Impact of Community-Based Larviciding on the Prevalence of Malaria Infection in Dar es Salaam, Tanzania.

The use of larval source management is not prioritized by contemporary malaria control programs in sub-Saharan Africa despite historical success. Larviciding, in particular, could be effective in urban areas where transmission is focal and accessibility to Anopheles breeding habitats is generally easier than in rural settings. The objective of this study is to assess the effectiveness of a community-based microbial larviciding intervention to reduce the prevalence of malaria infection in Dar es Salaam, United Republic of Tanzania. Larviciding was implemented in 3 out of 15 targeted wards of Dar es Salaam in 2006 after two years of baseline data collection. This intervention was subsequently scaled up to 9 wards a year later, and to all 15 targeted wards in 2008. Continuous randomized cluster sampling of malaria prevalence and socio-demographic characteristics was carried out during 6 survey rounds (2004-2008), which included both cross-sectional and longitudinal data (N = 64,537). Bayesian random effects logistic regression models were used to quantify the effect of the intervention on malaria prevalence at the individual level. Effect size estimates suggest a significant protective effect of the larviciding intervention. After adjustment for confounders, the odds of individuals living in areas treated with larviciding being infected with malaria were 21% lower (Odds Ratio = 0.79; 95% Credible Intervals: 0.66-0.93) than those who lived in areas not treated. The larviciding intervention was most effective during dry seasons and had synergistic effects with other protective measures such as use of insecticide-treated bed nets and house proofing (i.e., complete ceiling or window screens). A large-scale community-based larviciding intervention significantly reduced the prevalence of malaria infection in urban Dar es Salaam

Quantum Acoustics with Surface Acoustic Waves

It has recently been demonstrated that surface acoustic waves (SAWs) can interact with superconducting qubits at the quantum level. SAW resonators in the GHz frequency range have also been found to have low loss at temperatures compatible with superconducting quantum circuits. These advances open up new possibilities to use the phonon degree of freedom to carry quantum information. In this paper, we give a description of the basic SAW components needed to develop quantum circuits, where propagating or localized SAW-phonons are used both to study basic physics and to manipulate quantum information. Using phonons instead of photons offers new possibilities which make these quantum acoustic circuits very interesting. We discuss general considerations for SAW experiments at the quantum level and describe experiments both with SAW resonators and with interaction between SAWs and a qubit. We also discuss several potential future developments.Comment: 14 pages, 12 figure

The sigma and f_0(980) from Ke4 + pi-pi scatterings data

We systematically reconsider, within an improved "analytic K-matrix model", the extraction of the sigma = f_0(600) and f_0(980) masses, widths and hadronic couplings using new Ke4 = K-->pi-pi e nu_e data on pi-pi phase shift below 390 MeV and different sets of pi-pi--> pi-pi / K-K scatterings data from 400 MeV to 1.4 GeV. Our results are summarized in Tables 1, 2 and 5. In units of MeV, the complex poles are: M_sigma=452(12) - i 260(15) and M_f=981(34) -i 18(11), which are comparable with some recent high-precision determinations and with PDG values. Besides some other results, we find: |g_{sigma K+K-}|/|g_{sigma pi+pi-}|=0.37(6) which confirms a sizeable g_{sigma K+K-} coupling found earlier, and which disfavours a large pi-pi molecule or four-quark component of the sigma, while its broad pi-pi width (relative to the one of the rho-meson) cannot be explained within a \bar qq scenario. The narrow pi-pi width of the f_0(980) and the large value: |g_{f K+K-}|/|g_{f pi+pi-}|=2.59(1.34), excludes its pure (\bar uu+\bar dd) content. A significant gluonium component eventually mixed with \bar qq appears to be necessary for evading the previous difficulties.Comment: 9 pages, 3 figures, 6 table

Roy-Steiner-equation analysis of pion-nucleon scattering

We review the structure of Roy-Steiner equations for pion-nucleon scattering, the solution for the partial waves of the t-channel process $\pi\pi\to \bar N N$, as well as the high-accuracy extraction of the pion-nucleon S-wave scattering lengths from data on pionic hydrogen and deuterium. We then proceed to construct solutions for the lowest partial waves of the s-channel process $\pi N\to \pi N$ and demonstrate that accurate solutions can be found if the scattering lengths are imposed as constraints. Detailed error estimates of all input quantities in the solution procedure are performed and explicit parameterizations for the resulting low-energy phase shifts as well as results for subthreshold parameters and higher threshold parameters are presented. Furthermore, we discuss the extraction of the pion-nucleon $\sigma$-term via the Cheng-Dashen low-energy theorem, including the role of isospin-breaking corrections, to obtain a precision determination consistent with all constraints from analyticity, unitarity, crossing symmetry, and pionic-atom data. We perform the matching to chiral perturbation theory in the subthreshold region and detail the consequences for the chiral convergence of the threshold parameters and the nucleon mass.Comment: 101 pages, 28 figures; journal versio

Syndecan 4 Is Involved in Mediating HCV Entry through Interaction with Lipoviral Particle-Associated Apolipoprotein E

Hepatitis C virus (HCV) is a major cause of liver disease worldwide and HCV infection represents a major health problem. HCV associates with host lipoproteins forming host/viral hybrid complexes termed lipoviral particles. Apolipoprotein E (apoE) is a lipoprotein component that interacts with heparan sulfate proteoglycans (HSPG) to mediate hepatic lipoprotein uptake, and may likewise mediate HCV entry. We sought to define the functional regions of apoE with an aim to identify critical apoE binding partners involved in HCV infection. Using adenoviral vectors and siRNA to modulate apoE expression we show a direct correlation of apoE expression and HCV infectivity, whereas no correlation exists with viral protein expression. Mutating the HSPG binding domain (HSPG-BD) of apoE revealed key residues that are critical for mediating HCV infection. Furthermore, a novel synthetic peptide that mimics apoE's HSPG-BD directly and competitively inhibits HCV infection. Genetic knockdown of the HSPG proteins syndecan (SDC) 1 and 4 revealed that SDC4 principally mediates HCV entry. Our data demonstrate that HCV uses apoE-SDC4 interactions to enter hepatoma cells and establish infection. Targeting apoE-SDC interactions could be an alternative strategy for blocking HCV entry, a critical step in maintaining chronic HCV infection

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Ancient Martian aeolian processes and palaeomorphology reconstructed from the Stimson formation on the lower slope of Aeolis Mons, Gale crater, Mars

Reconstruction of the palaeoenvironmental context of Martian sedimentary rocks is central to studies of ancient Martian habitability and regional palaeoclimate history. This paper reports the analysis of a distinct aeolian deposit preserved in Gale crater, Mars, and evaluates its palaeomorphology, the processes responsible for its deposition, and its implications for Gale crater geological history and regional palaeoclimate. Whilst exploring the sedimentary succession cropping out on the northern flank of Aeolis Mons, Gale crater, the Mars Science Laboratory rover Curiosity encountered a decametre‐thick sandstone succession, named the Stimson formation, unconformably overlying lacustrine deposits of the Murray formation. The sandstone contains sand grains characterized by high roundness and sphericity, and cross‐bedding on the order of 1 m in thickness, separated by sub‐horizontal bounding surfaces traceable for tens of metres across outcrops. The cross‐beds are composed of uniform thickness cross‐laminations interpreted as wind‐ripple strata. Cross‐sets are separated by sub‐horizontal bounding surfaces traceable for tens of metres across outcrops that are interpreted as dune migration surfaces. Grain characteristics and presence of wind‐ripple strata indicate deposition of the Stimson formation by aeolian processes. The absence of features characteristic of damp or wet aeolian sediment accumulation indicate deposition in a dry aeolian system. Reconstruction of the palaeogeomorphology suggests that the Stimson dune field was composed largely of simple sinuous crescentic dunes with a height of ca 10 m, and wavelengths of ca 150 m, with local development of complex dunes. Analysis of cross‐strata dip azimuths indicates that the general dune migration direction and hence net sediment transport was towards the north‐east. The juxtaposition of a dry aeolian system unconformably above the lacustrine Murray formation represents starkly contrasting palaeoenvironmental and palaeoclimatic conditions. Stratigraphic relationships indicate that this transition records a significant break in time, with the Stimson formation being deposited after the Murray formation and stratigraphically higher Mount Sharp group rocks had been buried, lithified and subsequently eroded