A global metagenomic map of urban microbiomes and antimicrobial resistance.

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

Limited role of children in transmission of SARS-CoV-2 virus in households-Immunological analysis of 26 familial clusters.

BACKGROUND: The impact of children on the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains uncertain. This study provides an insight into distinct patterns of SARS-CoV-2 household transmission in case of pediatric and adult index cases as well as age-dependent susceptibility to SARS-CoV-2 infection. METHODS: Immune analysis, medical interviewing, and contact tracing of 26 families with confirmed SARS-CoV-2 infection cases have been conducted. Blood samples were analyzed serologically with the use of a SARS-CoV-2-specific IgG assay and virus neutralization test (VNT). Uni- and multivariable linear regression and mixed effect logistic regression models were used to describe potential risk factors for higher contagiousness and susceptibility to SARS-CoV-2 infection. RESULTS: SARS-CoV-2 infection could be confirmed in 67 of 124 family members. Fourteen children and 11 adults could be defined as index cases in their households. Forty of 82 exposed family members were defined as secondarily infected. The mean secondary attack rate in households was 0.48 and was significantly higher in households with adult than with pediatric index cases (0.85 vs 0.19; p < 0.0001). The age (grouped into child and adult) of index case, severity of disease, and occurrence of lower respiratory symptoms in index cases were significantly associated with secondary transmission rates in households. Children seem to be equally susceptible to acquire a SARS-CoV-2 infection as adults, but they suffer milder courses of the disease or remain asymptomatic. CONCLUSION: SARS-CoV-2 transmission from infected children to other household members occurred rarely in the first wave of the pandemic, despite close physical contact and the lack of hygienic measures.

A qualitative exploration of health-related present bias among HIV-positive adults in Uganda.

Decision-making errors such as present bias (PB) can have important consequences for health behaviors, but have been largely studied in the financial domain. We conducted a mixed-method study on PB in the context of ART adherence among clinic-enrolled adults in Uganda (n = 39). Specifically, we quantified PB by asking about preferences between medication available sooner to minimize headaches versus available later to cure headaches. We describe demographic similarities among PB participants and qualitatively explored how participants reflected on their PB (or absence thereof) in the context of health. Participants reporting PB were predominantly male, single/unmarried, older, had higher levels of education and income and more advanced HIV progression. Three common reasons for more present-biased choices provided were: (1) wanting to avoid pain, (2) wanting to return to work, and (3) fear of one's health worsening if s/he did not address their illness immediately. While PB in the financial domain often suggests that poorer individuals are more likely to prefer immediate rewards over their wealthier counterparts, our results suggest poor health is potentially a driving factor of PB. Further research is needed to build on these finding and inform how programs can frame key messages regarding ART adherence to patients displaying PB.Trial registration: ClinicalTrials.gov identifier: NCT03494777.

OPTICAL COHERENCE TOMOGRAPHY AND OCT ANGIOGRAPHY CHARACTERISTICS OF INDOCYANINE GREEN ANGIOGRAPHIC PLAQUES IN NONEXUDATIVE AGE-RELATED MACULAR DEGENERATION.

PURPOSE: To describe characteristics of indocyanine green (ICG) angiographic plaques in the nonexudative fellow eye of White patients with unilateral treatment-naïve exudative neovascular age-related macular degeneration through optical coherence tomography (OCT) and OCT angiography (OCTA). METHODS: In this retrospective cross-sectional study, nonexudative eyes with ICG angiographic plaques were analyzed by OCT B-scans for the sensitivity of a double-layer sign, a pigment epithelium detachment, outer retinal atrophy, hyperreflective dots, and subretinal hyperreflective material (SRHM). The ICG angiographic plaque was matched with a macular neovascularization in OCTA en face scans and color-coded B scans. RESULTS: In total, 35 ICG angiographic plaques in 33 of 291 (11%) nonexudative eyes were diagnosed. OCT revealed 27 double-layer sign (78%), eight pigment epithelium detachment (23%), 8 outer retinal atrophy (23%), eight hyperreflective dots (23%), and one subretinal hyperreflective material (3%). OCTA confirmed a macular neovascularization in 28 plaques (80%): 7 (20%) in en face scans, 3 (9%) in color-coded B scans, and 18 (51%) in both. The area size in OCTA was significantly smaller than that of ICG angiography ( P = 0.002). CONCLUSION: The diagnosis of an ICG angiographic plaque in nonexudative fellow eyes of Whites with unilateral treatment-naïve exudative neovascular age-related macular degeneration was highly suggestive of a typical macular neovascularization type 1 as characterized by OCT and OCTA.

Exploring differences in perceptions of gentrification, neighborhood satisfaction, social cohesion, and health among residents of two predominantly African American Pittsburgh neighborhoods (n = 60).

BACKGROUND: Gentrification often leads to changes in the social and physical environment of neighborhoods, which social capital theory has found are connected to aspects of resident health and wellbeing. A growing body of literature has explored the impact of gentrification on health and wellbeing of residents. The goal of this study is to qualitatively explore the ways in which gentrification may have impacted perceptions of neighborhood satisfaction, social cohesion, and health of neighborhood residents (n = 60) from two predominantly Black neighborhoods in Pittsburgh, Pennsylvania, one of which experienced Black gentrification during the study's time period. This analysis is unique in its ability to capture experiences of residents who remained in their neighborhood throughout the course of the study, as well as those who moved away from their neighborhood. METHODS: Participants were randomly selected from a larger cohort enrolled in a quasi-experimental study and categorized by whether they lived in a census tract that gentrified, whether they owned or rented their home, and whether they moved from the neighborhood or remained in the same place of residence between 2011 and 2018. Phone interviews lasting approximately 30 min were conducted with participants and were audio recorded and transcribed verbatim. Participants were provided a $40 gift card for their time. Interview data were analyzed using a directed content approach, and Cohen's Kappa was obtained (k = 0.924) to signal good inter-rater reliability. RESULTS: Results showed renters in gentrified census tracts overwhelmingly viewed gentrification trends as a negative change compared to homeowners. Overall, participants from gentrified census tracts reported being relatively satisfied with their neighborhood, though some suggested there were fewer resources in the neighborhood over time; felt their social cohesion had deteriorated over time; and more commonly reflected negative health changes over time. CONCLUSIONS: These findings suggest that while gentrification can bring much needed improvements to neighborhoods, it can also bring other disruptive changes that affect the health and wellbeing of existing residents.

Impact of adaptive filtering on power and false discovery rate in RNA-seq experiments.

BACKGROUND: In RNA-sequencing studies a large number of hypothesis tests are performed to compare the differential expression of genes between several conditions. Filtering has been proposed to remove candidate genes with a low expression level which may not be relevant and have little or no chance of showing a difference between conditions. This step may reduce the multiple testing burden and increase power. RESULTS: We show in a simulation study that filtering can lead to some increase in power for RNA-sequencing data, too aggressive filtering, however, can lead to a decline. No uniformly optimal filter in terms of power exists. Depending on the scenario different filters may be optimal. We propose an adaptive filtering strategy which selects one of several filters to maximise the number of rejections. No additional adjustment for multiplicity has to be included, but a rule has to be considered if the number of rejections is too small. CONCLUSIONS: For a large range of simulation scenarios, the adaptive filter maximises the power while the simulated False Discovery Rate is bounded by the pre-defined significance level. Using the adaptive filter, it is not necessary to pre-specify a single individual filtering method optimised for a specific scenario.

Mechanical aortic valve prostheses offer a survival benefit in 50-65 year olds: AUTHEARTVISIT study.

BACKGROUND: The present population-based cohort study investigated long-term mortality after surgical aortic valve replacement (AVR) with bioprosthetic (B) or mechanical aortic valve prostheses (M) in a European social welfare state. METHODS: We analysed patient data from health insurance records covering 98% of the Austrian population between 2010 and 2018. Subsequent patient-level record linkage with national health data provided patient characteristics and clinical outcomes. Further reoperation, myocardial infarction, heart failure and stroke were evaluated as secondary outcomes. RESULTS: A total of 13,993 patients were analysed and the following age groups were examined separately: <50 years (727 patients: 57.77% M, 42.23% B), 50-65 years (2612 patients: 26.88% M, 73.12% B) and >65 years (10,654 patients: 1.26% M, 98.74% B). Multivariable Cox regression revealed that the use of B-AVR was significantly associated with higher mortality in patients aged 50-65 years compared to M-AVR (HR = 1.676 [1.289-2.181], p < 0.001). B-AVR also performed worse in a competing risk analysis regarding reoperation (HR = 3.483 [1.445-8.396], p = 0.005) and myocardial infarction (HR = 2.868 [1.255-6.555], p = 0.012). However, the risk of developing heart failure and stroke did not differ significantly after AVR in any age group. CONCLUSIONS: Patients aged 50-65 years who underwent M-AVR had better long-term survival, and a lower risk of reoperation and myocardial infarction. Even though anticoagulation is crucial in patients with M-AVR, we did not observe significantly increased stroke rates in patients with M-AVR. This evident survival benefit in recipients of mechanical aortic valve prostheses aged <65 years critically questions current guideline recommendations.

Implementation of South Africa's Central Chronic Medicine Dispensing and Distribution Program for HIV Treatment: A Qualitative Evaluation.

We used the Practical, Robust Implementation and Sustainability Model to evaluate implementation of South Africa's Central Chronic Medicine Dispensing and Distribution (CCMDD) program, a differentiated service delivery program which allows clinically stable HIV-positive patients to receive antiretroviral therapy refills at clinic- or community-based pick-up points. Across ten clinics, we conducted 109 semi-structured interviews with stakeholders (pick-up point staff, CCMDD service providers and administrators) and 16 focus groups with 138 patients. Participants had highly favorable attitudes and said CCMDD decreased stigma concerns. Patient-level barriers included inadequate education about CCMDD and inability to get refills on designated dates. Organizational-level barriers included challenges with communication and transportation, errors in medication packaging and tracking, rigid CCMDD rules, and inadequate infrastructure. Recommendations included: (1) provide patient education and improve communication around refills (at the patient level); (2) provide dedicated space and staff, and ongoing training (at the organizational/clinic level); and (3) allow for prescription renewal at pick-up points and less frequent refills, and provide feedback to clinics (at the CCMDD program level).

Is the Deep Endometriosis or the Surgery the Cause of Postoperative Bladder Dysfunction?

STUDY OBJECTIVE: To assess whether deep endometriosis surgery affects the bladder function. DESIGN: Prospective multicenter observational study (Canadian Task Force classification II-2). SETTING: Academic research centers. PATIENTS: Thirty-two patients with diagnosis of deep endometriosis requiring surgery. INTERVENTIONS: Women were evaluated with urodynamic studies, International Consultation on Incontinence Questionnaire - Urinary Incontinence Short Form, and International Consultation on Incontinence Questionnaire Overactive Bladder Module questionnaires before and 3 months after surgery. MEASUREMENTS AND MAIN RESULTS: The main outcome measure was the impact of deep endometriosis surgery on urodynamic parameters. All cystomanometric parameters showed an improvement postoperatively: in particular, the first desire to void (120 vs 204 mL; p <.001) and the bladder capacity (358 vs 409 mL; p = .011) increased significantly after surgery. Of the uroflow parameters, the maximal voiding flow improved significantly postoperatively (19 vs 25 mL/s; p = .026). The International Consultation on Incontinence Questionnaire - Urinary Incontinence Short Form (2.5 vs 0; p = .0005) and International Consultation on Incontinence Questionnaire Overactive Bladder Module (4.3 vs 1.2; p <.001) questionnaires showed a significant postoperative improvement too. CONCLUSION: Our data show that in a selected population of patients with deep infiltrating endometriosis (not requiring bowel or ureteral resection), the bladder function improves after surgery, both during filling and on voiding urodynamic phases. Postoperatively, patients with deep infiltrating endometriosis become aware of bladder filling later, have a higher bladder capacity, and have a higher maximal flow. The postoperative urodynamic results are corroborated by the improved scores on the bladder questionnaires.

A Comprehensive Evaluation of the Performance of Prediction Algorithms on Clinically Relevant Missense Variants.

The rapid integration of genomic technologies in clinical diagnostics has resulted in the detection of a multitude of missense variants whose clinical significance is often unknown. As a result, a plethora of computational tools have been developed to facilitate variant interpretation. However, choosing an appropriate software from such a broad range of tools can be challenging; therefore, systematic benchmarking with high-quality, independent datasets is critical. Using three independent benchmarking datasets compiled from the ClinVar database, we evaluated the performance of ten widely used prediction algorithms with missense variants from 21 clinically relevant genes, including BRCA1 and BRCA2. A fourth dataset consisting of 1053 missense variants was also used to investigate the impact of type 1 circularity on their performance. The performance of the prediction algorithms varied widely across datasets. Based on Matthews Correlation Coefficient and Area Under the Curve, SNPs&GO and PMut consistently displayed an overall above-average performance across the datasets. Most of the tools demonstrated greater sensitivity and negative predictive values at the expense of lower specificity and positive predictive values. We also demonstrated that type 1 circularity significantly impacts the performance of these tools and, if not accounted for, may confound the selection of the best performing algorithms.

Immune checkpoints and liver resection after neoadjuvant chemotherapy including bevacizumab in patients with microsatellite-stable colorectal liver metastases.

BACKGROUND: The clinical value of immune checkpoint expression as prognostic biomarker in bevacizumab-pretreated patients with resected microsatellite-stable (MMS) colorectal liver metastases is unclear and was retrospectively investigated in this study. METHODS: Expression analyses of IDO-1, PD-L1, and CTLA-4 were performed by immunohistochemistry in resected bevacizumab-pretreated colorectal liver metastases. Association of immune checkpoint expression in tumor cells and immune cells with response and clinical outcome was investigated. Expression profiles were compared with those of patients with anti-EGFR-targeted therapy and lung metastases, respectively. RESULTS: One hundred thirty-six patients with MMS disease were investigated (79 (58.1%) male/57 (41.9%) female, median age 62.9 years (range 31.0-80.4)). High expression of IDO-1 in immune cells was associated with longer OS (not reached versus 44.8 months, HR 0.23 (95% CI 0.09, 0.55), P = 0.001). Low expression of CTLA-4 in tumor cells was associated with better histological response (26 major, 19 partial, 18 none versus 14 major, 23 partial, 30 none, P = 0.032). Expression profiles differed compared to patients with anti-EGFR-targeted therapy and patients with lung metastases. CONCLUSION: Immune checkpoint expression was associated with response and survival. IDO-1 may serve as a novel prognostic and/or predictive biomarker in patients with MMS colorectal liver metastases.

Tamock: simulation of habitat-specific benchmark data in metagenomics.

BACKGROUND: Simulated metagenomic reads are widely used to benchmark software and workflows for metagenome interpretation. The results of metagenomic benchmarks depend on the assumptions about their underlying ecosystems. Conclusions from benchmark studies are therefore limited to the ecosystems they mimic. Ideally, simulations are therefore based on genomes, which resemble particular metagenomic communities realistically. RESULTS: We developed Tamock to facilitate the realistic simulation of metagenomic reads according to a metagenomic community, based on real sequence data. Benchmarks samples can be created from all genomes and taxonomic domains present in NCBI RefSeq. Tamock automatically determines taxonomic profiles from shotgun sequence data, selects reference genomes accordingly and uses them to simulate metagenomic reads. We present an example use case for Tamock by assessing assembly and binning method performance for selected microbiomes. CONCLUSIONS: Tamock facilitates automated simulation of habitat-specific benchmark metagenomic data based on real sequence data and is implemented as a user-friendly command-line application, providing extensive additional information along with the simulated benchmark data. Resulting benchmarks enable an assessment of computational methods, workflows, and parameters specifically for a metagenomic habitat or ecosystem of a metagenomic study. AVAILABILITY: Source code, documentation and install instructions are freely available at GitHub ( https://github.com/gerners/tamock ).

Food Insecurity in a Low-Income, Predominantly African American Cohort Following the COVID-19 Pandemic.

Objectives. To examine the impact of COVID-19 shutdowns on food insecurity among a predominantly African American cohort residing in low-income racially isolated neighborhoods.Methods. Residents of 2 low-income African American food desert neighborhoods in Pittsburgh, Pennsylvania, were surveyed from March 23 to May 22, 2020, drawing on a longitudinal cohort (n = 605) previously followed from 2011 to 2018. We examined longitudinal trends in food insecurity from 2011 to 2020 and compared them with national trends. We also assessed use of food assistance in our sample in 2018 versus 2020.Results. From 2018 to 2020, food insecurity increased from 20.7% to 36.9% (t = 7.63; P < .001) after steady declines since 2011. As a result of COVID-19, the United States has experienced a 60% increase in food insecurity, whereas this sample showed a nearly 80% increase, widening a preexisting disparity. Participation in the Supplemental Nutrition Assistance Program (52.2%) and food bank use (35.9%) did not change significantly during the early weeks of the pandemic.Conclusions. Longitudinal data highlight profound inequities that have been exacerbated by COVID-19. Existing policies appear inadequate to address the widening gap.

Lessons from low seroprevalence of SARS-CoV-2 antibodies in schoolchildren: A cross-sectional study.

BACKGROUND: Children are discussed as hidden SARS-CoV-2 virus reservoir because of predominantly mild or even asymptomatic course of disease. The objective of this cross-sectional study in May-July 2020 was to assess the prevalence of SARS-CoV-2 antibodies and virus RNA in schoolchildren, consistent with previous infection by contact tracing. METHODS: School authorities approached parents for voluntary participation. Interested families were contacted by the study team. A nasal and oropharyngeal swab, a blood sample, and a questionnaire were employed. Primary endpoint was the frequency of SARS-CoV-2 real-time PCR (RT-PCR) and antibody-positive children. Antibody positivity was assessed by a highly sensitive first-line ELISA, and a neutralization assay and two other immunoassays as confirmatory assays. RESULTS: Of 2069 children (median age 13 years, IQR 10-15), 2 cases (0.1%) tested positive for SARS-CoV-2 RNA and 26 cases (1.3%) tested positive for specific antibodies. SARS-CoV-2-specific antibodies exhibited detectable virus-neutralizing activity in 92% (24 of 26 samples). Seropositivity was associated with a history of mild clinical symptoms in 14 children (53.8%), while 12 children (46.2%) remained asymptomatic. Among 13 seropositive children being tested concomitantly with their siblings, only one pair of siblings was seropositive. Contact tracing revealed adult family members and school teachers as potential index cases. CONCLUSION: In schoolchildren, the infection rate with SARS-CoV-2 is low and associated with a mild or asymptomatic course of disease. Virus spreading seemed to occur more likely in intergenerational contacts than among siblings in the same household. The presence of neutralizing SARS-CoV-2 antibodies in children may reflect protective adaptive immunity.

The acceptability and feasibility of a pilot study examining the impact of a mobile technology-based intervention informed by behavioral economics to improve HIV knowledge and testing frequency among Latinx sexual minority men and transgender women.

BACKGROUND: We developed a novel intervention that uses behavioral economics incentives and mobile-health text messages to increase HIV knowledge and testing frequency among Latinx sexual minority men and Latinx transgender women. Here we provide a theoretically-grounded assessment regarding the intervention's acceptability and feasibility. METHODS: We conducted 30-min exit interviews with a stratified sample of participants (n = 26 Latinx sexual minority men, 15 Latinx transgender women), supplemented with insights from study staff (n = 6). All interviews were recorded, transcribed, and translated for a content analysis using Dedoose. Cohen's Kappa was 89.4% across coded excerpts. We evaluated acceptability based on how participants cognitively and emotionally reacted to the intervention and whether they considered it to be appropriate. We measured feasibility based on resource, scientific and process assessments (e.g., functionality of text messaging service, feedback on study recruitment procedures and surveys). RESULTS: Regarding acceptability, most participants clearly understood the intervention as a program to receive information about HIV prevention methods through text messages. Participants who did not complete the intervention shared they did not fully understand what it entailed at their initial enrollment, and thought it was a one-time engagement and not an ongoing program. Though some participants with a higher level of education felt the information was simplistic, most appreciated moving beyond a narrow focus on HIV to include general information on sexually transmitted infections; drug use and impaired sexual decision-making; and differential risks associated with sexual positions and practices. Latinx transgender women in particular appreciated receiving information about Pre-Exposure Prophylaxis. While participants didn't fully understand the exact chances of winning a prize in the quiz component, most enjoyed the quizzes and chance of winning a prize. Participants appreciated that the intervention required a minimal time investment. Participants shared that the intervention was generally culturally appropriate. Regarding feasibility, most participants reported the text message platform worked well though inactive participants consistently said technical difficulties led to their disengagement. Staff shared that clients had varying reactions to being approached while being tested for HIV, with some unwilling to enroll and others being very open and curious about the program. Both staff and participants relayed concerns regarding the length of the recruitment process and study surveys. CONCLUSIONS: Our theoretically-grounded assessment shows the intervention is both acceptable and feasible. TRIAL REGISTRATION: The trial was registered on May 5, 2017 with the ClinicalTrials.gov registry [ NCT03144336 ].

The effect of oral Δ-9-tetrahydrocannabinol on the minimal alveolar concentration of sevoflurane: A randomised, controlled, observer-blinded experimental study.

BACKGROUND: Cannabis has increasingly been used for medical and recreational purposes. The main pharmacological compound in cannabis is tetrahydrocannabinol (THC), which has sedative, anxiolytic and analgesic effects. In some animal models, THC has also been shown to reduce the minimum alveolar concentration (MAC) of halothane and cyclopropane, but its effect on sevoflurane, currently the most commonly used inhalational anaesthetic agent, has not been investigated. OBJECTIVE: To investigate the effect of THC on the MAC of sevoflurane in rats. METHODS: Observer-blinded, randomised controlled trial. SETTING: Centre for Biomedical Research of the Medical University of Vienna, 2019. INDIVIDUALS: Thirty-eight adult Wistar rats. INTERVENTIONS: The rats were allocated randomly into one of two groups. Group A received THC 10 mg kg and group B received the corresponding volume of placebo via gastric gavage (administration through a tube placed in the distal oesophagus). The rats were then individually anaesthetised in an airtight sevoflurane-flooded chamber, and the MAC in both groups was determined using Dixon's up-and-down method. Blood samples were drawn to measure serum concentrations of THC. MAIN OUTCOME MEASURES: The primary outcome was the MAC of sevoflurane in Groups A and B. RESULTS: The bootstrap estimate of the MAC of sevoflurane was 2.1 (95% confidence interval 1.8 to 2.4) vol% in the THC group and 2.8 (95% confidence interval 2.7 to 2.9) vol% in the placebo group, corresponding to a significant MAC reduction of 26% in response to THC. CONCLUSION: Gastric administration of THC 10 mg kg significantly reduced the MAC of sevoflurane by 26%. TRIAL REGISTRATION: Not applicable.

Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family.

Many yeasts differentiate into multicellular phenotypes in adverse environmental conditions. Here, we investigate pseudohyphal growth in Komagataella phaffii and the involvement of the flocculin (FLO) gene family in its regulation. The K. phaffii FLO family consists of 13 members, and the conditions inducing pseudohyphal growth are different from Saccharomyces cerevisiae. So far, this phenotype was only observed when K. phaffii was cultivated at slow growth rates in glucose-limited chemostats, but not upon nitrogen starvation or the presence of fusel alcohols. Transcriptional analysis identified that FLO11, FLO400 and FLO5-1 are involved in the phenotype, all being controlled by the transcriptional regulator Flo8. The three genes exhibit a complex mechanism of expression and repression during transition from yeast to pseudohyphal form. Unlike in S. cerevisiae, deletion of FLO11 does not completely prevent the phenotype. In contrast, deletion of FLO400 or FLO5-1 prevents pseudohyphae formation, and hampers FLO11 expression. FAIRE-Seq data shows that the expression and repression of FLO400 and FLO5-1 are correlated to open or closed chromatin regions upstream of these genes, respectively. Our findings indicate that K. phaffii Flo400 and/or Flo5-1 act as upstream signals that lead to the induction of FLO11 upon glucose limitation in chemostats at slow growth and chromatin modulation is involved in the regulation of their expression.

A subcellular proteome atlas of the yeast Komagataella phaffii.

The compartmentalization of metabolic and regulatory pathways is a common pattern of living organisms. Eukaryotic cells are subdivided into several organelles enclosed by lipid membranes. Organelle proteomes define their functions. Yeasts, as simple eukaryotic single cell organisms, are valuable models for higher eukaryotes and frequently used for biotechnological applications. While the subcellular distribution of proteins is well studied in Saccharomyces cerevisiae, this is not the case for other yeasts like Komagataella phaffii (syn. Pichia pastoris). Different to most well-studied yeasts, K. phaffii can grow on methanol, which provides specific features for production of heterologous proteins and as a model for peroxisome biology. We isolated microsomes, very early Golgi, early Golgi, plasma membrane, vacuole, cytosol, peroxisomes and mitochondria of K. phaffii from glucose- and methanol-grown cultures, quantified their proteomes by liquid chromatography-electrospray ionization-mass spectrometry of either unlabeled or tandem mass tag-labeled samples. Classification of the proteins by their relative enrichment, allowed the separation of enriched proteins from potential contaminants in all cellular compartments except the peroxisomes. We discuss differences to S. cerevisiae, outline organelle specific findings and the major metabolic pathways and provide an interactive map of the subcellular localization of proteins in K. phaffii.

Lessons learned from a mobile technology-based intervention informed by behavioral economics to improve ART adherence among youth in Uganda.

Evidence suggests that simple text messaging interventions may not suffice to improve ART adherence among youth in low-resource settings. To address this shortcoming, we developed an intervention that shared weekly real-time adherence feedback to youth in Uganda using short message services (SMS), based on information tracked by an electronic device (Wisepill). We present results from 7 formative and 6 exit focus groups (FGs) in Mulago and Entebbe, Uganda with youth ages 15-24, providers, and Community Advisory Board members. Participants consistently conveyed positive impressions of Wisepill, noting that it helped store their medications, facilitated travel, served as a reminder, and motivated adherence. Participants raised phone-related issues before the study; most were addressed but some remained (e.g., limited network access, electricity for powering phones). Further, they highlighted the importance of carefully crafting text messages (e.g., use slang rather than potentially stigmatizing words) and viewed personalizing messages favorably but were divided on the desirability of including their name in study-related texts. Exit FGs confirmed that sharing group adherence levels with participants tapped into the competitive spirit common among youth. Our results suggest future mobile technology-based interventions can be improved by providing messages that go beyond simple reminders to provide individual and group-level adherence feedback.

A randomized controlled trial study of the acceptability, feasibility, and preliminary impact of SITA (SMS as an Incentive To Adhere): a mobile technology-based intervention informed by behavioral economics to improve ART adherence among youth in Uganda.

BACKGROUND: Studies report serious adherence problems among youth (individuals age 15-24 years of age) in Uganda. Recent growth in mobile phone ownership has highlighted the potential of using text-based interventions to improve antiretroviral treatment (ART) adherence among Ugandan youth. We piloted a randomized controlled trial of a text-based intervention providing weekly real-time antiretroviral adherence feedback, based on information from a smart pill box, to HIV-positive Ugandan youth. In this paper, we report the acceptability, feasibility, and preliminary impact of the intervention. METHODS: We randomized participants to a control group, or to receive messages with information on either their own adherence levels (Treatment 1 - T1), or their own adherence and peer adherence levels (Treatment 2 - T2). We conducted six focus groups from December 2016 to March 2017 with providers and youth ages 15-24, double coded 130 excerpts, and achieved a pooled Cohen's Kappa of 0.79 and 0.80 based on 34 randomly selected excerpts. RESULTS: The quantitative and qualitative data show that the intervention was deemed acceptable and feasible. After controlling for baseline adherence, the T1 group had 3.8 percentage point lower adherence than the control group (95% CI -9.9, 2.3) and the T2 group had 2.4 percentage points higher adherence than the control group (95% CI -3.0, 7.9). However, there was an increasing treatment effect over time for the T2 group with the largest effect towards the end of the study; a 2.5 percentage point increase in the initial 9-weeks that grows steadily to 9.0 percentage points by the last 9-weeks of the study. We find negative treatment effects for T1 in 3 of the 4 9-week intervals. This pilot study was not designed to detect statistically significant differences. CONCLUSIONS: Improving youth's adherence by supplementing information about their adherence with information about the adherence of peers is a promising new strategy that should be further evaluated in a fully-powered study. Providing one's own adherence information alone appears to have less potential. TRIAL REGISTRATION: NCT02514356 07/30/2015.