Emerging applications of single-cell diagnostics

The performance of DNA sequencers (next generation sequencing) is rapidly enhanced these days, being used for genetic diagnostics. Although many phenomena could be elucidated with such massive genome data, it is still a big challenge to obtain comprehensive understanding of diseases and the relevant biology at the cellular level. In general terms, the data obtained to date are averages of ensembles of cells, but it is not certain whether the same features are the same inside an individual cell. Accordingly, important information may be masked by the averaging process. As the technologies for analyzing bio-molecular components in single cells are being developed, single cell analysis seems promising to address the current limitations due to averaging problems. Although the technologies for single cell analysis are still at the infant stage, the single cell approach has the potential to improve the accuracy of diagnosis based on knowledge of intra- and inter-cellular networks. In this review several technologies and applications (especially medical applications) of genome and transcriptome analysis or single cells are described.

Localized distributions of quasi-two-dimensional electronic states near defects artificially created at graphite surfaces in magnetic fields

We measured the local density of states of a quasi two-dimensional electron system (2DES) near defects, artificially created by Ar-ion sputtering, on surfaces of highly oriented pyrolytic graphite (HOPG) with scanning tunneling spectroscopy (STS) in high magnetic fields. At valley energies of the Landau level spectrum, we found two typical localized distributions of the 2DES depending on the defects. These are new types of distributions which are not observed in the previous STS work at the HOPG surface near a point defect [Y. Niimi, Phys. Rev. Lett. 97, 236804 (2006).10.1103/PhysRevLett.97.236804]. With increasing energy, we observed gradual transformation from the localized distributions to the extended ones as expected for the integer quantum Hall state. We show that the defect potential depth is responsible for the two localized distributions from comparison with theoretical calculations.

Construction of a versatile ultralow temperature scanning tunneling microscope

We constructed a dilution-refrigerator (DR)-based ultralow temperature scanning tunneling microscope (ULT-STM) which works at temperatures down to 30 mK, in magnetic fields up to 6 T and in ultrahigh vacuum (UHV). Besides these extreme operation conditions, this STM has several unique features not available in other DR-based ULT-STMs. One can load STM tips as well as samples with clean surfaces prepared in an UHV environment to a STM head keeping low temperature and UHV conditions. After then, the system can be cooled back to near the base temperature within 3 h. Due to these capabilities, it has a variety of applications not only for cleavable materials but also for almost all conducting materials. The present ULT-STM has also an exceptionally high stability in the presence of magnetic field and even during field sweep. We describe details of its design, performance, and applications for low temperature physics.

Learning arm's posture control using reinforcement learning and feedback-error-learning

In this paper, we propose a learning model using the Actor-Critic method and the feedback-error-learning scheme. The Actor-Critic method, which is one of the major frameworks in reinforcement learning, has attracted attention as a computational learning model in the basal ganglia. Meanwhile, the feedback-error-learning is learning architecture proposed as a computationally coherent model of cerebellar motor learning. This learning architecture's purpose is to acquire a feed-forward controller by using a feedback controller's output as an error signal. In past researches, a predetermined constant gain feedback controller was used for the feedback-error-learning. We use the Actor-Critic method for obtaining a feedback controller in the feedback-error-earning. By applying the proposed learning model to an arm's posture control, we show that high-performance feedback and feed-forward controller can be acquired from only by using a scalar value of reward.

Real-space imaging of alternate localization and extension of quasi-two-dimensional electronic States at graphite surfaces in magnetic fields

We measured the local density of states (LDOS) of a quasi-two-dimensional (2D) electron system near point defects on a surface of highly oriented pyrolytic graphite with scanning tunneling microscopy and spectroscopy. Differential tunnel conductance images taken at very low temperatures and in high magnetic fields show a clear contrast between localized and extended spatial distributions of the LDOS at the valley and peak energies of the Landau level spectrum, respectively. The localized electronic state has a single circular distribution around the defects with a radius comparable to the magnetic length. The localized LDOS is in good agreement with a spatial distribution of a calculated wave function for a single electron in 2D in a Coulomb potential in magnetic fields.

STS observations of Landau levels at graphite surfaces

Scanning tunneling spectroscopy (STS) measurements were made on surfaces of two different kinds of graphite samples, Kish graphite and highly oriented pyrolytic graphite (HOPG), at very low temperatures and in high magnetic fields. We observed a series of peaks in the tunnel spectra associated with Landau quantization of the quasi-two-dimensional electrons and holes. A comparison with the calculated local density of states at the surface layers allows us to identify Kish graphite as bulk graphite and HOPG as graphite with a finite thickness of 40 layers. This explains the qualitative difference between the two graphites reported in the recent transport measurements which suggested the quantum-Hall effect in HOPG. This work demonstrates how powerful the combined approach between the high quality STS measurement and the first-principles calculation is in material science.

Inclusive double-pomeron exchange at the fermilab tevatron p p collider

We report results from a study of events with a double-Pomeron exchange topology produced in p p collisions at sqrt[s]=1800 GeV. The events are characterized by a leading antiproton and a large rapidity gap on the outgoing proton side. We find that the differential production cross section agrees in shape with predictions based on Regge theory and factorization, and that the ratio of double-Pomeron exchange to single diffractive production rates is relatively unsuppressed as compared to the O(10) suppression factor previously measured in single diffractive production.

Search for Kaluza-Klein graviton emission in pp collisions at square root[s] = 1.8 TeV using the missing energy signature

We report on a search for direct Kaluza-Klein graviton production in a data sample of 84 pb(-1) of ppmacr; collisions at sqrt[s]=1.8 TeV, recorded by the Collider Detector at Fermilab. We investigate the final state of large missing transverse energy and one or two high energy jets. We compare the data with the predictions from a (3+1+n)-dimensional Kaluza-Klein scenario in which gravity becomes strong at the TeV scale. At 95% confidence level (C.L.) for n=2, 4, and 6 we exclude an effective Planck scale below 1.0, 0.77, and 0.71 TeV, respectively.

Search for pair production of scalar top quarks in R-parity violating decay modes in pp collisions at square root of s=1.8 TeV

We present the results of a search for pair production of scalar top quarks (t(1)) in an R-parity violating supersymmetry scenario in 106 pb(-1) of pp collisions at square root of s=1.8 TeV collected by the Collider Detector at Fermilab. In this mode each t(1) decays into a tau lepton and a b quark. We search for events with two tau's, one decaying leptonically (e or mu) and one decaying hadronically, and two jets. No candidate events pass our final selection criteria. We set a 95% confidence level lower limit on the t(1) mass at 122 GeV/c(2) for Br(t(1)-->tau b)=1.

Search for lepton flavor violating decays of a heavy neutral particle in p(-)p collisions at sqrt[s]=1.8 TeV

We report on a search for a high mass, narrow width particle that decays directly to emu, etau, or microtau. We use approximately 110 pb(-1) of data collected with the Collider Detector at Fermilab from 1992 to 1995. No evidence of lepton flavor violating decays is found. Limits are set on the production and decay of sneutrinos with R-parity violating interactions.

Comparative analysis for expressed genes by polymerase chain reaction using module-shuffling primers

We have developed a method for comparative analysis of gene expression. It is based on competitive PCR amplification with module-shuffling primers, followed by gel electrophoresis in a fluorescent DNA sequencer. In this method, tagged-cDNA restriction fragments derived from different sources were amplified in one tube at the same amplification efficiency. The method can detect different amounts of each expressed gene, up to difference in amounts of 30%. The method was successfully used for comparative analysis of expressed genes in yeast.

Classified fingerprinting: A method of comprehensive analysis for comparing megabase genomes

The objective of the work we describe is to establish elementary methods for investigating the functions of genes; specifically, a fingerprinting method for analyzing entire DNA fragments in a mixture. Our goal is to develop a method for comparing genes with a size of several megabases. We improved a method of amplified fragment length polymorphism (AFLP) so that it could be used to analyze all the restriction fragments in a mixture. This method could be used to detect 90% of the DNA fragments produced from 100-kb model genomes by using a four-base cutter enzyme.

DNA hybridization using "bead-array": probe-attached beads arrayed in a capillary in a predetermined order

We present a DNA analysis device called "Bead-Array", in which DNA-probe-attached beads (100 microns) are arrayed in a capillary in a predetermined order. We developed this device to overcome the problems of using DNA microarray technology, including high cost and a lengthy analysis time. Bead-arrays can easily be mass-produced even for many different probe combinations, and the small reaction volume and the use of sample flows enables faster hybridization. To demonstrate this, we examined DNA hybridization experiments using 18-mer DNA probes and targets and compared them to ones with beads in tubes. The results show that hybridization in bead-arrays progresses more than 100 times faster and reach the plateau in less than three min. These features suggest that the bead-array particularly meets the need for high-speed and disposable devices, for example diagnosis devices.

Central pseudorapidity gaps in events with a leading antiproton at the fermilab tevatron pp collider

We report a measurement of the fraction of events with a large pseudorapidity gap deltaeta within the pseudorapidity region available to the proton dissociation products X in p+p-->p+X. For a final state p of fractional momentum loss xi(p) and 4-momentum transfer squared t(p) within 0.06<xi(p)<0.09 and |t(p)|<1.0 [0.2] GeV2 at sqrt[s]=1800 [630] GeV, the fraction of events with deltaeta>3 is found to be 0.246+/-0.001 (stat)+/-0.042 (syst) [0.184+/-0.001 (stat)+/-0.043 (syst)]. Our results are compared with gap fractions measured in minimum bias pp collisions and with theoretical expectations.

Search for the supersymmetric partner of the top quark in dilepton events from pp collisions at square root of s=1.8 TeV

We have searched for pair production of the supersymmetric partner of the top quark (stop) in 107 pb(-1) of pp collisions at square root of s=1.8 TeV collected by the Collider Detector at Fermilab (CDF). Each stop is assumed to decay into a lepton, bottom quark, and supersymmetric neutrino. Such a scenario would give rise to events with two leptons, two hadronic jets, and a substantial imbalance of transverse energy. No evidence of such a stop signal has been found. We exclude stop masses in the region (80</=m(t)</=135 GeV/c(2)) in the mass plane of stop versus sneutrino.

Search for associated production of Upsilon and vector boson in pp collisions at sqrt[s]=1.8 TeV

We present a search for associated production of the Upsilon(1S) and a vector boson in 83 pb(-1) of ppmacr; collisions at sqrt[s]=1.8 TeV collected by the CDF experiment in 1994-1995. We find no evidence of the searched signal in the data, and set upper limits to the production cross sections.

Search for long-lived charged massive particles in pp collisions at square root s = 1.8 TeV

We report a search for the production of long-lived charged massive particles in a data sample of 90 pb(-1) of square root[s]=1.8 TeV pp collisions recorded by the Collider Detector at Fermilab. The search uses the muonlike penetration and anomalously high ionization energy loss signature expected for such a particle to discriminate it from backgrounds. The data are found to agree with background expectations, and cross section limits of O(1) pb are derived using two reference models, a stable quark and a stable scalar lepton.

Search for a W' boson decaying to a top and bottom quark pair in 1.8 TeV pp collisions

We report the results of a search for a W' boson produced in pp; collisions at a center-of-mass energy of 1.8 TeV using a 106 pb(-1) data sample recorded by the Collider Detector at Fermilab. We observe no significant excess of events above background for a W' boson decaying to a top and bottom quark pair. In a model where this boson would mediate interactions involving a massive right-handed neutrino (nu(R)) and have standard model strength couplings, we use these data to exclude a W' boson with mass between 225 and 536 GeV/c(2) at 95% confidence level for M(W')>>M(nu(R)) and between 225 and 566 GeV/c(2) at 95% confidence level for M(W')<M(nu(R)).

Limits on extra dimensions and new particle production in the exclusive photon and missing energy signature in pp collisions at square root [s]=1.8 TeV

The exclusive gammaE(T) signal has a small standard model cross section and is thus a channel sensitive to new physics. This signature is predicted by models with a superlight gravitino or with large extra spatial dimensions. We search for such signals at the Collider Detector at Fermilab, using 87 pb(-1) of data at square root [s]=1.8 TeV, and extract 95% C.L. limits on these processes. A limit of 221 GeV is set on the scale |F|(1/2) in supersymmetric models. For 4, 6, and 8 extra dimensions, model-dependent limits on the fundamental mass scale M(D) of 0.55, 0.58, and 0.60 TeV, respectively, are found. We also specify a "pseudo-model-independent" method of comparing the results to theoretical predictions.

Search for new physics in photon-lepton events in pp collisions at sqrt[s] = 1.8 TeV

We present the results of a search in pp collisions at sqrt[s] = 1.8 TeV for anomalous production of events containing a photon and a lepton (e or mu), both with large transverse energy, using 86 pb(-1) of data collected with the Collider Detector at Fermilab during the 1994-1995 collider run at the Fermilab Tevatron. The presence of large missing transverse energy (E(T)), additional photons, or additional leptons in these events is also analyzed. The results are consistent with standard model expectations, with the possible exception of photon-lepton events with large E(T), for which the observed total is 16 events and the expected mean total is 7.6+/-0.7 events.

Amicrobial pustular dermatosis in two patients with immunological abnormalities

We report two patients with severe amicrobial pustular dermatosis with immunological abnormalities: a 63-year-old woman with a 30-year-history of discoid lupus erythematosus and sicca syndrome, and a 35-year-old woman with high levels of gamma-globulinemia and positive antinuclear antibodies. Both patients presented with crusty and eroded erythematous plaques studded with aseptic pustules on the back, face, and scalp. Histological examination showed acanthosis, neutrophilic exocytosis to the epidermis, and neutrophilic and lymphocytic infiltration with nuclear dust in the dermis. These patients were diagnosed as having "amicrobial pustulosis associated with autoimmune diseases". The eruptions improved with combination treatment of oral prednisolone with cyclosporin A or diaminodiphenylsulphone. Although the pathogenesis remains unclear, amicrobial pustular dermatosis might be one of the cutaneous complications in autoimmune diseases.

Upsilon production and polarization in p p macro collisions at square root of s = 1.8 TeV

We report on measurements of the Upsilon(1S), Upsilon(2S), and Upsilon(3S) differential cross sections (d(2)sigma/dp(T)dy)(/y/<0.4), as well as on the Upsilon(1S) polarization in p p macro collisions at square root of s = 1.8 TeV using a sample of 77+/-3 pb(-1) collected by the collider detector at Fermilab. The three resonances were reconstructed through the decay Upsilon-->mu(+)mu(-). The measured angular distribution of the muons in the Upsilon(1S) rest frame is consistent with unpolarized meson production.

Diffractive dijet production at sqrt[s] = 630 and 1800 GeV at the Fermilab Tevatron

We report a measurement of the diffractive structure function F(D)(jj) of the antiproton obtained from a study of dijet events produced in association with a leading antiproton in pp collisions at sqrt[s] = 630 GeV at the Fermilab Tevatron. The ratio of F(D)(jj) at sqrt[s] = 630 GeV to F(D)(jj) obtained from a similar measurement at sqrt[s] = 1800 GeV is compared with expectations from QCD factorization and other theoretical predictions. We also report a measurement of the xi ( x-Pomeron) and beta ( x of parton in Pomeron) dependence of F(D)(jj) at sqrt[s] = 1800 GeV. In the region 0.035<xi<0.095, /t/<1 GeV2, and beta<0.5, F(D)(jj)(beta,xi) is found to be of the form beta(-1.0+/-0.1)xi(-0.9+/-0.1), which obeys beta-xi factorization.

Search for new heavy particles in the WZ0 final state in pp collisions at square root[s] = 1.8 TeV

We present the first general search for new heavy particles, X, which decay via X --> WZ0 --> e(nu)+jj as a function of M(X) and Gamma(X) in pp collisions at square root[s] = 1.8 TeV. No evidence is found for production of X in 110 pb(-1) of data collected by the Collider Detector at Fermilab. General cross section limits are set at the 95% C.L. as a function of mass and width of the new particle. The results are further interpreted as mass limits on the production of new heavy charged vector bosons which decay via W' --> WZ0 in an extended gauge model as a function of the width, Gamma(W'), and mixing factor between the W' and the standard model W bosons.

Study of B0 --> J/psiK(*)0pi(+)pi(-) decays with the collider detector at Fermilab

We report a study of the decays B0 --> J/psiK(*)0pi(+)pi(-), which involve the creation of a uu or dd quark pair in addition to a b -->c(cs) decay. The data sample consists of 110 pb(-1) of pp collisions at square root[s] = 1.8 TeV collected by the CDF detector at the Fermilab Tevatron collider during 1992-1995. We measure the branching fractions to be B(B0 --> J/psiK(*0)pi(+)pi(-)) = (6.6 +/- 1.9 +/- 1.1)x10(-4) and B(B0 --> J/psiK0pi(+)pi(-)) = (10.3 +/- 3.3 +/- 1.5)x10(-4). Evidence is seen for contributions from psi(2S)K(*)0, J/psiK0rho(0), J/psiK(*+)pi(-), and J/psiK1(1270).

Search for gluinos and scalar quarks in pp collisions at square root[s] = 1.8 TeV using the missing energy plus multijets signature

We have performed a search for gluinos (g) and scalar quarks (q) in a data sample of 84 pb(-1) of pp collisions at square root[s] = 1.8 TeV, recorded by the Collider Detector at Fermilab. We investigate the final state of large missing transverse energy and three or more jets, a characteristic signature in R-parity-conserving supersymmetric models. The analysis has been performed "blind," in that the inspection of the signal region is made only after the predictions from standard model backgrounds have been calculated. Comparing the data with predictions of constrained supersymmetric models, we exclude gluino masses below 195 GeV/c2 (95% C.L.), independent of the squark mass. For the case m(q) approximately m(g), gluino masses below 300 GeV/c2 are excluded.

Measurement of the strong coupling constant from inclusive jet production at the Tevatron pp collider

We report a measurement of the strong coupling constant, alpha(s)(MZ), extracted from inclusive jet production in pp collisions at square root[s] = 1800 GeV. The QCD prediction for the evolution of alpha(s) with jet transverse energy ET is tested over the range 40<ET<450 GeV using ET for the renormalization scale. The data show good agreement with QCD in the region below 250 GeV. The value of alpha(s) at the mass of the Z0 boson averaged over the range 40<ET<250 GeV is found to be alpha(s)(MZ) = 0.1178+/-0.0001(stat)+0.0081(-0.0095)(expt. syst). The associated theoretical uncertainties are mainly due to the choice of renormalization scale ((+6%)(-4%)) and input parton distribution functions (5%).

Search for gluinos and squarks using like-sign dileptons in pp macro collisions at square root of s = 1.8 TeV

We present results of the first search for like-sign dilepton ( e(+/-)e(+/-), e(+/-)mu(+/-), mu(+/-)mu(+/-)) events associated with multijets and large missing energy using 106 pb(-1) of data in pp macro collisions at square root of s = 1.8 TeV collected during 1992-1995 by the CDF experiment. Finding no events that pass our selection, we examine pair production of gluinos (tilde g) and squarks (tilde q) in a constrained framework of the minimal supersymmetric standard model. At tan beta = 2 and mu = -800 GeV/c(2), we set 95% confidence level limits of M(tilde g)>221 GeV/c(2) for M(tilde g) approximately M(tilde q), and M(tilde q)>168 GeV/c(2) for M(tilde q)>>M(tilde g), both with small variation as a function of mu.

Observation of diffractive J/psi production at the Fermilab Tevatron

We report the first observation of diffractive J/psi(--> mu+mu-) production in pp collisions at root square[s] = 1.8 TeV. Diffractive events are identified by their rapidity gap signature. In a sample of events with two muons of transverse momentum p(mu)T>2 GeV/c within the pseudorapidity region /eta/ < 1.0, the ratio of diffractive to total J/psi production rates is found to be R(J/psi) = [1.45 +/- 0.25]%. The ratio R(J/psi)(x) is presented as a function of x-Bjorken. By combining it with our previously measured corresponding ratio R(jj)(x) for diffractive dijet production, we extract a value of 0.59 +/- 0.15 for the gluon fraction of the diffractive structure function of the proton.

Search for quark-lepton compositeness and a heavy W' Boson using the enu channel in p p macro collisions at square root of [s] = 1.8 TeV

We present searches for quark-lepton compositeness and a heavy W' boson at high electron-neutrino transverse mass. We use approximately 110 pb(-1) of data collected in p p macro collisions at square root of [s] = 1.8 TeV by the CDF Collaboration during 1992-1995. The data are consistent with standard model expectations. Limits are set on the quark-lepton compositeness scale Lambda, the ratio of partial cross sections sigma(W'-->enu)/sigma(W-->enu), and the mass of a W' boson with standard model couplings. We exclude Lambda<2.81 TeV and a W' boson with mass below 754 GeV/c(2) at the 95% confidence level. Combining with our previously published limit obtained using the muon channel, we exclude a W' boson with mass below 786 GeV/c(2) at the 95% confidence level.

Charged-particle multiplicity pp collisions at square root of (s) = 1.8 TeV

We report on a measurement of the mean charged-particle multiplicity of jets in dijet events with dijet masses in the range 80-630 GeV/c(2), produced at the Tevatron in pp collisions with square root (s) = 1.8 TeV and recorded by the Collider Detector at Fermilab. The data are fit to perturbative-QCD calculations carried out in the framework of the modified leading log approximation and the hypothesis of local parton-hadron duality. The fit yields values for two parameters in that framework: the ratio of parton multiplicities in gluon and quark jets, r identical withN(g-jet)(partons)/N(q-jet)(partons) = 1.7+/-0.3, and the ratio of the number of charged hadrons to the number of partons in a jet, K(charged)(LPHD) identical with N(charged)(hadrons)/N(partons) = 0.57+/-0.11.

Double diffraction dissociation at the Fermilab Tevatron collider

We present results from a measurement of double diffraction dissociation in pp collisions at the Fermilab Tevatron collider. The production cross section for events with a central pseudorapidity gap of width Deltaeta(0)>3 (overlapping eta = 0) is found to be 4.43+/-0.02(stat)+/-1.18(syst) mb [ 3.42+/-0.01(stat)+/-1.09(syst) mb] at square root of (s) = 1800[630] GeV. Our results are compared with previous measurements and with predictions based on Regge theory and factorization.

Miniaturized pyrosequencer for DNA analysis with capillaries to deliver deoxynucleotides

As the human genome project proceeds, various types of DNA analysis tools are required for life sciences and medical sciences including DNA diagnostics. For example, a small DNA sequencer for sequencing a short DNA is required for bed-side DNA testing as well as DNA analysis in a small laboratory. Here, a new handy DNA sequencing system (pyrosequencer) based on the detection of inorganic pyrophosphate (PPi) released by polymerase incorporation is demonstrated. The system uses the bioluminescence detection system. The key point for the miniaturized DNA sequencer is to make a deoxynucleotide triphosphate (dNTP) delivery system small and inexpensive. It has been realized by using narrow capillaries to connect a reaction chamber and four dNTP reservoirs. Each dNTP is introduced into the reaction chamber by applying a pressure to the reservoir. Compared with other microdispensers, it is much cheaper and easier. By optimizing the conditions, an excellent sequencing ability is achieved while it is a simple and inexpensive system. In most cases, more than 40 bases can be successfully sequenced. A homopolymeric region, which can not be easily sequenced by a conventional gel-based DNA sequencer, is readily sequenced with this system. The new system is successfully applied to sequence a GC rich region or a region close to a priming region where misreading frequently occurs. A rapid analysis for a short DNA was easily achieved with this small instrument.

Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER)

A new method for SNP analysis based on the detection of pyrophosphate (PPi) is demonstrated, which is capable of detecting small allele frequency differences between two DNA pools for genetic association studies other than SNP typing. The method is based on specific primer extension reactions coupled with PPi detection. As the specificity of the primer-directed extension is not enough for quantitative SNP analysis, artificial mismatched bases are introduced into the 3'-terminal regions of the specific primers as a way of improving the switching characteristics of the primer extension reactions. The best position in the primer for such artificial mismatched bases is the third position from the primer 3'-terminus. Contamination with endogenous PPi, which produces a large background signal level in SNP analysis, was removed using PPase to degrade the PPi during the sample preparation process. It is possible to accurately and quantitatively analyze SNPs using a set of primers that correspond to the wild-type and mutant DNA segments. The termini of these primers are at the mutation positions. Various types of SNPs were successfully analyzed. It was possible to very accurately determine SNPs with frequencies as low 0.02. It is very reproducible and the allele frequency difference can be determined. It is accurate enough to detect meaningful genetic differences among pooled DNA samples. The method is sensitive enough to detect 14 amol ssM13 DNA. The proposed method seems very promising in terms of realizing a cost-effective, large-scale human genetic testing system.

Measurement of d sigma/dM and forward-backward charge asymmetry for high-mass Drell-Yan e(+)e(-) pairs from pp macro collisions at square root of s = 1.8 TeV

We report on a measurement of the mass dependence of the forward-backward charge asymmetry, A(FB), and production cross section d sigma/dM for e(+)e(-) pairs with mass M(ee)>40 GeV/c(2). The data sample consists of 108 pb(-1) of pp macro collisions at square root of s = 1.8 TeV taken by the Collider Detector at Fermilab during 1992-1995. The measured asymmetry and d sigma/dM are compared with the predictions of the standard model and a model with an extra Z' gauge boson.

Measurement of the top quark p(T) distribution

We have measured the p(T) distribution of top quarks that are pair produced in pp collisions at sqrt[s] = 1.8 TeV using a sample of tt decays in which we observe a single high- p(T) charged lepton, a neutrino, and four or more jets. We use a likelihood technique that corrects for the experimental bias introduced due to event reconstruction and detector resolution effects. The observed distribution is consistent with the standard model prediction. We use these data to place limits on the production of high- p(T) top quarks suggested in some models of anomalous top quark pair production.

Multiplex polymerase chain reaction (PCR) with color-tagged module-shuffling primers for comparing gene expression levels in various cells

A method based on the multiplex polymerase chain reaction (PCR) and gel electrophoresis for the comparative analysis of gene expression levels was developed. Using the method many cDNA fragments from different sources can be compared simultaneously. Competitive PCR amplification of expressed genes from different sources was performed by using 'module-shuffling primers' (MPSs). The MPSs (labeled with different fluorophores) consist of sequence modules of 3 or 4 nt. The modules are arranged in different orders in each primer; therefore, the base sequences of the primers are different but their melting temperatures are identical. The genes expressed in different sources are ligated with tags complementary with the MPSs. Tag-ligated fragments are mixed in one tube and amplified at the same amplification efficiency by the MPSs. Amplified fragments are detected separately by multiple-color gel electrophoresis. This method can detect different amounts of each expressed gene, up to a difference in amounts of 30%, and its detection limit is 0.1 amol per assay.

Search for neutral supersymmetric Higgs bosons in pp collisions at sqrt[s] = 1.8TeV

We present the results of a search for neutral Higgs bosons produced in association with b quarks in pp-->bb(phi)-->bbb final states with 91+/-7 pb(-1) of pp collisions at sqrt[s] = 1.8 TeV recorded by the Collider Detector at Fermilab. We find no evidence of such a signal and the data are interpreted in the context of the neutral Higgs sector of the minimal supersymmetric extension of the standard model. With basic parameter choices for the supersymmetric scale and the stop-quark mixing, we derive 95% C.L. lower mass limits for neutral Higgs bosons for tan(beta) values in excess of 35.

Production of chi(c1) and chi(c2) in pp collisions at sqrt[S] = 1.8 TeV

We have measured the ratio of prompt production rates of the charmonium states chi(c1) and chi(c2) in 110 pb(-1) of pp collisions at sqrt[s] = 1.8 TeV. The photon from their decay into J/psi(gamma) is reconstructed through conversion into e+e- pairs. The energy resolution this technique provides makes the resolution of the two states possible. We find the ratio of production cross sections sigma(chi(c2))/sigma(chi(c1)) = 0.96+/-0.27(stat)+/-0.11(syst) for events with pT(J/psi) > 4.0 GeV/c, /eta(J/psi)/ < 0.6, and pT(gamma) > 1.0 GeV/c.

First measurement of the ratio B(t --> Wb)/B(t --> Wq) and associated limit on the Cabibbo-Kobayashi-Maskawa element /V(tb)/

We present the first measurement of the ratio of branching fractions R identical withB(t-->Wb)/B(t-->Wq) from p_p collisions at sqrt[s] = 1.8 TeV. The data set corresponds to 109 pb(-1) of data recorded by the Collider Detector at Fermilab during the 1992-95 Tevatron run. We measure R = 0.94(+0.31)(-0.24)(stat+syst) or R>0.61 (0.56) at 90% (95)% C.L., in agreement with the standard model predictions. This measurement yields a limit on the Cabibbo-Kobayashi-Maskawa quark mixing matrix element /V(tb)/ under the assumption of three generations and unitarity.