Dory: Computation of persistence diagrams up to dimension two for Vietoris-Rips filtrations of large data sets.

Persistent homology (PH) is an approach to topological data analysis (TDA) that computes multi-scale topologically invariant properties of high-dimensional data that are robust to noise. While PH has revealed useful patterns across various applications, computational requirements have limited applications to small data sets of a few thousand points. We present Dory, an efficient and scalable algorithm that can compute the persistent homology of sparse Vietoris-Rips complexes on larger data sets, up to and including dimension two and over the field .

Expression of concern: Gadolinium embedded iron oxide nanoclusters as - dual-modal MRI-visible vectors for safe and efficient siRNA delivery.

Expression of concern for 'Gadolinium embedded iron oxide nanoclusters as - dual-modal MRI-visible vectors for safe and efficient siRNA delivery' by Xiaoyong Wang , , 2013, , 8098-8104, https://doi.org/10.1039/C3NR02797J.

Optimizing ancestral trait reconstruction of large HIV Subtype C datasets through multiple-trait subsampling.

Large datasets along with sampling bias represent a challenge for phylodynamic reconstructions, particularly when the study data are obtained from various heterogeneous sources and/or through convenience sampling. In this study, we evaluate the presence of unbalanced sampled distribution by collection date, location, and risk group of human immunodeficiency virus Type 1 Subtype C using a comprehensive subsampling strategy and assess their impact on the reconstruction of the viral spatial and risk group dynamics using phylogenetic comparative methods. Our study shows that a most suitable dataset for ancestral trait reconstruction can be obtained through subsampling by all available traits, particularly using multigene datasets.

Prediction of multiclass surgical outcomes in glaucoma using multimodal deep learning based on free-text operative notes and structured EHR data.

Objective: Surgical outcome prediction is challenging but necessary for postoperative management. Current machine learning models utilize pre- and post-op data, excluding intraoperative information in surgical notes. Current models also usually predict binary outcomes even when surgeries have multiple outcomes that require different postoperative management.

To boldly go: Unpacking the NHGRI's bold predictions for human genomics by 2030.

The 2020 strategic vision for human genomics, written by the National Human Genome Research Institute (NHGRI), was punctuated by a set of provocatively audacious "bold predictions for human genomics by 2030." Starting here, these will be unpacked and discussed in an upcoming series in the American Journal of Human Genetics.

Therapeutic Potential of the Genus Phytochemicals: A Theoretical ADME/Tox Analysis.

Natural products (NPs) are essential in the search for new drugs to treat a wide range of diseases, including infectious and malignant disorders. However, despite the discovery of many bioactive NPs, they often do not make it to market as drugs due to toxicity and other challenges. The development of NPs into drugs is a long and expensive process, and many promising compounds are abandoned along the way.

Clinical trial data sharing: a cross-sectional study of outcomes associated with two U.S. National Institutes of Health models.

The impact and effectiveness of clinical trial data sharing initiatives may differ depending on the data sharing model used. We characterized outcomes associated with models previously used by the U.S.

Community and partner engagement in dissemination and implementation research at the National Institutes of Health: an analysis of recently funded studies and opportunities to advance the field.

Background: As the focus has grown in recent years on both engaged research and dissemination and implementation (D&I) research, so too has federal funding to support these areas. The purpose of this analysis is to provide an overall perspective about the range of practices and approaches being used to engage partners in D&I research, with special attention to disparities-relevant research, and to identify gaps and opportunities in research funded by the US National Institutes of Health (NIH) in this space.

Methods: This analysis examined a portfolio of active D&I research grants funded in fiscal years 2020 and 2021 across the NIH.

Safety of COVID-19 vaccines during pregnancy: A systematic review and meta-analysis.

Background: Assessment of COVID-19 vaccines safety during pregnancy is urgently needed.

Methods: We conducted a systematic review and meta-analysis to evaluate the safety of COVID-19 vaccines, including their components and technological platforms used in other vaccines during pregnancy and animal studies to complement direct evidence. We searched literature databases from its inception to September 2021 without language restriction, COVID-19 vaccine websites, and reference lists of other systematic reviews and the included studies.

County-level associations between food retailer availability and violent crime rate.

Background: Violent crime (i.e., homicide, armed robbery, aggravated assault, and rape) continues to be a major public health concern in America.

Distinct cardiovascular phenotypes are associated with prognosis in systemic sclerosis: a cardiovascular magnetic resonance study.

Aims: Cardiovascular involvement in systemic sclerosis (SSc) is heterogeneous and ill-defined. This study aimed to: (i) discover cardiac phenotypes in SSc by cardiovascular magnetic resonance (CMR); (ii) provide a CMR-based algorithm for phenotypic classification; and (iii) examine for associations between phenotypes and mortality.

Methods And Results: A retrospective, single-centre, observational study of 260 SSc patients who underwent clinically indicated CMR including native myocardial T1 and T2 mapping from 2016 to 2019 was performed.

Tooth retention, health, and quality of life in older adults: a scoping review.

Objective: This scoping review describes the relationship between tooth retention, health, and quality of life in older adults.

Methods: Seven databases were searched for English language articles for subjects ≥ 65 y from 1981 to 2021. Exposure was tooth retention (≥ 20), and outcomes were general/systemic health and quality of life.

The ironic effects of dietary restraint in situations that undermine self-regulation.

Dietary restraint, defined as the cognitive effort to restrict eating, can paradoxically make individuals more susceptible to unhealthy eating when their ability to self-regulate is threatened. Past experiments have found that, in situations that elicit low self-control and/or unhealthy cravings, participants with higher dietary restraint eat more than those with lower restraint. However, these relationships have never been examined in a free-living environment.

The geography of emergency department-based HIV testing in South Africa: Can patients link to care?

Background: Emergency Departments (EDs) can serve as clinical sites for identification of new HIV infections and their entry into care. We examined if HIV-positive patients who present to EDs in South Africa are able to successfully link to care.

Methods: We conducted a one-year longitudinal prospective cohort study in four hospitals across the Eastern Cape, South Africa, with participants followed between July 2016 and July 2018.

Phenotyping hypertrophic cardiomyopathy using cardiac diffusion magnetic resonance imaging: the relationship between microvascular dysfunction and microstructural changes.

Aims: Microvascular dysfunction in hypertrophic cardiomyopathy (HCM) is predictive of clinical decline, however underlying mechanisms remain unclear. Cardiac diffusion tensor imaging (cDTI) allows in vivo characterization of myocardial microstructure by quantifying mean diffusivity (MD), fractional anisotropy (FA) of diffusion, and secondary eigenvector angle (E2A). In this cardiac magnetic resonance (CMR) study, we examine associations between perfusion and cDTI parameters to understand the sequence of pathophysiology and the interrelation between vascular function and underlying microstructure.

Safety of components and platforms of COVID-19 vaccines considered for use in pregnancy: A rapid review.

Background: Rapid assessment of COVID-19 vaccine safety during pregnancy is urgently needed.

Methods: We conducted a rapid systematic review, to evaluate the safety of COVID-19 vaccines selected by the COVID-19 Vaccines Global Access-Maternal Immunization Working Group in August 2020, including their components and their technological platforms used in other vaccines for pregnant persons. We searched literature databases, COVID-19 vaccine pregnancy registries, and explored reference lists from the inception date to February 2021 without language restriction.

Triglyceride-rich lipoproteins and their remnants: metabolic insights, role in atherosclerotic cardiovascular disease, and emerging therapeutic strategies-a consensus statement from the European Atherosclerosis Society.

Recent advances in human genetics, together with a large body of epidemiologic, preclinical, and clinical trial results, provide strong support for a causal association between triglycerides (TG), TG-rich lipoproteins (TRL), and TRL remnants, and increased risk of myocardial infarction, ischaemic stroke, and aortic valve stenosis. These data also indicate that TRL and their remnants may contribute significantly to residual cardiovascular risk in patients on optimized low-density lipoprotein (LDL)-lowering therapy. This statement critically appraises current understanding of the structure, function, and metabolism of TRL, and their pathophysiological role in atherosclerotic cardiovascular disease (ASCVD).

Building Capacity for Global Cancer Research: Existing Opportunities and Future Directions.

Cancer incidence and mortality are increasing in low- and middle-income countries (LMICs), where more than 75% of global cancer burden will occur by the year 2040. The primary drivers of cancer morbidity and mortality in LMICs are environmental and behavioral risk factors, inadequate prevention and early detection services, presence of comorbidities, and poor access to treatment and palliation. These same drivers also contribute to marked cancer health disparities in high-income countries.

Automated, open-source segmentation of the Hippocampus and amygdala with the open Vanderbilt archive of the temporal lobe.

Examining volumetric differences of the amygdala and anterior-posterior regions of the hippocampus is important for understanding cognition and clinical disorders. However, the gold standard manual segmentation of these structures is time and labor-intensive. Automated, accurate, and reproducible techniques to segment the hippocampus and amygdala are desirable.

NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index.

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources.

Ancestry-specific associations identified in genome-wide combined-phenotype study of red blood cell traits emphasize benefits of diversity in genomics.

Background: Quantitative red blood cell (RBC) traits are highly polygenic clinically relevant traits, with approximately 500 reported GWAS loci. The majority of RBC trait GWAS have been performed in European- or East Asian-ancestry populations, despite evidence that rare or ancestry-specific variation contributes substantially to RBC trait heritability. Recently developed combined-phenotype methods which leverage genetic trait correlation to improve statistical power have not yet been applied to these traits.

Protein Stability and Functional Characterization of Intra-Melanosomal Domain of Human Recombinant Tyrosinase-Related Protein 1.

Pigmentation is the result of a complex process by which the biopolymer melanin is synthesized and packed into melanosomes of melanocytes. Various types of oculocutaneous albinism (OCA), a series of autosomal recessive disorders, are associated with reduced pigmentation in the skin, eyes, and hair due to genetic mutations of proteins involved in melanogenesis. Human tyrosinase (Tyr) and tyrosinase-related protein 1 (Tyrp1) drives the enzymatic process of pigment bio-polymerization.