NCBI taxonomy: enhanced access via NCBI datasets.

The NCBI Taxonomy resource (https://www.ncbi.nlm.nih.gov/taxonomy) has long been a trusted, curated hub for organism names, classifications, and links to related data for all taxonomic nodes. NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/) is an improved way to leverage the rich data available at NCBI so users can effectively browse, search, and download information. While taxonomy data has been a cornerstone of NCBI Datasets since its inception, we recently extended the taxonomy information available via NCBI Datasets by updating the existing NCBI Datasets taxonomy page, implementing a new taxonomy name details page, expanding programmatic access to taxonomic information via command-line tools and APIs and improving the way we handle taxonomic queries to connect users to gene and genome data. This paper highlights these improvements and provides examples to help users effectively harness these new features.

Improving Enforcement Measures and Establishing Clear Criteria: A Content Analysis of Tobacco-Brand-Owned Instagram Accounts.

INTRODUCTION: This study examines limitations of the current regulatory framework for tobacco advertising on Instagram. We first investigate compliance with Food and Drug Administration (FDA) warning label requirements for posts by tobacco-owned accounts. Next, we examine the prevalence of content that has been restricted in broadcast or print for its youth appeal, followed by content meeting more expansive criteria for youth appeal set forth in the FDA's guidance document. AIMS AND METHODS: Posts by tobacco-brand-owned accounts between January 1, 2021, and February 14, 2022, were sampled from Mintel's Comperemedia Omni database. Instagram posts from 15 accounts were examined for violations of FDA warning label requirements and content that has been restricted on other mediums, including cartoons, sports branding, unauthorized claims, and young models (N = 1243). Finally, a subsample of n = 453 unambiguously branded posts was coded for themes that met the FDA's criteria of resonating with younger audiences, particularly that "adolescents rely on external information as they seek to shape their own identities." RESULTS: Only 12.8% of posts had fully compliant warning labels. Content that has been in some way regulated on other mediums, such as cartoons (1.6%), unauthorized health claims (<1%), sports branding (<1%), and young models (4.4%) were infrequent. However, a conservative analysis focusing only on branded posts found that posts frequently highlighted tech elements (45%), device customizability (24.5%), vaper identity (17.7%), stylized product photography (33.6%), social media engagement (32.2%), and memes (5.7%). CONCLUSIONS: Enforcement of existing regulations on Instagram is minimal. Explicit content restrictions applying evidence-based guidance on youth-appealing advertising are needed. IMPLICATIONS: This research has important implications for enforcing and expanding advertising regulations on social media. First, Instagram's self-imposed regulations are ineffective, permitting tobacco companies to post ads from brand-owned accounts despite claiming to restrict tobacco promotion on the platform. Second, policymakers should seek to apply FDA guidance on youth-appealing advertising informed by decades of research to create explicit enforceable content restrictions that extend beyond cartoons, sports figures, and young models to include content likely to situate tobacco use within the developing self-concept of vulnerable youth such as presenting e-cigarettes as hi-tech devices, highlighting vaper identity, or infiltrating online social media culture. Finally, greater resources for enforcement are needed given the only applicable regulation, warning labels, remains largely ignored.

Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets.

To explore complex biological questions, it is often necessary to access various data types from public data repositories. As the volume and complexity of biological sequence data grow, public repositories face significant challenges in ensuring that the data is easily discoverable and usable by the biological research community. To address these challenges, the National Center for Biotechnology Information (NCBI) has created NCBI Datasets. This resource provides straightforward, comprehensive, and scalable access to biological sequences, annotations, and metadata for a wide range of taxa. Following the FAIR (Findable, Accessible, Interoperable, and Reusable) data management principles, NCBI Datasets offers user-friendly web interfaces, command-line tools, and documented APIs, empowering researchers to access NCBI data seamlessly. The data is delivered as packages of sequences and metadata, thus facilitating improved data retrieval, sharing, and usability in research. Moreover, this data delivery method fosters effective data attribution and promotes its further reuse. This paper outlines the current scope of data accessible through NCBI Datasets and explains various options for exploring and downloading the data.

Impact and costs of targeted recruitment of minorities to the National Lung Screening Trial.

BACKGROUND: To promote results in the National Lung Screening Trial (NLST) that are generalizable across the entire US population, a subset of NLST sites developed dedicated strategies for minority recruitment. PURPOSE: To report the effects of targeted strategies on the accrual of underrepresented groups, to describe participant characteristics, and to estimate the costs of targeted enrollment. METHODS: The 2002-2004 Tobacco Use Supplement was used to estimate eligible proportions of racial and ethnic categories. Strategic planning included meetings/conferences with key stakeholders and minority organizations. Potential institutions were selected based upon regional racial/ethnic diversity and proven success in recruitment of underrepresented groups. Seven institutions submitted targeted recruitment strategies with budgets. Accrual by racial/ethnic category was tracked for each institution. Cost estimates were based on itemized receipts for minority strategies relative to minority accrual. RESULTS: Of 18,842 participants enrolled, 1576 (8.4%) were minority participants. The seven institutions with targeted recruitment strategies accounted for 1223 (77.6%) of all minority participants enrolled. While there was a significant increase in the rate of minority accrual pre-implementation to post-implementation for the institutions with targeted recruitment (9.3% vs. 15.2%, p < 0.0001), there was no significant difference for the institutions without (3.5% vs. 3.8%, p = 0.46). Minority enrollees at the seven institutions tended to have less than a high school education, be economically disadvantaged, and were more often uninsured. These socio-demographic differences persisted at the seven institutions even after adjusting for race and ethnicity. The success of different strategies varied by institution, and no one strategy was successful across all institutions. Costs for implementation were also highly variable, ranging from $146 to $749 per minority enrollee. LIMITATIONS: Data on minority recruitment processes were not consistently kept at the individual institutions. In addition, participant responses via newspaper advertisements and the efforts of minority staff hired by the institutions could not be coded on Case Report Forms. CONCLUSIONS: Strategic efforts were associated with significant increases in minority enrollment. The greatest successes require that a priori goals be established based on eligible racial/ethnic proportions; the historical performance of sites in minority accrual should factor into the selection of sites; recruitment planning must begin well in advance of trial launch; and there must be endorsement by prominent representatives of the racial groups of interest.

Feasibility of measuring pericoronary fat from precontrast scans: Effect of iodinated contrast on pericoronary fat attenuation.

BACKGROUND: Pericoronary adipose tissue (PCAT) attenuation has been identified as a marker for cardiovascular risk. The effect of contrast enhancement on fat attenuation is unknown. We aim to compare precontrast coronary scans to postcontrast CCTA for quantification of pericoronary fat volume and attenuation. METHODS: Thin slice pre- and post-contrast studies obtained at 120 kVp, heart rate <60, with no plaque or artifact in the right coronary artery (RCA) were selected. Analysis was limited to pixels -30 Hounsfield units (HU) to -190 HU and from 10 mm to 50 mm distal to the RCA origin at a radial distance equal to the vessel diameter. A subgroup with no plaque across all coronaries was also analyzed. RESULTS: Of 119 study pairs, the average RCA diameter was highly correlated at 3.85 mm (postcontrast) and 3.84 mm (precontrast), r = 0.97, p < 0.0001. The mean attenuation of pre- and postcontrast images was also highly correlated at -87.02 ±â€¯7.15 HU and -82.74 ±â€¯6.54 HU, respectively (r = 0.65, p < 0.0001). Pericoronary fat volume in the -190 to -30 HU range was 396 mm³ lower in the post contrast versus pre-contrast, consistent with higher attenuation (less negative) voxels postcontrast (p < 0.0001). Inter- and intra-reader agreement ranged 95-100% and 90% for precontrast and 85-90% for postcontrast studies, respectively. Subgroup analysis revealed precontrast attenuation -85.59 ±â€¯7.53 HU and postcontrast -82.21 ±â€¯7.15 HU were highly correlated r = 0.67, p < 0.0001. CONCLUSION: Pericoronary fat enhances with iodinated contrast, potentially explaining some of its risk-predictive capabilities. Fat attenuation and volume can be reliably measured from precontrast calcium scans, with volume quantification showing particularly strong correlation. Excellent inter- and intra-reader agreement is also demonstrated.

Advanced imaging programs: maximizing a multislice CT investment.

Advanced image processing has moved from a luxury to a necessity in the practice of medicine. A hospital's adoption of sophisticated 3D imaging entails several important steps with many factors to consider in order to be successful. Like any new hospital program, 3D post-processing should be introduced through a strategic planning process that includes administrators, physicians, and technologists to design, implement, and market a program that is scalable-one that minimizes up front costs while providing top level service. This article outlines the steps for planning, implementation, and growth of an advanced imaging program.

Cellular factors required for protection from hyperoxia toxicity in Saccharomyces cerevisiae.

Prolonged exposure to hyperoxia represents a serious danger to cells, yet little is known about the specific cellular factors that affect hyperoxia stress. By screening the yeast deletion library, we have identified genes that protect against high-O2 damage. Out of approx. 4800 mutants, 84 were identified as hyperoxia-sensitive, representing genes with diverse cellular functions, including transcription and translation, vacuole function, NADPH production, and superoxide detoxification. Superoxide plays a significant role, since the majority of hyperoxia-sensitive mutants displayed cross-sensitivity to superoxide-generating agents, and mutants with compromised SOD (superoxide dismutase) activity were particularly vulnerable to hyperoxia. By comparison, factors known to guard against H2O2 toxicity were poorly represented amongst hyperoxia-sensitive mutants. Although many cellular components are potential targets, our studies indicate that mitochondrial glutathione is particularly vulnerable to hyperoxia damage. During hyperoxia stress, mitochondrial glutathione is more susceptible to oxidation than cytosolic glutathione. Furthermore, two factors that help maintain mitochondrial GSH in the reduced form, namely the NADH kinase Pos5p and the mitochondrial glutathione reductase (Glr1p), are critical for hyperoxia resistance, whereas their cytosolic counterparts are not. Our findings are consistent with a model in which hyperoxia toxicity is manifested by superoxide-related damage and changes in the mitochondrial redox state.

Whistleblowers: there ain't no cure, but there is prevention.

Under federal and an increasing number of state laws, disgruntled and former employees are given significant financial incentives to report fraud to federal and state regulators. This article addresses strategies for reducing the likelihood that your practice will be the target of a whistleblower suit.

A patient, an internet article, and thou: challenges of the Internet in clinical practice.

This article addresses issues a physician should consider when responding to medical research gathered by a patient from the Internet, discussing both potential medical malpractice liability and offering specific, recommended responses for physicians whose patients conduct online medical research.

The new Medicare prescription drug benefit: important issues for physician practices.

Beginning January 1, 2006, Medicare beneficiaries will have the option of enrolling in a new Medicare program covering prescription drugs. This article summarizes the new benefit, suggests the factors beneficiaries and their physicians might consider when selecting a prescription drug plan, and outlines practice implications for physician offices.

Physicians heal thy laws: ten steps to becoming an effective citizen lobbyist.

By bringing information on medical issues to the attention of their representatives at the national and local levels, physicians can play an important role in molding policies that will affect their patients and their modes of practice. This article outlines the specific steps by which practitioners may engage law makers and their staffers to express their viewpoints and impact the legislative process.

Fraud and abuse enforcement trends. What's hot for physicians and physician practices.

The Department of Health and Human Services Office of Inspector General (OIG) has dramatically expanded the scope and frequency of physician fraud and abuse investigations. Further, OIG has increasingly extracted financial settlements and obtained sanctions against physicians. This article identifies seven areas of investigation that will be given highest priority.

3D volume segmentation of MRA data sets using level sets: image processing and display.

In this article, we use a level set-based segmentation algorithm to extract the vascular tree from magnetic resonance angiography (MRA) data sets. The classification approach depends on initializing the level sets in the 3D volume, and the level sets evolve with time to yield the blood vessels. This work introduces a high-quality initialization for the level set functions, allowing extraction of the blood vessels in 3D and elimination of non-vessel tissues. A comparison between the 2D and 3D segmentation approaches is made. The results are validated using a phantom that simulates the MRA data and show good accuracy.

Stark II final regulations: hot issues for physician practices.

The Stark law, first passed in 1989 and repeatedly expanded and clarified since then, has long created questions for group practices. Its primary intent is to prohibit physician referrals to entities in which the physician has a financial interest, but the details have proven confusing. The Stark law's Phase II regulations, as put forth by the Centers for Medicare and Medicaid Services, went into effect in July and attempt to offer further clarification. In this article the authors explain some of the complexities of this most recent set of Stark law regulations, especially as they apply to smaller, multi-specialty practices.

Health care privacy: exceptions to the rule preparing for the brave new world, Part III.

As physicians prepare for implementation of HIPAA, there will be times when they are asked to and may be required to release individual health information without patient consent and authorization. This third article in a four-part series highlights the situations in which a doctor may release health information without a patient's knowledge.

Preparing for the brave new world, Part 4: "Minimum necessary" disclosures under HIPAA.

"Minimum information given with maximum politeness," Jacqueline Kennedy once directed a White House press secretary. Decades later, a pending federal health-privacy rule says nothing about courtesy but does explicitly require a "minimum necessary" standard for most disclosures of personally identifiable information. Physician practices that understand these two key words will have a head start in complying with the privacy regulations, which were published in December 2000 under authority of the Health Insurance Portability and Accountability Act of 1996 (HIPAA). This article, the final installment of a four-part series on how the HIPAA privacy rule will affect the day-to-day lives of physicians and their staffs, focuses on what the U.S. Department of Health and Human Services (DHHS) means by "minimum necessary."

Automatic Detection of 2D and 3D Lung Nodules in Chest Spiral CT Scans.

Automatic detection of lung nodules is an important problem in computer analysis of chest radiographs. In this paper, we propose a novel algorithm for isolating lung abnormalities (nodules) from spiral chest low-dose CT (LDCT) scans. The proposed algorithm consists of three main steps. The first step isolates the lung nodules, arteries, veins, bronchi, and bronchioles from the surrounding anatomical structures. The second step detects lung nodules using deformable 3D and 2D templates describing typical geometry and gray-level distribution within the nodules of the same type. The detection combines the normalized cross-correlation template matching and a genetic optimization algorithm. The final step eliminates the false positive nodules (FPNs) using three features that robustly define the true lung nodules. Experiments with 200 CT data sets show that the proposed approach provided comparable results with respect to the experts.

3D shape analysis for early diagnosis of malignant lung nodules.

An alternative method for diagnosing malignant lung nodules by their shape rather than conventional growth rate is proposed. The 3D surfaces of the detected lung nodules are delineated by spherical harmonic analysis, which represents a 3D surface of the lung nodule supported by the unit sphere with a linear combination of special basis functions, called spherical harmonics (SHs). The proposed 3D shape analysis is carried out in five steps: (i) 3D lung nodule segmentation with a deformable 3D boundary controlled by two probabilistic visual appearance models (the learned prior and the estimated current appearance one); (ii) 3D Delaunay triangulation to construct a 3D mesh model of the segmented lung nodule surface; (iii) mapping this model to the unit sphere; (iv) computing the SHs for the surface, and (v) determining the number of the SHs to delineate the lung nodule. We describe the lung nodule shape complexity with a new shape index, the estimated number of the SHs, and use it for the K-nearest classification to distinguish malignant and benign lung nodules. Preliminary experiments on 327 lung nodules (153 malignant and 174 benign) resulted in the 93.6% correct classification (for the 95% confidence interval), showing that the proposed method is a promising supplement to current technologies for the early diagnosis of lung cancer.

3D shape analysis for early diagnosis of malignant lung nodules.

An alternative method of diagnosing malignant lung nodules by their shape, rather than conventional growth rate, is proposed. The 3D surfaces of the detected lung nodules are delineated by spherical harmonic analysis that represents a 3D surface of the lung nodule supported by the unit sphere with a linear combination of special basis functions, called Spherical Harmonics (SHs). The proposed 3D shape analysis is carried out in five steps: (i) 3D lung nodule segmentation with a deformable 3D boundary controlled by a new prior visual appearance model; (ii) 3D Delaunay triangulation to construct a 3D mesh model of the segmented lung nodule surface; (iii) mapping this model to the unit sphere; (iv) computing the SHs for the surface; and (v) determining the number of the SHs to delineate the lung nodule. We describe the lung nodule shape complexity with a new shape index, the estimated number of the SHs, and use it for the K-nearest classification into malignant and benign lung nodules. Preliminary experiments on 327 lung nodules (153 malignant and 174 benign) resulted in a classification accuracy of 93.6%, showing that the proposed method is a promising supplement to current technologies for the early diagnosis of lung cancer.

Elastic phantoms generated by microfluidics technology: validation of an imaged-based approach for accurate measurement of the growth rate of lung nodules.

This paper focuses on validating our approach for monitoring the development of lung nodules detected in successive chest low-dose computed tomography (LDCT) scans of a patient. Our methodology for monitoring detected lung nodules includes 3D LDCT data registration, which is a non-rigid technique and involves two steps: (i) global target-to-prototype alignment of one scan to another using the experience gained from a prior appearance model, followed by (ii) local alignment to correct for intricate relative deformations. We propose a new approach for validating the accuracy of our algorithm for elastic lung phantoms constructed with state-of-the-art microfluidics technology and in vivo data. Fabricated from a flexible transparent polymer, i.e. polydimethylsiloxane (PDMS), the phantoms mimic the contractions and expansions of the lung and nodules as seen during normal breathing. The in vivo data in our study had been collected from a small control group of four subjects and a larger test group of 27 subjects with known ground truth (biopsy diagnosis. The growth rate and diagnostic results for both phantoms and in vivo data confirm the high accuracy of our algorithm.