Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics.

The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.

A Health Equity Approach for Implementation of JYNNEOS Vaccination at Large, Community-Based LGBTQIA+ Events - Georgia, August 27-September 5, 2022.

Gay, bisexual, and other men who have sex with men (MSM) have been disproportionately affected during the 2022 U.S. monkeypox outbreak, with Black or African American (Black) MSM being the most affected demographic group (1). As of September 28, 2022, Georgia had reported 1,784 monkeypox cases; 98% of which occurred in males and 77% among Black persons (2). As of September 13, 2022, 60% of reported cases were among persons with HIV infection, and 50% of persons with monkeypox had a sexually transmitted infection within the past year (3). Because of racial disparities in the incidence of monkeypox cases and a large proportion of cases among MSM in Georgia, early vaccination beginning in July focused on improving equitable access by establishing new and leveraging existing partnerships with community-based organizations that serve affected populations, including persons with HIV infection. Despite these efforts, disparities persisted because of high demand and limited vaccine supply. The Georgia Department of Public Health (DPH) requested CDC support for a vaccine pilot and received an additional allocation of 5,500 doses of JYNNEOS vaccine for administration at events leading up to and throughout a Black gay Pride festival in Atlanta, a multiday event held Labor Day weekend (September 2-5, 2022). The event celebrates lesbian, gay, bisexual, transgender, queer or questioning, intersex, asexual, and other (LGBTQIA+) communities of color and hosts more than 125,000 attendees each year. Before the festival (as of August 24), 17,546 persons had been vaccinated in Georgia, of whom 96% were male, 34% aged 25-36 years, 44% Black, and 8% Hispanic or Latino (Hispanic) (4).

Randomised controlled trial of real-time feedback and brief coaching to reduce indoor smoking.

BACKGROUND: Previous secondhand smoke (SHS) reduction interventions have provided only delayed feedback on reported smoking behaviour, such as coaching, or presenting results from child cotinine assays or air particle counters. DESIGN: This SHS reduction trial assigned families at random to brief coaching and continuous real-time feedback (intervention) or measurement-only (control) groups. PARTICIPANTS: We enrolled 298 families with a resident tobacco smoker and a child under age 14. INTERVENTION: We installed air particle monitors in all homes. For the intervention homes, immediate light and sound feedback was contingent on elevated indoor particle levels, and up to four coaching sessions used prompts and praise contingent on smoking outdoors. Mean intervention duration was 64 days. MEASURES: The primary outcome was 'particle events' (PEs) which were patterns of air particle concentrations indicative of the occurrence of particle-generating behaviours such as smoking cigarettes or burning candles. Other measures included indoor air nicotine concentrations and participant reports of particle-generating behaviour. RESULTS: PEs were significantly correlated with air nicotine levels (r=0.60) and reported indoor cigarette smoking (r=0.51). Interrupted time-series analyses showed an immediate intervention effect, with reduced PEs the day following intervention initiation. The trajectory of daily PEs over the intervention period declined significantly faster in intervention homes than in control homes. Pretest to post-test, air nicotine levels, cigarette smoking and e-cigarette use decreased more in intervention homes than in control homes. CONCLUSIONS: Results suggest that real-time particle feedback and coaching contingencies reduced PEs generated by cigarette smoking and other sources. TRIAL REGISTRATION NUMBER: NCT01634334; Post-results.

Survival of Polyploid hybrid salamander embryos.

BACKGROUND: Animals with polyploid, hybrid nuclei offer a challenge for models of gene expression and regulation during embryogenesis. To understand how such organisms proceed through development, we examined the timing and prevalence of mortality among embryos of unisexual salamanders in the genus Ambystoma. RESULTS: Our regional field surveys suggested that heightened rates of embryo mortality among unisexual salamanders begin in the earliest stages of embryogenesis. Although we expected elevated mortality after zygotic genome activation in the blastula stage, this is not what we found among embryos which we reared in the laboratory. Once embryos entered the first cleavage stage, we found no difference in mortality rates between unisexual salamanders and their bisexual hosts. Our results are consistent with previous studies showing high rates of unisexual mortality, but counter to reports that heightened embryo mortality continues throughout embryo development. CONCLUSIONS: Possible causes of embryonic mortality in early embryogenesis suggested by our results include abnormal maternal loading of RNA during meiosis and barriers to insemination. The surprising survival rates of embryos post-cleavage invites further study of how genes are regulated during development in such polyploid hybrid organisms.

Does obesity cause type 2 diabetes mellitus (T2DM)? Or is it the opposite?

Obesity is believed to be a promoter of type 2 diabetes mellitus (T2DM). Reports indicate that severe obesity in childhood and adolescence increases the risk of T2DM in youth and young adults. T2DM, which is commonly asymptomatic, frequently is not recognized until random blood glucose is measured. Screening blood glucose levels measured in obese individuals are more effective for identifying undiagnosed persons, than screening the general population and therefore introduces a selection bias for discovery. The following commentary will indicate why these observations do not indicate that obesity is the cause of T2DM. Also, it will be shown that the insulin resistance of T2DM occurs primarily in the muscles of lean individuals predisposed to diabetes before they become obese. This insulin resistance is not secondary to, but instead, is the cause of the excessive fat accumulation associated with T2DM. Moreover, this early muscle insulin resistance is the etiology of the hyperlipidemia and excess fat accumulation characteristic of T2DM.

Screening eye exams in youth with type 1 diabetes under 18 years of age: Once may be enough?

Case series and registry data suggest that diabetic retinopathy requiring treatment is rare in youth with type 1 diabetes (T1D) prior to 18 years of age. We evaluated this question in the standardized clinical trial setting by retrospectively reviewing diabetic retinopathy examinations from participants in the Diabetes Control and Complications Trial (DCCT) who were 13 to <18 years of age at randomization. Standardized stereoscopic 7-field fundus photographs were obtained every 6 months during DCCT (1983-1993). Photographs were graded centrally using the Early Treatment Diabetic Retinopathy Study (ETDRS) scale. Transitions in diabetic retinopathy status over time were described. A total of 195 participants with median baseline glycated hemoglobin (HbA1c) of 9.3% (103 in the conventional and 92 in the intensive treatment groups) had an average of 5.3 diabetic retinopathy assessments during 2.3 years of follow-up (range 1-11) while under 18 years of age during the DCCT. No participant developed severe non-proliferative diabetic retinopathy or proliferative diabetic retinopathy and only one participant (in the intensive group) reached clinically significant macular edema (CSME) while less than 18 years of age. In this incident case, baseline characteristics included diabetes duration 9.3 years, HbA1c 10.3%, LDL 131 mg/dL, and mild non-proliferative diabetic retinopathy (35/35 ETDRS scale); CSME resolved without treatment. Similar analyses using age cut-offs of <19, 20, or 21 years showed a slight rise in diabetic retinopathy requiring treatment over late adolescence. Clinical trial evidence suggests that frequent eye exams may not be universally necessary in youth <18 years of age with T1D.

Malaria in Burkina Faso (West Africa) during the twenty-first century.

Temperature and rainfall predicted for the twenty-first century by global coupled models as reported by IPCC, (2014a, and b) were obtained regionally for Burkina Faso and through the Paluclim project, 2011-2014. One of the goals of this project was to assess the upcoming evolution of malaria transmission dynamics. From an impact model on malaria risk linked to climate variability, temperature and rainfall indices were derived. Malaria transmission dynamics were then predicted using the derived temperature and rainfall for the twenty-first century. Similar to the historical evidence of rainfall being an important factor for regulating the seasonal density of malaria vectors, this study also reports a definitive link between low-frequency rainfall variability and malaria in the region under the influence of the Atlantic Multidecadal Oscillation (AMO). This finding can be used by local stakeholders involved with the geography-based population health planning. Moreover, the predicted increase in temperature during the twenty-first century suggests a reduction of larvae survival in Burkina Faso and thus the malaria risk. More generally, the temperature increase could become a new limiting factor for malaria transmission dynamics in the Sahel Region (as reported by Mordecai et al. (2013).

Ecological niche models for sand fly species and predicted distribution of Lutzomyia longipalpis (Diptera: Psychodidae) and visceral leishmaniasis in Bahia state, Brazil.

Visceral leishmaniasis is a public health problem in Brazil. This disease is endemic in most of Bahia state, with increasing reports of cases in new areas. Ecological niche models (ENM) can be used as a tool for predicting potential distribution for disease, vectors, and to identify risk factors associated with their distribution. In this study, ecological niche models (ENMs) were developed for visceral leishmaniasis (VL) cases and 12 sand fly species captured in Bahia state. Sand fly data was collected monthly by CDC light traps from July 2009 to December 2012. MODIS satellite imagery was used to calculate NDVI, NDMI, and NDWI vegetation indices, MODIS day and night land surface temperature (LST), enhanced vegetation index (EVI), and 19 Bioclim variables were used to develop the ENM using the maximum entropy approach (Maxent). Mean diurnal range was the variable that most contributed to all the models for sand flies, followed by precipitation in wettest month. For Lutzomyia longipalpis (L. longipalpis), annual precipitation, precipitation in wettest quarter, precipitation in wettest month, and NDVI were the most contributing variables. For the VL model, the variables that contributed most were precipitation in wettest month, annual precipitation, LST day, and temperature seasonality. L. longipalpis was the species with the widest potential distribution in the state. The identification of risk areas and factors associated with this distribution is fundamental to prioritize resource allocation and to improve the efficacy of the state's program for surveillance and control of VL.

Enantiopurity and absolute configuration determination of arene cis-dihydrodiol metabolites and derivatives using chiral boronic acids.

The relative merits of the methods employed to determine enantiomeric excess (ee) values and absolute configurations of chiral arene and alkene cis-1,2-diol metabolites, including boronate formation, using racemic or enantiopure (+) and (-)-2-(1-methoxyethyl)phenylboronic acid (MEPBA), are discussed. Further applications of: 1) MEPBA derived boronates of chiral mono- and poly-cyclic arene cis-dihydrodiol, cyclohex-2-en-1-one cis-diol, heteroarene cis/trans-2,3-diol, and catechol metabolites in estimating their ee values, and 2) new chiral phenylboronic acids, 2-[1-methoxy-2,2-dimethylpropyl]phenyl boronic acid (MDPBA) and 2-[1-methoxy-1-phenylmethyl]phenyl boronic acid (MPPBA) and their advantages over MEPBA, as reagents for stereochemical analysis of arene and alkene cis-diol metabolites, are presented.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

Stereodynamics and edge-to-face CH-π aromatic interactions in imino compounds containing heterocyclic rings.

By comparison with close contact interactions between benzene rings there is a paucity of experimental data available for attractive interactions involving aromatic heterocyclic rings, especially for small molecules in solution. Herein we describe aromatic heterocyclic and carbocyclic edge-to face interactions and conformational stereodynamics of N-1,2-diphenylethyl imines bearing a phenyl group and either a 2-pyridyl, 3-pyridyl, 2-thiophene or 2-furanyl moiety on the imino carbon. X-ray crystal structures have been determined for two compounds. Slow rotation about the phenyl-imino bond in the E-isomers and around the heterocycle-imino bond in the Z-isomers of the pyridyl compounds was observed at low temperatures by NMR. Abnormally large shielding of one ortho hydrogen indicates that both the imino phenyl and heterocycle rings can engage in an edge-to-face interaction with the N-terminal phenyl moiety in the appropriate isomer. Some rotational barriers around the phenyl-imino and heterocycle-imino bonds were measured.

The developmental transcriptome of Drosophila melanogaster.

Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

Chemoenzymatic synthesis of enantiopure hydroxy sulfoxides derived from substituted arenes.

Enantiopure ß-hydroxy sulfoxides and catechol sulfoxides were obtained, by chemoenzymatic synthesis, involving dioxygenase-catalysed benzylic hydroxylation or arene cis-dihydroxylation and cis-diol dehydrogenase-catalysed dehydrogenation. Absolute configurations of chiral hydroxy sulfoxides were determined by X-ray crystallography, ECD spectroscopy and stereochemical correlation. The application of a new range of ß-hydroxy sulfoxides as chiral ligands was examined.

Disentangling the relationship between sex-biased gene expression and X-linkage.

X chromosomes are preferentially transmitted through females, which may favor the accumulation of X-linked alleles/genes with female-beneficial effects. Numerous studies have shown that genes with sex-biased expression are under- or over-represented on the X chromosomes of a wide variety of organisms. The patterns, however, vary between different animal species, and the causes of these differences are unresolved. Additionally, genes with sex-biased expression tend to be narrowly expressed in a limited number of tissues, and narrowly expressed genes are also non-randomly X-linked in a taxon-specific manner. It is therefore unclear whether the unique gene content of the X chromosome is the result of selection on genes with sex-biased expression, narrowly expressed genes, or some combination of the two. To address this problem, we measured sex-biased expression in multiple Drosophila species and at different developmental time points. These data were combined with available expression measurements from Drosophila melanogaster and mouse to reconcile the inconsistencies in X-chromosome content among taxa. Our results suggest that most of the differences between Drosophila and mammals are confounded by disparate data collection/analysis approaches as well as the correlation between sex bias and expression breadth. Both the Drosophila and mouse X chromosomes harbor an excess of genes with female-biased expression after controlling for the confounding factors, suggesting that the asymmetrical transmission of the X chromosome favors the accumulation of female-beneficial mutations in X-linked genes. However, some taxon-specific patterns remain, and we provide evidence that these are in part a consequence of constraints imposed by the dosage compensation mechanism in Drosophila.

Toluene dioxygenase-catalyzed synthesis and reactions of cis-diol metabolites derived from 2- and 3-methoxyphenols.

Using toluene dioxygenase as biocatalyst, enantiopure cis-dihydrodiol and cis-tetrahydrodiol metabolites, isolated as their ketone tautomers, were obtained from meta and ortho methoxyphenols. Although these isomeric phenol substrates are structurally similar, the major bioproducts from each of these biotransformations were found at different oxidation levels. The relatively stable cyclohexenone cis-diol metabolite from meta methoxyphenol was isolated, while the corresponding metabolite from ortho methoxyphenol was rapidly bioreduced to a cyclohexanone cis-diol. The chemistry of the 3-methoxycyclohexenone cis-diol product was investigated and elimination, aromatization, hydrogenation, regioselective O-exchange, Stork-Danheiser transposition and O-methylation reactions were observed. An offshoot of this technology provided a two-step chemoenzymatic synthesis, from meta methoxyphenol, of a recently reported chiral fungal metabolite; this synthesis also established the previously unassigned absolute configuration.

Faster-X evolution of gene expression in Drosophila.

DNA sequences on X chromosomes often have a faster rate of evolution when compared to similar loci on the autosomes, and well articulated models provide reasons why the X-linked mode of inheritance may be responsible for the faster evolution of X-linked genes. We analyzed microarray and RNA-seq data collected from females and males of six Drosophila species and found that the expression levels of X-linked genes also diverge faster than autosomal gene expression, similar to the "faster-X" effect often observed in DNA sequence evolution. Faster-X evolution of gene expression was recently described in mammals, but it was limited to the evolutionary lineages shortly following the creation of the therian X chromosome. In contrast, we detect a faster-X effect along both deep lineages and those on the tips of the Drosophila phylogeny. In Drosophila males, the dosage compensation complex (DCC) binds the X chromosome, creating a unique chromatin environment that promotes the hyper-expression of X-linked genes. We find that DCC binding, chromatin environment, and breadth of expression are all predictive of the rate of gene expression evolution. In addition, estimates of the intraspecific genetic polymorphism underlying gene expression variation suggest that X-linked expression levels are not under relaxed selective constraints. We therefore hypothesize that the faster-X evolution of gene expression is the result of the adaptive fixation of beneficial mutations at X-linked loci that change expression level in cis. This adaptive faster-X evolution of gene expression is limited to genes that are narrowly expressed in a single tissue, suggesting that relaxed pleiotropic constraints permit a faster response to selection. Finally, we present a conceptional framework to explain faster-X expression evolution, and we use this framework to examine differences in the faster-X effect between Drosophila and mammals.

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs.

Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28 152 genomewide single nucleotide polymorphisms from polytypic barking frogs (Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (i) a rapid Pliocene-Pleistocene radiation that produced at least nine distinct lineages and (ii) that geographic features of the arid Central Mexican Plateau contributed to two independent northward expansions. Despite clear lineage differentiation (many private alleles and high between-lineage FST scores), D-statistic tests, which differentiate introgression from ancestral polymorphism, allowed us to identify two putative instances of reticulate gene flow. Partitioned D-statistics provided evidence that these events occurred in the same direction between clades but at different points in time. After correcting for geographic distance, we found that lineages involved in hybrid gene flow interactions had higher levels of genetic variation than independently evolving lineages. These findings suggest that the nature of hybrid compatibility can be conserved overlong periods of evolutionary time and that hybridization between diverging lineages may contribute to standing levels of genetic variation.

Reactions of enantiopure cyclic diols with sulfuryl chloride.

Monocyclic allylic cis-1,2-diols reacted with sulfuryl chloride at 0 °C in a regio- and stereo-selective manner to give 2-chloro-1-sulfochloridates, which were hydrolysed to yield the corresponding trans-1,2-chlorohydrins. At -78 °C, with very slow addition of sulfuryl chloride, cyclic sulfates were formed in good yields, proved to be very reactive with nucleophiles and rapidly decomposed on attempted storage. Reaction of a cyclic sulfate with sodium azide yielded a trans-azidohydrin without evidence of allylic rearrangement occurring. An enantiopure bicyclic cis-1,2-diol reacted with sulfuryl chloride to give, exclusively, a trans-1,2-dichloride enantiomer with retention of configuration at the benzylic centre and inversion at the non-benzylic centre; a mechanism is presented to rationalise the observation.

Neuromuscular electrical stimulation during recovery from exercise: a systematic review.

The use of subtetanic low-intensity neuromuscular electrical stimulation (NMES) for the purpose of promoting recovery from exercise has increased in recent years. The aim of this systematic review was to assess the effects of NMES on exercise recovery. A computerized database search of PubMed, CINAHL Plus, Sport Discus, and Cochrane Library electronic databases was conducted for the time period of January 1, 1970 to March 8, 2012. Only studies that used healthy uninjured humans and motor threshold electrical stimulation compared with at least one other recovery modality for the purpose of promoting recovery from exercise were eligible for selection. Thirteen studies satisfied the inclusion criteria and were included for analysis (11 randomized crossover trials, 1 randomized control trial [RCT], and 1 classified as other [OTH]). A quality assessment rating of the studies was performed using an extended version of The Cochrane Collaboration's tool for assessing risk of bias. Because of the heterogeneity of the study protocols, a qualitative review (best evidence synthesis) was performed for all outcomes, whereas the results for blood lactate (BLa) were also included in a meta-analysis. Eight studies were classified as high quality, 4 as medium quality, and 1 as low quality. Three studies found a positive outcome for a subjective measure of muscle pain, 3 for BLa, 1 for lowering creatine kinase, and only 1 for a performance parameter. The meta-analysis showed no evidence in favor of NMES vs. active (ACT) and mixed evidence vs. passive (PAS) recovery for BLa. In conclusion, although there may be some subjective benefits for postexercise recovery, evidence is not convincing to support NMES for enhancing subsequent performance.

Did John B. Watson Really "Found" Behaviorism?

Developments culminating in the nineteenth century, along with the predictable collapse of introspective psychology, meant that the rise of behavioral psychology was inevitable. In 1913, John B. Watson was an established scientist with impeccable credentials who acted as a strong and combative promoter of a natural science approach to psychology when just such an advocate was needed. He never claimed to have founded "behavior psychology" and, despite the acclaim and criticism attending his portrayal as the original behaviorist, he was more an exemplar of a movement than a founder. Many influential writers had already characterized psychology, including so-called mental activity, as behavior, offered many applications, and rejected metaphysical dualism. Among others, William Carpenter, Alexander Bain, and (early) Sigmund Freud held views compatible with twentieth-century behaviorism. Thus, though Watson was the first to argue specifically for psychology as a natural science, behaviorism in both theory and practice had clear roots long before 1913. If behaviorism really needs a "founder," Edward Thorndike might seem more deserving, because of his great influence and promotion of an objective psychology, but he was not a true behaviorist for several important reasons. Watson deserves the fame he has received, since he first made a strong case for a natural science (behaviorist) approach and, importantly, he made people pay attention to it.