Azimuthal angle correlations for rapidity separated Hadron pairs in d+Au collisions at square root of sNN=200 GeV

Deuteron-gold (d+Au) collisions at the Relativistic Heavy Ion Collider provide ideal platforms for testing QCD theories in dense nuclear matter at high energy. In particular, models suggesting strong saturation effects for partons carrying small nucleon momentum fraction (x) predict modifications to jet production at forward rapidity (deuteron-going direction) in d+Au collisions. We report on two-particle azimuthal angle correlations between charged hadrons at forward/backward (deuteron/gold going direction) rapidity and charged hadrons at midrapidity in d+Au and p+p collisions at square root of sNN=200 GeV. Jet structures observed in the correlations are quantified in terms of the conditional yield and angular width of away-side partners. The kinematic region studied here samples partons in the gold nucleus with x~0.1 to ~0.01. Within this range, we find no x dependence of the jet structure in d+Au collisions.

Acellular extracellular matrix for inguinal hernia repair

To investigate the clinical safety and effectiveness of acellular extracellular matrix (AEM) for inguinal hernia repair, 53 well-conducted and well-chosen sequential cases with inguinal hernia (56 inguinal hernias) were included in our multi-center study. All the inguinal hernias were repaired using conventional tension-free surgical procedures after being classified with Gilbert methods. No rejection was observed after operation. All the incisions healed well and no recurrence was found at the sixth month follow-up. At the seventh month after operation, one case of recurrence of right-side bilateral inguinal hernia (type IV) and another case of recurrence of left-side inguinal hernia (type V) were found. No other recurrence was observed at the 18th month follow-up. The AEM material has good histocompatibility and biomechanics characters and can be used for inguinal hernia repair. We observed no infection, chronic pain, funiculotesticular reaction, local nodular or feeling of discomfort after operation. But a further study of the usage of AEM in the repair of type IV and V inguinal hernias is still needed.

Common suppression pattern of eta and pi0 mesons at high transverse momentum in Au + Au collisions at square root S(NN) = 200 GeV

Inclusive transverse momentum spectra of eta mesons have been measured within p(T) = 2-10 GeV/c at midrapidity by the PHENIX experiment in Au + Au collisions at square root S(NN) = 200 GeV. In central Au+Au the eta yields are significantly suppressed compared to peripheral Au + Au, d + Au, and p + p yields scaled by the corresponding number of nucleon-nucleon collisions. The magnitude, centrality, and p(T) dependence of the suppression is common, within errors, for eta and pi0. The ratio of eta to pi0 spectra at high p(T) amounts to 0.40 < R(eta/pi)0 < 0.48 for the three systems, in agreement with the world average measured in hadronic and nuclear reactions and, at large scaled momentum, in e+e- collisions.

Single electrons from heavy-flavor decays in collisions at

The invariant differential cross section for inclusive electron production in p+p collisions at [FORMULA: SEE TEXT] has been measured by the PHENIX experiment at the BNL Relativistic Heavy Ion Collider over the transverse momentum range 0.4<or=pT<OR=5.0 GeV/c in the central rapidity region ([FORMULA: SEE TEXT]). The contribution to the inclusive electron spectrum from semileptonic decays of hadrons carrying heavy flavor, i.e., charm quarks or, at high , bottom quarks, is determined via three independent methods. The resulting electron spectrum from heavy-flavor decays is compared to recent leading and next-to-leading order perturbative QCD calculations. The total cross section of charm quark-antiquark pair production is determined to be [FORMULA: SEE TEXT].

Measurement of identified and inclusive photon second-harmonic parameter and implications for direct photon production in [FORMULA: SEE TEXT] Au+Au

The azimuthal distribution of identified pi0 and inclusive photons has been measured in [FORMULA: SEE TEXT] Au+Au collisions with the PHENIX experiment at the Relativistic Heavy-Ion Collider (RHIC). The second-harmonic parameter (nu2) was measured to describe the observed anisotropy of the azimuthal distribution. The measured inclusive photon is consistent with the value expected for the photons from hadron decay and is also consistent with the lack of direct photon signal over the measured pT range 1-6 GeV/c. An attempt is made to extract nu2 of direct photons.

Nuclear modification of electron spectra and implications for heavy quark energy loss in Au+Au collisions at [FORMULA: SEE TEXT]

The PHENIX experiment has measured midrapidity ([FORMULA: SEE TEXT]) transverse momentum spectra ([FORMULA: SEE TEXT]) of electrons as a function of centrality in Au+Au collisions at [FORMULA: SEE TEXT]. Contributions from photon conversions and from light hadron decays, mainly Dalitz decays of pi0 and eta mesons, were removed. The resulting nonphotonic electron spectra are primarily due to the semileptonic decays of hadrons carrying heavy quarks. Nuclear modification factors were determined by comparison to nonphotonic electrons in p+p collisions. A significant suppression of electrons at high pT is observed in central Au+Au collisions, indicating substantial energy loss of heavy quarks.

J/psi production and nuclear effects for d + Au and p + p collisions at square root of S(NN) = 200 GeV

J/psi production in d + Au and p + p collisions at square root of S(NN) = 200 GeV has been measured by the PHENIX experiment at rapidities -2.2 < y < +2.4. The cross sections and nuclear dependence of J/psi production versus rapidity, transverse momentum, and centrality are obtained and compared to lower energy p + A results and to theoretical models. The observed nuclear dependence in d + Au collisions is found to be modest, suggesting that the absorption in the final state is weak and the shadowing of the gluon distributions is small and consistent with Dokshitzer-Gribov-Lipatov-Altarelli-Parisi-based parametrizations that fit deep-inelastic scattering and Drell-Yan data at lower energies.

Measurement of transverse single-spin asymmetries for midrapidity production of neutral pions and charged hadrons in polarized p + p collisions at square root(s) = 200 GeV

Transverse single-spin asymmetries to probe the transverse-spin structure of the proton have been measured for neutral pions and nonidentified charged hadrons from polarized proton-proton collisions at midrapidity and square root(s) = 200 GeV. The data cover a transverse momentum (pT) range 1.0-5.0 GeV/c for neutral pions and 0.5-5.0 GeV/c for charged hadrons, at a Feynman-x value of approximately zero. The asymmetries seen in this previously unexplored kinematic region are consistent with zero within errors of a few percent. In addition, the inclusive charged hadron cross section at midrapidity from 0.5 < pT < 7.0 GeV/c is presented and compared to next-to-leading order perturbative QCD (pQCD) calculations. Successful description of the unpolarized cross section above approximately 2 GeV/c suggests that pQCD is applicable in the interpretation of the asymmetry results in the relevant kinematic range.

Delimitation of the rice wide compatibility gene S5 ( n ) to a 40-kb DNA fragment

Wide compatibility varieties (WCVs) are a special class of rice (Oryza sativa L.) germplasm that produces hybrids with normal pollen and spikelet fertility when crossed with both indica and japonica subspecies. The wide compatibility gene S5 ( n ) has been used extensively in inter-subspecific hybrid breeding programs. We previously mapped the S5 locus to a 2.2-cM genomic region between RM253 and R2349 on chromosome 6, using a population of 356 F(1) plants derived from the three-way cross 02428/Nanjing11//Balilla. In this study, a chromosome walking strategy was employed to construct a physical map covering this genomic region using these two closest markers as the starting points. A physical map consisting of six overlapping BAC clones was formed, spanning a genomic region of 540-kb in length. By analyzing recombination events from a population of 8,000 F(1) plants derived from a three-way cross based on near isogenic lines of the S5 locus, the S5 locus was localized to a DNA fragment of 40-kb in length, flanked by two shotgun subclones, 7B1 and 15D2. Sequence analysis of this fragment predicted five open reading frames, encoding xyloglucan fucosyltransferases, dnak-type molecular chaperone BiP, a putative eukaryotic aspartyl protease, and a hypothetical protein. This result will be very useful in molecular cloning of the S5 ( n ) allele and marker-assisted transferring of the wide compatibility gene in rice breeding programs.

Saturation of azimuthal anisotropy in Au + Au collisions at (square root)s(NN) = 62-200 GeV

New measurements are presented for charged hadron azimuthal correlations at midrapidity in Au+Au collisions at (square root)s(NN) = 62.4 and 200 GeV. They are compared to earlier measurements obtained at (square root)s(NN) = 130 GeV and in Pb + Pb collisions at (square root)s(NN) = 17.2 GeV. Sizeable anisotropies are observed with centrality and transverse momentum (pT) dependence characteristic of elliptic flow (upsilon2). For a broad range of centralities, the observed magnitudes and trends of the differential anisotropy, upsilon2(pT), change very little over the collision energy range (square root)s(NN) = 62-200 GeV, indicating saturation of the excitation function for upsilon2 at these energies. Such a saturation may be indicative of the dominance of a very soft equation of state for (square root)s(NN) approximately 60-200 GeV.

Centrality dependence of direct photon production in (square root)S(NN) = 200 GeV Au + Au collisions

The first measurement of direct photons in Au + Au collisions at (square root)S(NN) = 200 GeV is presented. The direct photon signal is extracted as a function of the Au + Au collision centrality and compared to next-to-leading order perturbative quantum chromodynamics calculations. The direct photon yield is shown to scale with the number of nucleon-nucleon collisions for all centralities.

Localization of pms3, a gene for photoperiod-sensitive genic male sterility, to a 28.4-kb DNA fragment

Photoperiod-sensitive genic male-sterile (PSGMS) rice, in which pollen fertility is regulated by day-length, originally arose as a natural mutant in the rice cultivar Nongken 58 (Oryza sativa ssp. japonica). Previous studies identified pms3 on chromosome 12 as the locus of the original PSGMS mutation. In this study we have assigned the pms3 locus to a 28.4-kb DNA fragment by genetic and physical mapping. A cross between Nongken 58S (PSGMS line) and DH80 was used to produce an F2 population of about 7000 plants, from which 892 highly sterile individuals were obtained for recombination analysis. By analyzing recombination events in the sterile individuals using a total of 157 RFLP probes from a BAC contig covering the pms3 region, the pms3 locus was localized to a sub-region of less than 1.7 cM. Further analysis of recombination events using 49 additional probes isolated from this sub-region identified markers flanking the pms3 region on each side; these markers are only 28.4-kb apart. Sequence analysis of this fragment predicted the presence of five ORFs, found high homology with two ESTs in public databases, and detected three SNPs between the mutant and the wild-type parents, which may be helpful for identifying a candidate gene for pms3.

Deuteron and antideuteron production in Au+Au collisions at square root of s(NN)=200 GeV

The production of deuterons and antideuterons in the transverse momentum range 1.1<p(T)<4.3 GeV/c at midrapidity in Au+Au collisions at square root of s(NN)=200 GeV has been studied by the PHENIX experiment at RHIC. A coalescence analysis, comparing the deuteron and antideuteron spectra with that of proton and antiproton, has been performed. The coalescence probability is equal for both deuterons and antideuterons and it increases as a function of p(T), which is consistent with an expanding collision zone. Comparing (anti)proton yields, p /p=0.73+/-0.01, with (anti)deuteron yields, d /d=0.47+/-0.03, we estimate that n /n=0.64+/-0.04. The nucleon phase space density is estimated from the coalescence measurement.

Centrality dependence of charm production from a measurement of single electrons in Au+Au collisions at sqrt[s(NN)]=200 GeV

The PHENIX experiment has measured midrapidity transverse momentum spectra (0.4<p(T)<4.0 GeV/c) of single electrons as a function of centrality in Au+Au collisions at sqrt[s(NN)]=200 GeV. Contributions from photon conversions and Dalitz decays of light neutral mesons are measured by introducing a thin (1.7% X0) converter into the PHENIX acceptance and are statistically removed. The subtracted nonphotonic electron spectra are primarily due to the semileptonic decays of hadrons containing heavy quarks, mainly charm at lower p(T). For all centralities, the charm production cross section is found to scale with the nuclear overlap function, T(AA). For minimum-bias collisions the charm cross section per binary collision is N(cc )/T(AA)=622+/-57(stat)+/-160(syst) microb.

Nuclear modification factors for hadrons at forward and backward rapidities in deuteron-gold collisions at sqrt[s(NN)]=200 GeV

We report on charged hadron production in deuteron-gold reactions at sqrt[s(NN)]=200 GeV. Our measurements in the deuteron direction cover 1.4<eta<2.2, referred to as forward rapidity, and in the gold direction -2.0<eta<-1.4, referred to as backward rapidity, and a transverse momentum range p(T)=0.5-4.0 GeV/c. We compare the relative yields for different deuteron-gold collision centrality classes. We observe a suppression relative to binary collision scaling at forward rapidity, sensitive to low momentum fraction (x) partons in the gold nucleus, and an enhancement at backward rapidity, sensitive to high momentum fraction partons in the gold nucleus.

High-resolution refinement of the hexagonal A-DNA octamer d(GTGTACAC) at 1.4 A

The hexagonal crystal form of the octamer d(GTGTACAC), grown in the presence of spermine, has unit-cell dimensions a = b = 32.18 and c = 78.51 A, space group P6(1)22, with one DNA strand in the asymmetric unit. The structure has been refined starting with the earlier lower resolution model and using high-resolution 1.4 A data collected on a Siemens-Xentronics area detector at 258 K. There were 4365 unique reflections greater than 2sigma(F) in the resolution range 5-1.4 A. The model was refitted into 3F(o) - 2F(c). Sim-weighted omit maps and difference maps were used to locate water molecules. The final model with 161 DNA atoms and 37 water molecules gave an R factor of 19.8%. Crystals of the same octamer were also grown in the presence of spermidine instead of spermine, and refinement using nominal 1.45 A resolution data, 3292 unique reflections, final R = 19.1%, gave virtually identical DNA parameters. No bound spermine or spermidine was detected in either of these structure analyses. The electron density was clear for the DNA and showed holes in the center of the six-membered rings of bases, and also in the center of some of the sugar rings. The high-resolution structure has provided more precise DNA parameters and confirmed the features observed in the earlier 2 A study including the packing-induced distortion in the A7 (A15) sugar pucker from C(3')-endo and C(2')-endo. This change causes the end base pairs to bend away from the helix axis while the rest of the duplex is nearly linear. The hydration patterns in the deep and shallow grooves have been characterized. Chains of water molecules were found, but no rings. The familiar intermolecular contact region between the end base pair and the minor groove of a symmetry-related duplex, involving four residues on one strand and two on the other, has been analyzed. One of these interactions is a hydrogen bond.

Genetic dissection of embryo sac fertility, pollen fertility, and their contributions to spikelet fertility of intersubspecific hybrids in rice

The partial sterility of hybrids has been a major barrier for utilization of the strong heterosis expressed in hybrids between Oryza sativa ssp. indica and O. sativa ssp. japonica. Wide-compatibility varieties, comprising a special class of germplasm, are able to produce fertile hybrids when crossed to both indica and japonica varieties. However, all the work on wide compatibility and majority of studies on indica/japonica hybrid sterility reported so far were based only on spikelet fertility; thus, it is not known to what extent male and female gamete abortions influence hybrid sterility. In this study, we investigated pollen fertility, embryo sac fertility, and spikelet fertility in an F1 population of 202 true hybrid plants derived from a three-way cross ('02428'/'Nanjing 11'//'Balilla'). A partial regression analysis showed that the pollen and embryo sac fertility contributed almost equally to spikelet fertility. QTL analysis based on a linkage map of 191 polymorphic marker loci identified two QTLs for pollen fertility, one QTL for embryo sac fertility, and three QTLs for spikelet fertility. The S5 locus, previously identified as a locus for wide compatibility by spikelet fertility analysis, is a major locus for embryo sac fertility, and a QTL on chromosome 5 had a major effect on pollen fertility. These two loci coincided with the two major QTLs for spikelet fertility. The study also detected a QTL on chromosome 8, showing a large effect on spikelet fertility but no effect on either pollen or embryo sac fertility. Very little interaction among the QTLs was detected. The implications of the findings in rice breeding programs are discussed.

Double helicity asymmetry in inclusive midrapidity pi0 production for polarized p+p collisions at square root s = 200 GeV

We present a measurement of the double longitudinal spin asymmetry in inclusive pi(0) production in polarized proton-proton collisions at sqrt[s]=200 GeV. The data were taken at the Relativistic Heavy Ion Collider with average beam polarizations of 0.27. The measurements are the first in a program to study the longitudinal spin structure of the proton, using strongly interacting probes, at collider energies. The asymmetry is presented for transverse momenta 1-5 GeV/c at midrapidity, where next-to-leading-order perturbative quantum chromodynamic (NLO pQCD) calculations well describe the unpolarized cross section. The observed asymmetry is small and is compared to a NLO pQCD calculation with a range of polarized gluon distributions.

Bose-Einstein correlations of charged pion pairs in Au + Au collisions at square root sNN = 200 GeV

Bose-Einstein correlations of identically charged pion pairs were measured by the PHENIX experiment at midrapidity in Au + Au collisions at square root s(NN)=200 GeV. The Bertsch-Pratt radius parameters were determined as a function of the transverse momentum of the pair and as a function of the centrality of the collision. Using the standard core-halo partial Coulomb fits, and a new parametrization which constrains the Coulomb fraction as determined from the unlike-sign pion correlation, the ratio R(out)/R(side) is within 0.8-1.1 for 0.25< <k(T)> <1.2 GeV/c. The centrality dependence of all radii is well described by a linear scaling in N(1/3)(part), and R(out)/R(side) for <k(T)> approximately 0.45 GeV/c is approximately constant at unity as a function of centrality.

Measurement of nonrandom event-by-event fluctuations of average transverse momentum in square root of (sNN)=200 GeV Au+Au and p+p collisions

Event-by-event fluctuations of the average transverse momentum of produced particles near midrapidity have been measured by the PHENIX Collaboration in square root of (sNN)=200 GeV Au+Au, and p+p collisions at the Relativistic Heavy Ion Collider. The fluctuations are observed to be in excess of the expectation for statistically independent particle emission for all centralities. The excess fluctuations exhibit a dependence on both the centrality of the collision and on the pT range over which the average is calculated. Both the centrality and pT dependence can be well reproduced by a simulation of random particle production with the addition of contributions from hard-scattering processes.

J/psi production from proton-proton collisions at square root of s=200 GeV

J/psi production has been measured in proton-proton collisions at square root of s=200 GeV over a wide rapidity and transverse momentum range by the PHENIX experiment at the Relativistic Heavy Ion Collider. Distributions of the rapidity and transverse momentum, along with measurements of the mean transverse momentum and total production cross section are presented and compared to available theoretical calculations. The total J/psi cross section is 4.0+/-0.6(stat)+/-0.6(syst)+/-0.4(abs) mu b. The mean transverse momentum is 1.80+/-0.23(stat)+/-0.16(syst) GeV/c.

The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines derived from an indica by japonica cross

Delayed leaf-senescence, or stay-green, has been regarded as a desired characteristic for the production of a number of crops including rice. In this study, we analyzed the genetic basis of stay-green using a population of 190 doubled haploid lines from the cross between an indica parent Zhenshan 97 and a stay-green japonica parent Wuyujing 2. The population was tested in replicated field trials in 2 consecutive years, and six traits were defined to evaluate the stay-green characteristics. A genetic linkage map with 179 SSR (simple sequence repeat) marker loci was constructed. The software QTLMapper, based on a mixed linear model approach, was applied to detect QTLs, epistatic effects and their environmental interactions for these traits. A total of 46 main-effect QTLs was detected for the six traits that can be localized to 25 chromosomal regions. The individual effects of all the QTLs were small. Fifty digenic interactions were resolved that involved 66 loci distributed on all 12 chromosomes. Environmental interactions were detected for 18 of the main-effect QTLs and 14 of the epistatic interactions. Collectively, the epistatic effects and QTL by year interactions accounted for large proportions of the phenotypic variations. The results also showed that most of the stay-green traits were negatively correlated with yield and its component traits. The implications of the results in crop improvement were discussed.