Abstract
Quantifying mutant or variable allele frequencies (VAFs) of ≤10−3 using next-generation sequencing (NGS) has utility in both clinical and nonclinical settings. Two common approaches for ...quantifying VAFs using NGS are tagged single-strand sequencing and duplex sequencing. While duplex sequencing is reported to have sensitivity up to 10−8 VAF, it is not a quick, easy, or inexpensive method. We report a method for quantifying VAFs that are ≥10−4 that is as easy and quick for processing samples as standard sequencing kits, yet less expensive than the kits. The method was developed using PCR fragment-based VAFs of Kras codon 12 in log10 increments from 10−5 to 10−1, then applied and tested on native genomic DNA. For both sources of DNA, there is a proportional increase in the observed VAF to input VAF from 10−4 to 100% mutant samples. Variability of quantitation was evaluated within experimental replicates and shown to be consistent across sample preparations. The error at each successive base read was evaluated to determine if there is a limit of read length for quantitation of ≥10−4, and it was determined that read lengths up to 70 bases are reliable for quantitation. The method described here is adaptable to various oncogene or tumor suppressor gene targets, with the potential to implement multiplexing at the initial tagging step. While easy to perform manually, it is also suited for robotic handling and batch processing of samples, facilitating detection and quantitation of genetic carcinogenic biomarkers before tumor formation or in normal-appearing tissue.
•Post-synthesis annealing of arc-melted polycrystalline Fe3Ga4 leads to controllable changes in magnetic ordering temperatures.•External applied pressure showed a similar trend as observed in unit ...cell volume changes induced by thermal annealing.•Reduced volume in the lattice reduced antiferromagnetic-to-ferromagnetic transition temperature to the room-temperature regime.•The tuning of this transition to room-temperature opens the possibility for exploiting this magnetic ordering change in devices.•Volume changes alter the low temperature transition in the as well as the metamagnetic behavior in the antiferromagnetic phase.
The effects of post-synthesis annealing temperature on arc-melted samples of Fe3Ga4 has been studied to investigate changes in crystallographic and magnetic properties induced by annealing. Results show a significant trend in the evolution of the (incommensurate spin density wave) ISDW-FM (ferromagnetic) transition temperature as a function of the refined unit cell volume in annealed samples. Strikingly, this trend allowed for the tuning of the transition temperature down to room-temperature (300 K) whilst maintaining a sharp transition in temperature, opening the door to the use of Fe3Ga4 in functional devices. Crystallographic analysis through Rietveld refinement of high-resolution x-ray diffraction data has showed that arc-melted stoichiometric Fe3Ga4 is multi-phase regardless of annealing temperature with a minor phase of FeGa3 decreasing in phase fraction at higher annealing temperature. In order to validate the trend in ISDW-FM transition temperature with regard to unit cell volume, high pressure magnetometry was performed. This showed that the FM-ISDW (~ 68 K) and ISDW-FM (~ 360 K) transition temperatures could be tuned, increased and decreased respectively, linearly with external pressure. Thus, external pressure and the ensuing crystallographic changes minimize the temperature range of the stability of the ISDW pointing toward the importance of structural properties on the mechanism for the formation of the intermediate ISDW phase. These results show how this model system can be tuned as well as highlighting the need for future high-pressure crystallography and related single crystal measurements to understand the mechanism and nature of the intermediate ISDW phase to be exploited in future devices.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
IntroductionEffective communication can help optimise healthcare interactions and patient outcomes. However, few interventions have been tested clinically, subjected to cost-effectiveness analysis or ...are sufficiently brief and well-described for implementation in primary care. This paper presents the protocol for determining the effectiveness and cost-effectiveness of a rigorously developed brief eLearning tool, EMPathicO, among patients with and without musculoskeletal pain.Methods and analysisA cluster randomised controlled trial in general practitioner (GP) surgeries in England and Wales serving patients from diverse geographic, socioeconomic and ethnic backgrounds. GP surgeries are randomised (1:1) to receive EMPathicO e-learning immediately, or at trial end. Eligible practitioners (eg, GPs, physiotherapists and nurse practitioners) are involved in managing primary care patients with musculoskeletal pain. Patient recruitment is managed by practice staff and researchers. Target recruitment is 840 adults with and 840 without musculoskeletal pain consulting face-to-face, by telephone or video. Patients complete web-based questionnaires at preconsultation baseline, 1 week and 1, 3 and 6 months later. There are two patient-reported primary outcomes: pain intensity and patient enablement. Cost-effectiveness is considered from the National Health Service and societal perspectives. Secondary and process measures include practitioner patterns of use of EMPathicO, practitioner-reported self-efficacy and intentions, patient-reported symptom severity, quality of life, satisfaction, perceptions of practitioner empathy and optimism, treatment expectancies, anxiety, depression and continuity of care. Purposive subsamples of patients, practitioners and practice staff take part in up to two qualitative, semistructured interviews.Ethics approval and disseminationApproved by the South Central Hampshire B Research Ethics Committee on 1 July 2022 and the Health Research Authority and Health and Care Research Wales on 6 July 2022 (REC reference 22/SC/0145; IRAS project ID 312208). Results will be disseminated via peer-reviewed academic publications, conference presentations and patient and practitioner outlets. If successful, EMPathicO could quickly be made available at a low cost to primary care practices across the country.Trial registration number ISRCTN18010240.
We studied coatings on five glass‐rich basalts from the Big Island of Hawaii. The coatings are characterized by complex morphologies and their thicknesses range from 3 to 80 μm. Coating chemistries ...are predominantly hydrated silica with minor amounts of Fe‐, Ti‐, and S‐bearing materials. Visible, near infrared, and thermal infrared spectra of the coatings demonstrate that coatings as thin as 3 μm mask the spectral character of the substrate basalt. The Fe‐, Ti‐, and S‐bearing components control the VNIR coating spectra. The hydrated silica component of the coatings dominates the thermal infrared coating spectra. The coating chemistries are consistent with leaching and/or dissolution of basalt glass or tephra in aqueous, acidic, and oxidizing conditions and subsequent precipitation of insoluble phases. Similar alteration conditions are thought to have occurred on Mars, making formation of such coatings on Martian lithologies feasible. Given the capabilities of various Mars missions, if coatings like those of this study were present on Martian lithologies, their chemical and/or spectral signatures would be detectable. Chemical and spectral data from thin (≤10 μm), Fe‐ and Ti‐bearing coatings are consistent with phases capable of explaining the high‐SiO2 component of Type 2 surfaces previously identified in the Thermal Emission Spectrometer data set and are potentially consistent with spectral data from the Mars Exploration Rovers.
Abstract
4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is one of the key tobacco-specific nitrosamines that plays an important role in human lung carcinogenesis. However, repeated inhalation ...toxicity data on NNK, which is more directly relevant to cigarette smoking, are currently limited. In the present study, the subacute inhalation toxicity of NNK was evaluated in Sprague Dawley rats. Both sexes (9–10 weeks age; 16 rats/sex/group) were exposed by nose-only inhalation to air, vehicle control (75% propylene glycol), or 0.8, 3.2, 12.5, or 50 mg/kg body weight (BW)/day of NNK (NNK aerosol concentrations: 0, 0, 0.03, 0.11, 0.41, or 1.65 mg/L air) for 1 h/day for 14 consecutive days. Toxicity was evaluated by assessing body and organ weights; food consumption; clinical pathology; histopathology observations; blood, urine, and tissue levels of NNK, its major metabolite 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), and their glucuronides (reported as total NNK, tNNK, and total NNAL, tNNAL, respectively); O6-methylguanine DNA adduct formation; and blood and bone marrow micronucleus frequency. Whether the subacute inhalation toxicity of NNK followed Haber’s Rule was also determined using additional animals exposed 4 h/day. The results showed that NNK exposure caused multiple significant adverse effects, with the most sensitive endpoint being non-neoplastic histopathological lesions in the nose. The lowest-observed-adverse-effect level (LOAEL) was 0.8 mg/kg BW/day or 0.03 mg/L air for 1 h/day for both sexes. An assessment of Haber’s Rule indicated that 14-day inhalation exposure to the same dose at a lower concentration of NNK aerosol for a longer time (4 h daily) resulted in greater adverse effects than exposure to a higher concentration of NNK aerosol for a shorter time (1 h daily).
Abstract
The tobacco-specific nitrosamine NNK 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone is found in tobacco products and tobacco smoke. NNK is a potent genotoxin and human lung carcinogen; ...however, there are limited inhalation data for the toxicokinetics (TK) and genotoxicity of NNK in vivo. In the present study, a single dose of 5 × 10−5, 5 × 10−3, 0.1, or 50 mg/kg body weight (BW) of NNK, 75% propylene glycol (vehicle control), or air (sham control) was administered to male Sprague-Dawley (SD) rats (9–10 weeks age) via nose-only inhalation (INH) exposure for 1 h. For comparison, the same doses of NNK were administered to male SD rats via intraperitoneal injection (IP) and oral gavage (PO). Plasma, urine, and tissue specimens were collected at designated time points and analyzed for levels of NNK and its major metabolite 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) and tissue levels of DNA adduct O6-methylguanine by LC/MS/MS. TK data analysis was performed using a non-linear regression program. For the genotoxicity subgroup, tissues were collected at 3 h post-dosing for comet assay analysis. Overall, the TK data indicated that NNK was rapidly absorbed and metabolized extensively to NNAL after NNK administration via the three routes. The IP route had the greatest systemic exposure to NNK. NNK metabolism to NNAL appeared to be more efficient via INH than IP or PO. NNK induced significant increases in DNA damage in multiple tissues via the three routes. The results of this study provide new information and understanding of the TK and genotoxicity of NNK.
4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is one of the key tobacco-specific nitrosamines that plays an important role in human lung carcinogenesis. Repeated dose inhalation toxicity data ...on NNK, particularly relevant to cigarette smoking, however, is surprisingly limited. Hence, there is a lack of direct information available on the carcinogenic and potential non-carcinogenic effects of NNK via inhalational route exposure. In the present study, the subchronic inhalation toxicity of NNK was evaluated in Sprague Dawley rats. Both sexes (9–10 weeks age; 23 rats/sex/group) were exposed by nose-only inhalation to air, vehicle control (75% propylene glycol), or 0.2, 0.8, 3.2, or 7.8 mg/kg body weight (BW)/day of NNK (NNK aerosol concentrations: 0, 0, 0.0066, 0.026, 0.11, or 0.26 mg/L air) for 1 h/day for 90 consecutive days. Toxicity was evaluated by assessing body weights; food consumption; clinical pathology; histopathology; organ weights; blood, urine, and tissue levels of NNK, its major metabolite 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), and their glucuronides (reported as total NNK, tNNK, and total NNAL, tNNAL, respectively); tissue levels of the DNA adduct O6-methylguanine; blood and bone marrow micronucleus (MN) frequency; and bone marrow DNA strand breaks (comet assay). The results showed that NNK exposure caused multiple significant adverse effects, with the most sensitive endpoint being non-neoplastic lesions in the nose. Although the genotoxic biomarker O6-methylguanine was detected, genotoxicity from NNK exposure was negative in the MN and comet assays. The Lowest-Observed-Adverse-Effect-Level (LOAEL) was 0.8 mg/kg BW/day or 0.026 mg/L air of NNK for 1 h/day for both sexes. The No-Observed-Adverse-Effect-Level (NOAEL) was 0.2 mg/kg BW/day or 0.0066 mg/L air of NNK for 1 h/day for both sexes. The results of this study provide new information relevant to assessing the human exposure hazard of NNK.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data ...stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Metallic Fe3Ga4 displays a complex magnetic phase diagram that supports an intermediate antiferromagnetic (AFM) helical spin structure (HSS) state at room temperature which lies between two ...ferromagnetic (FM) phases. Magnetic measurements along the three crystallographic axes were performed in order to develop a model for the temperature and field dependence of the HSS state. These results show that the AFM state is a helically ordered spiral propagating along the c-axis with the magnetic moments rotating in the ab-plane. Under applied magnetic field, the AFM state exhibits a metamagnetic transition to conical ordering before entering a fully field-polarized FM state at high fields. The conical ordering in the AFM state is anisotropic even within the ab-plane and may gives rise to Berry phase effects in transport measurements. Metallic conductivity from density of states computations was confirmed through resistivity measurements and no anomalous behavior was observed through the various magnetic transitions.
•Magnetic measurements on aligned single crystals of Fe3Ga4 were performed to understand the magnetic ordering.•Metamagnetic transitions were observed in the AFM phase as the ab-plane helical order evolves with increased field.•The metallic nature of Fe3Ga4 was confirmed though electrical resistivity measurements and through density of states calculations.•Extensive density functional theory (DFT) calculations were performed to understand the magnetic ground state of this system.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Localized provoked vulvodynia (LPV) is a chronic pain condition without an identifiable cause that is localized to a portion of the vulva and provoked by pressure or touch. LPV is a commonly ...occurring but poorly understood condition lacking consensus on management.
This scoping review used Arksey and O'Malley's approach to identify and evaluate literature published between 2010 and 2023 that addressed the question: What is the current evidence on the efficacy or effectiveness of pharmacological treatments in the management of LPV?
This review evaluated 18 papers reporting on the efficacy or effectiveness of oral, topical, and injectable medications. Seven of the studies were randomized controlled trials. Oral gabapentin and oral desipramine showed some improvement in sexual function compared to placebo. Small sample sizes and methodological issues limited confidence in interpreting findings. Pain was reduced in descriptive studies of tricyclic antidepressants, milnacipran, injectable anesthetics, and botulinum toxin. Where pain did not improve with treatment, some oral medications improved participants' mood and sexual function. Some topical agents may be effective in reducing peripherally mediated neuropathic pain. Botulinum toxin was the most well-studied injectable but yielded mixed outcomes related to pain, quality of life, and sexual function.
There is a lack of convincing evidence to draw conclusions about the efficacy or effectiveness of pharmacological therapies for LPV. The breadth of therapies for treating LPV warrants the development of evidence-based, consensus guidelines for measuring treatment outcomes and improving comparisons across studies. Recommendations for research include addressing methodological shortcomings and diversifying the participant pool to increase the generalizability of findings.
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IJS, NUK, UL, UM, UPUK, VSZLJ
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