Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements

We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, $ \le$2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.

Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The E. coli RRS Elements

We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, ≤2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.

Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 1,4,[5],12:i:- ST34 in Southeast Asia

Salmonella enterica serotype 1,4,[5],12:i:- (Typhimurium monophasic variant) of sequence type (ST) 34 has emerged as the predominant pandemic genotype in recent decades. Despite increasing reports of resistance to antimicrobials in Southeast Asia, Salmonella ST34 population structure and evolution remained understudied in the region. Here we performed detailed genomic investigations on 454 ST34 genomes collected from Vietnam and diverse geographical sources to elucidate the pathogen's epidemiology, evolution and antimicrobial resistance. We showed that ST34 has been introduced into Vietnam in at least nine occasions since 2000, forming five co-circulating major clones responsible for paediatric diarrhoea and bloodstream infection. Most expansion events were associated with acquisitions of large multidrug resistance plasmids of IncHI2 or IncA/C2. Particularly, the self-conjugative IncA/C2 pST34VN2 (co-transferring blaCTX-M-55, mcr-3.1, and qnrS1) underlies local expansion and intercontinental spread in two separate ST34 clones. At the global scale, Southeast Asia was identified as a potential hub for the emergence and dissemination of multidrug resistant Salmonella ST34, and mutation analysis suggests of selection in antimicrobial responses and key virulence factors.

Understanding the barriers and facilitators of COVID-19 risk mitigation strategy adoption and COVID-19 vaccination in refugee settlements in Uganda: a qualitative study

BACKGROUND

Perspectives on COVID-19 risk and the willingness and ability of persons living in refugee settlements to adopt COVID-19 prevention strategies have not been rigorously evaluated. The realities of living conditions in Ugandan refugee settlements may limit the extent to which refugees can uptake strategies to mitigate COVID-19 risk.

METHODS

In-depth qualitative interviews were conducted between April 2021 and April 2022 to assess COVID-19 knowledge, risk perception, prevention strategy adoption including COVID-19 vaccination, and COVID-19 impact on living conditions in refugee settlements in Uganda. Interview participants included 28 purposively selected refugees who called into "Dial-COVID", a free telephone COVID-19 information collection and dissemination platform that was advertised in refugee settlements by community health workers. Interviews were analyzed using a combination of deductive and inductive content analysis. Emerging themes were mapped onto the Theoretical Domains Framework to identify domains influencing prevention behavior. Results were synthesized to provide intervention and policy recommendations for risk mitigation in refugee settlements for COVID-19 and future infectious disease outbreaks.

RESULTS

The COVID-19 pandemic detrimentally impacted economic and food security as well as social interactions in refugee settlements. Youth were considered especially impacted, and participants reported incidents of child marriage and teenage pregnancy following school closures. Participants displayed general knowledge of COVID-19 and expressed willingness to protect themselves and others from contracting COVID-19. Risk mitigation strategy uptake including COVID-19 vaccination was influenced by COVID-19 knowledge, emotions surrounding COVID-19, the environmental context and resources, personal goals, beliefs about the consequences of (non)adoption, social influences, and behavior reinforcement. Resource constraints, housing conditions, and competing survival needs challenged the adoption of prevention strategies and compliance decreased over time.

CONCLUSIONS

Contextual challenges impact the feasibility of COVID-19 risk mitigation strategy uptake in refugee settlements. Pre-existing hardships in this setting were amplified by the COVID-19 pandemic and related lockdowns. Targeted dispelling of myths, alignment of information across communication mediums, supporting survival needs and leveraging of respected role models are strategies that may hold potential to mitigate risk of infectious diseases in this setting.

REGISTRATION DETAILS

World Pandemic Research Network - 490,652.

RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli

Single-stranded DNA (ssDNA) gapped regions are common intermediates in DNA transactions. Using a new non-denaturing bisulfite treatment combined with ChIP-seq, abbreviated 'ssGap-seq', we explore RecA and SSB binding to ssDNA on a genomic scale in E. coli in a wide range of genetic backgrounds. Some results are expected. During log phase growth, RecA and SSB assembly profiles coincide globally, concentrated on the lagging strand and enhanced after UV irradiation. Unexpected results also abound. Near the terminus, RecA binding is favored over SSB, binding patterns change in the absence of RecG, and the absence of XerD results in massive RecA assembly. RecA may substitute for the absence of XerCD to resolve chromosome dimers. A RecA loading pathway may exist that is independent of RecBCD and RecFOR. Two prominent and focused peaks of RecA binding revealed a pair of 222 bp and GC-rich repeats, equidistant from dif and flanking the Ter domain. The repeats, here named RRS for replication risk sequence, trigger a genomically programmed generation of post-replication gaps that may play a special role in relieving topological stress during replication termination and chromosome segregation. As demonstrated here, ssGap-seq provides a new window on previously inaccessible aspects of ssDNA metabolism.

Fabrication of a Low-Cost Microfluidic Device for High-Throughput Drug Testing on Static and Dynamic Cancer Spheroid Culture Models

Drug development is a complex and expensive process from new drug discovery to product approval. Most drug screening and testing rely on in vitro 2D cell culture models; however, they generally lack in vivo tissue microarchitecture and physiological functionality. Therefore, many researchers have used engineering methods, such as microfluidic devices, to culture 3D cells in dynamic conditions. In this study, a simple and low-cost microfluidic device was fabricated using Poly Methyl Methacrylate (PMMA), a widely available material, and the total cost of the completed device was USD 17.75. Dynamic and static cell culture examinations were applied to monitor the growth of 3D cells. α-MG-loaded GA liposomes were used as the drug to test cell viability in 3D cancer spheroids. Two cell culture conditions (i.e., static and dynamic) were also used in drug testing to simulate the effect of flow on drug cytotoxicity. Results from all assays showed that with the velocity of 0.005 mL/min, cell viability was significantly impaired to nearly 30% after 72 h in a dynamic culture. This device is expected to improve in vitro testing models, reduce and eliminate unsuitable compounds, and select more accurate combinations for in vivo testing.

Leveraging interactive voice response technology to mitigate COVID-19 risk in refugee settlements in Uganda: Lessons learned implementing "Dial-COVID" a toll-free mobile phone symptom surveillance and information dissemination tool

BACKGROUND

Persons living in refugee settlements in sub-Saharan Africa may be at increased risk for COVID-19 and experience barriers to accessing COVID-19 information. We aimed to evaluate the implementation of "Dial-COVID" a multi-lingual, toll free, telephone platform that uses interactive voice response (IVR) to track COVID-19 symptoms/exposure and disseminate COVID-19 health information in refugee settlements in Uganda. We hypothesized that IVR could provide an alternative way to screen for COVID-19 and communicate public health information to humanitarian populations when physical access and testing capacity were limited.

METHODS

The Dial-COVID IVR platform was created in ten languages and advertised by community health workers in refugee settlements for participants to call into toll free. In a recorded IVR symptom survey, participants were screened for COVID-19 symptoms/exposures and based on their responses, received tailored public health messages about COVID-19 risk mitigation in accordance with Uganda Ministry of Health guidelines. Here we report the challenges and lessons learned implementing this research during the pandemic.

RESULTS

Between February 2021 and March 2022, 15,465 calls were received by the Dial-COVID platform from all 31 refugee settlements in Uganda through which 6,913 symptom surveys were completed and 10,411 public health messages were disseminated in all study languages. Uptake of Dial-COVID fluctuated with the national COVID-19 caseload and was impacted by phone ownership and connectivity in refugee settlements. Intensified advertising efforts promoted Dial-COVID uptake. Flexibility to adapt IVR messages was contingent on translation capacity.

CONCLUSION

Refugees living in refugee settlements across Uganda accessed Dial-COVID to share and obtain COVID-19 information suggesting that IVR holds potential for rapid information dissemination and screening of humanitarian populations during future infectious disease outbreaks and may be a valuable tool for routine public health programs. IVR adaptation flexibility and reach are influenced by language constraints and by contextual factors related to platform access.

REGISTRATION DETAILS

World Pandemic Research Network- 490652.

Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization

We describe a purified biochemical system to produce monoclonal antibodies (Abs) in vitro using activation-induced deoxycytidine deaminase (AID) and DNA polymerase η (Polη) to diversify immunoglobulin variable gene (IgV) libraries within a phage display format. AID and Polη function during B-cell affinity maturation by catalyzing somatic hypermutation (SHM) of immunoglobulin variable genes (IgV) to generate high-affinity Abs. The IgV mutational motif specificities observed in vivo are conserved in vitro. IgV mutations occurred in antibody complementary determining regions (CDRs) and less frequently in framework (FW) regions. A unique feature of our system is the use of AID and Polη to perform repetitive affinity maturation on libraries reconstructed from a preceding selection step. We have obtained scFv Abs against human glucagon-like peptide-1 receptor (GLP-1R), a target in the treatment of type 2 diabetes, and VHH nanobodies targeting Fatty Acid Amide Hydrolase (FAAH), involved in chronic pain, and artemin, a neurotropic factor that regulates cold pain. A round of in vitro affinity maturation typically resulted in a 2- to 4-fold enhancement in Ab-Ag binding, demonstrating the utility of the system. We tested one of the affinity matured nanobodies and found that it reduced injury-induced cold pain in a mouse model.

Maintaining health professional education during war: A scoping review

PURPOSE

War negatively impacts health professional education when health care is needed most. The aims of this scoping review are to describe the scope of barriers and targeted interventions to maintaining health professional education during war and summarise the research.

METHODS

We conducted a scoping review between 20 June 2018 and 2 August 2018. The search was restricted to English publications including peer-reviewed publications without date ranges involving war and health professional education (medical school, residency training and nursing school), with interventions described to maintain educational activities. Two independent reviewers completed inclusion determinations and data abstraction. Thematic coding was performed using an inductive approach allowing dominant themes to emerge. The frequency of barrier and intervention themes and illustrative quotes were extracted. Articles were divided into modern/postmodern categories to permit temporal and historical analysis of thematic differences.

RESULTS

Screening identified 3271 articles, with 56 studies meeting inclusion criteria. Publication dates ranged from 1914-2018 with 17 unique wars involving 17 countries. The studies concerned medical students (61.4%), residents (28.6%) and nursing students (10%). Half involved the modern era and half the postmodern era. Thematic coding identified five categories of barriers and targeted interventions in maintaining health professions education during war: curriculum, personnel, wellness, resources, and oversight, with most involving curriculum and personnel. The distribution of themes among various health professional trainees was similar. The frequency and specifics changed temporally reflecting innovations in medical education and war, with increased focus on oversight and personnel during the modern era and greater emphasis on wellness, curriculum, and resources during the postmodern era.

CONCLUSIONS

There are overarching categories of barriers and targeted interventions in maintaining health professional education during war which evolve over time. These may serve as a useful framework to strategically support future research and policy efforts.

Effect of Cationic Groups on the Selectivity of Ternary Antimicrobial Polymers

Antimicrobial polymers (AMPs) have emerged as a promising approach to combat multidrug-resistant pathogens. Developed from binary polymers, which contain cationic and hydrophobic groups, ternary polymers are enhanced by adding neutral hydrophilic monomers to improve their biocompatibility. Cationic groups have attracted significant attention owing to their pivotal role in AMPs. Although many studies have investigated the effect of cationic groups on antimicrobial activity of binary AMPs, there is a lack of comprehensive and systematic evaluation for ternary AMPs. Therefore, a library of 31 statistical amphiphilic ternary polymers containing different cationic groups, including primary amine, guanidine and sulfonium groups was prepared to investigate the impact of cationic groups on antimicrobial activity and biocompatibility. We show that the cationic balance appears to be a critical factor influencing polymers' antibacterial activity and selectivity. Our results reveal that the polymers that have the ratio of the cationic groups ranging between 50-60%, coupled with a cationic/hydrophobic ratio in the range of [1.4-2] and an appropriate neutral hydrophilic/hydrophobic balance, exhibited the highest selectivity toward mammalian cells. Furthermore, selectivity can be improved with suitable cationic moieties and good neutral hydrophilic candidates. In the present study, a lysine-mimicking monomer and PEG chain were the best choices for cationic and hydrophilic sources to develop the most selective AMPs, displaying an impressive selectivity for HC₅₀ and IC₅₀ greater than 83 and 21, respectively. This study elucidates a structure-property-performance relationship for ternary AMPs, which contributes to the development of AMPs capable of selectively targeting gram-negative pathogens. This article is protected by copyright. All rights reserved.

Evaluation of change in emergency care knowledge and skills among front-line healthcare providers in Ukraine with the Basic Emergency Care course: a pretest/post-test study

OBJECTIVE

Evaluate the change in participant emergency care knowledge and skill confidence after implementation of the WHO-International Committee of the Red Cross (ICRC) Basic Emergency Care (BEC) course.

DESIGN

Pretest/post-test quasi-experimental study.

SETTING

Mechnikov Hospital in Dnipro, Ukraine.

PARTICIPANTS

Seventy-nine participants engaged in the course, of whom 50 (63.3%) completed all assessment tools. The course was open to healthcare providers of any level who assess and treat emergency conditions as part of their practice. The most common participant profession was resident physician (24%), followed by health educator (18%) and prehospital provider (14%).

INTERVENTIONS

The 5-day WHO-ICRC BEC course.

PRIMARY AND SECONDARY OUTCOME MEASURES

Change in pre-course and post-course knowledge and skill confidence assessments. Open-ended written feedback was collected upon course completion and analysed for common themes.

RESULTS

Participant knowledge assessment scores improved from 19 (IQR 15-20) to 22 (IQR 19-23) on a 25-point scale (p<0.001). Participant skill confidence self-assessment scores improved from 2.5 (IQR 2.1-2.8) to 2.9 (IQR 2.5-3.3) on a 4-point scale (p<0.001). The most common positive feedback themes were high-quality teaching and useful skill sessions. The most common constructive feedback themes were translation challenges and request for additional skill session time.

CONCLUSIONS

This first implementation of the WHO-ICRC BEC course for front-line healthcare providers in Ukraine was successful and well received by participants. This is also the first report of a BEC implementation outside of Africa and suggests that the course is also effective in the European context, particularly in humanitarian crisis and conflict settings. Future research should evaluate long-term knowledge retention and the impact on patient outcomes. Further iterations should emphasise local language translation and consider expanding clinical skills sessions.

The mRNA tether model for activation-induced deaminase and its relevance for Ig somatic hypermutation and class switch recombination

Activation-induced deaminase (AID) only deaminates cytosine within single-stranded DNA. Transcription is known to increase AID deamination on duplex DNA substrates during transcription. Using a purified T7 RNA polymerase transcription system, we recently found that AID deamination of a duplex DNA substrate is reduced if RNase A is added during transcription. This finding prompted us to consider that the mRNA tail may contribute to AID action at the nearby transcribed strand (TS) or non-transcribed strand (NTS) of DNA, which are transiently single-stranded in the wake of RNA polymerase movement. Here, we used a purified system to test whether a single-stranded oligonucleotide (oligo) consisting of RNA in the 5' portion and DNA in the 3' portion (i.e., 5'RNA-DNA3', also termed an RNA-DNA fusion substrate) could be deaminated equally efficiently as the same sequence when it is entirely DNA. We found that AID acts on the RNA-DNA fusion substrate and the DNA-only substrate with similar efficiency. Based on this finding and our recent observation on the importance of the mRNA tail, we propose a model in which the proximity and length of the mRNA tail provide a critical site for AID loading to permit a high local collision frequency with the NTS and TS in the transient wake of the RNA polymerase. When the mRNA tail is not present, we know that AID action drops to levels equivalent to when there is no transcription at all. This mRNA tether model explains several local and global features of Ig somatic hypermutation and Ig class switch recombination, while integrating structural and functional features of AID.

Genomic landscape of single-stranded DNA gapped intermediates in Escherichia coli

Single-stranded (ss) gapped regions in bacterial genomes (gDNA) are formed on W- and C-strands during replication, repair, and recombination. Using non-denaturing bisulfite treatment to convert C to U on ssDNA, combined with deep sequencing, we have mapped gDNA gap locations, sizes, and distributions in Escherichia coli for cells grown in mid-log phase in the presence and absence of UV irradiation, and in stationary phase cells. The fraction of ssDNA on gDNA is similar for W- and C-strands, ∼1.3% for log phase cells, ∼4.8% for irradiated log phase cells, and ∼8.5% for stationary phase cells. After UV irradiation, gaps increased in numbers and average lengths. A monotonic reduction in ssDNA occurred symmetrically between the DNA replication origin of (OriC) and terminus (Ter) for log phase cells with and without UV, a hallmark feature of DNA replication. Stationary phase cells showed no OriC → Ter ssDNA gradient. We have identified a spatially diverse gapped DNA landscape containing thousands of highly enriched ‘hot’ ssDNA regions along with smaller numbers of ‘cold’ regions. This analysis can be used for a wide variety of conditions to map ssDNA gaps generated when DNA metabolic pathways have been altered, and to identify proteins bound in the gaps.

Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam

Extra-intestinal pathogenic Escherichia coli (ExPEC) ST1193, a globally emergent fluoroquinolone-resistant clone, has become an important cause of bloodstream infections (BSIs) associated with significant morbidity and mortality. Previous studies have reported the emergence of fluoroquinolone-resistant ExPEC ST1193 in Vietnam; however, limited data exist regarding the genetic structure, antimicrobial resistance (AMR) determinants and transmission dynamics of this pandemic clone. Here, we performed genomic and phylogenetic analyses of 46 ST1193 isolates obtained from BSIs and healthy individuals in Ho Chi Minh City, Vietnam, to investigate the pathogen population structure, molecular mechanisms of AMR and potential transmission patterns. We further examined the phylogenetic structure of ST1193 isolates in a global context. We found that the endemic E. coli ST1193 population was heterogeneous and highly dynamic, largely driven by multiple strain importations. Several well-supported phylogenetic clusters (C1-C6) were identified and associated with distinct bla _CTX-M variants, including bla _CTXM-27 (C1-C3, C5), bla _CTXM-55 (C4) and bla _CTXM-15 (C6). Most ST1193 isolates were multidrug-resistant and carried an extensive array of AMR genes. ST1193 isolates also exhibited the ability to acquire further resistance while circulating in Vietnam. There were phylogenetic links between ST1193 isolates from BSIs and healthy individuals, suggesting these organisms may both establish long-term colonization in the human intestinal tract and induce infections. Our study uncovers factors shaping the population structure and transmission dynamics of multidrug-resistant ST1193 in Vietnam, and highlights the urgent need for local One Health genomic surveillance to capture new emerging ExPEC clones and to better understand the origins and transmission patterns of these pathogens.

Fear, distress, and perceived risk shape stigma toward Ebola survivors: a prospective longitudinal study

Background

During the 2014–15 Ebola Virus Disease (EVD) epidemic, thousands of people in Sierra Leone were infected with the devastating virus and survived. Years after the epidemic was declared over, stigma toward EVD survivors and others affected by the virus is still a major concern, but little is known about the factors that influence stigma toward survivors. This study examines how key personal and ecological factors predicted EVD-related stigma at the height of the 2014–2015 epidemic in Sierra Leone, and the personal and ecological factors that shaped changes in stigma over time.

Methods

Using three waves of survey data from a representative sample in the Western Urban and Western Rural districts of Sierra Leone, this study examines factors associated with self-reported personal stigma toward Ebola survivors (11 items, α = 0.77) among 1008 adults (74.6% retention rate) from 63 census enumeration areas of the Western Rural and Western Urban districts of Sierra Leone. Participants were randomly sampled at the height of the EVD epidemic and followed up as the epidemic was waning and once the epidemic had been declared over by the WHO. Three-level mixed effects models were fit using Stata 16 SE to examine cross-sectional associations as well as predictors of longitudinal changes in stigma toward EVD survivors.

Results

At the height of the EVD epidemic, female sex, household wealth, post-traumatic stress, EVD-related fear and perceived infection risk are a few of the factors which predicted higher levels of stigma toward survivors. On average, stigma toward EVD survivors decreased significantly as the epidemic declined in Sierra Leone, but female sex, EVD fear, and risk perceptions predicted a slower rate of change.

Conclusion

This study identified key individual and psychosocial characteristics which may predict higher levels of stigma toward infectious disease survivors. Future studies should pursue a better understanding of how personal characteristics and perceptions, including psychosocial distress, fear, and perceived infection risk serve as pathways for stigma in communities affected by infectious disease.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-021-12146-0.

Leveraging Case Narratives to Enhance Patient Age Ascertainment from Adverse Event Reports

INTRODUCTION

Missing age presents a significant challenge when evaluating individual case safety reports (ICSRs) in the FDA Adverse Event Reporting System (FAERS). When age is missing in an ICSR's structured field, it may be in the report's free-text narrative.

OBJECTIVES

This study aimed to evaluate the performance and assess the potential impact of a rule-based natural language processing (NLP) tool that utilizes a text string search to identify patients' numerical age from unstructured narratives.

METHODS

Using FAERS ICSRs from 2002 to 2018, we evaluated the annual proportion of ICSRs with age missing in the structured field before and after NLP application. Reviewers manually identified patients' age from ICSR narratives (gold standard) from a random sample of 1500 ICSRs. The gold standard was compared to the NLP-identified age.

RESULTS

During the study period, the percentage of ICSRs missing age in the structured field increased from 21.9 to 43.8%. The NLP tool performed well among the random sample: sensitivity 98.5%, specificity 92.9%, positive predictive value (PPV) 94.9%, and F-measure 96.7%. It also performed well for the subset of ICSRs missing age in the structured field; when applied to these cases, NLP identified age for an additional one million ICSRs (10% of the total number of ICSRs from 2002 to 2018) and decreased the percentage of ICSRs missing age to 27% overall.

CONCLUSIONS

NLP has potential utility to extract patients' age from ICSR narratives. Use of this tool would enhance pharmacovigilance and research using FAERS data.

Factors influencing utilization and perception of health care: a qualitative study among traumatized Yazidi refugees in Germany

BACKGROUND

Ensuring adequate utilization of healthcare services for displaced populations is critical, yet there are well-documented treatment gaps. Yazidi women captured by the Islamic State (IS) were subjected to extreme trauma and violence. This study aims to understand perceptions of healthcare providers and utilization of these services among women who experienced extreme trauma.

METHODS

This is a qualitative study with voluntary participation offered to approximately 400 women resettled through the Special Quota Program. An empirical approach was used to collect data and a grounded theory approach was used for content analysis. Participants ranked their interactions with providers on a Likert scale. Posttraumatic stress disorder (PTSD) symptoms were assessed using the impact of event scale-revised questionnaire.

RESULTS

A total of 116 Yazidi women participated in this study. The women experienced an average of 6.8 months of captivity by IS and 93% met criteria for probable PTSD. Eighty-three percent of the women interacted with a physician; 80% found this interaction helpful. Sixty-nine percent interacted with psychologists; 61% found this interaction helpful. Six themes emerged: "reminders of trauma" and "hopelessness" in relation to the traumatic experience; "immediate relief" and "healing through pharmaceutical treatment" in relation to provider interventions, and "support" and "cultural differences" in relation to interactions with providers.

CONCLUSIONS

There exist major barriers to care for Yazidi women who experienced extreme trauma, particularly in regards to psychiatric care. Perceptions of healthcare providers and perceived effectiveness of therapy are critical factors that must be taken into consideration to improve healthcare utilization and outcomes.

Longitudinal Changes in Posttraumatic Stress Disorder After Resettlement Among Yazidi Female Refugees Exposed to Violence

IMPORTANCE

Posttraumatic stress disorder (PTSD) is highly prevalent among refugees surviving mass atrocities, especially among women. Longitudinal studies investigating factors associated with PTSD course are essential to enable adequate treatment yet widely lacking.

OBJECTIVE

To identify longitudinal changes in PTSD severity and posttraumatic coping among severely traumatized female refugees as well as risk and protective factors for PTSD course.

DESIGN, SETTING, AND PARTICIPANTS

This prospective cohort study took place in 14 German cities in the context of a humanitarian admission program that resettled 1000 especially vulnerable women and children from northern Iraq to Germany. Approximately 400 adult beneficiaries of the humanitarian admission program were eligible for the study. At baseline, a total of 116 of the 400 beneficiaries (29.0%) participated, with 96 (82.8%) of these women participating in the follow-up assessment. The study included a baseline assessment conducted 2 years after resettlement (September 1, 2017, to January 12, 2018) and a 1-year follow-up (August 29, 2018, to January 15, 2019).

EXPOSURES

Violence and/or captivity during the 2014 genocide in northern Iraq by the so-called Islamic State.

MAIN OUTCOMES AND MEASURES

Posttraumatic stress disorder severity and coping strategies were assessed in interpreter-aided interviews using the Impact of Event Scale-Revised.

RESULTS

A total of 116 women (mean [SD] age, 32.2 [8.2] years; 115 [99.1%] Yazidi; 1 [0.9%] Christian) participated at baseline. According to the Impact of Event Scale-Revised, a high PTSD severity was found (mean [SD] raw sum score, 60.88 [15.75] of 88, with higher scores indicating greater distress), with no significant change over time. Helpful coping strategies included prayer, belief in collective strength, and belief in personal strength. Earlier symptoms of intrusions (β = 0.389, P = .007) and longer captivity (β = 0.218, P = .02) were identified as being associated with PTSD severity 1 year later. Longer captivity was associated with PTSD aggravation over time (β = 0.227, P = .04). Posttraumatic strengthening in faith (β = -0.206, P = .05) and in social relationships (β = -0.221, P = .03) were associated with a reduction in PTSD symptoms.

CONCLUSIONS AND RELEVANCE

These findings suggest that female refugee survivors of genocide are at high risk for severe and chronic PTSD beyond the initial years of resettlement. The findings provide suggestions for mental health care specialized for particularly vulnerable populations.

Effect of hydrophilic groups on the bioactivity of antimicrobial polymers

Antimicrobial polymers have recently been investigated as potential treatments to combat multidrug-resistant pathogens.

AID-RNA polymerase II transcription-dependent deamination of IgV DNA

Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) in immunoglobulin variable (IgV) genes to produce high-affinity antibodies. SHM requires IgV transcription by RNA polymerase II (Pol II). A eukaryotic transcription system including AID has not been reported previously. Here, we reconstitute AID-catalyzed deamination during Pol II transcription elongation in conjunction with DSIF transcription factor. C→T mutations occur at similar frequencies on non-transcribed strand (NTS) and transcribed strand (TS) DNA. In contrast, bacteriophage T7 Pol generates NTS mutations predominantly. AID-Pol II mutations are strongly favored in WRC and WGCW overlapping hot motifs (W = A or T, R = A or G) on both DNA strands. Single mutations occur on 70% of transcribed DNA clones. Mutations are correlated over a 15 nt distance in multiply mutated clones, suggesting that deaminations are catalyzed processively within a stalled or backtracked transcription bubble. Site-by-site comparisons for biochemical and human memory B-cell mutational spectra in an IGHV3-23*01 target show strongly favored deaminations occurring in the antigen-binding complementarity determining regions (CDR) compared to the framework regions (FW). By exhibiting consistency with B-cell SHM, our in vitro data suggest that biochemically defined reconstituted Pol II transcription systems can be used to investigate how, when and where AID is targeted.

Association of Oral Anticoagulants and Verapamil or Diltiazem With Adverse Bleeding Events in Patients With Nonvalvular Atrial Fibrillation and Normal Kidney Function

IMPORTANCE

Direct oral anticoagulants (DOACs) are purported to have fewer drug-drug interactions than warfarin. However, potential interactions with coprescribed medications are still a safety concern. Verapamil hydrochloride and diltiazem hydrochloride are combined P-glycoprotein (P-gp) and CYP3A4 inhibitors and may be associated with increases in the risk of bleeding with DOACs.

OBJECTIVE

To evaluate the risk of bleeding with DOACs and verapamil or diltiazem using an active comparator design.

DESIGN, SETTING, AND PARTICIPANTS

A comparative effectiveness active comparator cohort study was conducted using US population-based data (2010-2015) analyzed between January 1 and July 15, 2019. Data were obtained on 48 442 patients with nonvalvular atrial fibrillation who had received an index prescription of dabigatran, rivaroxaban, or apixaban between October 19, 2010, through June 30, 2015, with final follow-up on October 1, 2015. Analysis was restricted to individuals with no history of kidney disease who were receiving standard doses of the DOACs.

EXPOSURES

Patients with initial prescriptions of DOACs who were receiving verapamil or diltiazem were compared with those receiving amlodipine or metoprolol.

MAIN OUTCOMES AND MEASURES

Overall and gastrointestinal major, moderate, and minor bleeding using primary or secondary diagnoses. Hazard ratios and 95% CIs were estimated using inverse probability of treatment weights in Cox proportional hazards regression models.

RESULTS

Of the 48 442 patients reviewed, analysis was conducted on 1764 patients receiving DOACs with verapamil or diltiazem compared with 3105 receiving amlodipine and 1793 patients receiving DOACs with verapamil or diltiazem compared with 3224 receiving metoprolol. Depending on the comparison, approximately 60% of the cohort were younger than 65 years and male, which differed by treatment group. Rivaroxaban and apixaban were not associated with increased rates of bleeding for patients receiving verapamil or diltiazem compared with those receiving amlodipine or metoprolol. Among patients receiving dabigatran etexilate, the overall bleeding rate was 52% higher (hazard ratio, 1.52; 95% CI, 1.05-2.20) with verapamil or diltiazem vs amlodipine and 43% higher (hazard ratio, 1.43; 95% CI, 1.02-2.00) vs metoprolol. Bleeding rates for dabigatran with verapamil or diltiazem were higher overall for other bleeding types (244.9 vs 158.4 per 1000 person-years; adjusted hazard ratios of overall GI bleeding: 2.16; 95% CI, 1.30-3.60; minor bleeding: 1.56; 95% CI, 1.07-2.27; and minor GI bleeding: 2.16; 95% CI, 1.29-3.63). Sensitivity analyses showed consistent results for dabigatran when used with verapamil and diltiazem, with magnitudes ranging from 50% to 100% increased hazard rates and no significant results for apixaban or rivaroxaban.

CONCLUSIONS AND RELEVANCE

Current US prescribing information only recommends prescribing changes with dabigatran and P-gp inhibitors with lower kidney function. This study found increased bleeding risk associated with dabigatran when used concomitantly with the P-gp inhibitors verapamil and diltiazem in individuals with normal kidney function. Clinicians and patients may need to consider these drug-drug interactions when choosing oral anticoagulation.

Pain, somatic complaints, and subjective concepts of illness in traumatized female refugees who experienced extreme violence by the "Islamic State" (IS)

BACKGROUND

Refugees with a history of war or sexual violence often experience somatic symptoms along with mental disorders. After being held in captivity by the so-called "Islamic State" (IS), 1100 especially vulnerable Yazidi women and children (around 400 women) received special medical and psychological support. We report on their (psycho-) somatic complaints and concepts of illness.

METHODS

Female refugees (N = 116) were surveyed regarding their somatic complaints and concepts of illness. The Impact of Event Scale-Revised (IES-R) and self-developed questionnaire items with ratings on a five-point Likert scale from 0 ("not at all") to 4 ("extremely") were used. Subgroup analyses and a multiple linear regression model were computed.

RESULTS

Pain (M = 2.43, SD = 1.70) is the main somatic complaint with a moderate rated severity, followed by feelings of suffocation (M = 2.37, SD = 1.53), and movement disorders (M = 1.62, SD = 1.70). In a linear regression model, pain explains variance (R² = 0.325) in the refugees' self-reported health-related wellbeing. Somatic symptoms are mainly attributed to psychological causes, followed by physical (e.g., physical origin of symptoms), religious, and supernatural causes. Women with pain symptoms attributed their symptoms more to physical causes (M = 1.90, SD = 1.78) than did women without pain symptoms (M = 1.07, SD = 1.59).

CONCLUSION

Female Yazidi refugees being kept in IS captivity mainly suffer from pain, which is attributed to an explanatory psychological model. The study results show the specific psychosomatic and psychotherapeutic needs and demands for specifically tailored psychotherapy.

AttentiveVideo

Understanding a target audience's emotional responses to a video advertisement is crucial to evaluate the advertisement's effectiveness. However, traditional methods for collecting such information are slow, expensive, and coarse grained. We propose AttentiveVideo, a scalable intelligent mobile interface with corresponding inference algorithms to monitor and quantify the effects of mobile video advertising in real time. Without requiring additional sensors, AttentiveVideo employs a combination of implicit photoplethysmography (PPG) sensing and facial expression analysis (FEA) to detect the attention, engagement , and sentiment of viewers as they watch video advertisements on unmodified smartphones. In a 24-participant study, AttentiveVideo achieved good accuracy on a wide range of emotional measures (the best average accuracy = 82.6% across nine measures). While feature fusion alone did not improve prediction accuracy with a single model, it significantly improved the accuracy when working together with model fusion. We also found that the PPG sensing channel and the FEA technique have different strength in data availability, latency detection, accuracy, and usage environment. These findings show the potential for both low-cost collection and deep understanding of emotional responses to mobile video advertisements.

Random Walk Enzymes: Information Theory, Quantum Isomorphism, and Entropy Dispersion

Activation-induced deoxycytidine deaminase (AID) is a key enzyme in the human immune system. AID binds to and catalyzes random point mutations on the immunoglobulin (Ig) gene, leading to diversification of the Ig gene sequence by random walk motions, scanning for cytidines and turning them to uracils. The mutation patterns deposited by AID on its substrate DNA sequences can be interpreted as random binary words, and the information content of this stochastically generated library of mutated DNA sequences can be measured by its entropy. In this paper, we derive an analytical formula for this entropy and show that the stochastic scanning + catalytic dynamics of AID is controlled by a characteristic length that depends on the diffusion coefficient of AID and the catalytic rate. Experiments showed that the deamination rates have a sequence context dependence, where mutations are generated at higher intensities on DNA sequences with higher densities of mutable sites. We derive an isomorphism between this classical system and a quantum mechanical model and use this isomorphism to explain why AID appears to focus its scanning on regions with higher concentrations of deaminable sites. Using path integral Monte Carlo simulations of the quantum isomorphic system, we demonstrate how AID's scanning indeed depends on the context of the DNA sequence and how this affects the entropy of the library of generated mutant clones. Examining detailed features in the entropy of the experimentally generated clone library, we provide clear evidence that the random walk of AID on its substrate DNA is focused near hot spots. The model calculations applied to the experimental data show that the observed per-site mutation frequencies display similar contextual dependences as observed in the experiments, in which hot motifs are located adjacent to several different types of hot and cold motifs.

Resistance to Second-Generation HIV-1 Maturation Inhibitors

A betulinic acid-based compound, bevirimat (BVM), inhibits HIV-1 maturation by blocking a late step in protease-mediated Gag processing: the cleavage of the capsid-spacer peptide 1 (CA-SP1) intermediate to mature CA. Previous studies showed that mutations conferring resistance to BVM cluster around the CA-SP1 cleavage site. Single amino acid polymorphisms in the SP1 region of Gag and the C terminus of CA reduced HIV-1 susceptibility to BVM, leading to the discontinuation of BVM's clinical development. We recently reported a series of "second-generation" BVM analogs that display markedly improved potency and breadth of activity relative to the parent molecule. Here, we demonstrate that viral clones bearing BVM resistance mutations near the C terminus of CA are potently inhibited by second-generation BVM analogs. We performed de novo selection experiments to identify mutations that confer resistance to these novel compounds. Selection experiments with subtype B HIV-1 identified an Ala-to-Val mutation at SP1 residue 1 and a Pro-to-Ala mutation at CA residue 157 within the major homology region (MHR). In selection experiments with subtype C HIV-1, we identified mutations at CA residue 230 (CA-V230M) and SP1 residue 1 (SP1-A1V), residue 5 (SP1-S5N), and residue 10 (SP1-G10R). The positions at which resistance mutations arose are highly conserved across multiple subtypes of HIV-1. We demonstrate that the mutations confer modest to high-level maturation inhibitor resistance. In most cases, resistance was not associated with a detectable increase in the kinetics of CA-SP1 processing. These results identify mutations that confer resistance to second-generation maturation inhibitors and provide novel insights into the mechanism of resistance.IMPORTANCE HIV-1 maturation inhibitors are a class of small-molecule compounds that block a late step in the viral protease-mediated processing of the Gag polyprotein precursor, the viral protein responsible for the formation of virus particles. The first-in-class HIV-1 maturation inhibitor bevirimat was highly effective in blocking HIV-1 replication, but its activity was compromised by naturally occurring sequence polymorphisms within Gag. Recently developed bevirimat analogs, referred to as "second-generation" maturation inhibitors, overcome this issue. To understand more about how these second-generation compounds block HIV-1 maturation, here we selected for HIV-1 mutants that are resistant to these compounds. Selections were performed in the context of two different subtypes of HIV-1. We identified a small set of mutations at highly conserved positions within the capsid and spacer peptide 1 domains of Gag that confer resistance. Identification and analysis of these maturation inhibitor-resistant mutants provide insights into the mechanisms of resistance to these compounds.

NLPReViz: an interactive tool for natural language processing on clinical text

The gap between domain experts and natural language processing expertise is a barrier to extracting understanding from clinical text. We describe a prototype tool for interactive review and revision of natural language processing models of binary concepts extracted from clinical notes. We evaluated our prototype in a user study involving 9 physicians, who used our tool to build and revise models for 2 colonoscopy quality variables. We report changes in performance relative to the quantity of feedback. Using initial training sets as small as 10 documents, expert review led to final F1scores for the "appendiceal-orifice" variable between 0.78 and 0.91 (with improvements ranging from 13.26% to 29.90%). F1for "biopsy" ranged between 0.88 and 0.94 (-1.52% to 11.74% improvements). The average System Usability Scale score was 70.56. Subjective feedback also suggests possible design improvements.

Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses

Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. This model partly explains the association between synchronous stress-dependent epitranscriptomic marks and significant multi-codon usage skewing in families of translationally regulated transcripts. The model also predicts translational adaptation during viral infections.

Secondary Traumatization in Caregivers Working With Women and Children Who Suffered Extreme Violence by the "Islamic State"

Introduction: Refugees fleeing persecution, torture, or sexual violence are at high risk of developing both acute and chronic psychological disorders. Systematic violence, as committed against the Yazidi minority in Northern Iraq by the terror organization known as the Islamic State (IS), can be seen as a particularly traumatic burden to the victims, but also to caregivers providing treatments and assistance to them. The intense exposure to traumatic content may cause secondary traumatization in respective caregivers. This study aims (1) to identify the prevalence of secondary traumatization in caregivers working with traumatized women and children from Northern Iraq; (2) to determine the specific distressing factors and resources of the caregivers; as well as (3) to analyze whether caregivers' personal history of trauma or flight, attachment styles, working arrangements as well as support offers qualify as risk or resilience factors for secondary traumatization. Materials and Methods: In this cross-sectional study, N = 84 caregivers (social workers, psychotherapists/physicians, and interpreters) in the context of a Humanitarian Admission Program (HAP) for women and children traumatized by the so called IS were investigated about their work-related burdens and resources. Secondary traumatization was assessed with the Questionnaire for Secondary Traumatization (FST). To identify relevant determinants for secondary traumatization multiple linear regression analyses were performed. Results: Secondary traumatization was present in 22.9% of the participating caregivers, with 8.6% showing a severe symptom load. A personal history of traumatic experiences, a personal history of flight, a higher number of hours per week working in direct contact with refugees as well as a preoccupied attachment style were detected as risk factors for secondary traumatization. A secure attachment style could be identified as a resilience factor for secondary traumatization. Discussion: Caregivers working with traumatized refugees are at high risk of developing secondary traumatization. Based on the findings of this study and theoretical considerations, a framework of classification for different types of trauma-associated psychological burdens of caregivers working with traumatized refugees is proposed. Implications for the training and supervision of professionals in refugee- and trauma-care are discussed.

Urban disaster preparedness of Hong Kong residents: A territory-wide survey

OBJECTIVE

To assess the state of community disaster preparedness of Hong Kong residents and to identify factors associated with adequate preparedness behaviors.

DESIGN

A cross-sectional survey using random Global Positioning System (GPS) spatial sampling conducted from the 8 August 2015 to 6 September 2015.

PARTICIPANTS

Hong Kong residents aged 18 years or more.

METHOD

A 19-item questionnaire was developed to assess respondents' preparedness information acquisition, communication plan, evacuation strategies, first-aid and disaster knowledge, financial resilience, and preparedness behaviors. In total, 1023 residents were interviewed at 516 GPS locations. Multiple logistic regression was used to identify factors associated with preparedness behaviors, defined as having an evacuation kit in our study.

RESULTS

Television remains the key information source, both before and during disaster, with young respondents also favoring social media and the internet and elder residents preferring television and radio. Many respondents did not have adequate first-aid knowledge and few showed correct responses to a typhoon warning signal. Only 39.4% had an evacuation kit. In logistic regression, correct responses to first aid questions and a typhoon warning signal were significantly associated with kit preparation (OR 2.023, 95% CI 1.233-3.318, p=0.005). Residents with elderly household member(s) were significantly less likely to do so (OR 0.554, 95% CI 0.333-0.922, p=0.023).

CONCLUSIONS

Community resilience-building programs should tailor information provision to different age groups with a focus on the family caregivers of elderly residents. There is a need to promulgate first-aid training and disaster education in the community.

Preferential interactions of trehalose, L-arginine.HCl and sodium chloride with therapeutically relevant IgG1 monoclonal antibodies

Preferential interactions of weakly interacting formulation excipients govern their effect on the equilibrium and kinetics of several reactions of protein molecules in solution. Using vapor pressure osmometry, we characterized the preferential interactions of commonly used excipients trehalose, L-arginine.HCl and NaCl with three therapeutically-relevant, IgG1 monoclonal antibodies that have similar size and shape, but differ in their surface hydrophobicity and net charge. We further characterized the effect of these excipients on the reversible self-association, aggregation and viscosity behavior of these antibody molecules. We report that trehalose, L-arginine.HCl and NaCl are all excluded from the surface of the three IgG1 monoclonal antibodies, and that the exclusion behavior is linearly related to the excipient molality in the case of trehalose and NaCl, whereas a non-linear behavior is observed for L-arginine.HCl. Interestingly, we find that the magnitude of trehalose exclusion depends upon the nature of the protein surface. Such behavior is not observed in case of NaCl and L-arginine.HCl as they are excluded to the same extent from the surface of all three antibody molecules tested in this study. Analysis of data presented in this study provides further insight into the mechanisms governing excipient-mediated stabilization of mAb formulations.

Localised impedance monitoring device for the remote clinical assessment of home-based dialysis patients

BioImpedance Spectroscopy (BIS) has been clinically used to determine the hydrational status of patients undergoing haemodialysis (HD). In the present project we are developing a calf-localised, integrated impedimetric device to periodically and conveniently measure and transmit information on the hydrational status of home-based patients to a remote clinic. Surprisingly, we have found that simple postural changes before or during measurement lead to significant fluid shifts in the lower leg that are as important and as long lasting as the effects of haemodialysis. These must be taken into account if potentially hazardous errors are not to be made in assessing a patient's hydrational status.

Birefringence of flow-assembled chitosan membranes in microfluidics

Biopolymer membrane assembly in microfluidics offers precise spatial and temporal resolution for biomolecular and cellular interactions during and after assembly. Control over molecular transport across the biofabricated membranes requires microstructural characterization. This study investigates, for the first time, the birefringence of chitosan membranes assembled with flow in a microfluidic environment, and the effects of pH and flow rate on the membrane's micro-alignment. The optical anisotropy of the formed membranes was quantified using a de Sénarmont compensator for transmitted quantitative polarized light microscopy. The chitosan membranes were biofabricated within a small aperture in a microfluidic network with various flow and pH conditions of chitosan and alginate solutions. The measured optical retardance and parallelism index clearly indicate that the microstructure of the flow-assembled membrane was well organized and aligned along the direction of chitosan flow. Optical retardance increased significantly with the pH of the alginate solution, but was less sensitive to the variation of the flow rates of the polymer solutions during the biofabrication process. It was also determined that the birefringence signal dropped significantly across the membrane growth direction regardless of the molecular density in the membrane. The mechanism of the micro-alignment was discussed, which was presumably due to the molecular un-wrapping by shear flow. We envision that the current study paves a path to further understand and actively manipulate the microstructure of flow-assembled membranes for broad lab-on-a-chip applications.

Integrity of immunoglobulin variable regions is supported by GANP during AID-induced somatic hypermutation in germinal center B cells

Immunoglobulin affinity maturation depends on somatic hypermutation (SHM) in immunoglobulin variable (IgV) regions initiated by activation-induced cytidine deaminase (AID). AID induces transition mutations by C→U deamination on both strands, causing C:G→T:A. Error-prone repairs of U by base excision and mismatch repairs (MMRs) create transversion mutations at C/G and mutations at A/T sites. In Neuberger’s model, it remained to be clarified how transition/transversion repair is regulated. We investigate the role of AID-interacting GANP (germinal center-associated nuclear protein) in the IgV SHM profile. GANP enhances transition mutation of the non-transcribed strand G and reduces mutation at A, restricted to GYW of the AID hotspot motif. It reduces DNA polymerase η hotspot mutations associated with MMRs followed by uracil-DNA glycosylase. Mutation comparison between IgV complementary and framework regions (FWRs) by Bayesian statistical estimation demonstrates that GANP supports the preservation of IgV FWR genomic sequences. GANP works to maintain antibody structure by reducing drastic changes in the IgV FWR in affinity maturation.

Associations between Mental Health and Ebola-Related Health Behaviors: A Regionally Representative Cross-sectional Survey in Post-conflict Sierra Leone

BACKGROUND

Little attention has been paid to potential relationships between mental health, trauma, and personal exposures to Ebola virus disease (EVD) and health behaviors in post-conflict West Africa. We tested a conceptual model linking mental health and trauma to EVD risk behaviors and EVD prevention behaviors.

METHODS AND FINDINGS

Using survey data from a representative sample in the Western Urban and Western Rural districts of Sierra Leone, this study examines associations between war exposures, post-traumatic stress disorder (PTSD) symptoms, depression, anxiety, and personal EVD exposure (e.g., having family members or friends diagnosed with EVD) and EVD-related health behaviors among 1,008 adults (98% response rate) from 63 census enumeration areas of the Western Rural and Western Urban districts randomly sampled at the height of the EVD epidemic (January-April 2015). Primary outcomes were EVD risk behaviors (14 items, Cronbach's α = 0.84) and EVD prevention behaviors (16 items, Cronbach's α = 0.88). Main predictors comprised war exposures (8 items, Cronbach's α = 0.85), anxiety (10 items, Cronbach's α = 0.93), depression (15 items, Cronbach's α = 0.91), and PTSD symptoms (16 items, Cronbach's α = 0.93). Data were analyzed using two-level, population-weighted hierarchical linear models with 20 multiply imputed datasets. EVD risk behaviors were associated with intensity of depression symptoms (b = 0.05; 95% CI 0.00, 0.10; p = 0.037), PTSD symptoms (b = 0.10; 95% CI 0.03, 0.17; p = 0.008), having a friend diagnosed with EVD (b = -0.04; 95% CI -0.08, -0.00; p = 0.036), and war exposures (b = -0.09; 95% CI -0.17, -0.02; p = 0.013). EVD prevention behaviors were associated with higher anxiety (b = 0.23; 95% CI 0.06, 0.40; p = 0.008), having a friend diagnosed with EVD (b = 0.15; 95% CI 0.04, 0.27; p = 0.011), and higher levels of war exposure (b = 0.45; 95% CI 0.16, 0.74; p = 0.003), independent of mental health. PTSD symptoms were associated with lower levels of EVD prevention behavior (b = -0.24; 95% CI -0.43, -0.06; p = 0.009).

CONCLUSIONS

In post-conflict settings, past war trauma and mental health problems are associated with health behaviors related to combatting EVD. The associations between war trauma and both EVD risk behaviors and EVD prevention behaviors may be mediated through two key mental health variables: depression and PTSD symptoms. Considering the role of mental health in the prevention of disease transmission may help fight continuing and future Ebola outbreaks in post-conflict Sierra Leone. This sample is specific to Freetown and the Western Area and may not be representative of all of Sierra Leone. In addition, our main outcomes as well as personal EVD exposure, war exposures, and mental health predictors rely on self-report, and therefore raise the possibility of common methods bias. However, the findings of this study may be relevant for understanding dynamics related to EVD and mental health in other major capital cities in the EVD-affected countries of West Africa.

Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification

Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) and class-switch recombination (CSR) by deaminating C→U during transcription of Ig-variable (V) and Ig-switch (S) region DNA, which is essential to produce high-affinity antibodies. Here we report the crystal structure of a soluble human AID variant at 2.8Å resolution that favors targeting WRC motifs (W=A/T, R=A/G) in vitro, and executes Ig V SHM in Ramos B-cells. A specificity loop extending away from the active site to accommodate two purine bases next to C, differs significantly in sequence, length, and conformation from APOBEC proteins Apo3A and Apo3G, which strongly favor pyrimidines at -1 and -2 positions. Individual amino acid contributions to specificity and processivity were measured in relation to a proposed ssDNA binding cleft. This study provides a structural basis for residue contributions to DNA scanning properties unique to AID, and for disease mutations in human HIGM-2 syndrome.

Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution

Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble. When unconstrained on single-stranded (ss) DNA, AID moves in random bidirectional short slides/hops over the entire molecule while remaining bound for ∼5 min. Our analysis distinguishes dynamic scanning from static ssDNA creasing. That AID alone can track along with RNAP during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID can initiate SHM and CSR when properly regulated, yet when unregulated can access non-Ig genes and cause cancer.

Activation-induced deoxycytidine deaminase (AID) induces somatic hypermutation and class-switch recombination during transcription of immunoglobulin genes. Here the authors use single-molecule FRET to show that AID translocates together with RNA polymerase and scans within stalled transcription bubbles.

Random-walk enzymes

Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C→U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics.

An assessment of antenatal care among Syrian refugees in Lebanon

BACKGROUND

After more than three years of violence in Syria, Lebanon hosts over one million Syrian refugees creating significant public health concerns. Antenatal care delivery to tens of thousands of pregnant Syrian refugee women is critical to preventing maternal and fetal mortality but is not well characterized given the multiple factors obtaining health data in a displaced population. This study describes antenatal care access, the scope of existing antenatal care, and antenatal and family planning behaviors and practice among pregnant Syrian refugees in various living conditions and multiple geographic areas of Lebanon.

METHODS

A field-based survey was conducted between July and October 2013 in 14 main geographic sites of refugee concentration. The assessment evaluated antenatal services among a non-randomized sample of 420 self-identified pregnant Syrian refugee women that included demographics, gestational age, living accommodation, antenatal care coverage, antenatal care content, antenatal health behaviors, antenatal health literacy, and family planning perception and practices.

RESULTS

In total, 420 pregnant Syrian refugees living in Lebanon completed the survey. Of these, 82.9% (348) received some antenatal care. Of those with at least one antenatal visit, 222 (63.8%) received care attended by a skilled professional three or more times, 111 (31.9%) 1-2 times, and 15 (4.3%) had never received skilled antenatal care. We assessed antenatal care content defined by blood pressure measurement, and urine and blood sample analyses. Of those who had received any antenatal care, only 31.2% received all three interventions, 18.2% received two out of three, 32.1% received one out of three, and 18.5% received no interventions. Only (41.2%) had an adequate diet of vitamins, minerals, and folic acid. Access, content and health behaviors varied by gestational age, type of accommodation and location in Lebanon.

CONCLUSIONS

Standards of antenatal care are not being met for pregnant Syrian refugee women in Lebanon. This descriptive analysis of relative frequencies suggests reproductive health providers should focus attention on increasing antenatal care visits, particularly to third trimester and late gestational age patients and to those in less secure sheltering arrangements. With this approach they can improve care content by providing early testing and interventions per accepted guidelines designed to improve pregnancy outcomes.

Bioinformatic investigation of the cost management strategies of five oral microbes

Some amino acids are more energetically costly to synthesize de novo, therefore many microbes have evolved to regulate the metabolic expenditure of the cell and reduce the energy burden of extracellular unrecyclable proteins. Several oral bacterial species take up amino acids and peptides obtained from proteolysis of host proteins and hence do not rely only on de novo synthesis. The aim of this study was to investigate if five oral bacterial species implement cost management strategies to reduce the energy burden of extracellular unrecyclable proteins. Since the relative de novo amino acid synthesis costs are proportional to the masses of the amino acids, the energy costs of producing proteins were assessed by calculating the mean amino acid mass for each protein. For Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia and Streptococcus sanguinis, the outer membrane/extracellular proteins are made up of a much larger percentage of lower average mass amino acids whereas cytoplasmic proteins are made up of a larger proportion of higher average mass amino acid residues. These results are consistent with the five oral bacterial species employing energy-saving mechanisms in the production of extracellular unrecyclable proteins. Interestingly, the P. gingivalis and S. sanguinis genomes exhibited significantly lower predicted mean amino acid masses compared with those of the genomes of the other three species, suggesting that this may provide them with an energy advantage with respect to protein biosynthetic cost.

Evidence for the role of EPHX2 gene variants in anorexia nervosa

Anorexia nervosa (AN) and related eating disorders are complex, multifactorial neuropsychiatric conditions with likely rare and common genetic and environmental determinants. To identify genetic variants associated with AN, we pursued a series of sequencing and genotyping studies focusing on the coding regions and upstream sequence of 152 candidate genes in a total of 1205 AN cases and 1948 controls. We identified individual variant associations in the Estrogen Receptor-ß (ESR2) gene, as well as a set of rare and common variants in the Epoxide Hydrolase 2 (EPHX2) gene, in an initial sequencing study of 261 early-onset severe AN cases and 73 controls (P=0.0004). The association of EPHX2 variants was further delineated in: (1) a pooling-based replication study involving an additional 500 AN patients and 500 controls (replication set P=0.00000016); (2) single-locus studies in a cohort of 386 previously genotyped broadly defined AN cases and 295 female population controls from the Bogalusa Heart Study (BHS) and a cohort of 58 individuals with self-reported eating disturbances and 851 controls (combined smallest single locus P<0.01). As EPHX2 is known to influence cholesterol metabolism, and AN is often associated with elevated cholesterol levels, we also investigated the association of EPHX2 variants and longitudinal body mass index (BMI) and cholesterol in BHS female and male subjects (N=229) and found evidence for a modifying effect of a subset of variants on the relationship between cholesterol and BMI (P<0.01). These findings suggest a novel association of gene variants within EPHX2 to susceptibility to AN and provide a foundation for future study of this important yet poorly understood condition.