Search Results (9)

A vast proportion of scientific data remains locked behind dynamic web interfaces, often called the deep web—inaccessible to conventional search engines and standard crawlers. This gap between data availability and machine usability hampers the goals of open science and automation. While registries like FAIRsharing offer structured metadata describing data standards, repositories, and policies aligned with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles, they do not enable seamless, programmatic access to the underlying datasets. We present FAIRFind, a system designed to bridge this accessibility gap. FAIRFind autonomously discovers, interprets, and operationalizes access paths to biological databases on the deep web, regardless of their FAIR compliance. Central to our approach is the Deep Web Communication Protocol (DWCP), a resource description language that represents web forms, HyperText Markup Language (HTML) tables, and file-based data interfaces in a machine-actionable format. Leveraging large language models (LLMs), FAIRFind combines a specialized deep web crawler and web-form comprehension engine to transform passive web metadata into executable workflows. By indexing and embedding these workflows, FAIRFind enables natural language querying over diverse biological data sources and returns structured, source-resolved results. Evaluation across multiple open-source LLMs and database types demonstrates over 90% success in structured data extraction and high semantic retrieval accuracy. FAIRFind advances existing registries by turning linked resources from static references into actionable endpoints, laying a foundation for intelligent, autonomous data discovery across scientific domains. Full article

Habitat fragmentation and degradation in natural wetlands has resulted in declines in the populations of shorebirds in the Indian subcontinent. Shorebirds rely on these wetlands as wintering or stop-over sites along the southern extent of the Central Asian Flyway. Shorebirds are known to utilize agroecosystems as alternate foraging habitats. The suitability of agroecosystems as foraging areas for overwintering migratory shorebirds has not been well studied in the Indian subcontinent. We conducted a comprehensive assessment of published literature and compiled field observations to investigate the importance of inland and coastal agroecosystems for shorebirds in India. We assessed the shorebird populations at natural wetlands: mudflats and mangroves of Kadalundi Vallikkunnu Community Reserve (KVCR) and Puthuvypu sand beach, as well as adjacent agroecosystems on the west coast of India, including Sanketham Wetlands, Manthalakkadavu, Vazhakkad, Elamaram, Kodinhi, and Kooriyad. On the east coast, we assessed the natural wetland habitats of Valinokkam, Point Calimere, and Pichavaram and evaluated inland agroecosystems in regions, such as Jammu and Kashmir, Punjab, Rajasthan, Gujarat, Uttar Pradesh, Tamil Nadu, and Kerala. Fifty-three shorebird species utilize diverse agroecosystems from various parts of India. While studies on the use of agroecosystems by shorebirds are limited on the east coast, evidence suggests that major wintering sites are adjacent to paddy fields, fostering substantial shorebird diversity. In Pichavaram, Point Calimere, and Gulf of Mannar regions, 22 shorebird species utilize agroecosystems, including the notable near-threatened Eurasian Curlew. Seventeen of these species are winter arrivals, highlighting the crucial role agroecosystems play as stopover areas. On the west coast, 19 shorebird species appear to utilize agroecosystems in Kooriyad, Manthalakkadavu, Vazhakkad, Sanketham Wetlands, Elamaram, and Kodinhi. Few species use agricultural fields in the north (Jammu and Kashmir). Paddy fields, that are flooded as part of the cropping cycle, support diverse prey species, such as macroinvertebrates, amphibians, and small fish, that could attract and support migratory shorebirds. Agricultural practices like fallowing, flooding, and ploughing could further increase the abundance and accessibility of prey for shorebirds, drawing them in greater numbers. It is crucial to recognize that unsustainable and unethical agricultural methods could detrimentally affect shorebird numbers. The accumulation of pesticide residues and the contamination from heavy metals could also threaten shorebirds. As a result, there is an urgent need for detailed research to better evaluate the importance of agroecosystems in supporting resident or migratory shorebirds. Systematic studies that explain the population dynamics, habitat selection trends, habitat utilization, and the over-summering behavior of the migratory birds at agroecosystems are needed. Implementing sustainable conservation strategies and adopting environmentally friendly agricultural practices are essential to support the rich biodiversity of the region. Full article

Flavonoids are a large subgroup of polyphenols known to be sourced from over 6000 natural products, including fruits, vegetables, bark, and herbs. Due to their antioxidant properties, flavonoids have been implicated as a therapy source for many diseases and conditions, including inflammation, vasculitis, venous insufficiency, and hemorrhoids. Currently, some flavonoids are being researched for their antioxidant ability concerning neuroprotection. These flavonoids can penetrate the blood–brain barrier and, depending on the specific flavonoid, retain adequate bioavailability in certain brain regions. Further data suggest that flavonoids could have a strong anti-inflammatory effect in the brain, which not only could be a robust therapeutic source for known neuroinflammatory diseases such as Alzheimer’s Disease or Parkinson’s Disease but also could be a therapeutic source for ischemic or hemorrhagic conditions such as a stroke. While flavonoid toxicity exists, they are relatively safe and non-invasive drugs from natural origins. As such, exploring the known mechanisms and therapies may highlight and establish flavonoid therapy as a viable source of therapy for stroke patients. As stated, many flavonoids are already being isolated, purified, and implemented in both in vitro and in vivo experiments. As these flavonoids proceed to clinical trials, it will be important to understand how they function as a therapy, primarily as antioxidants, and by other secondary mechanisms. This review aims to elucidate those mechanisms and explore the neuroprotective role of flavonoids. Full article

Radiation therapy (RT) in the management of pelvic cancers remains a clinical challenge to urologists given the sequelae of urethral stricture disease secondary to fibrosis and vascular insults. The objective of this review is to understand the physiology of radiation-induced stricture disease and to educate urologists in clinical practice regarding future prospective options clinicians have to deal with this condition. The management of post-radiation urethral stricture consists of conservative, endoscopic, and primary reconstructive options. Endoscopic approaches remain an option, but with limited long-term success. Despite concerns with graft take, reconstructive options such as urethroplasties in this population with buccal grafts have shown long-term success rates ranging from 70 to 100%. Robotic reconstruction is augmenting previous options with faster recovery times. Radiation-induced stricture disease is challenging with multiple interventions available, but with successful outcomes demonstrated in various cohorts including urethroplasties with buccal grafts and robotic reconstruction. Full article

For a few decades, globally, erectile dysfunction (ED) has become more prominent even in young adults and represents a mounting health concern causing a significant effect on men’s quality of life. There is an expectation that by the end of 2025, the number of ED cases can rise to 322 million. We aimed to comprehensively analyze the scientific output of scholarly articles and studies in the field of ED (2016–2021). Data from scholarly articles were collected using Pubmed, and clinical trials-related information was accessed from the clinical trials website. An extensive patent search was conducted using databases such as USPTO (United States patent and trademark office) and EPO (European patent office), WIPO (World Intellectual Property Organization), etc. Owing to the high market value of ED drugs, considerable interest was attained to grab the opportunities. The race to replace the phosphodiesterase type 5 inhibitor (PDE5 inhibitor-PDE5i) can be identified as evident from the significant number of patents filed and the inventions cleared with clinical trials. Some other intriguing interventions are identified for ED treatment but have yet to gain public acceptance. The current analysis confirms the overall evolution and unexplored corners of research on ED treatment strategies with a current global projection. Full article

Blinding mitigates several sources of bias which, if left unchecked, can quantitively affect study outcomes. Blinding remains under-utilized, particularly in non-pharmaceutical clinical trials, but is often highly feasible through simple measures. Although blinding is generally viewed as an effective method by which to eliminate bias, blinding does also pose some inherent limitations, and it behooves clinicians and researchers to be aware of such caveats. This article will review general principles for blinding in clinical trials, including examples of useful blinding techniques for both pharmaceutical and non-pharmaceutical trials, while also highlighting the limitations and potential consequences of blinding. Appropriate reporting on blinding in trial protocols and manuscripts, as well as future directions for blinding research, will also be discussed. Full article

Evidence-based medicine is predicated on the integration of best available research evidence with clinical expertise and patient values to inform care. In medical research, several distinct measures are commonly used to describe the associations between variables, and a sound understanding of these pervasive measures is foundational in the clinician’s ability to interpret, synthesize, and apply available evidence from the medical literature. Accordingly, this article aims to provide an educational tutorial/topic primer on some of the most ubiquitous measures of association and risk quantification in medical research, including odds ratios, relative risk, absolute risk, and number needed to treat, using several real-world examples from the medical literature. Full article

Sensitivity, which denotes the proportion of subjects correctly given a positive assignment out of all subjects who are actually positive for the outcome, indicates how well a test can classify subjects who truly have the outcome of interest. Specificity, which denotes the proportion of subjects correctly given a negative assignment out of all subjects who are actually negative for the outcome, indicates how well a test can classify subjects who truly do not have the outcome of interest. Positive predictive value reflects the proportion of subjects with a positive test result who truly have the outcome of interest. Negative predictive value reflects the proportion of subjects with a negative test result who truly do not have the outcome of interest. Sensitivity and specificity are inversely related, wherein one increases as the other decreases, but are generally considered stable for a given test, whereas positive and negative predictive values do inherently vary with pre-test probability (e.g., changes in population disease prevalence). This article will further detail the concepts of sensitivity, specificity, and predictive values using a recent real-world example from the medical literature. Full article

Background: Primary small cell carcinoma of the kidney (PSCCK) is exceedingly rare and data on disease characteristics and outcomes are sparse. This study examines a nationally-representative cancer registry to better characterize PSCCK. Methods: We queried the National Cancer Database to identify patients with histology-confirmed PSCCK from 2004 to 2015. Adjusted Cox proportional hazards regression and Kaplan–Meier analyses were employed to assess predictors of mortality and estimate median survival time, respectively. Results: A total of 110 patients were included (47:53% female:male, 77% ≥60 years of age, 86% Caucasian). Significant predictors of mortality included female sex, age 60–69 years, treatment at an Integrated Network Cancer Program, stage cM1, and lack of surgical and chemoradiotherapy treatment. Independent protective factors were high socioeconomic status and treatment at an Academic Research Program. The estimated median overall survival time was 9.31 (95% CI 7.28–10.98) months for all patients. No differences in estimated survival time were observed across individual treatment modalities among those patients who underwent treatment (p = 0.214). Conclusions: PSCCK is an aggressive malignancy with a median survival time of less than one year. Future studies that correlate clinical tumor staging with specific treatment modalities are needed to optimize and individualize management. Full article