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Background Infectious disease forecasting aims to predict characteristics of both seasonal epidemics and future pandemics. Accurate and timely infectious disease forecasts could aid public health responses by informing key preparation and mitigation efforts. Main body For forecasts to be fully integrated into public health decision-making, federal, state, and local officials must understand how forecasts were made, how to interpret forecasts, and how well the forecasts have performed in the past. Since the 2013–14 influenza season, the Influenza Division at the Centers for Disease Control and Prevention (CDC) has hosted collaborative challenges to forecast the timing, intensity, and short-term trajectory of influenza-like illness in the United States. Additional efforts to advance forecasting science have included influenza initiatives focused on state-level and hospitalization forecasts, as well as other infectious diseases. Using CDC influenza forecasting challenges as an example, this paper provides an overview of infectious disease forecasting; applications of forecasting to public health; and current work to develop best practices for forecast methodology, applications, and communication. Conclusions These efforts, along with other infectious disease forecasting initiatives, can foster the continued advancement of forecasting science.

Objective: Despite large-scale efforts and expensive public education campaigns mounted by the government at all levels in the past decade, the improvements in disaster preparedness among the US Gulf Coast residents have been ineffectual at best. Some factors that contribute to better preparedness are past experience, awareness of what to do in a disaster scenario and availability, and access to informational and supportive resources. We examine whether an experience of a natural disaster brings about changes in preparedness and access to resources. Design: Our study is based on data from 2 cross-sectional random-digit-dialing surveys in 2008 (pre-Ike) and 2009 (post-Ike) with sample sizes of 1001 and 1009, respectively. Participants: Adults living in one of the 85 zip codes in Houston, Texas. Main Outcome Measure: Self-reported preparedness, evacuation plan, available resources (informational, financial and emotional). Results: We found no significant changes in preparedness or evacuation plans in residents of Houston prior to and a year after Hurricane Ike. Hispanics and other minority groups reported a significant increase in access to information and all residents reported an increase in perception of availability of financial support, if needed. Perceived availability of tangible (financial) support has been linked to positive physical and mental health effects and can contribute to resiliency and quicker recovery. The unchanged preparedness levels could be attributed to ceiling effects, that is, the already high levels of preparedness reported by Houston residents. Greater access to information reported by Hispanics and other minorities is encouraging and indicative of success in reaching out. Conclusions: Our results also indicate a greater need for appropriate targeted strategies to reach out to African Americans in Houston since this group reported poorer access to information. This has implications for planning and preparedness officials and the communication strategies used to reach the community.

In 2015, Harris County (Texas) Public Health responded to the Zika virus (ZIKV) threat by investigating every report of potential ZIKV infection, including those with negative laboratory results, through December 2017. Before investigations, 40.6% of patients who were indicated for testing received it in accordance with Centers for Disease Control and Prevention guidelines. By investigating reports with negative ZIKV results, we increased the number of patients receiving correct and complete laboratory testing to 54.5%, and improved dissemination of evolving guidelines to partners across the health care spectrum.

When Hurricane Harvey landed along the Texas coast on August 25, 2017, it caused massive flooding and damage and displaced tens of thousands of residents of Harris County, Texas. Between August 29 and September 23, Harris County, along with community partners, operated a megashelter at NRG Center, which housed 3365 residents at its peak. Harris County Public Health conducted comprehensive public health surveillance and response at NRG, which comprised disease identification through daily medical record reviews, nightly “cot-to-cot” resident health surveys, and epidemiological consultations; messaging and communications; and implementation of control measures including stringent isolation and hygiene practices, vaccinations, and treatment. Despite the lengthy operation at the densely populated shelter, an early seasonal influenza A (H3) outbreak of 20 cases was quickly identified and confined. Influenza outbreaks in large evacuation shelters after a disaster pose a significant threat to populations already experiencing severe stressors. A holistic surveillance and response model, which consists of coordinated partnerships with onsite agencies, in-time epidemiological consultations, predesigned survey tools, trained staff, enhanced isolation and hygiene practices, and sufficient vaccines, is essential for effective disease identification and control. The lessons learned and successes achieved from this outbreak may serve for future disaster response settings. (Disaster Med Public Health Preparedness. 2019;13:97-101)

Histone acetylation is a ubiquitous hallmark of transcription, but whether the link between histone acetylation and transcription is causal or consequential has not been addressed. Using immunoblot and chromatin immunoprecipitation-sequencing in S. cerevisiae , here we show that the majority of histone acetylation is dependent on transcription. This dependency is partially explained by the requirement of RNA polymerase II (RNAPII) for the interaction of H4 histone acetyltransferases (HATs) with gene bodies. Our data also confirms the targeting of HATs by transcription activators, but interestingly, promoter-bound HATs are unable to acetylate histones in the absence of transcription. Indeed, HAT occupancy alone poorly predicts histone acetylation genome-wide, suggesting that HAT activity is regulated post-recruitment. Consistent with this, we show that histone acetylation increases at nucleosomes predicted to stall RNAPII, supporting the hypothesis that this modification is dependent on nucleosome disruption during transcription. Collectively, these data show that histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases. Histone acetylation is a ubiquitous hallmark of transcription. Here the authors provide evidence that the majority of histone acetylation is dependent on transcription, specifically due to the requirement of RNAPII for the recruitment and activity of histone acetyltransferases.

Spatial transcriptomics has gained popularity over the past decade due to its ability to evaluate transcriptome data while preserving spatial information. Cell segmentation is a crucial step in spatial transcriptomic analysis, as it enables the avoidance of unpredictable tissue disentanglement steps. Although high-quality cell segmentation algorithms can aid in the extraction of valuable data, traditional methods are frequently non-spatial, do not account for spatial information efficiently, and perform poorly when confronted with the problem of spatial transcriptome cell segmentation with varying shapes. In this study, we propose ST-CellSeg, an image-based machine learning method for spatial transcriptomics that uses manifold for cell segmentation and is novel in its consideration of multi-scale information. We first construct a fully connected graph which acts as a spatial transcriptomic manifold. Using multi-scale data, we then determine the low-dimensional spatial probability distribution representation for cell segmentation. Using the adjusted Rand index (ARI), normalized mutual information (NMI), and Silhouette coefficient (SC) as model performance measures, the proposed algorithm significantly outperforms baseline models in selected datasets and is efficient in computational complexity.

Background: Treatment of wheat with the phytohormones abscisic acid (ABA) and gibberellic acid (GA) has been shown to affect Fusarium head blight (FHB) disease severity. However, the molecular mechanisms underlying the elicited phenotypes remain unclear. Toward addressing this gap in our knowledge, global transcriptomic profiling was applied to the FHB-susceptible wheat cultivar ‘Fielder’ to map the regulatory responses effected upon treatment with ABA, an ABA receptor antagonist (AS6), or GA in the presence or absence of Fusarium graminearum (Fg) challenge. Results: Spike treatments resulted in a total of 30,876 differentially expressed genes (DEGs) identified in ‘Fielder’ (26,004) and the Fg (4872) pathogen. Topology overlap and correlation analyses defined 9689 wheat DEGs as Fg-related across the treatments. Further enrichment analyses demonstrated that these included expression changes within ‘Fielder’ defense responses, cell structural metabolism, molecular transport, and membrane/lipid metabolism. Dysregulation of ABA and GA crosstalk arising from repression of ‘Fielder’ FUS3 was noted. As well, expression of a putative Fg ABA-biosynthetic cytochrome P450 was detected. The co-applied condition of Fg + ABA elicited further upregulation of phytohormone biosynthesis, as well as SA and ET signaling pathways and cell wall/polyphenolic metabolism. In contrast, co-applied Fg + GA mainly suppressed phytohormone biosynthesis and signaling, while modulating primary and secondary metabolism and flowering. Unexpectedly, co-applied Fg + AS6 did not affect ABA biosynthesis or signaling, but rather elicited antagonistic responses tied to stress, phytohormone transport, and FHB disease-related genes.

Presentation of the variant antigen, Plasmodium falciparum erythrocyte membrane protein 1 (EMP1), at knob-like protrusions on the surface of infected red blood cells, underpins the parasite’s pathogenicity. Here we describe a protein PF3D7_0301700 (PTP7), that functions at the nexus between the intermediate trafficking organelle, the Maurer’s cleft, and the infected red blood cell surface. Genetic disruption of PTP7 leads to accumulation of vesicles at the Maurer’s clefts, grossly aberrant knob morphology, and failure to deliver EMP1 to the red blood cell surface. We show that an expanded low complexity sequence in the C-terminal region of PTP7, identified only in the Laverania clade of Plasmodium , is critical for efficient virulence protein trafficking.

The sexual stage gametocytes of the malaria parasite, Plasmodium falciparum , adopt a falciform (crescent) shape driven by the assembly of a network of microtubules anchored to a cisternal inner membrane complex (IMC). Using 3D electron microscopy, we show that a non-mitotic microtubule organizing center (MTOC), embedded in the parasite’s nuclear membrane, orients the endoplasmic reticulum and the nascent IMC and seeds cytoplasmic microtubules. A bundle of microtubules extends into the nuclear lumen, elongating the nuclear envelope and capturing the chromatin. Classical mitotic machinery components, including centriolar plaque proteins, Pf centrin-1 and −4, microtubule-associated protein, End-binding protein-1, kinetochore protein, Pf NDC80 and centromere-associated protein, Pf CENH3, are involved in the nuclear microtubule assembly/disassembly process. Depolymerisation of the microtubules using trifluralin prevents elongation and disrupts the chromatin, centromere and kinetochore organisation. We show that the unusual non-mitotic hemispindle plays a central role in chromatin organisation, IMC positioning and subpellicular microtubule formation in gametocytes. The sexual blood stages of Plasmodium falciparum develop through five morphologically distinct stages culminating in mature crescent-shaped gametocytes that can be transmitted from the mammalian host to the mosquito vector. Here, Li et al. apply different microscopy and tomography approaches to characterize how the microtubule organizing center and cytoplasmic and nuclear microtubules are organized and oriented during these different stages in the absence of genome replication and mitosis.

Transmission of malaria parasites relies on the formation of a specialized blood form called the gametocyte. Gametocytes of the human pathogen, Plasmodium falciparum, adopt a crescent shape. Their dramatic morphogenesis is driven by the assembly of a network of microtubules and an underpinning inner membrane complex (IMC). Using super-resolution optical and electron microscopies we define the ultrastructure of the IMC at different stages of gametocyte development. We characterize two new proteins of the gametocyte IMC, called PhIL1 and PIP1. Genetic disruption of PhIL1 or PIP1 ablates elongation and prevents formation of transmission-ready mature gametocytes. The maturation defect is accompanied by failure to form an enveloping IMC and a marked swelling of the digestive vacuole, suggesting PhIL1 and PIP1 are required for correct membrane trafficking. Using immunoprecipitation and mass spectrometry we reveal that PhIL1 interacts with known and new components of the gametocyte IMC.