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The presence of HIV in sequestered reservoirs is a central impediment to a functional cure, allowing HIV to persist despite life-long antiretroviral therapy (ART), and driving a variety of comorbid conditions. Our understanding of the latent HIV reservoir in the central nervous system is incomplete, because of difficulties in accessing human central nervous system tissues. Microglia contribute to HIV reservoirs, but the molecular phenotype of HIV-infected microglia is poorly understood. We leveraged the unique "Last Gift" rapid autopsy program, in which people with HIV are closely followed until days or even hours before death. Microglial populations were heterogeneous regarding their gene expression profiles but showed similar chromatin accessibility landscapes. Despite ART, we detected occasional microglia containing cell-associated HIV RNA and HIV DNA integrated into open regions of the host's genome (∼0.005%). Microglia with detectable HIV RNA showed an inflammatory phenotype. These results demonstrate a distinct myeloid cell reservoir in the brains of people with HIV despite suppressive ART. Strategies for curing HIV and neurocognitive impairment will need to consider the myeloid compartment to be successful.

Abstract Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. For the 2021–22 and 2022–23 influenza seasons, 26 forecasting teams provided national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one-to-four weeks ahead. Forecast skill is evaluated using the Weighted Interval Score (WIS), relative WIS, and coverage. Six out of 23 models outperform the baseline model across forecast weeks and locations in 2021–22 and 12 out of 18 models in 2022–23. Averaging across all forecast targets, the FluSight ensemble is the 2nd most accurate model measured by WIS in 2021–22 and the 5th most accurate in the 2022–23 season. Forecast skill and 95% coverage for the FluSight ensemble and most component models degrade over longer forecast horizons. In this work we demonstrate that while the FluSight ensemble was a robust predictor, even ensembles face challenges during periods of rapid change.

Jessica Addison,1,2,* Areej Hassan,1,2,* Amy DiVasta1,2 1Division of Adolescent/Young Adult Medicine, Boston Children’s Hospital, Boston, MA, USA; 2Department of Pediatrics, Harvard Medical School, Boston, MA, USA*These authors contributed equally to this workCorrespondence: Jessica Addison, Division of Adolescent/Young Medicine, Boston Children’s Hospital, LO-306, 300 Longwood Ave, Boston, MA, 02115, USA, Tel +1 202-549-4001, Email jessica.addison@childrens.harvard.eduAbstract: Contraception is a significant part of comprehensive sexual and reproductive health (SRH) care for adolescents and young adults (AYA). While providers may assume that AYA with chronic illness are not sexually active, studies have shown that there are no differences in their sexual practices compared to their counterparts without an illness. This assumption may result in less SRH screening, preventative services, and counseling by providers resulting in decreased basic sexual knowledge, increased risk of unplanned pregnancy, and other health disparities. Sexually active AYA with medical complexity are particularly in need of contraception for a variety of reasons. A better understanding of the complexities around contraception counseling can help increase utilization rates, improve shared-decision making around family planning, and reduce the stigma around sexual health counseling in this population. We have included three sections. First, a general overview of contraception methods. Next, an overview of contraceptive methods currently available, their efficacy, and medical eligibility criteria for their use in AYA who have certain characteristics or medical conditions. Finally, cases adapted from real clinical scenarios to highlight specific recommendations for contraception in AYA women living HIV, autoimmune conditions, and those who have received a solid organ transplant. This information will help providers to consider the multiple factors that influence contraception decision-making (including clinical status, thrombosis risk, medication interactions, safety), and optimize care for AYA living with chronic illness.Keywords: adolescent, young adult, contraception, sexual health, chronic illness

We present a means of studying rare reactive pathways in open quantum systems using transition path theory and ensembles of quantum jump trajectories. This approach allows for the elucidation of reactive paths for dissipative, nonadiabatic dynamics when the system is embedded in a Markovian environment. We detail the dominant pathways and rates of thermally activated processes and the relaxation pathways and photoyields following vertical excitation in a minimal model of a conical intersection. We find that the geometry of the conical intersection affects the electronic character of the transition state as defined through a generalization of a committor function for a thermal barrier crossing event. Similarly, the geometry changes the mechanism of relaxation following a vertical excitation. Relaxation in models resulting from small diabatic coupling proceeds through pathways dominated by pure dephasing, while those with large diabatic coupling proceed through pathways limited by dissipation. The perspective introduced here for the nonadiabatic dynamics of open quantum systems generalizes classical notions of reactive paths to fundamentally quantum mechanical processes.

The structure of the human neocortex underlies species-specific traits and reflects intricate developmental programs. Here we sought to reconstruct processes that occur during early development by sampling adult human tissues. We analysed neocortical clones in a post-mortem human brain through a comprehensive assessment of brain somatic mosaicism, acting as neutral lineage recorders1,2. We combined the sampling of 25 distinct anatomic locations with deep whole-genome sequencing in a neurotypical deceased individual and confirmed results with 5 samples collected from each of three additional donors. We identified 259 bona fide mosaic variants from the index case, then deconvolved distinct geographical, cell-type and clade organizations across the brain and other organs. We found that clones derived after the accumulation of 90-200 progenitors in the cerebral cortex tended to respect the midline axis, well before the anterior-posterior or ventral-dorsal axes, representing a secondary hierarchy following the overall patterning of forebrain and hindbrain domains. Clones across neocortically derived cells were consistent with a dual origin from both dorsal and ventral cellular populations, similar to rodents, whereas the microglia lineage appeared distinct from other resident brain cells. Our data provide a comprehensive analysis of brain somatic mosaicism across the neocortex and demonstrate cellular origins and progenitor distribution patterns within the human brain.

Monosodium urate crystals (MSUc) induce inflammation in vivo without prior priming, raising the possibility of an initial cell-autonomous phase. Here, using genome-wide transcriptomic analysis and biochemical assays, we demonstrate that MSUc alone induce a metabolic-inflammatory transcriptional program in non-primed human and murine macrophages that is markedly distinct to that induced by LPS. Genes uniquely upregulated in response to MSUc belong to lipid and amino acid metabolism, glycolysis, and SLC transporters. This upregulation leads to a metabolic rewiring in sera from individuals and mice with acute gouty arthritis. Mechanistically, the initiating inflammatory-metabolic changes in acute gout flares are regulated through a persistent expression and increased binding of JUN to the promoter of target genes through JNK signaling-but not P38-in a process that is different than after LPS stimulation and independent of inflammasome activation. Finally, pharmacological JNK inhibition limits MSUc-induced inflammation in animal models of acute gouty inflammation.

The COVID-19 pandemic presented enormous data challenges in the United States. Policy makers, epidemiological modelers, and health researchers all require up-to-date data on the pandemic and relevant public behavior, ideally at fine spatial and temporal resolution. The COVIDcast API is our attempt to fill this need: Operational since April 2020, it provides open access to both traditional public health surveillance signals (cases, deaths, and hospitalizations) and many auxiliary indicators of COVID-19 activity, such as signals extracted from deidentified medical claims data, massive online surveys, cell phone mobility data, and internet search trends. These are available at a fine geographic resolution (mostly at the county level) and are updated daily. The COVIDcast API also tracks all revisions to historical data, allowing modelers to account for the frequent revisions and backfill that are common for many public health data sources. All of the data are available in a common format through the API and accompanying R and Python software packages. This paper describes the data sources and signals, and provides examples demonstrating that the auxiliary signals in the COVIDcast API present information relevant to tracking COVID activity, augmenting traditional public health reporting and empowering research and decision-making.

Short-term forecasts of traditional streams from public health reporting (such as cases, hospitalizations, and deaths) are a key input to public health decision-making during a pandemic. Since early 2020, our research group has worked with data partners to collect, curate, and make publicly available numerous real-time COVID-19 indicators, providing multiple views of pandemic activity in the United States. This paper studies the utility of five such indicators-derived from deidentified medical insurance claims, self-reported symptoms from online surveys, and COVID-related Google search activity-from a forecasting perspective. For each indicator, we ask whether its inclusion in an autoregressive (AR) model leads to improved predictive accuracy relative to the same model excluding it. Such an AR model, without external features, is already competitive with many top COVID-19 forecasting models in use today. Our analysis reveals that 1) inclusion of each of these five indicators improves on the overall predictive accuracy of the AR model; 2) predictive gains are in general most pronounced during times in which COVID cases are trending in "flat" or "down" directions; and 3) one indicator, based on Google searches, seems to be particularly helpful during "up" trends.

We introduce a heterodimer model in which multiple mechanisms of vibronic coupling and their impact on energy transfer can be explicitly studied. We consider vibronic coupling that arises through either Franck-Condon activity in which each site in the heterodimer has a local electron-phonon coupling or Herzberg-Teller activity in which the transition dipole moment coupling the sites has an explicit vibrational mode-dependence. We have computed two-dimensional electronic-vibrational (2DEV) spectra for this model while varying the magnitude of these two effects and find that 2DEV spectra contain static and dynamic signatures of both types of vibronic coupling. Franck-Condon activity emerges through a change in the observed excitonic structure, while Herzberg-Teller activity is evident in the appearance of significant side-band transitions that mimic the lower-energy excitonic structure. A comparison of quantum beating patterns obtained from analysis of the simulated 2DEV spectra shows that this technique can report on the mechanism of energy transfer, elucidating a means of experimentally determining the role of specific vibronic coupling mechanisms in such processes.

Neurons are the longest-lived cells in our bodies and lack DNA replication, which makes them reliant on a limited repertoire of DNA repair mechanisms to maintain genome fidelity. These repair mechanisms decline with age, but we have limited knowledge of how genome instability emerges and what strategies neurons and other long-lived cells may have evolved to protect their genomes over the human life span. A targeted sequencing approach in human embryonic stem cell-induced neurons shows that, in neurons, DNA repair is enriched at well-defined hotspots that protect essential genes. These hotspots are enriched with histone H2A isoforms and RNA binding proteins and are associated with evolutionarily conserved elements of the human genome. These findings provide a basis for understanding genome integrity as it relates to aging and disease in the nervous system.

The directed energy deposition (DED) parameters were determined for near-β alloy Ti-55511 by employing statistical design of experiments (DOEs) methods. Parameters resulting in fully dense freeform deposits were identified using two sequential DOEs. Single laser tracks were printed with several laser power, traverse rate, and powder feed rate settings in an initial DOE to identify promising build parameters. The capture efficiency and effective deposition rate were used to characterize and rank the single track deposits. The best parameters were then used to print a solid cube with various X–Y and Z overlaps (different hatch spacing, HS, and layer thickness, ZS) in a second DOE. Suitable deposition parameters were selected based on the cube density and microstructure and were used to fabricate larger tensile samples for mechanical testing. Multiple parameter sets were found to provide dense Ti-55511 deposits with acceptable mechanical properties and the parametric models showed statistical significance.

BackgroundHorehound (Marrubium vulgare) is a medicinal plant whose signature bioactive compounds, marrubiin and related furanoid diterpenoid lactones, have potential applications for the treatment of cardiovascular diseases and type II diabetes. Lack of scalable plant cultivation and the complex metabolite profile of M. vulgare limit access to marrubiin via extraction from plant biomass. Knowledge of the marrubiin-biosynthetic enzymes can enable the development of metabolic engineering platforms for marrubiin production. We previously identified two diterpene synthases, MvCPS1 and MvELS, that act sequentially to form 9,13-epoxy-labd-14-ene. Conversion of 9,13-epoxy-labd-14-ene by cytochrome P450 monooxygenase (P450) enzymes can be hypothesized to facilitate key functional modification reactions in the formation of marrubiin and related compounds.ResultsMining a M. vulgare leaf transcriptome database identified 95 full-length P450 candidates. Cloning and functional analysis of select P450 candidates showing high transcript abundance revealed a member of the CYP71 family, CYP71AU87, that catalyzed the hydroxylation of 9,13-epoxy-labd-14-ene to yield two isomeric products, 9,13-epoxy labd-14-ene-18-ol and 9,13-epoxy labd-14-ene-19-ol, as verified by GC-MS and NMR analysis. Additional transient Nicotiana benthamiana co-expression assays of CYP71AU87 with different diterpene synthase pairs suggested that CYP71AU87 is specific to the sequential MvCPS1 and MvELS product 9,13-epoxy-labd-14-ene. Although the P450 products were not detectable in planta, high levels of CYP71AU87 gene expression in marrubiin-accumulating tissues supported a role in the formation of marrubiin and related diterpenoids in M. vulgare.ConclusionsIn a sequential reaction with the diterpene synthase pair MvCPS1 and MvELS, CYP71AU87 forms the isomeric products 9,13-epoxy labd-14-ene-18/19-ol as probable intermediates in marrubiin biosynthesis. Although its metabolic relevance in planta will necessitate further genetic studies, identification of the CYP71AU87 catalytic activity expands our knowledge of the functional landscape of plant P450 enzymes involved in specialized diterpenoid metabolism and can provide a resource for the formulation of marrubiin and related bioactive natural products.

[This corrects the article DOI: 10.1371/journal.pone.0176507.].

Fluorescent GTP analogues are utilized for an assortment of nucleic acid and protein characterization studies. Non-hydrolysable analogues such as GTPγS offer the advantage of keeping proteins in a GTP-bound conformation due to their resistance to hydrolysis into GDP. Two novel fluorescent GTPγS molecules were developed by linking fluorescein and tetramethylrhodamine to the γ-thiophosphate of GTPγS. Chemical and biological analysis of these two compounds revealed their successful synthesis and ability to bind to the nucleotide-binding site of tubulin. These two new fluorescent non-hydrolysable nucleotides offer new possibilities for biophysical and biochemical characterization of GTP-binding proteins.

Plants produce an immense diversity of natural products (i.e. secondary or specialized metabolites) that offer a rich source of known and potentially new pharmaceuticals and other desirable bioproducts. The Traditional Chinese Medicinal plant Isodon rubescens (Lamiaceae) contains an array of bioactive labdane-related diterpenoid natural products. Of these, the ent-kauranoid oridonin is the most prominent specialized metabolite that has been extensively studied for its potent antimicrobial and anticancer efficacy. Mining of a previously established transcriptome of I. rubescens leaf tissue identified seven diterpene synthase (diTPSs) candidates. Here we report the functional characterization of four I. rubescens diTPSs. IrTPS5 and IrTPS3 were identified as an ent-copalyl diphosphate (CPP) synthase and a (+)-CPP synthase, respectively. Distinct transcript abundance of IrTPS5 and the predicted ent-CPP synthase IrTPS1 suggested a role of IrTPS5 in specialized ent-kaurene metabolism possibly en route to oridonin. Nicotiana benthamiana co-expression assays demonstrated that IrTPS4 functions sequentially with IrTPS3 to form miltiradiene. In addition, IrTPS2 converted the IrTPS3 product (+)-CPP into the hydroxylated tricyclic diterpene nezukol not previously identified in I. rubescens. Metabolite profiling verified the presence of nezukol in I. rubescens leaf tissue. The proposed IrTPS2-catalyzed reaction mechanism proceeds via the common ionization of the diphosphate group of (+)-CPP, followed by formation of an intermediary pimar-15-en-8-yl+ carbocation and neutralization of the carbocation by water capture at C-8 to yield nezukol, as confirmed by nuclear magnetic resonance (NMR) analysis. Oxygenation activity is rare for the family of class I diTPSs and offers new catalysts for developing metabolic engineering platforms to produce a broader spectrum of bioactive diterpenoid natural products.

Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. For the 2021–22 and 2022–23 influenza seasons, 26 forecasting teams provided national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one-to-four weeks ahead. Forecast skill is evaluated using the Weighted Interval Score (WIS), relative WIS, and coverage. Six out of 23 models outperform the baseline model across forecast weeks and locations in 2021–22 and 12 out of 18 models in 2022–23. Averaging across all forecast targets, the FluSight ensemble is the 2nd most accurate model measured by WIS in 2021–22 and the 5th most accurate in the 2022–23 season. Forecast skill and 95% coverage for the FluSight ensemble and most component models degrade over longer forecast horizons. In this work we demonstrate that while the FluSight ensemble was a robust predictor, even ensembles face challenges during periods of rapid change. This manuscript evaluates forecasts of laboratory-confirmed influenza hospital admissions, a new target for influenza forecasting in the United States. Across two influenza seasons, the FluSight ensemble is robust compared to submitted models. [ABSTRACT FROM AUTHOR]

The contribution of chronic peripheral inflammation to the pathogenesis of neurodegenerative diseases is an outstanding question. Sustained activation of the peripheral innate and adaptive immune systems occurs in the context of a broad array of disorders ranging from chronic infectious diseases to autoimmune and metabolic diseases. In addition, progressive systemic inflammation is increasingly recognized during aging. Peripheral immune cells could potentially modulate the cellular brain environment via the secretion of soluble molecules. There is an ongoing debate whether peripheral immune cells have the potential to migrate into the brain under certain permissive circumstances. In this perspective, we discuss the possible contribution of chronic peripheral inflammation to the pathogenesis of age-related neurodegenerative diseases with a focus on microglia, the resident immune cells of the brain parenchyma.

Summary: Monosodium urate crystals (MSUc) induce inflammation in vivo without prior priming, raising the possibility of an initial cell-autonomous phase. Here, using genome-wide transcriptomic analysis and biochemical assays, we demonstrate that MSUc alone induce a metabolic-inflammatory transcriptional program in non-primed human and murine macrophages that is markedly distinct to that induced by LPS. Genes uniquely upregulated in response to MSUc belong to lipid and amino acid metabolism, glycolysis, and SLC transporters. This upregulation leads to a metabolic rewiring in sera from individuals and mice with acute gouty arthritis. Mechanistically, the initiating inflammatory-metabolic changes in acute gout flares are regulated through a persistent expression and increased binding of JUN to the promoter of target genes through JNK signaling—but not P38—in a process that is different than after LPS stimulation and independent of inflammasome activation. Finally, pharmacological JNK inhibition limits MSUc-induced inflammation in animal models of acute gouty inflammation.

Abstract Background: Diversity, equity, and inclusion (DEI) in clinical and translational science (CTS) are paramount to driving innovation and increasing health equity. One important area for improving diversity is among trainees in CTS programs. This paper reports on findings from a special session at the November 2020 Clinical and Translational Science Award (CTSA) national program meeting that focused on advancing diversity and inclusion within CTS training programs. Methods: Using qualitative content analysis, we identified approaches brought forth to increase DEI in KL2 career development and other training programs aimed at early-stage CTS investigators, beyond the six strategies put forth to guide the breakout session (prioritizing representation, building partnerships, making it personal, designing program structure, improving through feedback, and winning endorsement). We used an inductive qualitative content analysis approach to identify themes from a transcript of the panel of KL2 program leaders centered on DEI in training programs. Results: We identified four themes for advancing DEI within CTS training programs: 1) institutional buy-in; 2) proactive recruitment efforts; 3) an equitable application process; and 4) high-quality, diverse mentorship. Conclusion: Implementing these strategies in CTS and other training programs will be an important step for advancing DEI. However, processes need to be established to evaluate the implementation and effectiveness of these strategies through continuous quality improvement, a key component of the CTSA program. Training programs within the CTSA are well-positioned to be leaders in this critical effort to increase the diversity of the scientific workforce.

Let's Be Reasonable: A Conservative Case for Liberal Education by Jonathan Marks Princeton University Press, 2021, $27.95; 228 pages. IN LET'S BE REASONABLE, Jonathan Marks argues that higher education should [...]

Introduction: To analyze the correlation between the many different emergency department (ED) treatment metric intervals and determine if the metrics directly impacted by the physician correlate to the “door to room” interval in an ED (interval determined by ED bed availability). Our null hypothesis was that the cause of the variation in delay to receiving a room was multifactorial and does not correlate to any one metric interval.Methods: We collected daily interval averages from the ED information system, Meditech©. Patient flow metrics were collected on a 24-hour basis. We analyzed the relationship between the time intervals that make up an ED visit and the “arrival to room” interval using simple correlation (Pearson Correlation coefficients). Summary statistics of industry standard metrics were also done by dividing the intervals into 2 groups, based on the average ED length of stay (LOS) from the National Hospital Ambulatory Medical Care Survey: 2008 Emergency Department Summary.Results: Simple correlation analysis showed that the doctor-to-discharge time interval had no correlation to the interval of “door to room (waiting room time)”, correlation coefficient (CC) (CC=0.000, p=0.96). “Room to doctor” had a low correlation to “door to room” CC=0.143, while “decision to admitted patients departing the ED time” had a moderate correlation of 0.29 (p

This study aimed at documenting the sexual harassment of Syrian female refugees in refugee camps in Jordan. A purposive sample of 187 Syrian female refugees in the Za’atari camp was selected. The results showed that the environment of the camp played an important role in motivating males to harass females owing to the weakness of the security measures and the lack of sanctions upon deviant behaviors. Our findings show that females were subjected to numerous forms of sexual harassment, including hearing sexual jokes and sexual expressions, and being subjected to suggestive looks, sexual letters, and unwanted touching. Additionally, our results revealed that participants responded to sexual harassment by keeping silent because they feared making their situation worse by provoking conflict within their families. This left the victims without protection or the chance to obtain justice.

Author(s): S. K. Praetorius (corresponding author) [1]; A. C. Mix [1]; M. H. Walczak [1]; M. D. Wolhowe [1]; J. A. Addison [2]; F. G. Prahl [1] Marine sediments from [...]