Robust and stable transcriptional repression in Giardia using CRISPRi.

Giardia lamblia is a binucleate protistan parasite causing significant diarrheal disease worldwide. An inability to target Cas9 to both nuclei, combined with the lack of nonhomologous end joining and markers for positive selection, has stalled the adaptation of CRISPR/Cas9-mediated genetic tools for this widespread parasite. CRISPR interference (CRISPRi) is a modification of the CRISPR/Cas9 system that directs catalytically inactive Cas9 (dCas9) to target loci for stable transcriptional repression. Using a Giardia nuclear localization signal to target dCas9 to both nuclei, we developed efficient and stable CRISPRi-mediated transcriptional repression of exogenous and endogenous genes in Giardia. Specifically, CRISPRi knockdown of kinesin-2a and kinesin-13 causes severe flagellar length defects that mirror defects with morpholino knockdown. Knockdown of the ventral disk MBP protein also causes severe structural defects that are highly prevalent and persist in the population more than 5 d longer than defects associated with transient morpholino-based knockdown. By expressing two guide RNAs in tandem to simultaneously knock down kinesin-13 and MBP, we created a stable dual knockdown strain with both flagellar length and disk defects. The efficiency and simplicity of CRISPRi in polyploid Giardia allows rapid evaluation of knockdown phenotypes and highlights the utility of CRISPRi for emerging model systems

Vortex Loop Phase Transitions in Liquid Helium, Cosmic Strings, and High-T_c Superconductors

The distribution of thermally excited vortex loops near a superfluid phase transition is calculated from a renormalized theory. The number density of loops with a given perimeter is found to change from exponential decay with increasing perimeter to algebraic decay as T_c is approached, in agreement with recent simulations of both cosmic strings and high-T_c superconductors. Predictions of the value of the exponent of the algebraic decay at T_c and of critical behavior in the vortex density are confirmed by the simulations, giving strong support to the vortex-folding model proposed by Shenoy.Comment: Version to appear in Phys. Rev. Lett, with a number of corrections and addition

Automated Fourier space region-recognition filtering for off-axis digital holographic microscopy

Automated label-free quantitative imaging of biological samples can greatly benefit high throughput diseases diagnosis. Digital holographic microscopy (DHM) is a powerful quantitative label-free imaging tool that retrieves structural details of cellular samples non-invasively. In off-axis DHM, a proper spatial filtering window in Fourier space is crucial to the quality of reconstructed phase image. Here we describe a region-recognition approach that combines shape recognition with an iterative thresholding to extracts the optimal shape of frequency components. The region recognition technique offers fully automated adaptive filtering that can operate with a variety of samples and imaging conditions. When imaging through optically scattering biological hydrogel matrix, the technique surpasses previous histogram thresholding techniques without requiring any manual intervention. Finally, we automate the extraction of the statistical difference of optical height between malaria parasite infected and uninfected red blood cells. The method described here pave way to greater autonomy in automated DHM imaging for imaging live cell in thick cell cultures

Critical properties of loop percolation models with optimization constraints

We study loop percolation models in two and in three space dimensions, in which configurations of occupied bonds are forced to form closed loop. We show that the uncorrelated occupation of elementary plaquettes of the square and the simple cubic lattice by elementary loops leads to a percolation transition that is in the same universality class as the conventional bond percolation. In contrast to this an optimization constraint for the loop configurations, which then have to minimize a particular generic energy function, leads to a percolation transition that constitutes a new universality class, for which we report the critical exponents. Implication for the physics of solid-on-solid and vortex glass models are discussed.Comment: 8 pages, 8 figure

Medication Management Program Among Elderly at a Residential Facility

Abstract This quality improvement project aimed to address medication management-related issues at a residential facility. The project\u27s population was elderly residents who self- administered their medications. A root cause analysis and SWOT analysis identified multiple factors contributing to medication management errors, including lack of resident education, resident competency, and technology limitations. An intervention plan was developed and implemented in two phases. Phase 1 involved conducting medication reconciliation, assessing resident competency, and 1:1 educational sessions with the residents. Educational retention was assessed by using a pre-test and a post-test. Phase 2, to be implemented in the future, will address technology limitations, incorporate an electronic medical records (EMR) system, and provide ongoing staff education. Results from Phase 1 include 80% recalled new information while 20% showed no change after completion of the educational session and the pre/post-test; from those residents assessed with the Medi-Cog, 55% scored above 8 out of 10 while 45% scored below the cutoff score of 8, and last 100% of the Medication Administration Records (MAR) were reviewed. Although time constraints prevented Phase 2 interventions from being implemented, implementing an EMR system and a professional development plan for staff education are expected to contribute to further improvements in medication management at the residential facility. Continued monitoring and collaboration with the residents and staff are vital for sustained success

Benefits and limitations of text messages to stimulate higher learning among community providers: participants’ views of an mHealth intervention to support continuing medical education in Vietnam

BACKGROUND: A randomized controlled trial was conducted in 2015 to evaluate a mobile continuing medical education (mCME) intervention that provided daily text messages to community-based physicians’ assistants (CBPAs) in Thai Nguyen Province, Vietnam. Although the intervention failed to improve medical knowledge over a 6-month period, a companion qualitative study provided insights on the views and experiences of intervention participants. METHODS: We conducted focus group discussions (FGDs) and in-depth interviews (IDIs) among participants randomized to receive text messages containing either simple medical facts or quiz questions. Trained interviewers collected data immediately following the conclusion of the trial in December 2015. Using semi-structured question guides, respondents were queried on their views of the intervention, positive and negative, and perceived impacts of the intervention. During analysis, after learning that the intervention had failed to increase knowledge among participants, we also examined reasons for lack of improvement in medical knowledge. All analyses were performed in NVivo using a thematic approach. RESULTS: A total of 70 CBPAs engaged in one of 8 FGDs or an IDI. One-half were men; average age among all respondents was 40 years. Most (81%) practiced in rural settings and most (51%) focused on general medicine. The mean length of work experience was 3 years. All respondents made positive comments about the intervention; convenience, relevance, and quick feedback (quiz format) were praised. Downsides encompassed lack of depth of information, weak interaction, technology challenges, and challenging/irrelevant messages. Respondents described perceived impacts encompassing increased motivation, knowledge, collegial discussions, Internet use to search for more information, and clinical skills. Overall, they expressed a desire for the intervention to continue and recommended expansion to other medical professionals. Overreliance on the text messages, lack of effective self-study, and technical/language-based barriers may be potential explanations for intervention failure. CONCLUSION: As a form of mCME, daily text messages were well-received by community-level health care providers in Vietnam. This mCME approach appears very promising in low-resource environments or where traditional forms of CME are impractical. Future models might consider enhancements to foster linkages to relevant medical materials, improve interaction with medical experts, and tailor medical content to the daily activities of medical staff

Machine Learning to Automate Network Segregation for Enhanced Security in Industry 4.0

The heavy reliance of Industry 4.0 on emerging communication technologies, notably Industrial Internet-of-Things (IIoT) and Machine-Type Communications (MTC), and the increasing exposure of these traditionally isolated infrastructures to the Internet, are tremendously increasing the attack surface. Network segregation is a viable solution to address this problem. It essentially splits the network into several logical groups (subnetworks) and enforces adequate security policy on each segment, e.g., restricting unnecessary intergroup communications or controlling the access. However, existing segregation techniques primarily depend on manual configurations, which renders them inefficient for cyber-physical production systems because they are highly complex and heterogeneous environments with massive number of communicating machines. In this paper, we incorporate machine learning to automate network segregation, by efficiently classifying network end-devices into several groups through examining the traffic patterns that they generate. For performance evaluation, we analysed the data collected from a large segment of Infineon’s network in the context of the EU funded ECSEL-JU project “SemI40”. In particular, we applied feature selection and trained several supervised learning algorithms. Test results, using 10-fold cross validation, revealed that the algorithms generalise very well and achieve an accuracy up to 99.4%

Banana Cultivar Field Screening for Resistance to Fusarium oxysporum f.sp. cubense Tropical Race 4 in the Northern Territory

Fusarium oxysporum f.sp. cubense, causal agent of Panama disease, is one of the biggest threats to global banana production, particularly the Cavendish competent tropical race 4 (Foc TR4). It continues to spread globally with detections occurring in regions of the Middle East and new continents such as Africa and South America in the last decade. As the search was on for new management strategies and resistant cultivars to combat the disease, a banana cultivar-screening trial took place in the Northern Territory of Australia, which examined the responses of 24 banana cultivars to the soil borne fungus. These cultivars included material from TBRI, FHIA and selections from Thailand, Indonesia and Australia and evaluated for their resistance to tropical race 4 for two cropping cycles. Several cultivars displayed considerable resistance to Foc TR4, including several FHIA parental lines and hybrids, the Cavendish (AAA) selections GCTCV 215 and GCTCV 247 from TBRI and an Indonesian selection CJ19 showed either very little to no plant death due to the disease

A vortex description of the first-order phase transition in type-I superconductors

Using both analytical arguments and detailed numerical evidence we show that the first order transition in the type-I 2D Abelian Higgs model can be understood in terms of the statistical mechanics of vortices, which behave in this regime as an ensemble of attractive particles. The well-known instabilities of such ensembles are shown to be connected to the process of phase nucleation. By characterizing the equation of state for the vortex ensemble we show that the temperature for the onset of a clustering instability is in qualitative agreement with the critical temperature. Below this point the vortex ensemble collapses to a single cluster, which is a non-extensive phase, and disappears in the absence of net topological charge. The vortex description provides a detailed mechanism for the first order transition, which applies at arbitrarily weak type-I and is gauge invariant unlike the usual field-theoretic considerations, which rely on asymptotically large gauge coupling.Comment: 4 pages, 6 figures, uses RevTex. Additional references added, some small corrections to the tex

Relation between falciparum malaria and bacteraemia in Kenyan children: a population-based, case-control study and a longitudinal study.

BACKGROUND: Many investigators have suggested that malaria infection predisposes individuals to bacteraemia. We tested this hypothesis with mendelian randomisation studies of children with the malaria-protective phenotype of sickle-cell trait (HbAS). METHODS: This study was done in a defined area around Kilifi District Hospital, Kilifi, Kenya. We did a matched case-control study to identify risk factors for invasive bacterial disease, in which cases were children aged 3 months to 13 years who were admitted to hospital with bacteraemia between Sept 16, 1999, and July 31, 2002. We aimed to match two controls, by age, sex, location, and time of recruitment, for every case. We then did a longitudinal case-control study to assess the relation between HbAS and invasive bacterial disease as malaria incidence decreased. Cases were children aged 0-13 years who were admitted to hospital with bacteraemia between Jan 1, 1999, and Dec 31, 2007. Controls were born in the study area between Jan 1, 2006, and June 23, 2009. Finally, we modelled the annual incidence of bacteraemia against the community prevalence of malaria during 9 years with Poisson regression. RESULTS: In the matched case-control study, we recruited 292 cases-we recruited two controls for 236, and one for the remaining 56. Sickle-cell disease, HIV, leucocyte haemozoin pigment, and undernutrition were positively associated with bacteraemia and HbAS was strongly negatively associated with bacteraemia (odds ratio 0·36; 95% CI 0·20-0·65). In the longitudinal case-control study, we assessed data from 1454 cases and 10,749 controls. During the study period, the incidence of admission to hospital with malaria per 1000 child-years decreased from 28·5 to 3·45, with a reduction in protection afforded by HbAS against bacteraemia occurring in parallel (p=0·0008). The incidence of hospital admissions for bacteraemia per 1000 child-years also decreased from 2·59 to 1·45. The bacteraemia incidence rate ratio associated with malaria parasitaemia was 6·69 (95% CI 1·31-34·3) and, at a community parasite prevalence of 29% in 1999, 62% (8·2-91) of bacteraemia cases were attributable to malaria. INTERPRETATION: Malaria infection strongly predisposes individuals to bacteraemia and can account for more than half of all cases of bacteraemia in malaria-endemic areas. Interventions to control malaria will have a major additional benefit by reducing the burden of invasive bacterial disease. FUNDING: Wellcome Trust