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DPAGT1-CDG is a Congenital Disorder of Glycosylation (CDG) that lacks effective therapies. It is caused by mutations in the gene DPAGT1 which encodes the first enzyme in N-linked glycosylation. We used a Drosophila rough eye model of DPAGT1-CDG with an improperly developed, small eye phenotype. We performed a drug repurposing screen on this model using 1,520 small molecules that are 98% FDA/EMA-approved to find drugs that improved its eye. We identified 42 candidate drugs that improved the DPAGT1-CDG model. Notably from this screen, we found that pharmacological and genetic inhibition of the dopamine D2 receptor partially rescued the DPAGT1-CDG model. Loss of both dopamine synthesis and recycling partially rescued the model, suggesting that dopaminergic flux and subsequent binding to D2 receptors is detrimental under DPAGT1 deficiency. This links dopamine signaling to N-glycosylation and represents a new potential therapeutic target for treating DPAGT1-CDG. We also genetically validate other top drug categories including acetylcholine-related drugs, COX inhibitors, and an inhibitor of NKCC1. These drugs and subsequent analyses reveal novel biology in DPAGT1 mechanisms, and they may represent new therapeutic options for DPAGT1-CDG.

Locomotion results from the interactions of highly nonlinear neural and biomechanical dynamics. Accordingly, understanding gait dynamics across behavioral conditions and individuals based on detailed modeling of the underlying neuromechanical system has proven difficult. Here, we develop a data-driven and generative modeling approach that recapitulates the dynamical features of gait behaviors to enable more holistic and interpretable characterizations and comparisons of gait dynamics. Specifically, gait dynamics of multiple individuals are predicted by a dynamical model that defines a common, low-dimensional, latent space to compare group and individual differences. We find that highly individualized dynamics-i.e., gait signatures-for healthy older adults and stroke survivors during treadmill walking are conserved across gait speed. Gait signatures further reveal individual differences in gait dynamics, even in individuals with similar functional deficits. Moreover, components of gait signatures can be biomechanically interpreted and manipulated to reveal their relationships to observed spatiotemporal joint coordination patterns. Lastly, the gait dynamics model can predict the time evolution of joint coordination based on an initial static posture. Our gait signatures framework thus provides a generalizable, holistic method for characterizing and predicting cyclic, dynamical motor behavior that may generalize across species, pathologies, and gait perturbations.

BackgroundSame-day HIV testing and antiretroviral therapy (ART) initiation is being widely implemented. However, the optimal timing of ART among patients with tuberculosis (TB) symptoms is unknown. We hypothesized that same-day treatment (TB treatment for those diagnosed with TB; ART for those not diagnosed with TB) would be superior to standard care in this population.Methods and findingsWe conducted an open-label trial among adults with TB symptoms at initial HIV diagnosis at GHESKIO in Haiti; participants were recruited and randomized on the same day. Participants were randomized in a 1:1 ratio to same-day treatment (same-day TB testing with same-day TB treatment if TB diagnosed; same-day ART if TB not diagnosed) versus standard care (initiating TB treatment within 7 days and delaying ART to day 7 if TB not diagnosed). In both groups, ART was initiated 2 weeks after TB treatment. The primary outcome was retention in care with 48-week HIV-1 RNA ConclusionsIn patients with TB symptoms at HIV diagnosis, we found that same-day treatment was not associated with superior retention and viral suppression. In this study, a short delay in ART initiation did not appear to compromise outcomes.Trial registrationThis study is registered with ClinicalTrials.gov NCT03154320.

Persistent inflammation contributes to the development of cardiovascular disease (CVD) as an HIV-associated comorbidity. Innate immune cells such as monocytes are major drivers of inflammation in men and women with HIV. The study objectives are to examine the contribution of circulating non-classical monocytes (NCM, CD14dimCD16+) and intermediate monocytes (IM, CD14+CD16+) to the host response to long-term HIV infection and HIV-associated CVD. Women with and without chronic HIV infection (H) were studied. Subclinical CVD (C) was detected as plaques imaged by B-mode carotid artery ultrasound. The study included H-C-, H+C-, H-C+, and H+C+ participants (23 of each, matched on race/ethnicity, age and smoking status), selected from among enrollees in the Women's Interagency HIV Study. We assessed transcriptomic features associated with HIV or CVD alone or comorbid HIV/CVD comparing to healthy (H-C-) participants in IM and NCM isolated from peripheral blood mononuclear cells. IM gene expression was little affected by HIV alone or CVD alone. In IM, coexisting HIV and CVD produced a measurable gene transcription signature, which was abolished by lipid-lowering treatment. In NCM, versus non-HIV controls, women with HIV had altered gene expression, irrespective of whether or not they had comorbid CVD. The largest set of differentially expressed genes was found in NCM among women with both HIV and CVD. Genes upregulated in association with HIV included several potential targets of drug therapies, including LAG3 (CD223). In conclusion, circulating monocytes from patients with well controlled HIV infection demonstrate an extensive gene expression signature which may be consistent with the ability of these cells to serve as potential viral reservoirs. Gene transcriptional changes in HIV patients were further magnified in the presence of subclinical CVD.

The analytical validation is reported for a targeted methylation-based cell-free DNA multi-cancer early detection test designed to detect cancer and predict the cancer signal origin (tissue of origin). A machine-learning classifier was used to analyze the methylation patterns of >105 genomic targets covering >1 million methylation sites. Analytical sensitivity (limit of detection [95% probability]) was characterized with respect to tumor content by expected variant allele frequency and was determined to be 0.07%-0.17% across five tumor cases and 0.51% for the lymphoid neoplasm case. Test specificity was 99.3% (95% confidence interval, 98.6-99.7%). In the reproducibility and repeatability study, results were consistent in 31/34 (91.2%) pairs with cancer and 17/17 (100%) pairs without cancer; between runs, results were concordant for 129/133 (97.0%) cancer and 37/37 (100%) non-cancer sample pairs. Across 3- to 100-ng input levels of cell-free DNA, cancer was detected in 157/182 (86.3%) cancer samples but not in any of the 62 non-cancer samples. In input titration tests, cancer signal origin was correctly predicted in all tumor samples detected as cancer. No cross-contamination events were observed. No potential interferent (hemoglobin, bilirubin, triglycerides, genomic DNA) affected performance. The results of this analytical validation study support continued clinical development of a targeted methylation cell-free DNA multi-cancer early detection test.

The conversion of supplemental greenhouse light energy into biomass is not always optimal. Recent trends in global energy prices and discussions on climate change highlight the need to reduce our energy footprint associated with the use of supplemental light in greenhouse crop production. This can be achieved by implementing "smart" lighting regimens which in turn rely on a good understanding of how fluctuating light influences photosynthetic physiology. Here, a simple fit-for-purpose dynamic model is presented. It accurately predicts net leaf photosynthesis under natural fluctuating light. It comprises two ordinary differential equations predicting: 1) the total stomatal conductance to CO2 diffusion and 2) the CO2 concentration inside a leaf. It contains elements of the Farquhar-von Caemmerer-Berry model and the successful incorporation of this model suggests that for tomato (Solanum lycopersicum L.), it is sufficient to assume that Rubisco remains activated despite rapid fluctuations in irradiance. Furthermore, predictions of the net photosynthetic rate under both 400ppm and enriched 800ppm ambient CO2 concentrations indicate a strong correlation between the dynamic rate of photosynthesis and the rate of electron transport. Finally, we are able to indicate whether dynamic photosynthesis is Rubisco or electron transport rate limited.

Sustained attention (SA) and working memory (WM) are critical processes, but the brain networks supporting these abilities in development are unknown. We characterized the functional brain architecture of SA and WM in 9- to 11-year-old children and adults. First, we found that adult network predictors of SA generalized to predict individual differences and fluctuations in SA in youth. A WM model predicted WM performance both across and within children-and captured individual differences in later recognition memory-but underperformed in youth relative to adults. We next characterized functional connections differentially related to SA and WM in youth compared to adults. Results revealed 2 network configurations: a dominant architecture predicting performance in both age groups and a secondary architecture, more prominent for WM than SA, predicting performance in each age group differently. Thus, functional connectivity (FC) predicts SA and WM in youth, with networks predicting WM performance differing more between youths and adults than those predicting SA.

Heme (iron-protoporphyrin IX) is an essential but potentially toxic cellular cofactor. While most organisms are heme prototrophs, many microorganisms can utilize environmental heme as iron source. The pathogenic yeast Candida albicans can utilize host heme in the iron-poor host environment, using an extracellular cascade of soluble and anchored hemophores, and plasma membrane ferric reductase-like proteins. To gain additional insight into the C. albicans heme uptake pathway, we performed an unbiased genetic selection for mutants resistant to the toxic heme analog Ga3+-protoporphyrin IX at neutral pH, and a secondary screen for inability to utilize heme as iron source. Among the mutants isolated were the genes of the pH-responsive RIM pathway, and a zinc finger transcription factor related to S. cerevisiae HAP1. In the presence of hemin in the medium, C. albicans HAP1 is induced, the Hap1 protein is stabilized and Hap1-GFP localizes to the nucleus. In the hap1 mutant, cytoplasmic heme levels are elevated, while influx of extracellular heme is lower. Gene expression analysis indicated that in the presence of extracellular hemin, Hap1 activates the heme oxygenase HMX1, which breaks down excess cytoplasmic heme, while at the same time it also activates all the known heme uptake genes. These results indicate that Hap1 is a heme-responsive transcription factor that plays a role both in cytoplasmic heme homeostasis and in utilization of extracellular heme. The induction of heme uptake genes by C. albicans Hap1 under iron satiety indicates that preferential utilization of host heme can be a dietary strategy in a heme prototroph.

Partial loss-of-function mutations in glycosylation pathways underlie a set of rare diseases called Congenital Disorders of Glycosylation (CDGs). In particular, DPAGT1-CDG is caused by mutations in the gene encoding the first step in N-glycosylation, DPAGT1, and this disorder currently lacks effective therapies. To identify potential therapeutic targets for DPAGT1-CDG, we performed CRISPR knockout screens in Drosophila cells for genes associated with better survival and glycoprotein levels under DPAGT1 inhibition. We identified hundreds of candidate genes that may be of therapeutic benefit. Intriguingly, inhibition of the mannosyltransferase Dpm1, or its downstream glycosylation pathways, could rescue two in vivo models of DPAGT1 inhibition and ER stress, even though impairment of these pathways alone usually causes CDGs. While both in vivo models ostensibly cause cellular stress (through DPAGT1 inhibition or a misfolded protein), we found a novel difference in fructose metabolism that may indicate glycolysis as a modulator of DPAGT1-CDG. Our results provide new therapeutic targets for DPAGT1-CDG, include the unique finding of Dpm1-related pathways rescuing DPAGT1 inhibition, and reveal a novel interaction between fructose metabolism and ER stress.

NGLY1 deficiency, a rare disease with no effective treatment, is caused by autosomal recessive, loss-of-function mutations in the N-glycanase 1 (NGLY1) gene and is characterized by global developmental delay, hypotonia, alacrima, and seizures. We used a Drosophila model of NGLY1 deficiency to conduct an in vivo, unbiased, small molecule, repurposing screen of FDA-approved drugs to identify therapeutic compounds. Seventeen molecules partially rescued lethality in a patient-specific NGLY1 deficiency model, including multiple serotonin and dopamine modulators. Exclusive dNGLY1 expression in serotonin and dopamine neurons, in an otherwise dNGLY1 deficient fly, was sufficient to partially rescue lethality. Further, genetic modifier and transcriptomic data supports the importance of serotonin signaling in NGLY1 deficiency. Connectivity Map analysis identified glycogen synthase kinase 3 (GSK3) inhibition as a potential therapeutic mechanism for NGLY1 deficiency, which we experimentally validated with TWS119, lithium, and GSK3 knockdown. Strikingly, GSK3 inhibitors and a serotonin modulator rescued size defects in dNGLY1 deficient larvae upon proteasome inhibition, suggesting that these compounds act through NRF1, a transcription factor that is regulated by NGLY1 and regulates proteasome expression. This study reveals the importance of the serotonin pathway in NGLY1 deficiency, and serotonin modulators or GSK3 inhibitors may be effective therapeutics for this rare disease. Author summary NGLY1 deficiency is a rare disease with no effective treatment. We conducted a drug repurposing screen and used the Connectivity Map, a transcriptional-based computational approach, to identify compounds that may serve as therapeutics for NGLY1 deficient individuals. The drug repurposing screen identified FDA-approved compounds acting through the serotonin and dopamine pathway that partially rescued lethality in an NGLY1 deficiency fly model. We also found that expressing dNGLY1 (the Drosophila ortholog of NGLY1) exclusively in serotonin neurons, in an otherwise dNGLY1 deficient fly, partially rescued lethality. These data indicate the importance of the serotonin and dopamine systems in NGLY1 deficiency. The Connectivity Map analyses found GSK3 inhibitors as potential therapeutic compounds, which were validated in vivo in the fly. Furthermore, knockdown of sgg (the Drosophila ortholog of GSK3) partially rescued lethality in dNGLY1 deficient flies, suggesting GSK3 as a therapeutic target for NGLY1 deficiency. Taken together, this work identifies therapeutic strategies for NGLY1 deficiency.

Aging affects almost all aspects of an organism-its morphology, its physiology, its behavior. Isolating which biological mechanisms are regulating these changes, however, has proven difficult, potentially due to our inability to characterize the full repertoire of an animal's behavior across the lifespan. Using data from fruit flies (D. melanogaster) we measure the full repertoire of behaviors as a function of age. We observe a sexually dimorphic pattern of changes in the behavioral repertoire during aging. Although the stereotypy of the behaviors and the complexity of the repertoire overall remains relatively unchanged, we find evidence that the observed alterations in behavior can be explained by changing the fly's overall energy budget, suggesting potential connections between metabolism, aging, and behavior.

Muscle Invasive bladder cancer is known to have an abundance of mutations, particularly in DNA damage response and chromatin modification genes. The role of these mutations in the development and progression of the disease is not well understood. However, a mutually exclusive mutation pattern between gene pairs could suggest gene mutations of significance. For example, a mutually exclusive mutation pattern could suggest an epistatic relationship where the outcome of a mutation in one gene would have the same outcome as a mutation in a different gene. The significance of a mutually exclusive relationship was determined by establishing a normal distribution of the conditional probabilities for having a mutation in one gene and not the other as well as the reverse relationship for each gene pairing. Then these distributions were used to determine the sigma–magnitude of standard deviation by which the observed value differed from the expected, a value that can also be interpreted as the ‘p-value’. This approach led to the identification of mutually exclusive mutation patterns in KDM6A and KMT2D as well as KDM6A and RB1 that suggested the observed mutation pattern did not happen by chance. Upon further investigation of these genes and their interactions, a potential similar outcome was identified that supports the concept of epistasis. Knowledge of these mutational interactions provides a better understanding of the mechanisms underlying muscle invasive bladder cancer development, and may direct therapeutic development exploiting genotoxic chemotherapy and synthetic lethality in these pathways.

Even early in the COVID-19 pandemic, adherence to physical distancing measures was variable, exposing some communities to elevated risk. While cognitive factors from the Health Belief Model (HBM) and resilience correlate with compliance with physical distancing, external conditions may preclude full compliance with physical distancing guidelines. Our objective was to identify HBM and resilience constructs that could be used to improve adherence to physical distancing even when full compliance is not possible. We examined adherence as expressed through 7-day non-work, non-household contact rates in two cohorts: 1) adults in households with children from Minnesota and Iowa; and 2) adults ≥50 years-old from Minnesota, one-third of whom had Parkinson’s disease. We identified multiple cognitive factors associated with physical distancing adherence, specifically perceived severity, benefits, self-efficacy, and barriers. However, the magnitude, and occasionally the direction, of these associations was population-dependent. In Cohort 1, perceived self-efficacy for remaining 6-feet from others was associated with a 29% lower contact rate (RR 0.71; 95% CI 0.65, 0.77). This finding was consistent across all race/ethnicity and income groups we examined. The barriers to adherence of having a child in childcare and having financial concerns had the largest effects among individuals from marginalized racial and ethnic groups and high-income households. In Cohort 2, self-efficacy to quarantine/isolate was associated with a 23% decrease in contacts (RR 0.77; 95% CI 0.66, 0.89), but upon stratification by education level, the association was only present for those with at least a Bachelor’s degree. Education also modified the effect of the barrier to adherence leaving home for work, increasing contacts among those with a Bachelor’s degree and reducing contacts among those without. Our findings suggest that public health messaging tailored to the identified cognitive factors has the potential to improve physical distancing adherence, but population-specific needs must be considered to maximize effectiveness.

The interactions between antibodies, SARS-CoV-2 and immune cells contribute to the pathogenesis of COVID-19 and protective immunity. To understand the differences between antibody responses in mild versus severe cases of COVID-19, we analyzed the B cell responses in patients 1.5 months post SARS-CoV-2 infection. Severe, and not mild, infection correlated with high titers of IgG against Spike receptor binding domain (RBD) that were capable of ACE2:RBD inhibition. B cell receptor (BCR) sequencing revealed that VH3-53 was enriched during severe infection. Of the 22 antibodies cloned from two severe donors, six exhibited potent neutralization against authentic SARS-CoV-2, and inhibited syncytia formation. Using peptide libraries, competition ELISA and mutagenesis of RBD, we mapped the epitopes of the neutralizing antibodies (nAbs) to three different sites on the Spike. Finally, we used combinations of nAbs targeting different immune-sites to efficiently block SARS-CoV-2 infection. Analysis of 49 healthy BCR repertoires revealed that the nAbs germline VHJH precursors comprise up to 2.7% of all VHJHs. We demonstrate that severe COVID-19 is associated with unique BCR signatures and multi-clonal neutralizing responses that are relatively frequent in the population. Moreover, our data support the use of combination antibody therapy to prevent and treat COVID-19.

BackgroundFace coverings constitute an important strategy for containing pandemics, such as COVID-19. Infection from airborne respiratory viruses including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can occur in at least three modes; tiny and/or dried aerosols (typically < 1.0 μm) generated through multiple mechanisms including talking, breathing, singing, large droplets (> 0.5 μm) generated during coughing and sneezing, and macro drops transmitted via fomites. While there is a growing number of studies looking at the performance of household materials against some of these situations, to date, there has not been any systematic characterization of household materials against all three modes.MethodsA three-step methodology was developed and used to characterize the performance of 21 different household materials with various material compositions (e.g. cotton, polyester, polypropylene, cellulose and blends) using submicron sodium chloride aerosols, water droplets, and mucous mimicking macro droplets over an aerosol-droplet size range of ~ 20 nm to 0.6 cm.ResultsExcept for one thousand-thread-count cotton, most single-layered materials had filtration efficiencies < 20% for sub-micron solid aerosols. However, several of these materials stopped > 80% of larger droplets, even at sneeze-velocities of up to 1700 cm/s. Three or four layers of the same material, or combination materials, would be required to stop macro droplets from permeating out or into the face covering. Such materials can also be boiled for reuse.ConclusionFour layers of loosely knit or woven fabrics independent of the composition (e.g. cotton, polyester, nylon or blends) are likely to be effective source controls. One layer of tightly woven fabrics combined with multiple layers of loosely knit or woven fabrics in addition to being source controls can have sub-micron filtration efficiencies > 40% and may offer some protection to the wearer. However, the pressure drop across such fabrics can be high (> 100 Pa).

Societal responses to crises require coordination at multiple levels of organization. Exploring early efforts to contain COVID-19 in the U.S., we argue that local governments can act to ensure systemic resilience and recovery when higher-level governments fail to do so. Event history analyses show that large, more urban areas experience COVID-19 more intensely due to high population density and denser socioeconomic networks. But metropolitan counties were also among the first to adopt shelter-in-place orders. Analyzing the statistical predictors of when counties moved before their states, we find that the hierarchy of counties by size and economic integration matters for the timing of orders, where both factors predict earlier shelter-in-place orders. In line with sociological theories of urban governance, we also find evidence of an important governance dimension to the timing of orders. Liberal counties in conservative states were more than twice as likely to adopt a policy and implement one earlier in the pandemic, suggesting that tensions about how to resolve collective governance problems are important in the socio-temporal dynamic of responses to COVID-19. We explain this behavior as a substitution effect in which more urban local governments, driven by risk and necessity, step up into the action vacuum left by higher levels of government and become national policy leaders and innovators.

We consider a proposed system that would place sensors in a number of wastewater manholes in a community in order to detect genetic remnants of SARS-Cov-2 found in the excreted stool of infected persons. These sensors would continually monitor the manhole's wastewater, and whenever virus remnants are detected, transmit an alert signal. In a recent paper, we described two new algorithms, each sequentially opening and testing successive manholes for genetic remnants, each algorithm homing in on a neighborhood where the infected person or persons are located. This paper extends that work in six important ways: (1) we introduce the concept of in-manhole sensors, as these sensors will reduce the number of manholes requiring on-site testing; (2) we present a realistic tree network depicting the topology of the sewer pipeline network; (3) for simulations, we present a method to create random tree networks exhibiting key attributes of a given community; (4) using the simulations, we empirically demonstrate that the mean and median number of manholes to be opened in a search follows a well-known logarithmic function; (5) we develop procedures for determining the number of sensors to deploy; (6) we formulate the sensor location problem as an integer nonlinear optimization and develop heuristics to solve it. Our sensor-manhole system, to be implemented, would require at least three additional steps in R&D: (a) an accurate, inexpensive and fast SARS-Cov-2 genetic-remnants test that can be done at the manhole; (b) design, test and manufacture of the sensors; (c) in-the-field testing and fine tuning of an implemented system.

Many eye-tracking data analyses rely on the Area-of-Interest (AOI) methodology, which utilizes AOIs to analyze metrics such as fixations. However, AOI-based methods have some inherent limitations including variability and subjectivity in shape, size, and location of AOIs. In this article, we propose an alternative approach to the traditional AOI dwell time analysis: Weighted Sum Durations (WSD). This approach decreases the subjectivity of AOI definitions by using Points-of-Interest (POI) while maintaining interpretability. In WSD, the durations of fixations toward each POI is weighted by the distance from the POI and summed together to generate a metric comparable to AOI dwell time. To validate WSD, we reanalyzed data from a previously published eye-tracking study (n = 90). The re-analysis replicated the original findings that people gaze less towards faces and more toward points of contact when viewing violent social interactions.

We aimed to apply the Systems Engineering Initiative for Patient Safety (SEIPS) model to increase effectiveness and sustainability of the World Health Organization’s (WHOs) hand hygiene (HH) guidelines within healthcare systems. Our cross-sectional, mixed-methods study took place at Jimma University Medical Center (JUMC), a tertiary care hospital in Jimma, Ethiopia, between November 2018 and August 2020 and consisted of three phases: baseline assessment, intervention, and follow-up assessment. We conducted questionnaires addressing HH knowledge and attitudes, interviews to identify HH barriers and facilitators within the SEIPS framework, and observations at the WHO’s 5 moments of HH amongst healthcare workers (HCWs) at JUMC. We then implemented HH interventions based on WHO guidelines and results from our baseline assessment. Follow-up HH observations were conducted months later during the Covid-19 pandemic. 250 HCWs completed questionnaires with an average knowledge score of 61.4% and attitude scores indicating agreement that HH promotes patient safety. Interview participants cited multiple barriers to HH including shortages and location of HH materials, inadequate training, minimal Infection Prevention Control team presence, and high workload. We found an overall baseline HH compliance rate of 9.4% and a follow-up compliance rate of 72.1%. Drastically higher follow-up compared to baseline compliance rates were likely impacted by our HH interventions and Covid-19. HCWs showed motivation for patient safety despite low HH knowledge. Utilizing the SEIPS model helped identify institution-specific barriers that informed targeted interventions beyond WHO guidelines aimed at increasing effectiveness and sustainability of HH efforts.

Inclusion of women in research on Alcohol Use Disorder (AUD) has shown that gender differences contribute to unique profiles of cognitive, emotional, and neuropsychological dysfunction. We employed functional magnetic resonance imaging (fMRI) of abstinent individuals with a history of AUD (21 women [AUDw], 21 men [AUDm]) and demographically similar non-AUD control (NC) participants without AUD (21 women [NCw], 21 men [NCm]) to explore how gender and AUD interact to influence brain responses during emotional processing and memory. Participants completed a delayed match-to-sample emotional face memory fMRI task, and brain activation contrasts between a fixation stimulus and pictures of emotional face elicited a similar overall pattern of activation for all four groups. Significant Group by Gender interactions revealed two activation clusters. A cluster in an anterior portion of the middle and superior temporal gyrus, elicited lower activation to the fixation stimulus than to faces for the AUDw as compared to the NCw; that abnormality was more pronounced than the one observed for men. Another cluster in the medial portion of the superior frontal cortex elicited higher activation to the faces by AUDm than NCm, a difference that was more evident than the one observed for women. Together, these findings have added new evidence of AUD-related gender differences in neural responses to facial expressions of emotion.

BackgroundInadequate and unequal distribution of health workers are significant barriers to provision of health services in Malawi, and challenges retaining health workers in rural areas have limited scale-up initiatives. This study therefore aims to estimate cost-effectiveness of monetary and non-monetary strategies in attracting and retaining nurse midwife technicians (NMTs) to rural areas of Malawi.MethodsThe study uses a discrete choice experiment (DCE) methodology to investigate importance of job characteristics, probability of uptake, and intervention costs. Interviews and focus groups were conducted with NMTs and students to identify recruitment and retention motivating factors. Through policymaker consultations, qualitative findings were used to identify job attributes for the DCE questionnaire, administered to 472 respondents. A conditional logit regression model was developed to produce probability of choosing a job with different attributes and an uptake rate was calculated to estimate the percentage of health workers that would prefer jobs with specific intervention packages. Attributes were costed per health worker year.ResultsQualitative results highlighted housing, facility quality, management, and workload as important factors in job selection. Respondents were 2.04 times as likely to choose a rural job if superior housing was provided compared to no housing (CI 1.71-2.44, pConclusionsOur results indicate housing and facility-level improvements have the greatest impact on rural job choice, while also creating longer-term improvements to health workers' living and working environments. These results provide practical evidence for policymakers to support development of workforce recruitment and retention strategies.

Background The population of women undergoing abdominal myomectomy for symptomatic large fibroid uterus is unique. We seek to characterize the timing, risk factors as well as the presenting symptoms which led patients to undergo repeat surgery in this patient population. Methods and findings We followed 592 patients who underwent an abdominal myomectomy from March 1998 to June 2010 at St. Vincent’s Catholic Medical Center and presented later during the study period with a recurrence of symptoms attributable to a reemergence of fibroids and who chose to undergo repeat surgical management. Twelve percent of patients exhibited symptoms of fibroid uterus which led to reoperation within the study period. The mean age at repeat surgery was 44.1 ± 0.6 years old (n = 69) and the mean time between operations was 7.9 ± 0.3 years. Presentation was variable but included bleeding, pain and infertility. Patients presented for surgery with a significantly smaller sized uterus than at their initial surgery. Timing between surgeries correlated with age at initial surgery and uterine size but race, number of fibroids, aggregate weight of fibroids removed, operative time or blood loss at the initial surgery did not correlate. Data is suggestive that intraperitoneal triamcinolone may reduce reoperation rates but not timing of recurrence. Conclusion These results may help in counseling patients, particularly younger women, on the risks of fibroid recurrence necessitating repeat surgery. Further research is necessary to assess if triamcinolone can alter fibroid reurrence in patients who undergo uterus sparing procedures.

Uncertainty about the importance of influenza transmission by airborne droplet nuclei generates controversy for infection control. Human challenge-transmission studies have been supported as the most promising approach to fill this knowledge gap. Healthy, seronegative volunteer 'Donors' (n = 52) were randomly selected for intranasal challenge with influenza A/Wisconsin/67/2005 (H3N2). 'Recipients' randomized to Intervention (IR, n = 40) or Control (CR, n = 35) groups were exposed to Donors for four days. IRs wore face shields and hand sanitized frequently to limit large droplet and contact transmission. One transmitted infection was confirmed by serology in a CR, yielding a secondary attack rate of 2.9% among CR, 0% in IR (p = 0.47 for group difference), and 1.3% overall, significantly less than 16% (p

OBJECTIVES:To develop, demonstrate and evaluate an automated deep learning method for multiple cardiovascular structure segmentation. BACKGROUND:Segmentation of cardiovascular images is resource-intensive. We design an automated deep learning method for the segmentation of multiple structures from Coronary Computed Tomography Angiography (CCTA) images. METHODS:Images from a multicenter registry of patients that underwent clinically-indicated CCTA were used. The proximal ascending and descending aorta (PAA, DA), superior and inferior vena cavae (SVC, IVC), pulmonary artery (PA), coronary sinus (CS), right ventricular wall (RVW) and left atrial wall (LAW) were annotated as ground truth. The U-net-derived deep learning model was trained, validated and tested in a 70:20:10 split. RESULTS:The dataset comprised 206 patients, with 5.130 billion pixels. Mean age was 59.9 ± 9.4 yrs., and was 42.7% female. An overall median Dice score of 0.820 (0.782, 0.843) was achieved. Median Dice scores for PAA, DA, SVC, IVC, PA, CS, RVW and LAW were 0.969 (0.979, 0.988), 0.953 (0.955, 0.983), 0.937 (0.934, 0.965), 0.903 (0.897, 0.948), 0.775 (0.724, 0.925), 0.720 (0.642, 0.809), 0.685 (0.631, 0.761) and 0.625 (0.596, 0.749) respectively. Apart from the CS, there were no significant differences in performance between sexes or age groups. CONCLUSIONS:An automated deep learning model demonstrated segmentation of multiple cardiovascular structures from CCTA images with reasonable overall accuracy when evaluated on a pixel level.

Several candidate HIV subunit vaccines based on recombinant envelope (Env) glycoproteins have been advanced into human clinical trials. To facilitate biopharmaceutical production, it is necessary to produce these in CHO (Chinese Hamster Ovary) cells, the cellular substrate used for the manufacturing of most recombinant protein therapeutics. However, previous studies have shown that when recombinant Env proteins from clade B viruses, the major subtype represented in North America, Europe, and other parts of the world, are expressed in CHO cells, they are proteolyzed and lack important glycan-dependent epitopes present on virions. Previously, we identified C1s, a serine protease in the complement pathway, as the endogenous CHO protease responsible for the cleavage of clade B laboratory isolates of -recombinant gp120s (rgp120s) expressed in stable CHO-S cell lines. In this paper, we describe the development of two novel CHOK1 cell lines with the C1s gene inactivated by gene editing, that are suitable for the production of any protein susceptible to C1s proteolysis. One cell line, C1s-/- CHOK1 2.E7, contains a deletion in the C1s gene. The other cell line, C1s-/- MGAT1- CHOK1 1.A1, contains a deletion in both the C1s gene and the MGAT1 gene, which limits glycosylation to mannose-5 or earlier intermediates in the N-linked glycosylation pathway. In addition, we compare the substrate specificity of C1s with thrombin on the cleavage of both rgp120 and human Factor VIII, two recombinant proteins known to undergo unintended proteolysis (clipping) when expressed in CHO cells. Finally, we demonstrate the utility and practicality of the C1s-/- MGAT1- CHOK1 1.A1 cell line for the expression of clinical isolates of clade B Envs from rare individuals that possess broadly neutralizing antibodies and are able to control virus replication without anti-retroviral drugs (elite neutralizer/controller phenotypes). The Envs represent unique HIV vaccine immunogens suitable for further immunogenicity and efficacy studies.

The continuing HIV pandemic calls for broad, multi-sectoral responses that foster community control of local prevention and care services, with the goal of leveraging high quality treatment as a means of reducing HIV incidence. Service system improvements require stakeholder input from across the care continuum to identify gaps and to inform strategic plans that improve HIV service integration and delivery. System dynamics modeling offers a participatory research approach through which stakeholders learn about system complexity and about ways to achieve sustainable system-level improvements. Via an intensive group model building process with a task force of community stakeholders with diverse roles and responsibilities for HIV service implementation, delivery and surveillance, we designed and validated a multi-module system dynamics model of the HIV care continuum, in relation to local prevention and care service capacities. Multiple sources of data were used to calibrate the model for a three-county catchment area of central Connecticut. We feature a core module of the model for the purpose of illustrating its utility in understanding the dynamics of treatment as prevention at the community level. We also describe the methods used to validate the model and support its underlying assumptions to improve confidence in its use by stakeholders for systems understanding and decision making. The model's generalizability and implications of using it for future community-driven strategic planning and implementation efforts are discussed.

Alcohol Use Disorder (AUD) has been associated with abnormalities in hippocampal volumes, but these relationships have not been fully explored with respect to sub-regional volumes, nor in association with individual characteristics such as age, gender differences, drinking history, and memory. The present study examined the impact of those variables in relation to hippocampal subfield volumes in abstinent men and women with a history of AUD. Using Magnetic Resonance Imaging at 3 Tesla, we obtained brain images from 67 participants with AUD (31 women) and 64 nonalcoholic control (NC) participants (31 women). The average duration of the most recent period of sobriety for AUD participants was 7.1 years. We used Freesurfer 6.0 to segment the hippocampus into 12 regions. These were imputed into statistical models to examine the relationships of brain volume with AUD group, age, gender, memory, and drinking history. Interactions with gender and age were of particular interest. Compared to the NC group, the AUD group had approximately 5% smaller subiculum, CA1, molecular layer, and hippocampal tail regions. Age was negatively associated with volumes for the AUD group in the subiculum and the hippocampal tail, but no significant interactions with gender were identified. The relationships for delayed and immediate memory with hippocampal tail volume differed for AUD and NC groups: Higher scores on tests of immediate and delayed memory were associated with smaller volumes in the AUD group, but larger volumes in the NC group. Length of sobriety was associated with decreasing CA1 volume in women (0.19% per year) and increasing volume size in men (0.38% per year). The course of abstinence on CA1 volume differed for men and women, and the differential relationships of subfield volumes to age and memory could indicate a distinction in the impact of AUD on functions of the hippocampal tail. These findings confirm and extend evidence that AUD, age, gender, memory, and abstinence differentially impact volumes of component parts of the hippocampus.

Introduction3D printing is being used more extensively in modern biomedicine. One of the problems is selecting a proper crosslinking method of bioprinted material. Amongst currently used techniques we can distinguish: physical crosslinking (e.g. Ca2+ and Sr2+) and chemical crosslinking-the UV light crosslinking causing the biggest discussion. UV radiation is selectively absorbed by DNA, mainly in the UV-B region but also (to some extent) in UV-A and UV-C regions. DNA excitement results in typical photoproducts. The amount of strand breaks may vary depending on the period of exposition, it can also differ when cells undergo incubation after radiation.AimThe aim of this study was to show whether and how the time of irradiation with 405 nm and 365 nm wavelengths affect DNA damage in cell lines and micro-organs (pancreatic islets).Materials and methodsThe degree of DNA damage caused by different wavelengths of radiation (405 nm and 365 nm) was evaluated by a comet assay. The test was performed on fibroblasts, alpha cells, beta cells and porcine pancreatic islets after 24 hours incubation period. Samples without radiation treatment were selected as a control group. Results analysis consisted of determining the percent of cells with damaged DNA and the tail intensity evaluation.ResultsThe degree of DNA damage in pancreatic islets after exposure to 405 nm wavelength oscillated between 2% and 6% depending on the tested time period (10 - 300 seconds). However, treating islets using 365 nm wavelength resulted in damage up to 50%. This clearly shows significantly less damage when using 405 nm wavelength. Similar results were obtained for the tested cell lines.ConclusionsCrosslinking with 405 nm is better for pancreatic islets than crosslinking with 365 nm UV light.

About 50% of individuals infected with the novel Coronavirus (SARS-CoV-2) suffer from intestinal infection as well as respiratory infection. They shed virus in their stool. Municipal sewage systems carry the virus and its genetic remnants. These viral traces can be detected in the sewage entering a wastewater treatment plant (WTP). Such virus signals indicate community infections but not locations of the infection within the community. In this paper, we frame and formulate the problem in a way that leads to algorithmic procedures homing in on locations and/or neighborhoods within the community that are most likely to have infections. Our data source is wastewater sampled and real-time tested from selected manholes. Our algorithms dynamically and adaptively develop a sequence of manholes to sample and test. The algorithms are often finished after 5 to 10 manhole samples, meaning that-in the field-the procedure can be carried out within one day. The goal is to provide timely information that will support faster more productive human testing for viral infection and thus reduce community disease spread. Leveraging the tree graph structure of the sewage system, we develop two algorithms, the first designed for a community that is certified at a given time to have zero infections and the second for a community known to have many infections. For the first, we assume that wastewater at the WTP has just revealed traces of SARS-CoV-2, indicating existence of a "Patient Zero" in the community. This first algorithm identifies the city block in which the infected person resides. For the second, we home in on a most infected neighborhood of the community, where a neighborhood is usually several city blocks. We present extensive computational results, some applied to a small New England city.

BackgroundStudies have suggested associations between self-reported engagement in health behaviors and reduced risk of cognitive decline. Most studies explore these relationships using one health behavior, often cross-sectionally or with dementia as the outcome. In this study, we explored whether several individual self-reported health behaviors were associated with cognitive decline when considered simultaneously, using data from the Wisconsin Registry for Alzheimer's Prevention (WRAP), an Alzheimer's disease risk-enriched cohort who were non-demented and in late midlife at baseline.MethodWe analyzed longitudinal cognitive data from 828 participants in WRAP, with a mean age at baseline cognitive assessment of 57 (range = 36-78, sd = 6.8) and an average of 6.3 years (standard deviation = 1.9, range = 2-10) of follow-up. The primary outcome was a multi-domain cognitive composite, and secondary outcomes were immediate/delayed memory and executive function composites. Predictors of interest were self-reported measures of physical activity, cognitive activity, adherence to a Mediterranean-style diet (MIND), and interactions with each other and age. We conducted linear mixed effects analyses within an Information-theoretic (IT) model averaging (MA) approach on a set of models including covariates and combinations of these 2- and 3-way interactions. The IT approach was selected due to the large number of interactions of interest and to avoid pitfalls of traditional model selection approaches.ResultsModel-averaged results identified no significant self-reported health behavior*age interactions in relationship to the primary composite outcome. In secondary outcomes, higher MIND diet scores associated with slower decline in executive function. Men showed faster decline than women on delayed memory, independent of health behaviors. There were no other significant interactions among any other health behaviors and cognitive trajectories.ConclusionsWhen multiple covariates and health behaviors were considered simultaneously, there were limited weak associations with cognitive decline in this age range. These results may be explained alone or in combination by three alternative explanations: 1) the range of cognitive decline is in middle age is too small to observe relationships with health behaviors, 2) the putative associations of these health behaviors on cognition may not be robust in this age range, or 3) the self-reported measures of the health behaviors may not be optimal for predicting cognitive decline. More study may be needed that incorporates sensitive measures of health behaviors, AD biomarker profiles, and/or other disease comorbidities.

When the fungus Candida albicans proliferates in the oropharyngeal cavity during experimental oropharyngeal candidiasis (OPC), it undergoes large-scale genome changes at a much higher frequency than when it grows in vitro. Previously, we identified a specific whole chromosome amplification, trisomy of Chr6 (Chr6x3), that was highly overrepresented among strains recovered from the tongues of mice with OPC. To determine the functional significance of this trisomy, we assessed the virulence of two Chr6 trisomic strains and a Chr5 trisomic strain in the mouse model of OPC. We also analyzed the expression of virulence-associated traits in vitro. All three trisomic strains exhibited characteristics of a commensal during OPC in mice. They achieved the same oral fungal burden as the diploid progenitor strain but caused significantly less weight loss and elicited a significantly lower inflammatory host response. In vitro, all three trisomic strains had reduced capacity to adhere to and invade oral epithelial cells and increased susceptibility to neutrophil killing. Whole genome sequencing of pre- and post-infection isolates found that the trisomies were usually maintained. Most post-infection isolates also contained de novo point mutations, but these were not conserved. While in vitro growth assays did not reveal phenotypes specific to de novo point mutations, they did reveal novel phenotypes specific to each lineage. These data reveal that during OPC, clones that are trisomic for Chr5 or Chr6 are selected and they facilitate a commensal-like phenotype.

Snow dynamics influence seasonal behaviors of wildlife, such as denning patterns and habitat selection related to the availability of food resources. Under a changing climate, characteristics of the temporal and spatial patterns of snow are predicted to change, and as a result, there is a need to better understand how species interact with snow dynamics. This study examines grizzly bear (Ursus arctos) spring habitat selection and use across western Alberta, Canada. Made possible by newly available fine-scale snow cover data, this research tests a hypothesis that grizzly bears select for locations with less snow cover and areas where snow melts sooner during spring (den emergence to May 31st). Using Integrated Step Selection Analysis, a series of models were built to examine whether snow cover information such as fractional snow covered area and date of snow melt improved models constructed based on previous knowledge of grizzly bear selection during the spring. Comparing four different models fit to 62 individual bear-years, we found that the inclusion of fractional snow covered area improved model fit 60% of the time based on Akaike Information Criterion tallies. Probability of use was then used to evaluate grizzly bear habitat use in response to snow and environmental attributes, including fractional snow covered area, date since snow melt, elevation, and distance to road. Results indicate grizzly bears select for lower elevation, snow-free locations during spring, which has important implications for management of threatened grizzly bear populations in consideration of changing climatic conditions. This study is an example of how fine spatial and temporal scale remote sensing data can be used to improve our understanding of wildlife habitat selection and use in relation to key environmental attributes.

A major challenge in HIV vaccine development is the identification of immunogens able to elicit broadly neutralizing antibodies (bNAbs). While remarkable progress has been made in the isolation and characterization of bNAbs, the epitopes they recognize appear to be poorly immunogenic. Thus, none of the candidate vaccines developed to date has induced satisfactory levels of neutralizing antibodies to the HIV envelope protein (Env). One approach to the problem of poor immunogenicity is to build vaccines based on envelope (env) genes retrieved from rare individuals termed elite neutralizers (ENs) who at one time possessed specific sequences that stimulated the formation of bNAbs. Env proteins selected from these individuals could possess uncommon, yet to be defined, structural features that enhance the immunogenicity of epitopes recognized by bNAbs. Here we describe the recovery of envs from an EN that developed unusually broad and potent bNAbs. As longitudinal specimens were not available, we combined plasma and provirus sequences acquired from a single time-point to infer a phylogenetic tree. Combining ancestral reconstruction data with virus neutralization data allowed us to sift through the myriad of virus quasi-species that evolved in this individual to identify envelope sequences from the nodes that appeared to define the transition from neutralization sensitive envs to the neutralization resistant envs that occur in EN plasma. Synthetic genes from these nodes were functional in infectivity assays and sensitive to neutralization by bNAbs, and may provide a novel source of immunogens for HIV vaccine development.

Pharmacogenetics studies have identified several allelic variants with the potential to reduce toxicity and improve treatment outcome. The present study was designed to determine if such findings are reproducible in a heterogenous population of patients with lung cancer undergoing therapy with paclitaxel. We designed a prospective multi-institutional study that recruited n = 103 patients receiving paclitaxel therapy with a 5-year follow up. All patients were genotyped using the Drug Metabolizing Enzymes and Transporters (DMET) platform, which ascertains 1931 genotypes in 235 genes. Progression-free survival (PFS) of paclitaxel therapy and clinically-significant paclitaxel toxicities were classified and compared according to genotype. Initial screening revealed eleven variants that are associated with PFS. Of these, seven variants in ABCB11 (rs4148768), ABCC3 (rs1051640), ABCG1 (rs1541290), CYP8B1 (rs735320), NR3C1 (rs6169), FMO6P (rs7889839), and GSTM3 (rs7483) were associated with paclitaxel PFS in a multivariate analysis accounting for clinical covariates. Multivariate analysis revealed four SNPs in VKORC1 (rs2884737), SLC22A14 (rs4679028), GSTA2 (rs6577), and DCK (rs4643786) were associated with paclitaxel toxicities. With the exception of a variant in VKORC1, the present study did not find the same genetic outcome associations of other published research on pharmacogenetics variants that affect paclitaxel outcomes. This finding suggests that prior pharmacogenomics research findings may not be reproduced in the most frequently-diagnosed malignancy, lung cancer.

IntroductionGeographic Information Systems (GIS) and spatial analysis are emerging tools for global health, but it is unclear to what extent they have been applied to HIV research in Africa. To help inform researchers and program implementers, this scoping review documents the range and depth of published HIV-related GIS and spatial analysis research studies conducted in Africa.MethodsA systematic literature search for articles related to GIS and spatial analysis was conducted through PubMed, EMBASE, and Web of Science databases. Using pre-specified inclusion criteria, articles were screened and key data were abstracted. Grounded, inductive analysis was conducted to organize studies into meaningful thematic areas.Results and discussionThe search returned 773 unique articles, of which 65 were included in the final review. 15 different countries were represented. Over half of the included studies were published after 2014. Articles were categorized into the following non-mutually exclusive themes: (a) HIV geography, (b) HIV risk factors, and (c) HIV service implementation. Studies demonstrated a broad range of GIS and spatial analysis applications including characterizing geographic distribution of HIV, evaluating risk factors for HIV, and assessing and improving access to HIV care services.ConclusionsGIS and spatial analysis have been widely applied to HIV-related research in Africa. The current literature reveals a diversity of themes and methodologies and a relatively young, but rapidly growing, evidence base.

BACKGROUND:Face-to-face brief interventions for problem drinking are effective, but they have found limited implementation in routine care and the community. Internet-based interventions could overcome this treatment gap. We investigated effectiveness and moderators of treatment outcomes in internet-based interventions for adult problem drinking (iAIs). METHODS AND FINDINGS:Systematic searches were performed in medical and psychological databases to 31 December 2016. A one-stage individual patient data meta-analysis (IPDMA) was conducted with a linear mixed model complete-case approach, using baseline and first follow-up data. The primary outcome measure was mean weekly alcohol consumption in standard units (SUs, 10 grams of ethanol). Secondary outcome was treatment response (TR), defined as less than 14/21 SUs for women/men weekly. Putative participant, intervention, and study moderators were included. Robustness was verified in three sensitivity analyses: a two-stage IPDMA, a one-stage IPDMA using multiple imputation, and a missing-not-at-random (MNAR) analysis. We obtained baseline data for 14,198 adult participants (19 randomised controlled trials [RCTs], mean age 40.7 [SD = 13.2], 47.6% women). Their baseline mean weekly alcohol consumption was 38.1 SUs (SD = 26.9). Most were regular problem drinkers (80.1%, SUs 44.7, SD = 26.4) and 19.9% (SUs 11.9, SD = 4.1) were binge-only drinkers. About one third were heavy drinkers, meaning that women/men consumed, respectively, more than 35/50 SUs of alcohol at baseline (34.2%, SUs 65.9, SD = 27.1). Post-intervention data were available for 8,095 participants. Compared with controls, iAI participants showed a greater mean weekly decrease at follow-up of 5.02 SUs (95% CI -7.57 to -2.48, p < 0.001) and a higher rate of TR (odds ratio [OR] 2.20, 95% CI 1.63-2.95, p < 0.001, number needed to treat [NNT] = 4.15, 95% CI 3.06-6.62). Persons above age 55 showed higher TR than their younger counterparts (OR = 1.66, 95% CI 1.21-2.27, p = 0.002). Drinking profiles were not significantly associated with treatment outcomes. Human-supported interventions were superior to fully automated ones on both outcome measures (comparative reduction: -6.78 SUs, 95% CI -12.11 to -1.45, p = 0.013; TR: OR = 2.23, 95% CI 1.22-4.08, p = 0.009). Participants treated in iAIs based on personalised normative feedback (PNF) alone were significantly less likely to sustain low-risk drinking at follow-up than those in iAIs based on integrated therapeutic principles (OR = 0.52, 95% CI 0.29-0.93, p = 0.029). The use of waitlist control in RCTs was associated with significantly better treatment outcomes than the use of other types of control (comparative reduction: -9.27 SUs, 95% CI -13.97 to -4.57, p < 0.001; TR: OR = 3.74, 95% CI 2.13-6.53, p < 0.001). The overall quality of the RCTs was high; a major limitation included high study dropout (43%). Sensitivity analyses confirmed the robustness of our primary analyses. CONCLUSION:To our knowledge, this is the first IPDMA on internet-based interventions that has shown them to be effective in curbing various patterns of adult problem drinking in both community and healthcare settings. Waitlist control may be conducive to inflation of treatment outcomes.

Over the last decade, multiple broadly neutralizing monoclonal antibodies (bN-mAbs) to the HIV-1 envelope protein (Env) gp120 have been described. Many of these recognize epitopes consisting of both amino acid and glycan residues. Moreover, the glycans required for binding of these bN-mAbs are early intermediates in the N-linked glycosylation pathway. This type of glycosylation substantially alters the mass and net charge of Envs compared to molecules with the same amino acid sequence but possessing mature, complex (sialic acid-containing) carbohydrates. Since cell lines suitable for biopharmaceutical production that limit N-linked glycosylation to mannose-5 (Man5) or earlier intermediates are not readily available, the production of vaccine immunogens displaying these glycan-dependent epitopes has been challenging. Here, we report the development of a stable suspension-adapted Chinese hamster ovary (CHO) cell line that limits glycosylation to Man5 and earlier intermediates. This cell line was created using the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing system and contains a mutation that inactivates the gene encoding Mannosyl (Alpha-1,3-)-Glycoprotein Beta-1,2-N-Acetylglucosaminyltransferase (MGAT1). Monomeric gp120s produced in the MGAT1- CHO cell line exhibit improved binding to prototypic glycan-dependent bN-mAbs directed to the V1/V2 domain (e.g., PG9) and the V3 stem (e.g., PGT128 and 10-1074) while preserving the structure of the important glycan-independent epitopes (e.g., VRC01). The ability of the MGAT1- CHO cell line to limit glycosylation to early intermediates in the N-linked glycosylation pathway without impairing the doubling time or ability to grow at high cell densities suggests that it will be a useful substrate for the biopharmaceutical production of HIV-1 vaccine immunogens.

Gene duplication facilitates functional diversification and provides greater phenotypic flexibility to an organism. Expanded gene families arise through repeated gene duplication but the extent of functional divergence that accompanies each paralogous gene is generally unexplored because of the difficulty in isolating the effects of single family members. The telomere-associated (TLO) gene family is a remarkable example of gene family expansion, with 14 members in the more pathogenic Candida albicans relative to two TLO genes in the closely-related species C. dubliniensis. TLO genes encode interchangeable Med2 subunits of the major transcriptional regulatory complex Mediator. To identify biological functions associated with each C. albicans TLO, expression of individual family members was regulated using a Tet-ON system and the strains were assessed across a range of phenotypes involved in growth and virulence traits. All TLOs affected multiple phenotypes and a single phenotype was often affected by multiple TLOs, including simple phenotypes such as cell aggregation and complex phenotypes such as virulence in a Galleria mellonella model of infection. No phenotype was regulated by all TLOs, suggesting neofunctionalization or subfunctionalization of ancestral properties among different family members. Importantly, regulation of three phenotypes could be mapped to individual polymorphic sites among the TLO genes, including an indel correlated with two phenotypes, growth in sucrose and macrophage killing. Different selective pressures have operated on the TLO sequence, with the 5' conserved Med2 domain experiencing purifying selection and the gene/clade-specific 3' end undergoing extensive positive selection that may contribute to the impact of individual TLOs on phenotypic variability. Therefore, expansion of the TLO gene family has conferred unique regulatory properties to each paralog such that it influences a range of phenotypes. We posit that the genetic diversity associated with this expansion contributed to C. albicans success as a commensal and opportunistic pathogen.

BackgroundThe extent to which the presence and extent of subclinical atherosclerosis by coronary computed tomography angiography influences a potential mortality benefit of statin is unknown. We evaluated the relationship between statin therapy, mortality, and subclinical atherosclerosis.MethodsIn the CONFIRM study, patients with normal or non-obstructive plaque (Results1.2% of patients experienced all-cause mortality. Patients not on baseline statin therapy had a stepwise increased risk of all-cause mortality by CAC (relative to CAC = 0; CAC 1-99: hazard ratio [HR] 1.65, CAC 100-299: HR 2.19, and CAC≥300: HR 2.98) or SIS (relative to SIS = 0; SIS 1: HR 1.62, SIS 2-3: 2.48 and SIS≥4: 2.95). Conversely, in patients on baseline statin therapy, there was no significant increase in mortality risk with increasing CAC (p value for interaction = 0.049) or SIS (p value for interaction = 0.007). The incidence of MACE was 2.1%. Similar to the all-cause mortality, the risk of MACE was increased with CAC or SIS strata in patient not on baseline statin therapy. However, this relation was not observed in patient on baseline statin therapy.ConclusionIn individuals with non-obstructive coronary artery disease, increased risk of adverse events occurs with increasing CAC or SIS who are not on baseline statin therapy. Statin therapy is associated with a mitigation of risk of cardiac events in the presence of increasing atherosclerosis, with no particular threshold of disease burden.

Damaged cartilage has very low regenerative potential which has led to the search for novel tissue-engineering approaches to help treat cartilage defects. While various approaches have been reported, there is no perfect treatment currently. In this study we evaluated the effects of a plant extract, chlorogenic acid (CGA), as part of chondrocyte transplantation on a model of knee joint injury in chicks. First, primary cultured chondrocytes used to evaluate the effects of CGA on chondrogenesis. Then using an articular cartilage injury model of chick knee we assessed the functional recovery after transplantation of the complexes containing chondrocytes and CGA in an alginate scaffold. Histological analysis, PCR, and western blot were further used to understand the underlying mechanisms. We showed that 60 μM CGA in alginate exhibited notable effects on stimulating chondrogenesis in vitro. Secondly, it was shown that the application of these complexes accelerated the recovery of injury-induced dysfunction by gait analysis when followed for 21 days. Histochemical analysis demonstrated that there was less abnormal vasculature formation, more chondrocyte proliferation and cartilage matrix synthesis in the presence of the complexes containing CGA. We discovered CGA treated transplantation up-regulated the expressions of Sox9 and Col2a1 which were responsible for the stimulation of chondrogenesis. Furthermore, the application of these complexes could suppress the abnormal angiogenesis and fibrosis at the injury site. Lastly, the elevated levels of inflammatory cytokines IL-1β, TNF-α, p-p65, and MMPs expression were decreased in the presence of CGA. This may be caused through adjusting cellular redox homeostasis associated with Nrf2. This study suggests that combining chondrocytes and CGA on an alginate scaffold can improve the recovery of damaged articular cartilage.

The production of envelope glycoproteins (Envs) for use as HIV vaccines is challenging. The yield of Envs expressed in stable Chinese Hamster Ovary (CHO) cell lines is typically 10-100 fold lower than other glycoproteins of pharmaceutical interest. Moreover, Envs produced in CHO cells are typically enriched for sialic acid containing glycans compared to virus associated Envs that possess mainly high-mannose carbohydrates. This difference alters the net charge and biophysical properties of Envs and impacts their antigenic structure. Here we employ a novel robotic cell line selection strategy to address the problems of low expression. Additionally, we employed a novel gene-edited CHO cell line (MGAT1- CHO) to address the problems of high sialic acid content, and poor antigenic structure. We demonstrate that stable cell lines expressing high levels of gp120, potentially suitable for biopharmaceutical production can be created using the MGAT1- CHO cell line. Finally, we describe a MGAT1- CHO cell line expressing A244-rgp120 that exhibits improved binding of three major families of bN-mAbs compared to Envs produced in normal CHO cells. The new strategy described has the potential to eliminate the bottleneck in HIV vaccine development that has limited the field for more than 25 years.

To date, the RV144 HIV vaccine trial has been the only study to show that immunization can confer protection from HIV infection. While encouraging, the modest 31.2% (P = 0.04) efficacy achieved in this study left significant room for improvement, and created an incentive to optimize the AIDSVAX B/E vaccine immunogens to increase the level of vaccine efficacy. Since the completion of the RV144 trial, our understanding of the antigenic structure of the HIV envelope protein, gp120, and of the specificity of broadly neutralizing monoclonal antibodies (bN-mAbs) that bind to it, has significantly improved. In particular, we have learned that multiple families of bN-mAbs require specific oligomannose glycans for binding. Both of the monomeric gp120 immunogens (MN- and A244-rgp120) in the AIDSVAX B/E vaccine used in the RV144 trial were enriched for glycans containing high levels of sialic acid, and lacked critical N-linked glycosylation sites required for binding by several families of bN-mAbs. The absence of these epitopes may have contributed to the low level of efficacy achieved in this study. In this report, we describe our efforts to improve the antigenic structure of the rgp120 immunogens used in the vaccine by optimizing glycan-dependent epitopes recognized by multiple bN-mAbs. Our results demonstrated that by shifting the location of one PNGS in A244-rgp120, and by adding two PNGS to MN-rgp120, in conjunction with the production of both proteins in a cell line that favors the incorporation of oligomannose glycans, we could significantly improve the binding by three major families of bN-mAbs. The immunogens described here represent a second generation of gp120-based vaccine immunogens that exhibit potential for use in RV144 follow-up studies.

Brain phenotypes showing environmental influence may help clarify unexplained associations between urban exposure and psychiatric risk. Heritable prefrontal fMRI activation during working memory (WM) is such a phenotype. We hypothesized that urban upbringing (childhood urbanicity) would alter this phenotype and interact with dopamine genes that regulate prefrontal function during WM. Further, dopamine has been hypothesized to mediate urban-associated factors like social stress. WM-related prefrontal function was tested for main effects of urbanicity, main effects of three dopamine genes-catechol-O-methyltransferase (COMT), dopamine receptor D1 (DRD1), and dopamine receptor D2 (DRD2)-and, importantly, dopamine gene-by-urbanicity interactions. For COMT, three independent human samples were recruited (total n = 487). We also studied 253 subjects genotyped for DRD1 and DRD2. 3T fMRI activation during the N-back WM task was the dependent variable, while childhood urbanicity, dopamine genotype, and urbanicity-dopamine interactions were independent variables. Main effects of dopamine genes and of urbanicity were found. Individuals raised in an urban environment showed altered prefrontal activation relative to those raised in rural or town settings. For each gene, dopamine genotype-by-urbanicity interactions were shown in prefrontal cortex-COMT replicated twice in two independent samples. An urban childhood upbringing altered prefrontal function and interacted with each gene to alter genotype-phenotype relationships. Gene-environment interactions between multiple dopamine genes and urban upbringing suggest that neural effects of developmental environmental exposure could mediate, at least partially, increased risk for psychiatric illness in urban environments via dopamine genes expressed into adulthood.

BACKGROUND:Cancers induce gene expression alterations in stroma surrounding tumors that supports cancer progression. However, it is actually not at all known the extent of altered stromal gene expression enacted by tumors nor the extent to which altered stromal gene expression penetrates the stromal tissue. Presently, post-surgical "tumor-free" stromal tissue is determined to be cancer-free based on solely on morphological normality-a criteria that has not changed in more than 100 years despite the existence of sophisticated gene expression data to the contrary. We therefore investigated the extent to which breast tumors alter stromal gene expression in three dimensions in women undergoing mastectomy with the intent of providing a genomic determination for development of future risk of recurrence criteria, and to inform the need for adjuvant full-breast irradiation. METHODS AND FINDINGS:Genome-wide gene expression changes were determined in histopathologically normal breast tissue in 33 women undergoing mastectomy for stage II and III primary invasive ductal carcinoma at serial distances in three dimensions from the tumor. Gene expression was determined by genome-wide mRNA analysis and subjected to metagene mRNA characterization. Tumor-like gene expression signatures in stroma were identified that surprisingly transitioned to a plastic, normalizing homeostatic signature with distance from tumor. Stroma closest to tumor displayed a pronounced tumor-like signature enriched in cancer-promoting pathways involved in disruption of basement membrane, cell migration and invasion, WNT signaling and angiogenesis. By 2 cm from tumor in all dimensions, stromal tissues were in transition, displaying homeostatic and tumor suppressing gene activity, while also expressing cancer supporting pathways. CONCLUSIONS:The dynamics of gene expression in the post-tumor breast stroma likely co-determines disease outcome: reversion to normality or transition to transformation in morphologically normal tissue. Our stromal genomic signature may be important for personalizing surgical and adjuvant therapeutic decisions and risk of recurrence.

Emergomyces africanus is a thermally dimorphic fungus that causes a systemic mycosis in immunocompromised persons in South Africa. Infection is presumed to follow inhalation of airborne propagules. We developed a quantitative PCR protocol able to detect as few as 5 Es. africanus propagules per day. Samples were collected in Cape Town, South Africa over 50 weeks by a Burkard spore trap with an alternate orifice. We detected Es. africanus in air samples from 34 days (10%) distributed over 11 weeks. These results suggest environmental exposure to airborne Es. africanus propagules occurs more commonly in endemic areas than previously appreciated.

In complex real-world scenes, image content is conveyed by a large collection of intertwined visual features. The visual system disentangles these features in order to extract information about image content. Here, we investigate the role of one integral component: the content of spatial frequencies in an image. Specifically, we measure the amount of image content carried by low versus high spatial frequencies for the representation of real-world scenes in scene-selective regions of human visual cortex. To this end, we attempted to decode scene categories from the brain activity patterns of participants viewing scene images that contained the full spatial frequency spectrum, only low spatial frequencies, or only high spatial frequencies, all carefully controlled for contrast and luminance. Contrary to the findings from numerous behavioral studies and computational models that have highlighted how low spatial frequencies preferentially encode image content, decoding of scene categories from the scene-selective brain regions, including the parahippocampal place area (PPA), was significantly more accurate for high than low spatial frequency images. In fact, decoding accuracy was just as high for high spatial frequency images as for images containing the full spatial frequency spectrum in scene-selective areas PPA, RSC, OPA and object selective area LOC. We also found an interesting dissociation between the posterior and anterior subdivisions of PPA: categories were decodable from both high and low spatial frequency scenes in posterior PPA but only from high spatial frequency scenes in anterior PPA; and spatial frequency was explicitly decodable from posterior but not anterior PPA. Our results are consistent with recent findings that line drawings, which consist almost entirely of high spatial frequencies, elicit a neural representation of scene categories that is equivalent to that of full-spectrum color photographs. Collectively, these findings demonstrate the importance of high spatial frequencies for conveying the content of complex real-world scenes.

Non-neutralizing IgG to the V1V2 loop of HIV-1 gp120 correlates with a decreased risk of HIV-1 infection but the mechanism of protection remains unknown. This V1V2 IgG correlate was identified in RV144 Thai trial vaccine recipients, who were primed with a canarypox vector expressing membrane-bound gp120 (vCP1521) and boosted with vCP1521 plus a mixture gp120 proteins from clade B and clade CRF01_AE (B/E gp120). We sought to determine whether the mechanism of vaccine protection might involve antibody-dependent complement activation. Complement activation was measured as a function of complement component C3d deposition on V1V2-coated beads in the presence of RV144 sera. Variable levels of complement activation were detected two weeks post final boosting in RV144, which is when the V1V2 IgG correlate was identified. The magnitude of complement activation correlated with V1V2-specific serum IgG and was stronger and more common in RV144 than in HIV-1 infected individuals and two related HIV-1 vaccine trials, VAX003 and VAX004, where no protection was seen. After adjusting for gp120 IgA, V1V2 IgG, gender, and risk score, complement activation by case-control plasmas from RV144 correlated inversely with a reduced risk of HIV-1 infection, with odds ratio for positive versus negative response to TH023-V1V2 0.42 (95% CI 0.18 to 0.99, p = 0.048) and to A244-V1V2 0.49 (95% CI 0.21 to 1.10, p = 0.085). These results suggest that complement activity may have contributed in part to modest protection against the acquisition of HIV-1 infection seen in the RV144 trial.