Minor Contributor Research Articles

Development and validation of a fast and automated DNA identification line

The importance of DNA evidence for gaining investigative leads demands a fast workflow for forensic DNA profiling performed in large volumes. Therefore, we developed software solutions for automated DNA profile analysis, contamination check, major donor inference, DNA database (DDB) comparison and reporting of the conclusions. This represents the Fast DNA IDentification Line (FIDL) and this study describes its development, validation and implementation in criminal casework at the authors’ institute. This first implementation regards single donor profiles and major contributors to mixtures. The validation included testing of the software components on their own and examination of the performance of different DDB search strategies. Furthermore, end-to-end testing was performed under three conditions: (1) testing of scenarios that can occur in DNA casework practice, (2) tests using three months of previous casework data, and (3) testing in a casework production environment in parallel to standard casework practices. The same DNA database candidates were retrieved by this automated line as by the manual workflow. The data flow was correct, results were reproducible and robust, results requiring manual analysis were correctly flagged, and reported results were as expected. Overall, we found FIDL valid for use in casework practice in our institute. The results from FIDL are automatically reported within three working days from receiving the trace sample. This includes the time needed for registration of the case, DNA extraction, quantification, polymerase chain reaction and capillary electrophoresis. FIDL itself takes less than two hours from intake of the raw CE data to reporting. Reported conclusions are one of five options: (1) candidate retrieved from DDB, (2) no candidate retrieved from DDB, (3) high evidential value with regards to reference within the case, (4) results require examination of expert, or (5) insufficient amount of DNA obtained to generate a DNA profile. In our current process, the automated report is sent within three working days and a complete report, with confirmation of the FIDL results, and signed by a reporting officer is sent at a later time. The signed report may include additional analyses regarding e.g. minor contributors. The automated report with first case results is quickly available to the police enabling them to act upon the DNA results prior to receiving the full DNA report. This line enables a uniform and efficient manner of handling large numbers of traces and cases and provides high value investigative leads in the early stages of the investigation.

Varus morphology and its surgical implication in osteoarthritic knee and total knee arthroplasty

BackgroundKnee varus alignment represents a notorious cause of knee osteoarthritis. It can be caused by tibial deformity, combined tibial–femoral deformity and/or ligament imbalance. Understanding malalignment is crucial in total knee arthroplasty to restore frontal plane neutral mechanical axis. The aim of this study was to determine which factor contributes the most to varus osteoarthritic knee and its related surgical implications in performing a total knee arthroplasty.MethodsWe retrospectively evaluated 140 patients operated for total knee arthroplasty due to a varus knee. Full-leg hip to ankle preoperative X-rays were taken. Radiological parameters recorded were: mechanical axis deviation, hip–knee–ankle, anatomical–mechanical angle, medial neck shaft angle, mechanical lateral distal femoral angle (mLDFA), medial proximal tibial angle (MPTA), joint line convergence angle (JLCA), lateral proximal femoral angle, lateral distal tibial angle (LDTA), femoral bowing, and length of tibia and femur. We also determined ideals tibial and femoral cuts in mm according to mechanical alignment technique. A R2 was calculated based on the linear regression between the predicted values and the observed data.ResultsThe greatest contributor to arthritic varus (R = 0.444) was MPTA. Minor contributors were mLDFA (R = 0.076), JLCA (R = 0.1554), LDTA (R = 0.065), and femoral bowing (R = 0.049). We recorded an average of 7.6 mm in lateral tibial cut thickness to restore neutral alignment.ConclusionsThe radiological major contributor to osteoarthritic varus knee alignment is related to proximal tibia deformity. As a surgical consequence, during performing total knee arthroplasty, the majority of the correction should therefore be made on tibial cut.

Potential estrogenic background in aquatic laboratory cultivations.

Aquatic biotests are important tools targeting various effects in ecotoxicology, including endocrine disruption. Unintentional exposure of bioassay organisms to endocrine disruptors during cultivation or testing may interfere with assessed endpoints. We illustrate this issue on the example of laboratory phytoplankton cultivation, where possible sources of estrogenic compounds have been revealed. Fifty-four blank samples (water and fresh or cultivated growth media) were assessed by in vitro biotests for their estrogenicity, and major known estrogens originating from plastic materials, bisphenol A and alkylphenols, were analyzed in selected samples. The samples of freshly prepared growth medium elicited weak estrogenic response in bioassays and some samples of the aerated media caused responses even above the 50% of maximum of the reference compound (17β-estradiol, E2), while the samples from diverse laboratory water sources did not show significant estrogenic activity. The results identified substances contained in the growth medium as minor but reproducible contributors to estrogenicity in the cultivations. Sporadic but significant effects (up to 4.9 ng E2 equivalent/L) can be ascribed to compounds released from the used plastic materials during aeration of the cultivations. The potential sources of unintentional exposure to estrogenic compounds need to be considered in aquatic cultivations and biotests, since they could impact their outcomes, especially in arrangements assessing reproduction or whole life cycle biotests, or production of bioactive compounds by phytoplankton. The findings emphasize the necessity to assess all relevant blanks, ideally by sensitive high throughput in vitro assays that reflect also unknown pollutants and minimize all potential sources of background contamination. In vitro assays show very good applicability for this purpose since they enable to screen for any background estrogenicity of the used media and materials without the need of analyzing individual compounds, which often might not be known.

A comprehensive characterization of MPS-STR stutter artefacts

Interpretation of DNA evidence involving mixtures is challenging when alleles from minor contributors coincide with stutters from major contributors. To accommodate this, it is important to have a good understanding of stutter sequence formation trends. Here, multiple stutter types were characterized based on massively parallel sequencing (MPS) data from 387 single source samples, using the Verogen ForenSeq™ DNA Signature Prep kit. A beta regression model was used to investigate the relationship between the stutter proportion and candidate explanatory variables. In the final model, stutter proportions were explained by the length of the parental uninterrupted stretch (PTUS), which is comparable to block length of the missing motif (BLMM). Also, different stutter types (n+1, n-1, n+2, n-2, n0) were analyzed separately per locus. The fitted stutter models were then integrated into an extended probabilistic genotyping model based on EuroForMix (MPSproto). An illustrative minor/major mock mixture example is discussed. Evaluation of multiple types of stutters on a per locus basis improved the probabilistic genotyping result compared to the conventional EuroForMix model, using the LUS+ nomenclature.

Implications of high-Mg# adakitic magmatism at Hunter Ridge for arc magmatism of the Fiji - Vanuatu region

The mostly submarine Hunter Ridge, located in the SW Pacific records a ∼12 Myr to present history of magmatism related to the opening of the North Fiji Basin and subduction of oceanic lithosphere of the South Fiji Basin. Although the Hunter Ridge is probably composed primarily of an older Vitiaz-related basement, young volcanic features are present from Matthew Island to Kadavu Island. Some dredged volcanic rocks from these features have low-FeO and high-Mg# affinities, ranging from picrites to high-Mg# andesites and dacites. Elevated Sr (500 – 3400 ppm) and Sr/Y (50 – 240) coupled to fractionated (adakitic) rare-earth element patterns (La/Yb = 5 – 40, Gd/Yb = 1.5 – 5.7) indicate a garnet-signature derived from the melting of eclogite-facies basalt. Pacific-type MORB Nd-Hf-Pb isotopic ratios of these rocks contrast with the Indian-type MORB nature of the underlying North Fiji mantle but match closely the subducted South Fiji ocean crust. Low values of Th/La (< 0.15), Ba/La (< 22), unradiogenic 87Sr/86Sr (0.7026 – 0.7032) and Pacific-MORB Nd-Hf-Pb isotopic ratios indicate that sediment is a minor contributor to the source. The isotopic data clearly connect Hunter Ridge arc rocks of all compositions (picrites, low- to medium K2O arc lavas, basalts, high-Mg# andesites and dacites) to source components predominantly within the subducting plate. Unradiogenic 87Sr/86Sr (0.7026 – 0.7029) at high Sr abundances (700 – 1400 ppm) are common in hot-slab localities and are interpreted to reflect flux-melting of MORB under eclogite-facies conditions driven by dehydration in the underlying mantle of the subducting plate. Such an adakitic slab-melt component can be detected in more common (non-adakitic) arc rocks along the Hunter Ridge and Vanuatu arc as well. Evidence of slab melting along the western Pacific indicates that melting of subducting oceanic lithosphere is likely a common occurrence at convergent margins.

A New Computational Deconvolution Algorithm for the Analysis of Forensic DNA Mixtures with SNP Markers.

Single nucleotide polymorphisms (SNPs) support robust analysis on degraded DNA samples. However, the development of a systematic method to interpret the profiles derived from the mixtures is less studied, and it remains a challenge due to the bi-allelic nature of SNP markers. To improve the discriminating power of SNPs, this study explored bioinformatic strategies to analyze mixtures. Then, computer-generated mixtures were produced using real-world massively parallel sequencing (MPS) data from the single samples processed with the Precision ID Identity Panel. Moreover, the values of the frequency of major allele reads (FMAR) were calculated and applied as key parameters to deconvolve the two-person mixtures and estimate mixture ratios. Four custom R language scripts (three for autosomes and one for Y chromosome) were designed with the K-means clustering method as a core algorithm. Finally, the method was validated with real-world mixtures. The results indicated that the deconvolution accuracy for evenly balanced mixtures was 100% or close to 100%, which was the same as the deconvolution accuracy of inferring the genotypes of the major contributor of unevenly balanced mixtures. Meanwhile, the accuracy of inferring the genotypes of the minor contributor decreased as its proportion in the mixture decreased. Moreover, the estimated mixture ratio was almost equal to the actual ratio between 1:1 and 1:6. The method proposed in this study provides a new paradigm for mixture interpretation, especially for inferring contributor profiles of evenly balanced mixtures and the major contributor profile of unevenly balanced mixtures.

Who feeds on whom in semi-aquatic moss ecosystems?

Moss patches growing at the interface between terrestrial and limnic ecosystems (in the splash-water zone) are colonized by terrestrial, semi-aquatic, and aquatic animals. Besides being a refuge, mosses provide food resources, such as micro-algae, particulate organic matter, and moss tissues themselves. In this study, the standing stocks and isotopic signatures of both resources and consumers were measured to analyze the trophic channels utilized by moss-dwelling consumers in two semi-aquatic moss ecosystems of a stream and a lake. The mean total invertebrate abundance (± SD) in the lake mosses was 1109.08 ± 230.33 ind. 10gmossDW−1, which was ~4-fold higher than in the stream (265.37 ± 184.62 ind. 10gmossDW−1). We found that moss tissues were a fairly minor contributor to the diets of the invertebrates; instead the most important resource for invertebrates was the epiphytic biofilms growing on them. The moss-dwelling community in the lake occupied a larger isotopic space than in the stream, suggesting a lower trophic redundancy of the community in the lake. This was especially the case for the δ13C range, which was 39% larger in the lake than in the stream, where δ13C signatures appeared more focused. In contrast, the δ15N range of the invertebrate community associated with mosses was rather large and did not differ substantially between stream and lake. Dorylaimid nematodes, predatory dipters and water mites showed enriched δ15N signatures suggesting they could occupy apex positions in moss food webs despite their small body sizes. Our results suggested that mosses were not an important food resource, but instead their textural complexity enabled a coherent and relatively large invertebrate food web composed of detritivores, algivores, omnivores, predators, and probably parasites.

Current Controversies in Radiology on Cost, Reimbursement, and Price Transparency: AJR Expert Panel Narrative Review.

Many believe that fundamental reform of the U.S. health care system is overdue and necessary given rising national health care expenditures, poor performance on key population health metrics, meaningful health disparities, concerns about potential financial toxicity of care, inadequate price transparency, pending insolvency of Medicare Part A, increasing commercial insurance premiums, and large uninsured and underinsured populations. The Medicare Payment Advisory Commission, an independent congressional agency, believes that part of this reform includes redistribution of reimbursements away from specialties such as radiology. Thus, despite an increase in the Medicare population and spending, Medicare payments for medical imaging have been decreasing for years. Further, the No Surprises Act, a federal law intended to curb the problem of surprise medical billing, was repurposed in federal rulemaking to reduce reimbursement from commercial payers to certain specialties, including radiology. In this article, we examine challenges facing the U.S. health care system, focusing on cost, reimbursement, and price transparency and the role of radiology in addressing such challenges. Medical imaging is a minor contributor to national health care expenditures but has an outsized impact on patient care. The radiology community should work together to reinforce the value of medical imaging and reduce inappropriate utilization of low-value care.

ParC Variants in Mycoplasma genitalium: Trends over Time and Association with Moxifloxacin Failure.

Prevalence, trends, and treatment outcome estimates were generated for parC variants in macrolide-resistant Mycoplasma genitalium. Among 539 cases, the most common amino acid change was S83I, which increased from 13% in 2012 to 2013, to 23% in 2019 to 2020 (Ptrend = 0.046). From 381 moxifloxacin treatments, failure occurred in 58.7% (95% confidence interval [CI], 46.7 to 69.9) of cases with S83I. Other changes affecting S83 or D87 were uncommon and minor contributors to failure. The absence of S83I was highly predictive of moxifloxacin cure (96.4%; 95% CI, 93.7 to 98.2), highlighting diagnostic potential.

Assessing non-LUS stutter in DNA sequence data

Forensic DNA analysis is among the most well-recognized and well-developed forensic disciplines. The field’s use of DNA markers known as short tandem repeats (STRs) offer a robust means of discriminating individuals while also introducing challenges to the analysis. One of these challenges, stutter, is the result of a non-biological artifact introduced during PCR. The formation and amplification of these stutter products can occur at rates as high as 15–20% of the parent allele. The challenge inherent in this process is differentiating stutter artifacts from true alleles, particularly in the presence of a minor contributor. Traditionally, DNA profiles are obtained using capillary electrophoresis (CE), where amplified DNA fragments are separated by size, not sequence, and the identification of stutter is performed on a locus-specific level. The use of CE-based fragment data rather than sequence-based data, has limited the community’s understanding of the precise behavior of stutter. Massively parallel sequencing (MPS) data provides an opportunity to better characterize stutter, permitting a more accurate means of detecting both size- or longest uninterrupted stretch (LUS)-based stutter but also allele and motif-specific stutter characteristics. This study sheds light on the value of characterizing motif- and allele-specific stutter, including non-LUS stutter, when using MPS methods. Analysis and characterization of stutter sequences was performed using data generated from 539 samples amplified with the ForenSeq and PowerSeq 46GY library preparation kit and sequenced on the Illumina MiSeq FGx. Assessment of non-LUS stutter begins with calculating stutter rates for all potential stutter products at a given locus (and allele), additionally, the occurrence of these discrete stutter products were quantified. Results show that although the LUS sequence stutters at a higher rate than non-LUS motifs, the non-LUS stutter products do occur at detectable levels and potentially influence sequence-based mixture analysis. The data indicate that the stutter from one motif or allele can be distinguished from another motif or allele based on their unique stutter rates; however, the number of stutter products from each motif or allele may similarly make up the overall pool of stutter products. Motif- and allele-specific stutter models provide the most comprehensive analysis of sequence stutter rates and provide the ability to differentiate stutter sequences more accurately from true allele stutter. This information provides a foundation for including the characterization of non-LUS stutter products when analyzing DNA profiles, specifically mixtures with potential low-level contributors.

Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures

BackgroundsY-chromosomal haplotypes based on Y-short tandem repeats (STRs) and Y-single nucleotide polymorphisms/insertion and deletion polymorphisms (SNPs/InDels) are used to characterize paternal lineages of unknown male trace donors. However, Y-chromosomal genetic markers are not currently sufficient for precise individual identification. Microhaplotype (MH), generally < 200 bp on autosomes and consisting of two or more SNPs, was recently introduced in forensic genetics with the development of massive parallel sequencing technology and may facilitate identification and DNA mixture deconvolution. Therefore, combining the two kinds of genetic markers may be beneficial in many forensic scenarios, especially crime scenes with male suspects, such as sexual assault cases. MethodsIn the present study, we developed a novel MPS-based panel, Microhaplotype and Y-SNP/STR (MY), by multiplex PCR and 150-bp paired-end sequencing, including 114 Y-SNPs (twelve dominant Y-DNA haplogroups), 45 Y-STRs (N-1 stutter < 0.09; estimated mutation rate < 5 × 10−3), and 22 MHs (allele coverage ratio > 0.91; pairwise distance > 10 Mb). Additionally, MY system-based genotype pattern recognition (GPR), a regression-based method to identify the genotype pattern for each MH locus, is proposed for two-person DNA mixture deconvolution. We integrated 26 two-person genotype combinations into nine genotype patterns and validated the application range of GPR based on DNA profiles of ten sets of simulated male-male DNA mixtures (1:10–1:2). ResultsThe effective number of alleles (Ae) ranged from 3.62 to 14.72, with an average of 7.17, in 100 Chinese Guangdong Han individuals. The cumulative discrimination power was 1–5.00 × 10−31, and the cumulative power of exclusion was 1–5.00 × 10−8 and 1–4.85 × 10−12 for duo and trio paternity testing, respectively. Furthermore, the actual mixing ratio-depth of coverage (DoC) ratio (RDoC) regression relationships were established for different genetic markers and genotype patterns. In five overlapping areas, genotype differentiation of the major and minor contributors required likelihood ratio methods. In nonoverlapping areas, the genotype pattern could be recognized by comparing the observed RDoC and RDoC ranges. ConclusionThe GPR can be used to deconvolute two-person DNA mixtures (application range: 1:10–1:2) for individual identification.

Allele frequencies and minor contributor match statistic convergence using simulated population replicates.

Probabilistic genotyping permits a comparison of forensic evidence given hypotheses regarding the origin of observed short tandem repeat alleles in a mixed DNA profile. Using the publicly available R package forensim, it has been proposed that mixtures with non-contributors from low genetic diversity populations are more likely to be mistakenly identified as contributors to a mixture than non-contributors from high genetic diversity populations. We hypothesized that these observations are attributed to the unique distribution of alleles in the reference population and may not generalize to other samplings of the same population. We used forensim to simulate 200 US populations (50 each of self-reported African-American, Asian-American, European-American, and Hispanic descent). We compared likelihood ratios for 2400 mixtures to those derived from published data and identified stark differences. A minimum of ten population replicates were required to reduce observed differences relative to published data. Deviations from Hardy-Weinberg equilibrium and allele frequency distributions suggest that simulated populations should be sufficiently evaluated for expectations of population genetic parameters prior to use in DNA mixture modeling experiments. Overall, our findings support the utility of forensim and further describe its suitability to model population genetic parameters but suggest that a single population replicate (directly ascertained or simulated) may be insufficient to make conclusions about a given DNA mixture.

Particle Size, Mass Concentration, and Microbiota in Dental Aerosols

Many dental procedures are considered aerosol-generating procedures that may put the dental operator and patients at risk for cross-infection due to contamination from nasal secretions and saliva. This aerosol, depending on the size of the particles, may stay suspended in the air for hours. The primary objective of the study was to characterize the size and concentrations of particles emitted from 7 different dental procedures, as well as estimate the contribution of the nasal and salivary fluids of the patient to the microbiota in the emitted bioaerosol. This cross-sectional study was conducted in an open-concept dental clinic with multiple operators at the same time. Particle size characterization and mass and particle concentrations were done by using 2 direct reading instruments: Dust-Trak DRX (Model 8534) and optical particle sizer (Model 3330). Active bioaerosol sampling was done before and during procedures. Bayesian modeling (SourceTracker2) of long-reads of the 16S ribosomal DNA was used to estimate the contribution of the patients’ nasal and salivary fluids to the bioaerosol. Aerosols in most dental procedures were sub-PM1 dominant. Orthodontic debonding and denture adjustment consistently demonstrated more particles in the PM1, PM2.5, PM4, and PM10 ranges. The microbiota in bioaerosol samples were significantly different from saliva and nasal samples in both membership and abundance (P < 0.05) but not different from preoperative ambient air samples. A median of 80.15% of operator exposure was attributable to sources other than the patients’ salivary or nasal fluids. Median operator’s exposure from patients’ fluids ranged from 1.45% to 2.75%. Corridor microbiota showed more patients’ nasal bioaerosols than oral bioaerosols. High-volume saliva ejector and saliva ejector were effective in reducing bioaerosol escape. Patient nasal and salivary fluids are minor contributors to the operator’s bioaerosol exposure, which has important implications for COVID-19. Control of bioaerosolization of nasal fluids warrants further investigation.

A Time-to-Event Exposure-Response Model for Amyloid-Related Imaging Abnormalities Following Administration of Aducanumab to Subjects With Early Alzheimer Disease.

Amyloid-related imaging abnormalities with edema (ARIA-E) have been reported in patients with early Alzheimer disease treated with aducanumab. ARIA-E incidence has been observed to be dependent on both dose and apolipoprotein E4 carrier status. A time-to-event (TTE) approach applying data from 2 phase 3 studies (studies 301 and 302) was used to describe the effect of aducanumab serum exposure on the instantaneous risk of 2 end points: the first incidence of ARIA-E and time to ARIA-E resolution. A total of 3251 subjects with 826 events supported the TTE model to characterize the first ARIA-E event. The TTE resolution model was supported by data from 768 of 826 subjects who had ARIA-E resolved. Relationships between drug concentrations and ARIA-E events were modeled with a hazard function dependent on time, aducanumab serum concentrations, attenuation of aducanumab exposure effects with time (ie, potential for tolerance to aducanumab exposure), study, and apolipoprotein E4 carrier status. The TTE model showed that ARIA-E incidence rates were higher during the first 200 days, followed by a reduction in rates. The change in event rate reflects the attenuation of drug effect, thereby providing support for the current proposed titration regimen. Time to ARIA-E resolution was characterized by a constant baseline hazard with a probability to resolution affected by baseline ARIA-E severity and aducanumab concentration. ARIA-E resolution was found to be driven primarily by baseline hazard and time and suggested that aducanumab concentration effect is a minor contributor to the time to resolution of ARIA-E.

Identification of the vaginal secretion donor in mixture stains using polymorphic cSNPs on mRNA biomarkers

In recent years, RNA profiling has become an important technique in identifying the origin of human body fluids/tissues. Both perpetrators and victims can be identified from stains involving vaginal secretions (VS), such as sperm/VS mixtures left on condoms, bed sheets, or papers, etc. Body fluid specific RNA typing could link the source of body fluids/tissues and the identity of the donor. In this study, we aimed to trace the donor of VS in mixture stains using body fluid-specific mRNA markers and construct a coding single nucleotide polymorphism (cSNP) typing system for VS. We screened 8 VS-specific mRNA biomarkers (MUC4, SFTA2, CYP2A6, MYOZ1, FUT6, ESR1, SPINK5, and SERPINB13) encompassing 18 cSNPs. The RNA obtained from various body fluid/tissue samples was treated with reverse transcription polymerase chain reaction (RT-PCR) and then followed by a multiplex PCR and SNaPshot mini-sequencing assay. The detection limit of the assay was 0.08 ng RNA. For single-source body fluid, the positive cSNP typing was only shown in VS and void in non-VS body fluids/tissues. For laboratory-generated VS-containing mixtures, the minor VS contributor could be successfully detected at a ratio of 1:10–1:500. We also confirmed the concordance of DNA typing and mRNA typing for the cSNPs in this system. In summary, we established an 18-cSNP typing system for VS with high sensitivity and specificity, which could identify both the donor and the tissue origin simultaneously. This was shown to be a powerful tool for identifying the VS donor in those VS-containing mixture stains.

Monte Carlo simulations of nanodosimetry and radiolytic species production for monoenergetic proton and electron beams: Benchmarking of GEANT4-DNA and LPCHEM codes.

In hadrontherapy, biophysical models can be used to predict the biological effect received by cancerous tissues and organs at risk. The input data of these models generally consist of information on nano/micro dosimetric quantities and, concerning some models, reactive species produced in water radiolysis. In order to fully account for the radiation stochastic effects, these input data have to be provided by Monte Carlo track structure (MCTS) codes allowing to estimate physical, physico-chemical, and chemical effects of radiation at the molecular scale. The objective of this study is to benchmark two MCTS codes, Geant4-DNA and LPCHEM, that are useful codes for estimating the biological effects of ions during radiation therapy treatments. In this study we considered the simulation of specific energy spectra for monoenergetic proton beams (10 MeV) as well as radiolysis species production for both electron (1 MeV) and proton (10 MeV) beams with Geant4-DNA and LPCHEM codes. Options 2, 4, and 6 of the Geant4-DNA physics lists have been benchmarked against LPCHEM. We compared probability distributions of energy transfer points in cylindrical nanometric targets (10nm) positioned in a liquid water box. Then, radiochemical species (· OH, , , H2 , and yields simulated between 10-12 and 10-6 s after irradiation are compared. Overall, the specific energy spectra and the chemical yields obtained by the two codes are in good agreement considering the uncertainties on experimental data used to calibrate the parameters of the MCTS codes. For 10 MeV proton beams, ionization and excitation processes are the major contributors to the specific energy deposition (larger than 90%) while attachment, solvation, and vibration processes are minor contributors. LPCHEM simulates tracks with slightly more concentrated energy depositions than Geant4-DNA which translates into slightly faster recombination than Geant4-DNA. Relative deviations (CEV ) with respect to the average of evolution rates of the radical yields between 10-12 and 10-6 s remain below 10%. When comparing execution times between the codes, we showed that LPCHEM is faster than Geant4-DNA by a factor of about four for 1000 primary particles in all simulation stages (physical, physico-chemical, and chemical). In multi-thread mode (four threads), Geant4-DNA computing times are reduced but remain slower than LPCHEM by ∼20% up to ∼50%. For the first time, the entire physical, physico-chemical, and chemical models of two track structure Monte Carlo codes have been benchmarked along with an extensive analysis on the effects on the water radiolysis simulation. This study opens up new perspectives in using specific energy distributions and radiolytic species yields from monoenergetic ions in biophysical models integrated to Monte Carlo software.

Cerato-platanin protein 1 is not critical for Fusarium graminearum growth and aggressiveness, but its overexpression provides an edge to Fusarium head blight in wheat

Fusarium graminearum is a mycotoxin-producing pathogen involved in Fusarium head blight (FHB) disease of cereals, and is responsible for compromising grain yield and quality.Over the course of infection, the fungus secretes various metabolites and proteins, of which only a handful have been fully characterized in the context of FHB. We report herein the role of a secreted cerato-platanin protein (FGSG_10212, FgCPP1) in the growth and aggressiveness of F. graminearum. Pathogen strains in which FgCPP1 was disrupted (Δfgcpp1) or overexpressed (FgCPP1-OX1) did not differ from the wild-type with respect to macroconidial germination or mycelial growth, nor in sensitivity to chemicals targeting fungal cell walls. Host—plant interaction studies were conducted including disease assays in wheat and host-cell localization of FgCPP1 in tobacco cells. Consistent with previous reports for FgCPP1 disruption mutants of F. graminearum, no difference was observed among FgCPP1-OX1, Δfgcpp1 and the wild-type in their ability to cause disease spread in point-inoculated wheat spikes. Spray inoculation of the wheat spikes with FgCPP1-OX1 resulted in an increase in diseased spikelets as early as 3 days post-inoculation in each of the three wheat genotypes assessed; however, this increase was not observed when the disease assay was repeated in the cultivar ‘Penhold’ with an additional FgCPP1-OX transformant, FgCPP1-OX2. FgCPP1-OX1 also resulted in increased levels of deoxynivalenol accumulation in axenic culture, as well as in spray-inoculated wheat spikes. We propose that FgCPP1 is a minor contributor to pathogen aggressiveness in wheat.

Single‐Atom Fe Catalysts for Fenton‐Like Reactions: Roles of Different N Species

AbstractRecognizing and controlling the structure–activity relationships of single‐atom catalysts (SACs) is vital for manipulating their catalytic properties for various practical applications. Herein, Fe SACs supported on nitrogen‐doped carbon (SA‐Fe/CN) are reported, which show high catalytic reactivity (97% degradation of bisphenol A in only 5 min), high stability (80% of reactivity maintained after five runs), and wide pH suitability (working pH range 3–11) toward Fenton‐like reactions. The roles of different N species in these reactions are further explored, both experimentally and theoretically. It is discovered that graphitic N is an adsorptive site for the target molecule, pyrrolic N coordinates with Fe(III) and plays a dominant role in the reaction, and pyridinic N, coordinated with Fe(II), is only a minor contributor to the reactivity of SA‐Fe/CN. Density functional theory (DFT) calculations reveal that a lower d‐band center location of pyrrolic‐type Fe sites leads to the easy generation of Fe‐oxo intermediates, and thus, excellent catalytic properties.

Role of the efflux transporters Abcb1 and Abcg2 in the brain distribution of olaparib in mice

Olaparib is a first-in-class poly (ADP-ribose) polymerase oral inhibitor used to treat various tumors. In this study, we clarified the roles of ABCB1/Abcb1 and ABCG2/Abcg2 transporters in restricting olaparib distribution to the brain. Olaparib was efficiently transported by human ABCG2, human ABCB1, and mouse Abcg2 in vitro. In the in vivo disposition study of olaparib using single or combination knockout mice, the systemic exposure of olaparib did not differ significantly between the strains over an 8-h period. However, the brain-to-plasma unbound concentration ratio of olaparib increased 5.6- and 8.1-fold in Abcb1a/1b and Abcb1a/1b;Abcg2 knockout mice, respectively, compared with wild-type mice. The Abcg2 single knockout mice exhibited a similar brain-to-plasma unbound concentration ratio to wild-type mice. Moreover, the brain distribution of olaparib could be modulated by the ABCB1/ABCG2 dual inhibitor elacridar to reach a similar degree of inhibition to Abcb1a/1b–/–. These findings suggest that olaparib is actively transported by both human and mouse ABCB1/Abcb1 and ABCG2/Abcg2; while Abcb1a/1b is a major determinant of olaparib brain penetration in mice, Abcg2 is likely to be a minor contributor. Concomitant treatment with temozolomide slightly increased the brain distribution of olaparib in mouse, but the clinical impact of the interaction was expected to be limited.

Forensic Identification of Fentanyl and its Analogs by Electrochemical-Surface Enhanced Raman Spectroscopy (EC-SERS) for the Screening of Seized Drugs of Abuse

Reliable identification of fentanyl and fentanyl analogs present in seized drug samples is imperative to the safety of first responders and laboratory personnel and informs the future analysis process and handling procedures. The electrochemical-surface enhanced Raman spectroscopy (EC-SERS) method developed in this work allows the in-situ preparation of the SERS substrate providing a rapid, efficient, and accurate approach to detect fentanyl, even at low percent by weight concentrations common in seized drugs. Optimization of the electrochemical potentials suitable for the SERS substrate preparation and adsorption of the analyte was achieved using multi-pulse amperometric detection. This method demonstrated large enhancement of the SERS response. This method was applied to six fentanyl analogs with substitutions to the amide group, representing small changes in the fentanyl core structure. Identification of these analogs through differences in the EC-SERS spectra was evident. Interference studies incorporating analytes frequently encountered with fentanyl including heroin, cocaine, methamphetamine, naltrexone, and naloxone were assessed and found to offer limited to no interference. The limits of detection of the fentanyl compounds were in the low to mid nanograms per milliliter range, with the most sensitive compound detected at 10 ng/ml. Application of the method to simulated drug mixtures was performed to determine fit-for-purpose. In all mixtures with fentanyl as the minor contributor, fentanyl was correctly identified, including mixture samples comprised of 5 and 1% fentanyl. This approach represents the first in-situ EC-SERS analysis of fentanyl and its analogs and provides accurate and efficient screening for fentanyl in seized drug samples.