Database resources of the National Center for Biotechnology Information.

The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for most of these databases. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, SciENcv, the NIH Comparative Genomics Resource (CGR), NCBI Virus, SRA, RefSeq, foreign contamination screening tools, Taxonomy, iCn3D, ClinVar, GTR, MedGen, dbSNP, ALFA, ClinicalTrials.gov, Pathogen Detection, antimicrobial resistance resources, and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.

Aziridination via Nitrogen-Atom Transfer to Olefins from Photoexcited Azoxy-Triazenes.

Herein, we report that readily accessible azoxy-triazenes can serve as nitrogen atom sources under visible light excitation for the phthalimido-protected aziridination of alkenes. This approach eliminates the need for external oxidants, precious transition metals, and photocatalysts, marking a departure from conventional methods. The versatility of this transformation extends to the selective aziridination of both activated and unactivated multisubstituted alkenes of varying electronic profiles. Notably, this process avoids the formation of competing C-H insertion products. The described protocol is operationally simple, scalable, and adaptable to photoflow conditions. Mechanistic studies support the idea that the photofragmentation of azoxy-triazenes results in the generation of a free singlet nitrene. Furthermore, a mild photoredox-catalyzed N-N cleavage of the protecting group to furnish the free aziridines is reported. Our findings contribute to the advancement of sustainable and practical methodologies for the synthesis of nitrogen-containing compounds, showcasing the potential for broader applications in synthetic chemistry.

Photosensitized Oxidative Damage from a New Perspective: The Influence of Before-Light and After-Light Reaction Conditions.

Photooxidative damage is heavily influenced by the presence of bioactive agents. Conversely, bioactive agents influence the local environment, which in turn is perturbed by photooxidative damage. These sorts of processes give rise to a version of the "chicken-and-egg" quandary. In this Perspective, we probe this issue by referring to photooxidative damage in one direction as the light-dark (L-D) sequence and in a second direction as the dark-light (D-L) sequence with a reversed cause and effect. The L-D sequence can lead to the downstream production of reactive molecular species (RMS) in the dark, whereas the D-L sequence can be a pre-irradiation period, such as an additive to limit cellular iron levels to enhance biosynthesized amounts of a protoporphyrin sensitizer. A third direction comes from L-D or D-L sequences, or both simultaneously, which can also be useful for optimizing photodynamics. Photodynamic optimization will benefit from understanding and quantitating unidirectional L-D and D-L pathways, and bidirectional L-D/D-L pathways, for improved control over photooxidative damage. Photooxidative damage, which occurs during anticancer photodynamic therapy (PDT), will be shown to involve RMS. Such RMS include persulfoxides (R2S+OO-), NO2•, peroxynitrate (O2NOO-), OOSCN-, SO3•-, selenocyanogen [(SeCN)2], the triselenocyanate anion [(SeCN)3-], I•, I2•-, I3-, and HOOI, as well as additives to destabilize membranes (e.g., caspofungin and saponin A16), inhibit DNA synthesis (5-fluorouracil), or sequester iron (desferrioxamine). In view of the success that additive natural products and repurposed drugs have had in PDT, a Perspective of additive types is expected to reveal mechanistic details for enhanced photooxidation reactions in general. Indeed, strategies for how to potentiate photooxidations with additives remain highly underexplored.

Database resources of the national center for biotechnology information.

The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the most of these databases. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, RefSeq, SRA, Virus, dbSNP, dbVar, ClinicalTrials.gov, MMDB, iCn3D and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

SUMMARY: Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences. AVAILABILITY AND IMPLEMENTATION: https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Implementation of CDC Guidelines for Recess: A Formative Research Study.

The American Academy of Pediatrics recognizes recess as an essential part of overall child development in schools, impacting children's cognitive, socioemotional and physical health and development. However, recess is often removed from the school curriculum in exchange for more classroom activities. The Centers for Disease Control and Prevention (CDC) and SHAPE America developed Strategies for Recess in Schools to promote high-quality recess through specific actions, yet is not known how these are successfully implemented, particularly, in underserved settings. This formative research study examined the implementation of the CDC strategy in an urban, inner-city charter elementary school to identify barriers and facilitators to successful recess implementation from the perspective of various stakeholders. Thirteen in-depth interviews and focus group discussions were conducted with parents, teachers, recess monitors, and school administrators. Interviews were recorded, transcribed, and coded for thematic analysis, supported by group discussion and analytic memos. Results suggested that although stakeholders recognized the importance of recess, the implementation of the CDC strategy was neither uniformly understood nor implemented, suggesting that additional frameworks may be helpful in implementing the CDC strategy in schools in underserved communities.

Warming in the land of the midnight sun: breeding birds may suffer greater heat stress at high- versus low-Arctic sites.

Rising global temperatures are expected to increase reproductive costs for wildlife as greater thermoregulatory demands interfere with reproductive activities. However, predicting the temperatures at which reproductive performance is negatively impacted remains a significant hurdle. Using a thermoregulatory polygon approach, we derived a reproductive threshold temperature for an Arctic songbird-the snow bunting (Plectrophenax nivalis). We defined this threshold as the temperature at which individuals must reduce activity to suboptimal levels (i.e. less than four-time basal metabolic rate) to sustain nestling provisioning and avoid overheating. We then compared this threshold to operative temperatures recorded at high (82° N) and low (64° N) Arctic sites to estimate how heat constraints translate into site-specific impacts on sustained activity level. We predict buntings would become behaviourally constrained at operative temperatures above 11.7°C, whereupon they must reduce provisioning rates to avoid overheating. Low-Arctic sites had larger fluctuations in solar radiation, consistently producing daily periods when operative temperatures exceeded 11.7°C. However, high-latitude birds faced entire, consecutive days when parents would be unable to sustain required provisioning rates. These data indicate that Arctic warming is probably already disrupting the breeding performance of cold-specialist birds and suggests counterintuitive and severe negative impacts of warming at higher latitude breeding locations.

Epidemiology and clinical manifestations of cardiac amyloidosis.

Cardiac amyloidosis, once considered a rare disease, has garnered significant attention over the last few years due to three key reasons: first, increased recognition of this disease in conjunction with various common cardiac conditions such as heart failure with preserved ejection fraction and aortic stenosis; second, due to the advent of promising new therapies for light chain disease (AL), transthyretin (ATTR) cardiomyopathy, and amyloid neuropathy; finally, the advancements in cardiac imaging including echocardiography, magnetic resonance imaging, and nuclear cardiac scintigraphy aid in non-biopsy diagnosis of ATTR cardiac amyloidosis. The hereditary forms of ATTR have further come into importance with the availability of genetic testing and increased prevalence of certain mutations in African Americans. Recognition of non-cardiac clues to this disease has gained importance and reiterates that high clinical suspicion, detailed patient history, and examination with appropriate use of imaging are vital to confirm the diagnosis.

Limited heat tolerance in a cold-adapted seabird: implications of a warming Arctic.

The Arctic is warming at approximately twice the global rate, with well-documented indirect effects on wildlife. However, few studies have examined the direct effects of warming temperatures on Arctic wildlife, leaving the importance of heat stress unclear. Here, we assessed the direct effects of increasing air temperatures on the physiology of thick-billed murres (Uria lomvia), an Arctic seabird with reported mortalities due to heat stress while nesting on sun-exposed cliffs. We used flow-through respirometry to measure the response of body temperature, resting metabolic rate, evaporative water loss and evaporative cooling efficiency (the ratio of evaporative heat loss to metabolic heat production) in murres while experimentally increasing air temperature. Murres had limited heat tolerance, exhibiting: (1) a low maximum body temperature (43.3°C); (2) a moderate increase in resting metabolic rate relative that within their thermoneutral zone (1.57 times); (3) a small increase in evaporative water loss rate relative that within their thermoneutral zone (1.26 times); and (4) a low maximum evaporative cooling efficiency (0.33). Moreover, evaporative cooling efficiency decreased with increasing air temperature, suggesting murres were producing heat at a faster rate than they were dissipating it. Larger murres also had a higher rate of increase in resting metabolic rate and a lower rate of increase in evaporative water loss than smaller murres; therefore, evaporative cooling efficiency declined with increasing body mass. As a cold-adapted bird, murres' limited heat tolerance likely explains their mortality on warm days. Direct effects of overheating on Arctic wildlife may be an important but under-reported impact of climate change.

Database resources of the National Center for Biotechnology Information.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 38 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Labs and a new sequence database search. Resources that were updated in the past year include PubMed, PMC, Bookshelf, genome data viewer, Assembly, prokaryotic genomes, Genome, BioProject, dbSNP, dbVar, BLAST databases, igBLAST, iCn3D and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Regio- and Diastereoselective Rhodium-Catalyzed Allylic Substitution with Unstabilized Benzyl Nucleophiles.

We have developed a highly regio- and diastereoselective rhodium-catalyzed allylic substitution of challenging alkyl-substituted secondary allylic carbonates with benzylzinc reagents, which are prepared from widely available benzyl halides. This process utilizes rhodium(III) chloride as a commercially available, high-oxidation state and bench-stable pre-catalyst to provide a rare example of a regio- and diastereoselective allylic substitution in the absence of an exogenous ligand. This reaction tolerates electronically diverse benzylzinc nucleophiles and an array of functionalized and/or challenging aliphatic allylic electrophiles. Finally, the configurational fluxionality of the rhodium-allyl intermediate is exploited to develop a novel diastereoselective process for the construction of vicinal acyclic ternary/ternary stereogenic centers, in addition to a cyclic ternary/quaternary derivative.

Evidence for Helical Hinge Zero Modes in an Fe-Based Superconductor.

Combining topology and superconductivity provides a powerful tool for investigating fundamental physics as well as a route to fault-tolerant quantum computing. There is mounting evidence that the Fe-based superconductor FeTe0.55Se0.45 (FTS) may also be topologically nontrivial. Should the superconducting order be s±, then FTS could be a higher order topological superconductor with helical hinge zero modes (HHZMs). To test the presence of these modes, we have fabricated normal-metal/superconductor junctions on different surfaces via 2D atomic crystal heterostructures. As expected, junctions in contact with the hinge reveal a sharp zero bias anomaly that is absent when tunneling purely into the c-axis. Additionally, the shape and suppression with temperature are consistent with highly coherent modes along the hinge and are incongruous with other origins of zero bias anomalies. Additional measurements with soft-point contacts in bulk samples with various Fe interstitial contents demonstrate the intrinsic nature of the observed mode. Thus, we provide evidence that FTS is indeed a higher order topological superconductor.

Avian thermoregulation in the heat: is evaporative cooling more economical in nocturnal birds?

Evaporative cooling is a prerequisite for avian occupancy of hot, arid environments, and is the only avenue of heat dissipation when air temperatures (Ta) exceed body temperature (Tb). Whereas diurnal birds can potentially rehydrate throughout the day, nocturnal species typically forgo drinking between sunrise and sunset. We hypothesized that nocturnal birds have evolved reduced rates of evaporative water loss (EWL) and more economical evaporative cooling mechanisms compared with diurnal species, permitting nocturnal species to tolerate extended periods of intense heat without becoming lethally dehydrated. We used phylogenetically informed regressions to compare EWL and evaporative cooling efficiency [ratio of evaporative heat loss (EHL) and metabolic heat production (MHP); EHL/MHP] among nocturnal and diurnal birds at high Ta We analyzed variation in three response variables: (1) slope of EWL at Ta between 40 and 46°C, (2) EWL at Ta=46°C and (3) EHL/MHP at Ta=46°C. Nocturnality emerged as a weak, negative predictor, with nocturnal species having slightly shallower slopes and reduced EWL compared with diurnal species of similar mass. In contrast, nocturnal activity was positively correlated with EHL/MHP, indicating a greater capacity for evaporative cooling in nocturnal birds. However, our analysis also revealed conspicuous differences among nocturnal taxa. Caprimulgids and Australian owlet-nightjars had shallower slopes and reduced EWL compared with similarly sized diurnal species, whereas owls had EWL rates comparable to those of diurnal species. Consequently, our results did not unequivocally demonstrate more economical cooling among nocturnal birds. Owls predominately select refugia with cooler microclimates, but the more frequent and intense heat waves forecast for the 21st century may increase microclimate temperatures and the necessity for active heat dissipation, potentially increasing owls' vulnerability to dehydration and hyperthermia.

Dependence of SERS enhancement on the chemical composition and structure of Ag/Au hybrid nanoparticles.

Noble metal nanoparticles (NPs) such as silver (Ag) and gold (Au) have unique plasmonic properties that give rise to surface enhanced Raman scattering (SERS). Generally, Ag NPs have much stronger plasmonic properties and, hence, provide stronger SERS signals than Au NPs. However, Ag NPs lack the chemical stability and biocompatibility of comparable Au NPs and typically exhibit the most intense plasmonic resonance at wavelengths much shorter than the optimal spectral region for many biomedical applications. To overcome these issues, various experimental efforts have been devoted to the synthesis of Ag/Au hybrid NPs for the purpose of SERS detections. However, a complete understanding on how the SERS enhancement depends on the chemical composition and structure of these nanoparticles has not been achieved. In this study, Mie theory and the discrete dipole approximation have been used to calculate the plasmonic spectra and near-field electromagnetic enhancements of Ag/Au hybrid NPs. In particular, we discuss how the electromagnetic enhancement depends on the mole fraction of Au in Ag/Au alloy NPs and how one may use extinction spectra to distinguish between Ag/Au alloyed NPs and Ag-Au core-shell NPs. We also show that for incident laser wavelengths between ∼410 nm and 520 nm, Ag/Au alloyed NPs provide better electromagnetic enhancement than pure Ag, pure Au, or Ag-Au core-shell structured NPs. Finally, we show that silica-core Ag/Au alloy shelled NPs provide even better performance than pure Ag/Au alloy or pure solid Ag and pure solid Au NPs. The theoretical results presented will be beneficial to the experimental efforts in optimizing the design of Ag/Au hybrid NPs for SERS-based detection methods.

Psychiatry Residents' Use of Educational Websites: A Pilot Survey Study.

OBJECTIVE: Psychiatry residents have numerous online educational resources readily available to them although currently there are no data regarding residents' use and perception of such websites. METHODS: A survey was offered to 62 residents from all four years of training as well as recent graduates of a single psychiatry residency training program. RESULTS: Residents reported utilizing online resources on average 68 % of the time, in comparison to 32 % on average for printed materials. Residents reported UpToDate, PubMed, and Wikipedia as the most visited websites and ranked each highly but for different purposes. Thirty-five percent of residents felt that insufficient faculty guidance was a barrier to use of these educational websites. CONCLUSIONS: Pilot data indicate psychiatry residents use online resources daily for their education in various settings. Resident perceptions of individual website's trustworthiness, ease of use, and sources of clinical decision-making and personal learning suggest potential opportunities for educators to better understand the current use of these resources in residency training. Reported barriers including lack of faculty guidance suggest opportunities for academic psychiatry. Further study is necessary at multiple sites before such results may be generalized.

Effect of a Comprehensive School-Based Health Center on Academic Growth in K-8th Grade Students.

OBJECTIVE: School-based health centers (SBHCs) improve health care access, but associations with educational outcomes are mixed and limited for elementary and middle school students. We investigated whether students enrolled in a comprehensive SBHC demonstrated more growth in standardized math and reading assessments over 4 school years versus nonenrolled students. We also explored changes in absenteeism. METHODS: Participants were students enrolled in 2 co-located Title I schools from 2015-19 (1 elementary, 1 middle, n = 2480). Analysis of math and reading was limited to students with baseline and postbaseline scores (math n = 1622; reading n = 1607). Longitudinal regression models accounting for within-subject clustering were used to estimate the association of SBHC enrollment with academic scores and daily absenteeism, adjusting for grade, sex, body mass index category, health conditions, baseline outcomes (scores or absenteeism), and outcome pretrends. RESULTS: More than 70% of SBHC-enrolled students had math (1194 [73.6%]) and reading 1186 [73.8%]) scores. Enrollees were more likely than nonenrollees to have asthma (39.7% vs 19.6%) and overweight/obesity (42.4% vs 33.6%). Adjusted baseline scores were significantly lower in math and reading for enrollees. Mean change from baseline for enrollees exceeded nonenrollees by 3.5 points (95% confidence interval [CI]: 2.2, 4.8) in math and 2.1 points (95% CI: 0.9, 3.3) in reading. The adjusted rate of decrease in daily absenteeism was 10.8% greater for enrollees (incident rate ratio 0.772 [95% CI: 0.623, 0.956]) than nonenrollees (incident rate ratio 0.865 [95% CI: 0.696, 1.076]). CONCLUSIONS: SBHC enrollees had greater health and educational risk but demonstrated more growth in math and reading and less absenteeism than nonenrollees.

An arctic breeding songbird overheats during intense activity even at low air temperatures.

Birds maintain some of the highest body temperatures among endothermic animals. Often deemed a selective advantage for heat tolerance, high body temperatures also limits birds' thermal safety margin before reaching lethal levels. Recent modelling suggests that sustained effort in Arctic birds might be restricted at mild air temperatures, which may require reductions in activity to avoid overheating, with expected negative impacts on reproductive performance. We measured within-individual changes in body temperature in calm birds and then in response to an experimental increase in activity in an outdoor captive population of Arctic, cold-specialised snow buntings (Plectrophenax nivalis), exposed to naturally varying air temperatures (- 15 to 36 °C). Calm buntings exhibited a modal body temperature range from 39.9 to 42.6 °C. However, we detected a significant increase in body temperature within minutes of shifting calm birds to active flight, with strong evidence for a positive effect of air temperature on body temperature (slope = 0.04 °C/ °C). Importantly, by an ambient temperature of 9 °C, flying buntings were already generating body temperatures ≥ 45 °C, approaching the upper thermal limits of organismal performance (45-47 °C). With known limited evaporative heat dissipation capacities in these birds, our results support the recent prediction that free-living buntings operating at maximal sustainable rates will increasingly need to rely on behavioural thermoregulatory strategies to regulate body temperature, to the detriment of nestling growth and survival.

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.

Singlet Oxygen's Potential Role as a Nonoxidative Facilitator of Disulfide S-S Bond Rotation†.

The role of singlet oxygen potentially mediating increased conformational flexibility of a disulfide was investigated. Density functional theory (DFT) calculations indicate that the singlet oxygenation of 1,2-dimethyldisulfane produces a peroxy intermediate. This intermediate adopts a structure with a longer S-S bond distance and a more planar torsional angle θ (C-S-S-C) compared with the nonoxygenated 1,2-dimethyldisulfane. The lengthened S-S bond enables a facile rotation about the torsional angle in the semicircle region 0° < θ < 210°, that is ~5 kcal mol-1 lower in energy than the disulfane. The peroxy intermediate bears nO → σS-S and nO → σ*S-S interactions that stabilize the S-O bond but destabilize the S-S bond, which contrasts with stabilizing nS → σ*S-S hyperconjugative effects in the disulfane S-S bond. Subsequent departure of O2 from the disulfane peroxy intermediate is reminiscent of peroxy intermediates which also expel O2 , yet facilitate cis-trans isomerizations of stilbenes, hexadienes, cyanines, and carotenes. "Non-oxidative" 1 O2 interactions with a variety of bond types are currently underappreciated. We hope to raise awareness of how these interactions can help elucidate the origins of molecular twisting.

Photoinduced Nitroarenes as Versatile Anaerobic Oxidants for Accessing Carbonyl and Imine Derivatives.

Herein, we report a protocol for the anaerobic oxidation of alcohols, amines, aldehydes, and imines promoted by photoexcited nitroarenes. Mechanistic studies support the idea that photoexcited nitroarenes undergo double hydrogen atom transfer (HAT) steps with alcohols and amines to provide the respective ketone and imine products. In the presence of aldehydes and imines, successive HAT and oxygen atom transfer (OAT) events occur to yield carboxylic acids and amides, respectively. This transformation is amenable to a continuous-photoflow setup, which led to reduced reaction times.