Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.

Dynamics of parasite growth in genetically diverse Plasmodium falciparum isolates

Multiple parasite lineages with different proliferation rates or fitness may coexist within a clinical malaria isolate, resulting in complex growth interactions and variations in phenotype. To elucidate the dynamics of parasite growth in multiclonal isolates, we measured growth rates (GRs) of three Plasmodium falciparum Cambodian isolates, including IPC_3445 (MRA-1236), IPC_5202 (MRA-1240), IPC_6403 (MRA-1285), and parasite lineages previously cloned from each of these isolates by limiting dilution. Following synchronization, in vitro cultures of each parasite line were maintained over four consecutive asexual cycles (192 h), with thin smears prepared at each 48-h cycle to estimate GR and fold change in parasitemia (FCP). Cell cycle time (CCT), the duration it takes for ring-stage parasites to develop into mature schizonts, was measured by monitoring the development of 0-3-h post-invasion rings for up to 52 h post-incubation. Laboratory lines 3D7 (MRA-102) and Dd2 (MRA-150) were used as controls. Significant differences in GR, FCP, and CCT were observed between parasite isolates and clonal lineages from each isolate. The parasite lines studied here have well-defined growth phenotypes and will facilitate basic malaria research and development of novel malaria interventions. These lines are available to malaria researchers through the MR4 collection of NIAID's BEI Resources Program.

Development and validation of a rapid and easy-to-perform point-of-care lateral flow immunoassay (LFIA) for the detection of SARS-CoV-2 spike protein

Development and validation of rapid and easy-to-perform diagnostics continue to be a high priority during the current COVID-19 pandemic. Although vaccines are now widely available, early detection and consistent transmission control provide ideal means to mitigate the spread of SARS-CoV-2. Nucleic acid-based real-time PCR tests are widely acknowledged as the gold standard for reliable diagnosis of COVID-19 infection. These tests are based on detecting viable or nonviable viral nucleic acids. SARS-CoV-2 spike protein is an alternative and ideal target for SARS-CoV-2 diagnosis in the early phase of infection, but point-of-care kits to detect the SARS-CoV-2 spike protein are limited. Here we describe a rapid and convenient method based on Lateral Flow Immunoassay (LFIA) to detect SARS-CoV-2 spike proteins, including SARS-CoV-2 variants (A.23.1, B.1.1.1, 1.617.2, B.1.1.7, B.1.351, P.1, N501Y, R.1, P681H, P3, UK, and South African) within 5 to 10 minutes. We generated highly specific monoclonal antibodies (mAbs) against rationally designed SARS-CoV-2 spike protein. Matched pair mAbs were selected by epitope mapping and employed as antigen capture reagents by spotting onto a nitrocellulose membrane and as detector reagents by conjugation with colloidal gold nanoparticles. We evaluated the performance of the LFIA using recombinant spike proteins of SARS-CoV-2 and several SARS-CoV-2 variants. The specificity of the LFIA was assessed using heat-inactivated SARS-CoV-2 and related human coronaviruses (HCoV-OC43, HCoV-229E, HCoV-HKU1, and HCoV-NL63) and an FDA-approved respiratory pathogens (RP) panel. The assay exhibited 98% specificity and acceptable performance with respect to the minimum limit of detection (25 ng/test) in validation tests. This new LFIA provides improved performance for the early diagnosis of SARS-CoV-2, particularly for home monitoring and in situations with limited access to molecular methods.

Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and to support rapid experimental examination of genome-informed vaccine and therapeutic designs. Given the broad range of methods applied to generate new viral genomes, it is critical that consensus and variant calling tools yield consistent results across disparate pipelines. Here we examine the impact of sequencing technologies (Illumina and Oxford Nanopore) and 7 different downstream bioinformatic protocols on SARS-CoV-2 variant calling as part of the NIH Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) Tracking Resistance and Coronavirus Evolution (TRACE) initiative, a public-private partnership established to address the COVID-19 outbreak. Our results indicate that bioinformatic workflows can yield consensus genomes with different single nucleotide polymorphisms, insertions, and/or deletions even when using the same raw sequence input datasets. We introduce the use of a specific suite of parameters and protocols that greatly improves the agreement among pipelines developed by diverse organizations. Such consistency among bioinformatic pipelines is fundamental to SARS-CoV-2 and future pathogen surveillance efforts. The application of analysis standards is necessary to more accurately document phylogenomic trends and support data-driven public health responses.

Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike

SARS-CoV-2 pathogenesis, vaccine, and therapeutic studies rely on the use of animals challenged with highly pathogenic virus stocks produced in cell cultures. Ideally, these virus stocks should be genetically and functionally similar to the original clinical isolate, retaining wild-type properties to be reliably used in animal model studies. It is well-established that SARS-CoV-2 isolates serially passaged on Vero cell lines accumulate mutations and deletions in the furin cleavage site; however, these can be eliminated when passaged on Calu-3 lung epithelial cell lines, as presented in this study. As numerous stocks of SARS-CoV-2 variants of concern are being grown in cell cultures with the intent for use in animal models, it is essential that propagation methods generate virus stocks that are pathogenic in vivo. Here, we found that the propagation of a B.1.351 SARS-CoV-2 stock on Calu-3 cells eliminated viruses that previously accumulated mutations in the furin cleavage site. Notably, there were alternative variants that accumulated at the same nucleotide positions in virus populations grown on Calu-3 cells at multiple independent facilities. When a Calu-3-derived B.1.351 virus stock was used to infect hamsters, the virus remained pathogenic and the Calu-3-specific variants persisted in the population. These results suggest that Calu-3-derived virus stocks are pathogenic but care should still be taken to evaluate virus stocks for newly arising mutations during propagation.

A cautionary perspective regarding the isolation and serial propagation of SARS-CoV-2 in Vero cells

An array of SARS-CoV-2 virus variants have been isolated, propagated and used in in vitro assays, in vivo animal studies and human clinical trials. Observations of working stocks of SARS-CoV-2 suggest that sequential propagation in Vero cells leads to critical changes in the region of the furin cleavage site, which significantly reduce the value of the working stock for critical research studies. Serially propagating SARS-CoV-2 in Vero E6 cells leads to rapid increases in genetic variants while propagation in other cell lines (e.g. Vero/hSLAM) appears to mitigate this risk thereby improving the overall genetic stability of working stocks. From these observations, investigators are urged to monitor genetic variants carefully when propagating SARS-CoV-2 in Vero cells.

Culturing Mycobacteria

Building upon the foundational research of Robert Koch, who demonstrated the ability to grow Mycobacterium tuberculosis for the first time in 1882 using media made of coagulated bovine serum, microbiologists have continued to develop new and more efficient ways to grow mycobacteria. Presently, all known mycobacterial species can be grown in the laboratory using either axenic culture techniques or in vivo passage in laboratory animals. This chapter provides conventional protocols to grow mycobacteria for diagnostic purposes directly from clinical specimens, as well as in research laboratories for scientific purposes. Detailed protocols used for production of M. tuberculosis in large scale (under normoxic and hypoxic conditions) in bioreactors and for production of obligate intracellular pathogens such as Mycobacterium leprae and "Mycobacterium lepromatosis" using athymic nude mice and armadillos are provided.

Measurements of Nonsinglet Moments of the Nucleon Structure Functions and Comparison to Predictions from Lattice QCD for Q^{2}=4 GeV^{2}

We present extractions of the nucleon nonsinglet moments utilizing new precision data on the deuteron F_{2} structure function at large Bjorken-x determined via the Rosenbluth separation technique at Jefferson Lab Experimental Hall C. These new data are combined with a complementary set of data on the proton previously measured in Hall C at similar kinematics and world datasets on the proton and deuteron at lower x measured at SLAC and CERN. The new Jefferson Lab data provide coverage of the upper third of the x range, crucial for precision determination of the higher moments. In contrast to previous extractions, these moments have been corrected for nuclear effects in the deuteron using a new global fit to the deuteron and proton data. The obtained experimental moments represent an order of magnitude improvement in precision over previous extractions using high x data. Moreover, recent exciting developments in lattice QCD calculations provide a first ever comparison of these new experimental results with calculations of moments carried out at the physical pion mass, as well as a new approach that first calculates the quark distributions directly before determining moments.

P41 Endoscopy in cerebellopontine angle lesions: feasibility and technical considerations

Objectives

To define selection criteria and describe technique nuances for the use of endoscopy in surgery for cerebello-pontine angle (CPA) lesions.

Design

Prospective observational study.

Subjects

Patients undergoing CPA lesion resection were selected for endoscope-assisted and/or endoscope-guided lesion resection.

Methods

CPA interventions without mass lesions were excluded. 10 CPA lesions were identified pre-operatively for intra-operative endoscopic use across two neurosurgical centres. We describe equipment and technique selection.

Results

10 cases were selected over a one year period. Histology revealed 3 vestibular schwannomas (VS) (30%), 1 cyst (10%), 3 epidermoids (30%), 3 meningiomata (30%). Three cases were planned and carried out fully endoscopically (including two VS and the cyst) based on patient factors and favourable anatomy. Four cases were carried out with endoscopic assistance. The endoscope was used in three cases for anatomical orientation ‘around the corner’ only. Techniques and equipment vary depending on surgical aims, surgical anatomy and working area. Tips and pitfalls are identified and described.

Conclusions

Endoscopy can be applied safely in CPA pathologies, as an alternative to the operating microscope for highly selected cases, or as an adjunct for specific surgical steps, especially when microscope optics do not allow angled visualisation. It is particularly useful in identifying lesion residuum and ‘working around the corner’. High level training is required before applying endoscopy to the CPA.

Mycobacterial biomaterials and resources for researchers

There are many resources available to mycobacterial researchers, including culture collections around the world that distribute biomaterials to the general scientific community, genomic and clinical databases, and powerful bioinformatics tools. However, many of these resources may be unknown to the research community. This review article aims to summarize and publicize many of these resources, thus strengthening the quality and reproducibility of mycobacterial research by providing the scientific community access to authenticated and quality-controlled biomaterials and a wealth of information, analytical tools and research opportunities.

Children's Psychological Health Status–the Impact of Liver Transplantation: A Review

Medical audit needs to encompass physical, psychological and social aspects to patient functioning. The aim of this paper is to review the psychosocial impact of liver transplantation on children and their families. Evidence suggests that end stage liver diseases are associated with developmental delays. Emotional and behavioural problems are common and have been found to relate to the child's developmental status, physical appearance as well as family functioning. Post transplant, children and families often experience an exacerbation of preexisting emotional problems. One year post transplant, children typically show continuing developmental delays. Longer term assessments of quality of life suggest that children may experience fewer hospital contacts and that over time psychological difficulties reduce. Many families continue to experience problems in normalizing their interactions within and outside the family. The findings demonstrate the importance of including psychosocial outcomes in auditing the efficacy of medical interventions.

Genetic relatedness reveals total population size of white sharks in eastern Australia and New Zealand

Conservation concerns exist for many sharks but robust estimates of abundance are often lacking. Improving population status is a performance measure for species under conservation or recovery plans, yet the lack of data permitting estimation of population size means the efficacy of management actions can be difficult to assess, and achieving the goal of removing species from conservation listing challenging. For potentially dangerous species, like the white shark, balancing conservation and public safety demands is politically and socially complex, often leading to vigorous debate about their population status. This increases the need for robust information to inform policy decisions. We developed a novel method for estimating the total abundance of white sharks in eastern Australia and New Zealand using the genetic-relatedness of juveniles and applying a close-kin mark-recapture framework and demographic model. Estimated numbers of adults are small (ca. 280-650), as is total population size (ca. 2,500-6,750). However, estimates of survival probability are high for adults (over 90%), and fairly high for juveniles (around 73%). This represents the first direct estimate of total white shark abundance and survival calculated from data across both the spatial and temporal life-history of the animal and provides a pathway to estimate population trend.

Procoagulant microparticles promote coagulation in a factor XI-dependent manner in human endotoxemia

Essentials The procoagulant effects of microparticles (MPs) on coagulation in endotoxemia are not known. MPs from endotoxemia volunteers were evaluated for procoagulant activity in a plasma milieu. MPs from endotoxemia volunteers shortened clotting times and enhanced thrombin generation. MP procoagulant effects were mediated in a factor XI-dependent manner.

SUMMARY

Background Human endotoxemia is characterized by acute inflammation and activation of coagulation, as well as increased numbers of circulating microparticles (MPs). Whether these MPs directly promote coagulation and through which pathway their actions are mediated, however, has not been fully explored. Objectives In this study, we aimed to further characterize endotoxin-induced MPs and their procoagulant properties using several approaches. Methods Enumeration and characterization of MPs were performed using a new-generation flow cytometer. Relative contributions of the extrinsic and intrinsic pathways in MP-mediated procoagulant activity were assessed using plasmas deficient in factor (F) VII or FXI or with blocking antibodies to tissue factor (TF) or FXIa. Results Total MPs and platelet MPs were significantly elevated in plasma at 6 h after infusion of endotoxin in healthy human subjects. MPs isolated from plasma following endotoxin infusion also demonstrated increased TF activity in a reconstituted buffer system. When added to recalcified platelet-poor plasma, these MPs also promoted coagulation, as judged by a decreased clotting time with shortening of the lag time and time to peak thrombin using calibrated automated thrombography (CAT). However, the use of FVII-deficient plasma or blocking antibody to TF did not inhibit these procoagulant effects. In contrast, plasma clotting time was prolonged in FXI-deficient plasma and a blocking antibody to FXIa inhibited all MP-mediated parameters in the CAT assay. Conclusions The initiation of coagulation by cellular TF in endotoxemia is in contrast to (and presumably complemented by) the intrinsic pathway-mediated procoagulant effects of circulating MPs.

Segregation or aggregation? Sex-specific patterns in the seasonal occurrence of white sharks Carcharodon carcharias at the Neptune Islands, South Australia

The seasonal patterns of occurrence of male and female white sharks Carcharodon carcharias at the Neptune Islands in South Australia were reviewed. Analyses of a 14 year data series indicate that females seasonally aggregate in late autumn and winter coinciding with the maximum in-water availability of lactating female long-nose fur seals and seal pups. During this period, observed male:female sex ratios were similar; whereas during late spring and summer, males continued to visit, but females were rarely recorded. There was no evidence for segregation by sex or size at the Neptunes, but the highly focused seasonal pattern of occurrence of females compared with the year-round records of males suggests that there are likely to be differences between the sexes in overall distribution and movement patterns across southern Australia. It is suggested that foraging strategies and prey selection differ between sexes in C. carcharias across the life-history stages represented and that sex-specific foraging strategies may play an important role in structuring movement patterns and the sex ratios observed at such aggregation sites. Differences between sexes in distribution, movement patterns and foraging strategies are likely to have implications for modelling the consequences of fisheries by-catch between regions or jurisdictions and other spatially or temporally discrete anthropogenic effects on C. carcharias populations. Such differences urge for caution when estimating the size of C. carcharias populations based on observations at pinniped colonies due to the likelihood of sex-specific differences in movements and patterns of residency. These differences also suggest a need to account for sex-specific movement patterns and distribution in population and movement models as well as under conservation actions.

The Use of Psychotropic Drug Therapy in Borderline Personality Disorder: a Case Report

It is estimated that around 75% of patients with Borderline Personality Disorder (BPD) are prescribed psychotropic medication during their treatment course, although this is not recommended as first line therapy. In the UK, there are no guidelines to advise which drug treatments to use in BPD, however, numerous, but mostly small scale studies, show evidence that different medications target specific core symptoms. We report a case of a 25 year old woman with BPD, who has received treatment with five different psychotropic medications. We go on to assess not only the efficacy of these treatments in this individual case, but also whether the use of these treatments is in line with best evidence according to currently available research.

The effect of level of crude protein and available lysine on finishing pig performance, nitrogen balance and nutrient digestibility

Two trials were conducted to investigate the effect of decreasing the crude protein (CP) content of diets for finishing pigs containing two levels of available lysine on nutrient digestibility, nitrogen (N) balance and production performance. Ten finishing diets containing five levels of CP (on average 144, 155, 168, 182 and 193 g/kg fresh basis) and two levels of available lysine (6.9 and 8.2 g/kg fresh basis) were formulated. The diets were offered to pigs on a performance trial (n = 800 Large White (LW)×Landrace (LR) pigs) from 10 wk of age until finish at 21 wks+5 d of age. Average daily gain (ADG), average daily feed intake (ADFI) and feed conversion ratio (FCR) were calculated. In addition, a digestibility/N balance trial was conducted using pigs (n = 80 LW×LR) housed in metabolism crates. Digestibility of dry matter (DM), CP, oil, fibre and energy was determined. N balance values were determined through analysis of N content of urine and faeces (‘as determined’). N balance values were also calculated using ADG values and assuming that 16% of growth is protein deposition (“as calculated”). Pig performance was poor between 10 and 13 wk of age which indicated that the dietary treatments were nutritionally inadequate for pigs less than 40 kg. There was a significant (p<0.01) quadratic effect of increasing CP level on feed intake, ADG and FCR from 10 to 13 wk which indicated that the lower CP levels did not supply adequate levels of essential or non-essential amino acids. There was no effect of increasing available lysine level throughout the early period, which in conjunction with the response in older pigs, suggested that both 8.2 and 6.9 g/kg available lysine were insufficient to drive optimum growth. There was a positive response (p<0.05) to increasing available lysine level from 13 wk to finish which indicated that 6.9 g/kg available lysine was not adequate for finishing pigs. Energy digestibility decreased with decreasing CP level of diets containing 6.9 g/kg available lysine which may be attributed to the higher fibre content of the lower CP diets. Nitrogen excretion (g/d) was lowered when dietary CP was reduced regardless of whether the values were determined through balance or calculated using ADG. Calculated N excretion decreased linearly (p<0.001) and quadratically (p<0.001) with decreasing dietary CP content. When the N balance figures calculated in this study were compared with those quoted in the Northern Ireland and English Nitrates Directive Action Programmes, N excretion was less per pig (wean to finish) offered a 169 g/kg CP, 8.2 g/kg available lysine diet (2.39 kg vs 3.41 kg (Northern Ireland) and 2.93 kg (England)).

Measurement of muon neutrino quasielastic scattering on a hydrocarbon target at Eν ~ 3.5 GeV

We report a study of ν(μ) charged-current quasielastic events in the segmented scintillator inner tracker of the MINERvA experiment running in the NuMI neutrino beam at Fermilab. The events were selected by requiring a μ- and low calorimetric recoil energy separated from the interaction vertex. We measure the flux-averaged differential cross section, dσ/dQ², and study the low energy particle content of the final state. Deviations are found between the measured dσ/dQ² and the expectations of a model of independent nucleons in a relativistic Fermi gas. We also observe an excess of energy near the vertex consistent with multiple protons in the final state.

Measurement of muon antineutrino quasielastic scattering on a hydrocarbon target at Eν ~ 3.5 GeV

We have isolated ν(μ) charged-current quasielastic (QE) interactions occurring in the segmented scintillator tracking region of the MINERvA detector running in the NuMI neutrino beam at Fermilab. We measure the flux-averaged differential cross section, dσ/dQ², and compare to several theoretical models of QE scattering. Good agreement is obtained with a model where the nucleon axial mass, M(A), is set to 0.99 GeV/c² but the nucleon vector form factors are modified to account for the observed enhancement, relative to the free nucleon case, of the cross section for the exchange of transversely polarized photons in electron-nucleus scattering. Our data at higher Q² favor this interpretation over an alternative in which the axial mass is increased.

Precise measurement of the neutron magnetic form factor G(M)n in the few-GeV2 region

The neutron elastic magnetic form factor was extracted from quasielastic electron scattering on deuterium over the range Q;{2}=1.0-4.8 GeV2 with the CLAS detector at Jefferson Lab. High precision was achieved with a ratio technique and a simultaneous in situ calibration of the neutron detection efficiency. Neutrons were detected with electromagnetic calorimeters and time-of-flight scintillators at two beam energies. The dipole parametrization gives a good description of the data.

Search for the photoexcitation of exotic mesons in the pi+pi+pi- system

A search for exotic mesons in the pi;{+}pi;{+}pi;{-} system photoproduced by the charge exchange reaction gammap-->pi;{+}pi;{+}pi;{-}(n) was carried out by the CLAS Collaboration at Jefferson Lab. A tagged-photon beam with energies in the 4.8 to 5.4 GeV range, produced through bremsstrahlung from a 5.744 GeV electron beam, was incident on a liquid-hydrogen target. A partial wave analysis was performed on a sample of 83 000 events, the highest such statistics to date in this reaction at these energies. The main objective of this study was to look for the photoproduction of an exotic J;{PC}=1;{-+} resonant state in the 1 to 2 GeV mass range. Our partial wave analysis shows production of the a_{2}(1320) and the pi_{2}(1670) mesons, but no evidence for the a_{1}(1260), nor the pi_{1}(1600) exotic state at the expected levels. An upper limit of 13.5 nb is determined for the exotic pi_{1}(1600) cross section, less than 2% of the a_{2}(1320) production.

Measurement of direct f0(980) photoproduction on the proton

We report on the results of the first measurement of exclusive f_{0}(980) meson photoproduction on protons for E_{gamma}=3.0-3.8 GeV and -t=0.4-1.0 GeV2. Data were collected with the CLAS detector at the Thomas Jefferson National Accelerator Facility. The resonance was detected via its decay in the pi;{+}pi;{-} channel by performing a partial wave analysis of the reaction gammap-->ppi;{+}pi;{-}. Clear evidence of the f_{0}(980) meson was found in the interference between P and S waves at M_{pi;{+}pi;{-}} approximately 1 GeV. The S-wave differential cross section integrated in the mass range of the f_{0}(980) was found to be a factor of about 50 smaller than the cross section for the rho meson. This is the first time the f_{0}(980) meson has been measured in a photoproduction experiment.

Measurement of deeply virtual compton scattering beam-spin asymmetries

The beam-spin asymmetries in the hard exclusive electroproduction of photons on the proton (e p-->epgamma) were measured over a wide kinematic range and with high statistical accuracy. These asymmetries result from the interference of the Bethe-Heitler process and of deeply virtual Compton scattering. Over the whole kinematic range (x(B) from 0.11 to 0.58, Q2 from 1 to 4.8 GeV2, -t from 0.09 to 1.8 GeV2), the azimuthal dependence of the asymmetries is compatible with expectations from leading-twist dominance, A approximately a sinphi/(1+c cosphi). This extensive set of data can thus be used to constrain significantly the generalized parton distributions of the nucleon in the valence quark sector.

Bayesian analysis of pentaquark signals from CLAS data

We examine the results of two measurements by the CLAS collaboration, one of which claimed evidence for a Theta(+) pentaquark, while the other found no such evidence. The unique feature of these two experiments was that they were performed with the same experimental setup. Using a Bayesian analysis, we find that the results of the two experiments are in fact compatible with each other, but that the first measurement did not contain sufficient information to determine unambiguously the existence of a Theta(+). Further, we suggest a means by which the existence of a new candidate particle can be tested in a rigorous manner.

Search for medium modifications of the rho meson

The photoproduction of vector mesons on various nuclei has been studied using the CLAS detector at Jefferson Laboratory. The vector mesons, rho, omega, and varphi, are observed via their decay to e;{+}e;{-}, in order to reduce the effects of final-state interactions in the nucleus. Of particular interest are possible in-medium effects on the properties of the rho meson. The rho mass spectrum is extracted from the data on various nuclei, 2H, C, Fe, and Ti. We observe no significant mass shift and some broadening consistent with expected collisional broadening for the rho meson.

Experimental study of exclusive 2H(e,e'p)n reaction mechanisms at high Q2

The reaction 2H(e,e'p)n has been studied with full kinematic coverage for photon virtuality 1.75<Q2<5.5 GeV2. Comparisons of experimental data with theory indicate that for very low values of neutron recoil momentum (p(n)<100 MeV/c) the neutron is primarily a spectator and the reaction can be described by the plane-wave impulse approximation. For 100<p(n)<750 MeV/c, proton-neutron rescattering dominates the cross section, while Delta production followed by the NDelta-->NN transition is the primary contribution at higher momenta.

Measurement of the N-->Delta(+)(1232) transition at high-momentum transfer by pi(0) electroproduction

We report a new measurement of the exclusive electroproduction reaction gamma(*)p-->pi(0)p to explore the evolution from soft nonperturbative physics to hard processes via the Q(2) dependence of the magnetic (M(1+)), electric (E(1+)), and scalar (S(1+)) multipoles in the N-->Delta transition. 9000 differential cross section data points cover W from threshold to 1.4 GeV/c(2), 4pi center-of-mass solid angle, and Q(2) from 3 to 6 GeV(2)/c(2), the highest yet achieved. It is found that the magnetic form factor G(M)(*) decreases with Q(2) more steeply than the proton magnetic form factor, the ratio E(1+)/M(1+) is small and negative, indicating strong helicity nonconservation, and the ratio S(1+)/M(1+) is negative, while its magnitude increases with Q(2).

Search for Theta++ pentaquarks in the exclusive reaction gammap-->K+K-p

The reaction gammap --> pK+K- was studied at Jefferson Lab with photon energies from 1.8 to 3.8 GeV using a tagged photon beam. The goal was to search for a Theta++ pentaquark, a narrow, doubly charged baryon state having strangeness S=+1 and isospin I=1, in the pK+ invariant mass spectrum. No statistically significant evidence of a Theta++ was found. Upper limits on the total and differential cross section for the reaction gammap --> K-Theta++ were obtained in the mass range from 1.5 to 2.0 GeV/c2, with an upper limit for a narrow resonance with a mass M(Theta++) = 1.54 GeV/c2 of about 0.15 nb, 95% C.L.. This result places a stringent upper limit on the Theta++ width Gamma(Theta++) <0.1 MeV/c2.

Measurement of deeply virtual compton scattering with a polarized-proton target

The longitudinal target-spin asymmetry AUL for the exclusive electroproduction of high-energy photons was measured for the first time in ep-->e;'pgamma. The data have been accumulated at JLab with the CLAS spectrometer using 5.7 GeV electrons and a longitudinally polarized NH3 target. A significant azimuthal angular dependence was observed, resulting from the interference of the deeply virtual Compton scattering and Bethe-Heitler processes. The amplitude of the sinvarphi moment is 0.252+/-0.042stat+/-0.020sys. Theoretical calculations are in good agreement with the magnitude and the kinematic dependence of the target-spin asymmetry, which is sensitive to the generalized parton distributions H and H.