JLab Measurements of the

The charge and magnetic form factors, F_{C} and F_{M}, respectively, of ^{3}He are extracted in the kinematic range 25 fm^{-2}≤Q^{2}≤61 fm^{-2} from elastic electron scattering by detecting ^{3}He recoil nuclei and scattered electrons in coincidence with the two High Resolution Spectrometers of the Hall A Facility at Jefferson Lab. The measurements find evidence for the existence of a second diffraction minimum for the magnetic form factor at Q^{2}=49.3 fm^{-2} and for the charge form factor at Q^{2}=62.0 fm^{-2}. Both minima are predicted to exist in the Q^{2} range accessible by this Jefferson Lab experiment. The data are in qualitative agreement with theoretical calculations based on realistic interactions and accurate methods to solve the three-body nuclear problem.

Publisher's Note: JLab Measurements of the

This corrects the article DOI: 10.1103/PhysRevLett.119.162501.

Measurement of the Target-Normal Single-Spin Asymmetry in Quasielastic Scattering from the Reaction (3)He(↑)(e,e').

We report the first measurement of the target single-spin asymmetry, A(y), in quasielastic scattering from the inclusive reaction (3)He(↑)(e,e') on a (3)He gas target polarized normal to the lepton scattering plane. Assuming time-reversal invariance, this asymmetry is strictly zero for one-photon exchange. A nonzero A(y) can arise from the interference between the one- and two-photon exchange processes which is sensitive to the details of the substructure of the nucleon. An experiment recently completed at Jefferson Lab yielded asymmetries with high statistical precision at Q(2)=0.13, 0.46, and 0.97 GeV(2). These measurements demonstrate, for the first time, that the (3)He asymmetry is clearly nonzero and negative at the 4σ-9σ level. Using measured proton-to-(3)He cross-section ratios and the effective polarization approximation, neutron asymmetries of -(1-3)% were obtained. The neutron asymmetry at high Q(2) is related to moments of the generalized parton distributions (GPDs). Our measured neutron asymmetry at Q(2)=0.97 GeV(2) agrees well with a prediction based on two-photon exchange using a GPD model and thus provides a new, independent constraint on these distributions.

Precision Measurement of the p(e,e

New results are reported from a measurement of π^{0} electroproduction near threshold using the p(e,e^{'}p)π^{0} reaction. The experiment was designed to determine precisely the energy dependence of s- and p-wave electromagnetic multipoles as a stringent test of the predictions of chiral perturbation theory (ChPT). The data were taken with an electron beam energy of 1192 MeV using a two-spectrometer setup in Hall A at Jefferson Lab. For the first time, complete coverage of the ϕ_{π}^{*} and θ_{π}^{*} angles in the pπ^{0} center of mass was obtained for invariant energies above threshold from 0.5 up to 15 MeV. The 4-momentum transfer Q^{2} coverage ranges from 0.05 to 0.155 (GeV/c)^{2} in fine steps. A simple phenomenological analysis of our data shows strong disagreement with p-wave predictions from ChPT for Q^{2}>0.07 (GeV/c)^{2}, while the s-wave predictions are in reasonable agreement.

Precision measurement of the neutron twist-3 matrix element d(2)(n): probing color forces.

Double-spin asymmetries and absolute cross sections were measured at large Bjorken x (0.25≤x≤0.90), in both the deep-inelastic and resonance regions, by scattering longitudinally polarized electrons at beam energies of 4.7 and 5.9 GeV from a transversely and longitudinally polarized (3)He target. In this dedicated experiment, the spin structure function g(2)((3)He) was determined with precision at large x, and the neutron twist-3 matrix element d(2)(n) was measured at ⟨Q(2)⟩ of 3.21 and 4.32 GeV(2)/c(2), with an absolute precision of about 10(-5). Our results are found to be in agreement with lattice QCD calculations and resolve the disagreement found with previous data at ⟨Q(2)⟩=5 GeV(2)/c(2). Combining d(2)(n) and a newly extracted twist-4 matrix element f(2)(n), the average neutron color electric and magnetic forces were extracted and found to be of opposite sign and about 30 MeV/fm in magnitude.

Measurement of the target-normal single-spin asymmetry in deep-inelastic scattering from the reaction (3)He(↑)(e,e')X.

We report the first measurement of the target-normal single-spin asymmetry in deep-inelastic scattering from the inclusive reaction 3)He(↑)(e,e')X on a polarized (3)He gas target. Assuming time-reversal invariance, this asymmetry is strictly zero in the Born approximation but can be nonzero if two-photon-exchange contributions are included. The experiment, conducted at Jefferson Lab using a 5.89 GeV electron beam, covers a range of 1.72 GeV, which is nonzero at the 2.89σ level. Our measured asymmetry agrees both in sign and magnitude with a two-photon-exchange model prediction that uses input from the Sivers transverse momentum distribution obtained from semi-inclusive deep-inelastic scattering.

Measurement of double-polarization asymmetries in the quasielastic (3)He[→](e[→],e(')d) process.

We present a precise measurement of double-polarization asymmetries in the ^{3}He[over →](e[over →],e^{'}d) reaction. This particular process is a uniquely sensitive probe of hadron dynamics in ^{3}He and the structure of the underlying electromagnetic currents. The measurements have been performed in and around quasielastic kinematics at Q^{2}=0.25(GeV/c)^{2} for missing momenta up to 270 MeV/c. The asymmetries are in fair agreement with the state-of-the-art calculations in terms of their functional dependencies on p_{m} and ω, but are systematically offset. Beyond the region of the quasielastic peak, the discrepancies become even more pronounced. Thus, our measurements have been able to reveal deficiencies in the most sophisticated calculations of the three-body nuclear system, and indicate that further refinement in the treatment of their two-and/or three-body dynamics is required.

JLab measurement of the 4He charge form factor at large momentum transfers.

The charge form factor of 4He has been extracted in the range 29 fm(-2) ≤ Q2 ≤ 77 fm(-2) from elastic electron scattering, detecting 4He recoil nuclei and electrons in coincidence with the high resolution spectrometers of the Hall A Facility of Jefferson Lab. The measurements have uncovered a second diffraction minimum for the form factor, which was predicted in the Q2 range of this experiment. The data are in qualitative agreement with theoretical calculations based on realistic interactions and accurate methods to solve the few-body problem.

Measurements of parity-violating asymmetries in electron-deuteron scattering in the nucleon resonance region.

We report on parity-violating asymmetries in the nucleon resonance region measured using inclusive inelastic scattering of 5-6 GeV longitudinally polarized electrons off an unpolarized deuterium target. These results are the first parity-violating asymmetry data in the resonance region beyond the Δ(1232). They provide a verification of quark-hadron duality-the equivalence of the quark- and hadron-based pictures of the nucleon-at the (10-15)% level in this electroweak observable, which is dominated by contributions from the nucleon electroweak γZ interference structure functions. In addition, the results provide constraints on nucleon resonance models relevant for calculating background corrections to elastic parity-violating electron scattering measurements.

Beam-target double-spin asymmetry A{LT} in charged pion production from deep inelastic scattering on a transversely polarized {3}He target at 1.4

We report the first measurement of the double-spin asymmetry A{LT} for charged pion electroproduction in semi-inclusive deep-inelastic electron scattering on a transversely polarized {3}He target. The kinematics focused on the valence quark region, 0.16

New precision limit on the strange vector form factors of the proton.

The parity-violating cross-section asymmetry in the elastic scattering of polarized electrons from unpolarized protons has been measured at a four-momentum transfer squared Q2 = 0.624 GeV2 and beam energy E(b) = 3.48 GeV to be A(PV) = -23.80 ± 0.78(stat) ± 0.36(syst) parts per million. This result is consistent with zero contribution of strange quarks to the combination of electric and magnetic form factors G(E)(s) + 0.517G(M)(s) = 0.003 ± 0.010(stat) ± 0.004(syst) ± 0.009(ff), where the third error is due to the limits of precision on the electromagnetic form factors and radiative corrections. With this measurement, the world data on strange contributions to nucleon form factors are seen to be consistent with zero and not more than a few percent of the proton form factors.

Single spin asymmetries in charged pion production from semi-inclusive deep inelastic scattering on a transversely polarized 3He Target at Q2 = 1.4-2.7 GeV2.

We report the first measurement of target single spin asymmetries in the semi-inclusive (3)He(e,e'π(±))X reaction on a transversely polarized target. The experiment, conducted at Jefferson Lab using a 5.9 GeV electron beam, covers a range of 0.16 < x < 0.35 with 1.4 < Q(2) < 2.7 GeV(2). The Collins and Sivers moments were extracted from the azimuthal angular dependence of the measured asymmetries. The π(±) Collins moments for (3)He are consistent with zero, except for the π(+) moment at x = 0.35, which deviates from zero by 2.3σ. While the π(-) Sivers moments are consistent with zero, the π(+) Sivers moments favor negative values. The neutron results were extracted using the nucleon effective polarization and measured cross section ratios of proton to (3)He, and are largely consistent with the predictions of phenomenological fits and quark model calculations.

Measurements of the electric form factor of the neutron up to Q2=3.4 GeV2 using the reaction 3He(e,e'n)pp.

The electric form factor of the neutron was determined from studies of the reaction 3He(e,e'n)pp in quasielastic kinematics in Hall A at Jefferson Lab. Longitudinally polarized electrons were scattered off a polarized target in which the nuclear polarization was oriented perpendicular to the momentum transfer. The scattered electrons were detected in a magnetic spectrometer in coincidence with neutrons that were registered in a large-solid-angle detector. More than doubling the Q2 range over which it is known, we find G(E)(n)=0.0236±0.0017(stat)±0.0026(syst), 0.0208±0.0024±0.0019, and 0.0147±0.0020±0.0014 for Q(2)=1.72, 2.48, and 3.41 GeV2, respectively.

Mixing ratios of carbonyls and BTEX in ambient air of Kolkata, India and their associated health risk.

Mixing ratios of 15 carbonyls and BTEX (benzene, toluene, ethyl benzene, xylenes) were measured for the first time in ambient air of Kolkata, India at three sites from March to June 2006 and their photochemical reactivity was evaluated. Day and nighttime samples were collected on weekly basis. Formaldehyde was the most abundant carbonyl (mean concentration ranging between 14.07 microg m(-3) to 26.12 microg m(-3) over the three sites) followed by acetaldehyde (7.60-18.67 microg m(-3)) and acetone (4.43-10.34 microg m(-3)). Among the high molecular weight aldehydes, nonanal showed the highest concentration. Among the mono-aromatic VOCs, mean concentration of toluene (27.65-103.31 microg m(-3)) was maximum, closely followed by benzene (24.97-79.18 microg m(-3)). Mean formaldehyde to acetaldehyde (1.4) and acetaldehyde to propanal ratios (5.0) were typical of urban air. Based on their photochemical reactivity towards OH. radical, the concentrations of the VOCs were scaled to formaldehyde equivalent, which showed that the high molecular weight carbonyls and xylenes contribute significantly to the total OH-reactive mass of the VOCs. Due to the toxic effect of the VOCs studied, an assessment for both cancer risk and non-cancer hazard due to exposure to the population were calculated. Integrated life time cancer risk (ILTCR) due to four carcinogens (benzene, ethyl benzene, formaldehyde and acetaldehyde) and non-cancer hazard index for the VOCs at their prevailing level were estimated to be 1.42E-04 and 5.6 respectively.

Studies on commuters' exposure to BTEX in passenger cars in Kolkata, India.

Commuters' exposure to volatile organic compounds (VOCs) especially BTEX travelling in passenger cars in Kolkata, India were quantified in Phase I (2001-2002) and Phase II (2003-2004). Monitoring was made inside and in the immediate outside of passenger cars fitted with and without catalytic converters using different types of fuels, along two congested urban routes. During Phase I of the study, the benzene content in gasoline was 5% and the mean concentration of in-vehicle benzene in cars without catalytic converter was found to be as high as 721.2 microg/m3. In Phase II when the benzene content was reduced to <3% and with modified engine type, the mean in-vehicle benzene concentration was reduced to 112.4 microg/m3. The in-vehicle concentration varied with engine type and age of the vehicle. Roadside ambient mean concentration of benzene was 214.8 microg/m3 and 30.8 microg/m3 in Phase I and Phase II respectively.

Mathematical characterization of Chaos Game Representation. New algorithms for nucleotide sequence analysis.

Chaos Game Representation (CGR) can recognize patterns in the nucleotide sequences, obtained from databases, of a class of genes using the techniques of fractal structures and by considering DNA sequences as strings composed of four units, G, A, T and C. Such recognition of patterns relies only on visual identification and no mathematical characterization of CGR is known. The present report describes two algorithms that can predict the presence or absence of a stretch of nucleotides in any gene family. The first algorithm can be used to generate DNA sequences represented by any point in the CGR. The second algorithm can simulate known CGR patterns for different gene families by setting the probabilities of occurrence of different di- or trinucleotides by a trial and error process using some guidelines and approximate rules-of-thumb. The validity of the second algorithm has been tested by simulating sequences that can mimic the CGRs of vertebrate non-oncogenes, proto-oncogenes and oncogenes. These algorithms can provide a mathematical basis of the CGR patterns obtained using nucleotide sequences from databases.

A novel mutant of the type I restriction-modification enzyme EcoR124I is altered at a key stage of the subunit assembly pathway.

The HsdS subunit of a type I restriction-modification (R-M) system plays an essential role in the activity of both the modification methylase and the restriction endonuclease. This subunit is responsible for DNA binding, but also contains conserved amino acid sequences responsible for protein-protein interactions. The most important protein-protein interactions are those between the HsdS subunit and the HsdM (methylation) subunit that result in assembly of an independent methylase (MTase) of stoichiometry M(2)S(1). Here, we analysed the impact on the restriction and modification activities of the change Trp(212)-->Arg in the distal border of the central conserved region of the EcoR124I HsdS subunit. We demonstrate that this point mutation significantly influences the ability of the mutant HsdS subunit to assemble with the HsdM subunit to produce a functional MTase. As a consequence of this, the mutant MTase has drastically reduced DNA binding, which is restored only when the HsdR (restriction) subunit binds with the MTase. Therefore, HsdR acts as a chaperon allowing not only binding of the enzyme to DNA, but also restoring the methylation activity and, at sufficiently high concentrations in vitro of HsdR, restoring restriction activity.

Quantification of human polyomavirus JC virus load in urine and blood samples of healthy tribal populations of North-Eastern part of West Bengal, India.

BACKGROUND: Human polyomavirus JC (JCV) is a widespread human virus with profound pathogenic potential. A study was undertaken to quantify JCV load in urine and peripheral blood samples of immunocompetent, apparently healthy tribal individuals of North-Eastern part of West Bengal, India for the first time. MATERIALS AND METHODS: One hundred and thirteen samples of urine or blood were collected from different tribal groups of this region. For the quantitative estimation of the viral load in each sample, real-time polymerase chain reaction method using the SYBR Green dye was employed. RESULTS: The viral load estimated was found in the range between 3.5 × 102 and 2.12 × 106 copies/ml of samples having a mean and median viral copy numbers of 8.67 × 105 and 9.19 × 105 copies/ml of sample respectively. CONCLUSION: The mean viral DNA load in urine samples of the studied immunocompetent population was found to be higher than that found in a study conducted in the USA, but lower than similar groups of Italy and healthy adult women in the USA. However when compared with median values of viral DNA loads in urine samples of immunocompetent human subjects of Kuwait, Portugal, and Switzerland the observed viral DNA load was found to be substantially higher.

Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias.

Biases in the codon usage and base compositions at three codon sites in different genes of A+T-rich Gram-negative bacterium Haemophillus influenzae and G+C-rich Gram-positive bacterium Mycobacterium tuberculosis have been examined to address the following questions: (1) whether the synonymous codon usage in organisms having highly skewed base compositions is totally dictated by the mutational bias as reported previously (Sharp, P.M., Devine, K.M., 1989. Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons. Nucleic Acids Res. 17, 5029-5039), or is also controlled by translational selection; (2) whether preference of G in the first codon positions by highly expressed genes, as reported in Escherichia coli (Gutierrez, G., Marquez, L., Marin, A., 1996. Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translational efficiency. Nucleic Acids Res. 24, 2525-2527), is true in other bacteria; and (3) whether the usage of bases in three codon positions is species-specific. Result presented here show that even in organisms with high mutational bias, translational selection plays an important role in dictating the synonymous codon usage, though the set of optimal codons is chosen in accordance with the mutational pressure. The frequencies of G-starting codons are positively correlated to the level of expression of genes, as estimated by their Codon Adaptation Index (CAI) values, in M. tuberculosis as well as in H. influenzae in spite of having an A+T-rich genome. The present study on the codon preferences of two organisms with oppositely skewed base compositions thus suggests that the preference of G-starting codons by highly expressed genes might be a general feature of bacteria, irrespective of their overall G+C contents. The ranges of variations in the frequencies of individual bases at the first and second codon positions of genes of both H. influenzae and M. tuberculosis are similar to those of E. coli, implying that though the composition of all three codon positions is governed by a selection-mutation balance, the mutational pressure has little influence in the choice of bases at the first two codon positions, even in organisms with highly biased base compositions.

High-level expression of the cloned genes encoding the subunits of and intact DNA methyltransferase, M.EcoR124.

We have cloned the genes coding for the two subunits (HsdM and HsdS) of the type-I DNA methyltransferase (MTase), M.EcoR124, into the specially constructed expression vector, pJ119. These subunits have been synthesized together as an intact MTase. We have also cloned the individual subunit-encoding genes under the control of the T7 gene 10 promoter or the lacUV5 promoter. High levels of expression have been obtained in all cases. While HsdM was found to be soluble, HsdS was insoluble. However, in the presence of the co-produced HsdM subunit, HsdS was found in the soluble fraction as part of an active MTase. We have partially purified the cloned multi-subunit enzyme and shown that it is capable of DNA methylation both in vivo and in vitro.