.12}, but no significant effect on Hope {F (1,36) = 0.64, p = 0.20, Partial Eta Squared = 0.04} or depressive symptoms {F (1,36) = 0.95, p = 0.34, Partial Eta Squared = 0.03}. All participants in the intervention arm found the book interesting and indicated that it helped them believe they could succeed despite having SCD. They expressed satisfaction with the intervention. This pilot Bibliotherapy intervention was feasible, well received and showed promising efficacy on self-esteem. Larger controlled trials are recommended to establish the generalisability of these findings in the region.Pan African Clinical Trial Registry (Registration Number PACTR202110602061985).

PMID:42363631 | DOI:10.1080/13548506.2026.2694730

Personal Ment Health. 2026 Aug;20(3):e70091. doi: 10.1002/pmh.70091.

ABSTRACT

We critically appraise the study by de Bruin et al., which examined whether avoidant personality traits and avoidant coping predict differential outcomes of cognitive-behavioral therapy (CBT) versus short-term psychodynamic psychotherapy (STPP) in adult depression. Although the authors address an important clinical question regarding dimensional personality assessment in treatment selection, several methodological issues may limit the strength of their conclusions. First, avoidant personality traits were operationalized using a composite score derived from subtracting extraversion from neuroticism on the NEO-FFI. Although dimensional models are increasingly encouraged, this approach may not adequately capture the multifaceted construct of avoidant personality pathology, which includes features such as rejection sensitivity, shame, social inhibition, and feelings of inadequacy, and may instead reflect broader negative affectivity or introversion. Second, the study may have been underpowered to detect moderation effects, which typically require larger samples than main effect analyses. Attrition and participant exclusion may have further reduced statistical power, limiting the ability to identify meaningful treatment interactions. Therefore, the absence of significant moderation effects should be interpreted cautiously and not taken as definitive evidence of equivalent treatment efficacy across levels of avoidant pathology. Despite these limitations, the study contributes to growing research on dimensional personality approaches in depression treatment, and further well-powered studies using validated measures are warranted.

PMID:42363611 | DOI:10.1002/pmh.70091