With the expansion of soil transmitted helminth (STH) intervention efforts and the corresponding decline in infection prevalence, there is an increased need for sensitive and specific STH diagnostic ...assays. Previously, through next generation sequencing (NGS)-based identification and targeting of non-coding, high copy-number repetitive DNA sequences, we described the development of a panel of improved quantitative real-time PCR (qPCR)-based assays for the detection of Necator americanus, Ancylostoma duodenale, Ancylostoma ceylanicum, Trichuris trichiura, and Strongyloides stercoralis. However, due to the phenomenon of chromosome diminution, a similar assay based on high copy-number repetitive DNA was not developed for the detection of Ascaris lumbricoides. Recently, the publication of a reference-level germline genome sequence for A. lumbricoides has facilitated our development of an improved assay for this human pathogen of vast global importance.
Repurposing raw DNA sequence reads from a previously published Illumina-generated, NGS-based A. lumbricoides germline genome sequencing project, we performed a cluster-based repeat analysis utilizing RepeatExplorer2 software. This analysis identified the most prevalent repetitive DNA element of the A. lumbricoides germline genome (AGR, Ascaris germline repeat), which was then used to develop an improved qPCR assay. During experimental validation, this assay demonstrated a fold increase in sensitivity of ~3,100, as determined by relative Cq values, when compared with an assay utilizing a previously published, frequently employed, ribosomal internal transcribed spacer (ITS) DNA target. A comparative analysis of 2,784 field-collected samples was then performed, successfully verifying this improved sensitivity.
Through analysis of the germline genome sequence of A. lumbricoides, a vastly improved qPCR assay has been developed. This assay, utilizing a high copy-number repeat target found in eggs and embryos (the AGR repeat), will improve prevalence estimates that are fundamental to the programmatic decision-making process, while simultaneously strengthening mathematical models used to examine STH infection rates. Furthermore, through the identification of an optimal target for PCR, future assay development efforts will also benefit, as the identity of the optimized repeat DNA target is likely to remain unchanged despite continued improvement in PCR-based diagnostic technologies.
Abstract
BACKGROUND
Osteoporotic and neoplastic vertebral compression fractures (VCF) are common and painful, threatening quality of life and increasing risk of morbidity and mortality. Balloon ...kyphoplasty is a percutaneous option for treating painful cancer- and osteoporosis-related VCFs, supported by 2 randomized trials demonstrating efficacy benefits of BKP over nonsurgical care.
OBJECTIVE
To investigate 12-mo disability, quality of life, and safety outcomes specifically in a Medicare-eligible population, representing characteristic patients seen in routine clinical practice.
METHODS
A total of 354 patients with painful VCFs were enrolled at 24 US sites with 350 undergoing kyphoplasty. Four coprimary endpoints—Numerical Rating Scale (NRS) back pain, Oswestry Disability Index (ODI), Short Form-36 Questionnaire Physical Component Summary (SF-36v2 PCS), EuroQol-5-Domain (EQ-5D)—were evaluated for statistically significant improvement 3 mo after kyphoplasty. Data were collected at baseline, 7 d, and 1, 3, 6, and 12 mo (www.clinicaltrials.gov registration NCT01871519).
RESULTS
At the 3-mo primary endpoint, NRS improved from 8.7 to 2.7 and ODI improved from 63.4 to 27.1; SF-36 PCS was 24.2 at baseline improving to 36.6, and EQ-5D improved from 0.383 to 0.746 (P < .001 for each). These outcomes were statistically significant at every follow-up time point. Five device-/procedure-related adverse events, intraoperative asymptomatic balloon rupture, rib pain, and aspiration pneumonia, and a new VCF 25 d postprocedure, and myocardial infarction 105 d postprocedure were reported and each resolved with proper treatment.
CONCLUSION
This large, prospective, clinical study demonstrates that kyphoplasty is a safe, effective, and durable procedure for treating patients with painful VCF due to osteoporosis or cancer.
Lack of uniformity and generation of defects including grain boundaries and wrinkles in graphene coatings synthesized using chemical vapour deposition (CVD) adversely affect the durability of these ...coatings. In order to control the defect density and to improve the durability of corrosion resistance of the resultant graphene coating, a fundamental understanding of the influence of the CVD parameters on the defect density is of utmost importance. In this study, the influences of hydrogen flow during graphene growth and the cooling rate on the defect density and barrier properties of a graphene coating have been investigated. A thorough microscopic and spectroscopic investigation revealed that (i) slow cooling hindered the formation of graphene coating irrespective of the presence or absence of hydrogen flow, and (ii) under rapid cooling condition, absence of hydrogen flow restricted wrinkle formation on the resultant coating. Diminished wrinkle formation in absence of hydrogen flow significantly improved the durability of the resultant coating. Based on an in-depth electrochemical impedance spectroscopic investigation, a mechanism has been proposed, which was further corroborated with the post-corrosion analyses using X-ray photoelectron spectroscopy and scanning electron microscopy. This study provides a new direction to achieve graphene coatings with minimal defect density and excellent barrier properties.
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•Pt0.25Cu0.75/C catalysts were prepared & tested for ethanol oxidation activity.•The preparation method alters the Pt-Cu particle size and crystalline composition.•Heat treatment at ...700°C leads to the formation of the Pt-Cu intermetallic phase.•The Pt-Cu intermetallic phase has increased activity towards ethanol oxidation.
In this study, the Pt-Cu/C alloy with nominal composition of Pt0.25Cu0.75 was produced via three different methods impregnation, impregnation in the presence of sodium citrate additive and microwave assisted polyol method. Each method produced catalysts with differing structural and electrochemical properties. These catalysts were also heat treated to induce changes in the crystalline structure which in turn altered the activity towards the ethanol oxidation reaction (EOR). The crystalline structure, particle dispersion and chemical composition of the Pt-Cu samples were studied by Thermogravimetric Analysis (TGA), X-ray Powder Diffraction (XRD), Transmission Electron Microscopy (TEM) Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES) and X-ray photoelectron spectroscopy (XPS). The ICP, XPS, TGA and TEM results indicate each synthetic method produced catalysts with different chemical composition, metal loadings and particle dispersion. The XRD analysis showed that the heat treatment of the Pt-Cu/C samples resulted in ordered intermetallic crystalline structures such as PtCu and PtCu3. The highest EOR activity was observed for samples rich in intermetallic ordered phases, PtCu in particular. XPS and CO stripping measurements indicates that the electronic structure of the Pt-rich surface of the Pt-Cu particles was altered due to formation of intermetallic phases and the Cu-rich core.
Mutations in the BRCA1 and BRCA2 genes are found in most families with cases of both breast and ovarian cancer or with many cases of early-onset breast cancer. However, in an outbred population, the ...prevalence of BRCA1 and BRCA2 mutations in patients with breast cancer who were unselected for a family history of this disease has not been determined.
Mutations in the BRCA1 and BRCA2 genes were detected in blood samples from two population-based series of young patients with breast cancer from Britain.
Mutations were detected in 15 (5.9%) of 254 women diagnosed with breast cancer before age 36 years (nine 3.5% in BRCA1 and six 2.4% in BRCA2) and in 15 (4.1%) of 363 women diagnosed from ages 36 through 45 years (seven 1.9% in BRCA1 and eight 2.2% in BRCA2). Eleven percent (six of 55) of patients with a first-degree relative who developed ovarian cancer or breast cancer by age 60 years were mutation carriers, compared with 45% (five of 11) of patients with two or more affected first- or second-degree relatives. The standardized incidence ratio for breast cancer in mothers and sisters was 365 (five observed and 1.37 expected) for 30 mutation carriers and 199 (64 observed and 32.13 expected) for 587 noncarriers. If we assume recent penetrance estimates, the respective proportions of BRCA1 and BRCA2 mutation carriers are 3.1% and 3.0%, respectively, of patients with breast cancer who are younger than age 50 years, 0.49% and 0.84% of patients with breast cancer who are age 50 years or older, and 0.11% and 0.12% of women in the general population.
Mutations in the BRCA1 and BRCA2 genes make approximately equal contributions to early-onset breast cancer in Britain and account for a small proportion of the familial risk of breast cancer.
Women genetically predisposed to breast cancer often develop the disease at a young age when dense breast tissue reduces the sensitivity of X-ray mammography. Our aim was, therefore, to compare ...contrast enhanced magnetic resonance imaging (CE MRI) with mammography for screening.
We did a prospective multicentre cohort study in 649 women aged 35–49 years with a strong family history of breast cancer or a high probability of a
BRCA1,
BRCA2, or
TP53 mutation. We recruited participants from 22 centres in the UK, and offered the women annual screening with CE MRI and mammography for 2–7 years.
We diagnosed 35 cancers in the 649 women screened with both mammography and CE MRI (1881 screens): 19 by CE MRI only, six by mammography only, and eight by both, with two interval cases. Sensitivity was significantly higher for CE MRI (77%, 95% CI 60–90) than for mammography (40%, 24–58; p=0·01), and was 94% (81–99) when both methods were used. Specificity was 93% (92–95) for mammography, 81% (80–83) for CE MRI (p<0·0001), and 77% (75–79) with both methods. The difference between CE MRI and mammography sensitivities was particularly pronounced in
BRCA1 carriers (13 cancers; 92%
vs 23%, p=0·004).
Our findings indicate that CE MRI is more sensitive than mammography for cancer detection. Specificity for both procedures was acceptable. Despite a high proportion of grade 3 cancers, tumours were small and few women were node positive. Annual screening, combining CE MRI and mammography, would detect most tumours in this risk group.
The Flinton Group is a metasedimentary succession of the Grenville Province in SE Ontario, potentially allowing insight into the tectono‐thermal evolution of continental crust during the ...Mesoproterozoic. At its Green Bay locality, Flinton Group metapelites of the staurolite zone contain abundant, post‐kinematic garnet porphyroblasts. Whereas the larger garnet crystals are typically impinged, smaller crystals are isolated from each other, occasionally exhibiting elongated shapes with apparently trigonal morphology. Central sections of the garnet population of a representative sample reveal that garnet is composed of different compositional and microstructural domains. In the largest crystals of the population, garnet contains rectangular to rhombic domains, marked by sharp increases in the concentrations of Nb, V, Ti, and Cr. These domains are associated with irregularly shaped patches, characterized by spatially heterogenous enrichments of Ca and LREE, and depletions in the contents of P, Y, MREE, and HREE, accompanied by increased densities of comparatively coarse‐grained quartz inclusions hosting apatite. Microstructural relationships indicate that these domains correspond to portions of garnet that pseudomorphed biotite, with the enrichments of Nb, V, Ti, and Cr outlining the original biotite shapes. The compositional patterns formed by Ca, P, Y, and REE indicate that apatite participated in the grain‐fluid interactions that operated during the metasomatic replacement of biotite by garnet. The statistical analyses of the garnet number and size distributions confirm that garnet initially nucleated on biotite, controlled by the kinetics of attachment and detachment processes at the garnet/biotite interface, resulting in the typical impingement habit. In situ Lu–Hf garnet geochronology applied to garnet that did not pseudomorph biotite, and hence is enriched in HREE, points to a first metamorphic event at c. 1080
± 31 Ma. Subsequent pseudomorphism of staurolite by white mica in a Al2O3‐ and FeO‐mobile system resulted in the concomitant crystallization of a new garnet generation, forming overgrowths on the first garnet generation and nuclei in the fine‐grained matrix. Garnet that nucleated during this event grew to isolated and elongated crystals with apparently trigonal morphology, aligned in a direction c. perpendicular to the rock matrix foliation. The open‐system behaviour during this event limits the use of whole‐rock‐based geochronological and thermobarometrical applications. However, previously published in situ U–Pb ages of monazite included in the rims of the garnet crystals and in the rock matrix indicate that this event took place at c. 976
± 4 Ma, likely associated with a period of increased hydrothermal activity late in the metamorphic history of the Grenvillian Orogeny. Diffusion geospeedometry calculations indicate that garnet growth during this hydrothermal event lasted for less than 6 Myr.
Intestinal homeostasis is underpinned by LGR5+ve crypt-base columnar stem cells (CBCs), but following injury, dedifferentiation results in the emergence of LGR5−ve regenerative stem cell populations ...(RSCs), characterized by fetal transcriptional profiles. Neoplasia hijacks regenerative signaling, so we assessed the distribution of CBCs and RSCs in mouse and human intestinal tumors. Using combined molecular-morphological analysis, we demonstrate variable expression of stem cell markers across a range of lesions. The degree of CBC-RSC admixture was associated with both epithelial mutation and microenvironmental signaling disruption and could be mapped across disease molecular subtypes. The CBC-RSC equilibrium was adaptive, with a dynamic response to acute selective pressure, and adaptability was associated with chemoresistance. We propose a fitness landscape model where individual tumors have equilibrated stem cell population distributions along a CBC-RSC phenotypic axis. Cellular plasticity is represented by position shift along this axis and is influenced by cell-intrinsic, extrinsic, and therapeutic selective pressures.
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•Tumors have Lgr5+ve crypt base columnar (CBC) and Lgr5−ve regenerative stem cells (RSCs)•Stem cell admixture can be measured from transcriptional data using the stem cell index•Stem phenotypes vary by genotype and subtype, shifting with cell signaling disruption•Phenotype shifts from selective pressures associate with poor response to chemotherapy
Gil Vasquez et al. demonstrate that intestinal tumors contain variable populations of stem cells whose admixture can be assessed using a transcriptional molecular tool—the stem cell index. Tumor stem cell molecular phenotype associated with lesion subtype and cell-intrinsic and extrinsic signaling disruption and shifted responsively to tumor selective pressures.
The Midcontinent Rift in the Lake Superior region of North America is one of the best preserved examples of an aborted Precambrian intercontinental rift, one that hosts a diverse suite of rock types ...in addition to the well-studied and voluminous rift-fill flood basalts. Although there is a growing database of high-precision age information for the main volcanic packages and the largest mafic intrusions, there is relatively little information available on the absolute timing of mafic-ultramafic intrusions, dyke swarms, and alkaline complexes, especially in the Ontario portion of the rift. We report new high-precision U-Pb ages for 29 samples, primarily collected in the Lake Nipigon area, Ontario. From these new age results, it is now possible to expand the known distribution of Geon 15 magmatism in the region, confirm an early stage of Midcontinent Rift mafic magmatism between 1150 and 1130 Ma, provide evidence that significant mafic-ultramafic magmatism occurred in the Lake Nipigon region slightly earlier (∼1115-1110 Ma) than the main stage of rift magmatism (1108-1094 Ma), and further document synchronous ∼1110-1100 Ma tholeiitic and alkaline magmatism.
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