Machine learning at the energy and intensity frontiers of particle physics.

Our knowledge of the fundamental particles of nature and their interactions is summarized by the standard model of particle physics. Advancing our understanding in this field has required experiments that operate at ever higher energies and intensities, which produce extremely large and information-rich data samples. The use of machine-learning techniques is revolutionizing how we interpret these data samples, greatly increasing the discovery potential of present and future experiments. Here we summarize the challenges and opportunities that come with the use of machine learning at the frontiers of particle physics.

DNAJC21 Mutations Link a Cancer-Prone Bone Marrow Failure Syndrome to Corruption in 60S Ribosome Subunit Maturation.

A substantial number of individuals with bone marrow failure (BMF) present with one or more extra-hematopoietic abnormality. This suggests a constitutional or inherited basis, and yet many of them do not fit the diagnostic criteria of the known BMF syndromes. Through exome sequencing, we have now identified a subgroup of these individuals, defined by germline biallelic mutations in DNAJC21 (DNAJ homolog subfamily C member 21). They present with global BMF, and one individual developed a hematological cancer (acute myeloid leukemia) in childhood. We show that the encoded protein associates with rRNA and plays a highly conserved role in the maturation of the 60S ribosomal subunit. Lymphoblastoid cells obtained from an affected individual exhibit increased sensitivity to the transcriptional inhibitor actinomycin D and reduced amounts of rRNA. Characterization of mutations revealed impairment in interactions with cofactors (PA2G4, HSPA8, and ZNF622) involved in 60S maturation. DNAJC21 deficiency resulted in cytoplasmic accumulation of the 60S nuclear export factor PA2G4, aberrant ribosome profiles, and increased cell death. Collectively, these findings demonstrate that mutations in DNAJC21 cause a cancer-prone BMF syndrome due to corruption of early nuclear rRNA biogenesis and late cytoplasmic maturation of the 60S subunit.

Coupling QCD-Scale Axionlike Particles to Gluons.

We present a novel data-driven method for determining the hadronic interaction strengths of axionlike particles (ALPs) with QCD-scale masses. Using our method, it is possible to calculate the hadronic production and decay rates of ALPs, along with many of the largest ALP decay rates to exclusive final states. To illustrate the impact on QCD-scale ALP phenomenology, we consider the scenario where the ALP-gluon coupling is dominant over the ALP coupling to photons, electroweak bosons, and all fermions for m_{π}≲m_{a}≲3 GeV. We emphasize, however, that our method can easily be generalized to any set of ALP couplings to standard model particles. Finally, using the approach developed here, we provide calculations for the branching fractions of η_{c}→VV decays; i.e., η_{c} decays into two vector mesons, which are consistent with the known experimental values.

Photoproduction of Axionlike Particles.

We explore the sensitivity of photon-beam experiments to axionlike particles (ALPs) with QCD-scale masses whose dominant coupling to the standard model is either to photons or gluons. We introduce a novel data-driven method that eliminates the need for knowledge of nuclear form factors or the photon-beam flux when considering coherent Primakoff production off a nuclear target, and show that data collected by the PrimEx experiment in 2004 could improve the sensitivity to ALPs with 0.03≲m_{a}≲0.3 GeV by an order of magnitude. Furthermore, we explore the potential sensitivity of running the GlueX experiment with a nuclear target and its planned PrimEx -like calorimeter. For the case where the dominant coupling is to gluons, we study photoproduction for the first time, and predict the future sensitivity of the GlueX experiment using its nominal proton target. Finally, we set world-leading limits for both the ALP-gluon coupling and the ALP-photon coupling based on public mass plots.

Whole exome sequencing identifies genetic variants in inherited thrombocytopenia with secondary qualitative function defects.

Inherited thrombocytopenias are a heterogeneous group of disorders characterized by abnormally low platelet counts which can be associated with abnormal bleeding. Next-generation sequencing has previously been employed in these disorders for the confirmation of suspected genetic abnormalities, and more recently in the discovery of novel disease-causing genes. However its full potential has not yet been exploited. Over the past 6 years we have sequenced the exomes from 55 patients, including 37 index cases and 18 additional family members, all of whom were recruited to the UK Genotyping and Phenotyping of Platelets study. All patients had inherited or sustained thrombocytopenia of unknown etiology with platelet counts varying from 11×109/L to 186×109/L. Of the 51 patients phenotypically tested, 37 (73%), had an additional secondary qualitative platelet defect. Using whole exome sequencing analysis we have identified "pathogenic" or "likely pathogenic" variants in 46% (17/37) of our index patients with thrombocytopenia. In addition, we report variants of uncertain significance in 12 index cases, including novel candidate genetic variants in previously unreported genes in four index cases. These results demonstrate that whole exome sequencing is an efficient method for elucidating potential pathogenic genetic variants in inherited thrombocytopenia. Whole exome sequencing also has the added benefit of discovering potentially pathogenic genetic variants for further study in novel genes not previously implicated in inherited thrombocytopenia.

Proposed Inclusive Dark Photon Search at LHCb.

We propose an inclusive search for dark photons A^{'} at the LHCb experiment based on both prompt and displaced dimuon resonances. Because the couplings of the dark photon are inherited from the photon via kinetic mixing, the dark photon A^{'}→µ^{+}µ^{-} rate can be directly inferred from the off-shell photon γ^{*}→µ^{+}µ^{-} rate, making this a fully data-driven search. For run 3 of the LHC, we estimate that LHCb will have sensitivity to large regions of the unexplored dark-photon parameter space, especially in the 210-520 MeV and 10-40 GeV mass ranges. This search leverages the excellent invariant-mass and vertex resolution of LHCb, along with its unique particle-identification and real-time data-analysis capabilities.

Intensity of factor VIII treatment and inhibitor development in children with severe hemophilia A: the RODIN study.

The objective of this study was to examine the association of the intensity of treatment, ranging from high-dose intensive factor VIII (FVIII) treatment to prophylactic treatment, with the inhibitor incidence among previously untreated patients with severe hemophilia A. This cohort study aimed to include consecutive patients with a FVIII activity < 0.01 IU/mL, born between 2000 and 2010, and observed during their first 75 FVIII exposure days. Intensive FVIII treatment of hemorrhages or surgery at the start of treatment was associated with an increased inhibitor risk (adjusted hazard ratio [aHR], 2.0; 95% confidence interval [CI], 1.3-3.0). High-dose FVIII treatment was associated with a higher inhibitor risk than low-dose FVIII treatment (aHR, 2.3; 95% CI, 1.0-4.8). Prophylaxis was only associated with a decreased overall inhibitor incidence after 20 exposure days of FVIII. The association with prophylaxis was more pronounced in patients with low-risk F8 genotypes than in patients with high-risk F8 genotypes (aHR, 0.61, 95% CI, 0.19-2.0 and aHR, 0.85, 95% CI, 0.51-1.4, respectively). In conclusion, our findings suggest that in previously untreated patients with severe hemophilia A, high-dosed intensive FVIII treatment increases inhibitor risk and prophylactic FVIII treatment decreases inhibitor risk, especially in patients with low-risk F8 mutations.

Uptake of Pharmaceuticals Influences Plant Development and Affects Nutrient and Hormone Homeostases.

The detection of a range of active pharmaceutical ingredients (APIs) in the soil environment has led to a number of publications demonstrating uptake by crops, however very few studies have explored the potential for impacts on plant development as a result of API uptake. This study investigated the effect of carbamazepine and verapamil (0.005-10 mg/kg) on a range of plant responses in zucchini (Cucurbita pepo). Uptake increased in a dose-dependent manner, with maximum leaf concentrations of 821.9 and 2.2 mg/kg for carbamazepine and verapamil, respectively. Increased carbamazepine uptake by zucchini resulted in a decrease in above (<60%) and below (<30%) ground biomass compared to the controls (p < 0.05). At soil concentrations >4 mg/kg the mature leaves suffered from burnt edges and white spots as well as a reduction in photosynthetic pigments but no such effects were seen for verapamil. For both APIs, further investigations revealed significant differences in the concentrations of selected plant hormones (auxins, cytokinins, abscisic acid and jasmonates), and in the nutrient composition of the leaves in comparison to the controls (p < 0.05). This is some of the first research to demonstrate that the exposure of plants to APIs is likely to cause impacts on plant development with unknown implications.

Differential Ly-6C expression identifies the recruited macrophage phenotype, which orchestrates the regression of murine liver fibrosis.

Although macrophages are widely recognized to have a profibrotic role in inflammation, we have used a highly tractable CCl(4)-induced model of reversible hepatic fibrosis to identify and characterize the macrophage phenotype responsible for tissue remodeling: the hitherto elusive restorative macrophage. This CD11B(hi) F4/80(int) Ly-6C(lo) macrophage subset was most abundant in livers during maximal fibrosis resolution and represented the principle matrix metalloproteinase (MMP) -expressing subset. Depletion of this population in CD11B promoter-diphtheria toxin receptor (CD11B-DTR) transgenic mice caused a failure of scar remodeling. Adoptive transfer and in situ labeling experiments showed that these restorative macrophages derive from recruited Ly-6C(hi) monocytes, a common origin with profibrotic Ly-6C(hi) macrophages, indicative of a phenotypic switch in vivo conferring proresolution properties. Microarray profiling of the Ly-6C(lo) subset, compared with Ly-6C(hi) macrophages, showed a phenotype outside the M1/M2 classification, with increased expression of MMPs, growth factors, and phagocytosis-related genes, including Mmp9, Mmp12, insulin-like growth factor 1 (Igf1), and Glycoprotein (transmembrane) nmb (Gpnmb). Confocal microscopy confirmed the postphagocytic nature of restorative macrophages. Furthermore, the restorative macrophage phenotype was recapitulated in vitro by the phagocytosis of cellular debris with associated activation of the ERK signaling cascade. Critically, induced phagocytic behavior in vivo, through administration of liposomes, increased restorative macrophage number and accelerated fibrosis resolution, offering a therapeutic strategy to this orphan pathological process.

Development and characterization of seven polymorphic microsatellite loci in Bembidion atrocaeruleum (Coleoptera: Carabidae).

We isolated seven polymorphic microsatellite loci from a ground beetle (Bembidion atrocaeruleum, Coleoptera, Carabidae (Stephens, 1826)) associated with naturally and regularly disturbed floodplain habitat in northwest Europe. Loci were tested on 157 individuals collected from five distinct habitat patches across two adjacent drainage basins in Wales, United Kingdom, to assess their potential for revealing population structure across a relatively short spatial extent. Alleles per locus ranged from 4 to 12. For a central representative population, expected heterozygosity ranged from 0.23 to 0.78 (mean: 0.63), and observed heterozygosity ranged from 0.16 to 0.94 (mean: 0.56). Analysis of molecular variance indicated significant structure among populations, even when one locus potentially containing null alleles was removed. These loci have the potential to aid the study of dispersal mechanisms of this important riparian species along and between river corridors, a recurring question in floodplain conservation studies. In addition, given the diversity of the Bembidion genus, they may have utility in the study of sister species.

Examining thermally induced movement of the fatal fire victim.

Investigating a fatal fire scene comprises analysis not only of the fire's development to identify the point of fire origin and ignition source, but analysis of a victim's position and their relationship within the scene. This work presents both qualitative and quantitative results from experimentation investigating the effect of a real fire environment on the human body, and how the position of a victim at the post burn investigation stage may be significantly different to the position at fire ignition. Qualitative observations were undertaken on the burning of 39 compartment and vehicle scenes from ignition through to suppression, each containing a human cadaver. The results of analysis question the validity of previous work based on cremation observations. Quantitative results were produced by recording 13 points on the body on the X, Y and Z axis, both pre and post burn on a smaller dataset of ten compartment burns. Results have enabled a more robust assessment of thermally induced movement of the body within the scene along each axis, evidencing that pugilism is not the universal reaction of the fatal victim to thermal exposure, with extension of the upper limbs far more common than has been previously reported.

Analysis of psychoactive cathinones and tryptamines by electrospray ionization atmospheric pressure ion mobility time-of-flight mass spectrometry.

The ability to use positive ion monitoring mode with an atmospheric pressure ion mobility time-of-flight mass spectrometer (APIM(tof)MS) to detect psychoactive cathinones and tryptamines from aqueous phase samples was evaluated. The study used a traditional electrospray ionization (ESI) source for sample introduction and ionization. A total of four cathinones (mephedrone, butylone, 4-Me-PPP, and 4-MEC) and five tryptamines (5-EtO-DPT, 5-EtO-DALT, 5-EtO-MIPT, 5-EtO-ALCHT, and 5-EtO-2MALET) were investigated, and we report on parent ions, collision induced dissociation (CID) fragment ions, reduced mobility (Ko), mass flight times, and detection limits obtained from a single instrument run for the psychoactive substances. Detection limits reported ranged from 3 to 11 µM concentration for the compounds studied. This detection limit range corresponded to 1-5 ng of material needed for improved detection on the instrument. This article demonstrates that it was possible to use a single instrument platform for the separation, detection, and identification of cathinones and tryptamines in less than 1 min. The application holds great promise for detecting and identifying a new class of drugs often referred to as "bath salts" or "legal highs" distributed over the Internet.

The use of multiple tracers for tracking wastewater discharges in freshwater systems.

The assessment of potential impacts of wastewater effluent discharges in freshwater systems requires an understanding of the likely degrees of dilution and potential zones of influence. In this study, four tracers commonly present in wastewater effluents were monitored to compare their relative effectiveness in determining areas in freshwater systems that are likely to be impacted by effluent discharges. The four tracers selected were the human pharmaceutical carbamazepine, anthropogenic gadolinium, fluorescent-dissolved organic matter (fDOM), and electrical conductivity (EC). The four tracers were monitored longitudinally in two distinct freshwater systems receiving wastewater effluents, where one site had a high level of effluent dilution (effluent <1% of total flow) and the other site had a low level of effluent dilution (effluent ∼50% of total flow). At both sites, the selected tracers exhibited a similar pattern of response intensity downstream of discharge points relative to undiluted wastewater effluent, although a number of anomalies were noted between the tracers. Both EC and fDOM are non-specific to human influences, and both had a high background response, relative to the highly sensitive carbamazepine and anthropogenic gadolinium responses, although the ease of measuring EC and fDOM would make them more adaptable in highly variable systems. However, the greater sensitivity and selectivity of carbamazepine and gadolinium would make their combination with EC and fDOM as tracers of wastewater effluent discharges highly desirable to overcome potential limitations of individual tracers.

Examination of misconceptions surrounding fatal fire victims.

Fire deaths are not unusual in forensic investigative practice but due to the destructive nature of fire they are often very difficult to investigate. With the need to identify the deceased and the events surrounding the manner and cause of death, knowledge of thermally induced alteration to the human body is important. Within the fire investigation community, a number of misconceptions have been present for years regarding the protrusion of the tongue as an indicator of life during the fire, and fractured skulls as the result of brains boiling and skulls exploding. This work presents qualitative analysis on the experimental burning of 42 unembalmed human donated cadavers by the San Luis Obispo Strike Team (SLOFIST) on their annual Forensic Fire Death Investigation Course (FFDIC) between 2017 and 2019. Prior to burning, the position of the tongue within the dental arch was confirmed and sharp, blunt, surgical and gunshot trauma to the cranium documented. Temperature was recorded from ignition through to suppression with thermocouples present both within the scene and the body. Post burn analysis on the position of the tongue, observation of cranial fractures and presence of brain tissue were recorded and analysed in conjunction with thermocouple data, fire scene dynamics and body demographics. The results provide a more comprehensive understanding of the thermal environmental factors involved in producing the phenomena that facilitate these misconceptions, identifying that a more thorough understanding of individual fire scenes and their development is essential when interpreting alteration and injury to the body of the fatal fire victim.

Quantification of the variability and penetration of per- and poly-fluoroalkyl substances through a concrete pad.

Historical use of aqueous film forming foams (AFFF) containing per- and poly-fluoroalkyl substances (PFAS) for fire-fighting activities has contributed to widespread contamination of infrastructure which can represent an ongoing source of PFAS to the surrounding environment. A concrete fire training pad with historical use of Ansulite and Lightwater AFFF formulations had PFAS concentrations measured to quantify spatial variability of PFAS within the pad. Surface chips and whole cores of concrete through to the underlying aggregate base were collected over the 24 × 9 m concrete pad and depth profiles of PFAS concentrations in nine cores were analysed. PFOS and PFHxS dominated the PFAS for surface samples, along the depth profile of cores and in the underlying plastic and aggregate material, with substantial variability in the concentrations of PFAS in the samples. Although there was variability of individual PFAS along the depth profile, higher surface concentrations of PFAS generally followed the designed movement of water across the pad. Total oxidisable precursor (TOP) assessments of one core indicated additional PFAS were present along the entire length of the core. This study highlights concentrations of PFAS (up to low µg/kg) from historical use of AFFF can occur throughout concrete, with the variable concentrations throughout the profile.

Dissipation of sulfamethoxazole and trimethoprim antibiotics from manure-amended soils.

In this study, the dissipation of two antibiotics, sulfamethoxazole (SMX) and trimethoprim (TRM), in three soils under both aerobic and anaerobic conditions are evaluated. Under aerobic conditions, SMX dissipated rapidly through biodegradation but TRM was more persistent. Within the first 20 days in biologically active soils, >50% of the SMX was lost from the clay loam and loamy sand soils, and >80% loss was noted in the loam soil. Anaerobic dissipation of both compounds was more rapid than aerobic dissipation. The addition of manure to the soil only slightly increased the initial dissipation rate of the two compounds. Little effect was found on glucose mineralisation in soil following the addition of SMX and TRM, even as mixtures at high concentrations.

Modelling the attenuation of flowback chemicals for a soil-groundwater pathway from a hypothetical spill accident.

Flowback water from shale gas operations contains formation-derived compounds, including trace metals, radionuclides, and organics. While accidental releases from storage tanks with flowback water are low-probability events if multiple containment barriers are put in place, they cannot be entirely excluded. Here the natural attenuation potential of deep unsaturated zones and groundwater was explored using predictive modelling involving a hypothetical leak from a storage tank. Actual chemical concentrations from flowback water at two shale gas wells with contrasting salinity (12,300 and 105,000 ppm TDS) in the Beetaloo Sub-basin (Northern Territory, Australia) served as input to the one-dimensional HYDRUS model for simulating chemical transport through the unsaturated zone, with groundwater at 50 and 100 m depth, respectively. Subsequent chemical transport in groundwater involved the use of a three-dimensional analytical transport model. For a total of 63 chemicals the long-term attenuation from dilution and dispersion in unsaturated sediments and groundwater was calculated. Predicted environmental concentrations for aquatic receptors were compared with no-effect levels of individual chemicals to derive risk quotients (RQ) and identify chemicals of no concern to ecosystem health (i.e. RQ <1). Except for salinity and radium-228 in one of the two wells, RQ < 1 for all other chemicals. The initial approach considered testing of toxicity to individual chemicals only. When direct toxicity assessments (DTAs) were used to account for effects of chemical mixtures, the required DTA-derived safe dilution factor for 95% species protection was 1.8 to 2.5 times higher than the dilution factor accounting for dispersion and dilution only. Accounting for biodegradation, sorption and radioactive decay decreased chemical concentrations in unsaturated sediments to safe levels using the DTA for all chemicals. The study highlighted the importance of incorporating DTA in chemical risk assessments involving complex chemical mixtures. Improved understanding of fate and transport of flowback chemicals will help effectively manage water-quality risks associated with shale gas extraction.

Sorption, degradation and microbial toxicity of chemicals associated with hydraulic fracturing fluid and produced water in soils.

Spills of hydraulic fracturing (HF) fluids and of produced water during unconventional gas extraction operations may cause soil contamination. We studied the degradation and microbial toxicity of selected HF chemical components including two biocides (methylisothiozolinone- MIT, chloromethylisothiozolinone- CMIT), a gel-breaker aid (triethanolamine -TEA), and three geogenic chemicals (phenol, m-cresol and p-cresol) in ultrapure water, HF fluid and produced water in five different soil types (surface and subsurface soils). The degradation of the two biocides (in soils treated with HF fluid or ultrapure water) and of the three geogenic chemicals (in soils treated with produced water) was rapid (in all cases DT50 values < 2 days in surface soils). In contrast, the loss of TEA was much slower in soils, especially in those treated with HF fluid (DT50 > 30 days). Sorption coefficients (Koc in L/Kg) in these soils ranged from 71 to 733 for TEA, 64-408 for MIT and 11-72 for CMIT. In terms of soil microbial toxicity, exposure to HF fluid and produced water reduced microbial respiration, albeit temporarily. The overall microbial activities in surface soils contaminated with produced water had fully recovered in most soils. In contrast, the HF fluid addition to soils completely inhibited the nitrification in all soils, with little recovery over the 60 day experimental period. In the case of produced water exposure, three out of five surface soils showed complete recovery in nitrification during the study period. The functional genes for nitrogen fixation (nifH) and carbon cycling (GA1) and microbial community composition (16 S rRNA) were significantly affected by HF fluid in some soils. Overall, the study shows that the HF fluid can have significant detrimental impact on soil microbial functions, especially on nitrogen cycling. More work is needed to identify the exact cause of microbial toxicity in soils contaminated with HF fluid.

Method for extraction and analysis of per- and poly-fluoroalkyl substances in contaminated asphalt.

The legacy use of aqueous film-forming foam (AFFF) has led to the generation of large volumes of per- and poly-fluoroalkyl substances (PFAS)-contaminated asphalt materials, especially at airports and fire training areas. The management of such PFAS-contaminated asphalt materials requires an understanding of PFAS concentrations in these materials. This study, therefore, aimed to develop a suitable extraction methodology for the analysis of 22 target PFAS (i.e., carboxylic acids, sulfonic acids and fluorotelomers) in asphalt materials. A series of experiments was conducted to optimise extraction solvent composition, as well as to assess the performance of the chosen method under various conditions (i.e., sonication temperature, PFAS contamination level, asphalt core composition and timing of stable isotope addition used as internal standard). The methanol-based extractants performed best due to their accuracy and precision, which were within the acceptable range (extraction efficiency between 70 and 130% and RSD < 20%). The method which involved three successive extractions with methanol/1% NH3 by ultrasonication at 25 °C was selected due to its performance and ease of operation. The mean recovery of a vast majority of PFAS was found to be in the acceptable range. Tests on the timing of addition of stable isotope (SI)-labelled PFAS internal standards indicate that the recoveries obtained, regardless of when the stable isotopes were added, were within the acceptable range for PFAS. The accuracy and precision of PFAS recoveries were not affected by PFAS spike level (2 µg kg-1 and 200 µg kg-1), as well as sample composition (based on the location of asphalt material in the field). Low RSDs were achieved for asphalt cores collected from a contaminated site covering a wide range of concentrations (from LOQ to 2135 mg kg-1), demonstrating the suitability of the sample preparation method for real-world samples. The results from the interlaboratory testing were also in good agreement and validated the proposed PFAS extraction and analytical approach.