On the Relationship Between the Pseudo- and Superconducting Gaps: Effects of Residual Pairing Correlations Below Tc

The existence of a normal state spectral gap in underdoped cuprates raises important questions about the associated superconducting phase. For example, how does this pseudogap evolve into its below Tc counterpart? In this paper we characterize this unusual superconductor by investigating the nature of the ``residual'' pseudogap below Tc and, find that it leads to an important distinction between the superconducting excitation gap and order parameter. Our approach is based on a conserving diagrammatic BCS Bose-Einstein crossover theory which yields the precise BCS result in weak coupling at any T<Tc and reproduces Leggett's results in the T=0 limit. We explore the resulting experimental implications.Comment: REVTeX, 4 pages, 1 EPS figure (included

Superconducting transitions from the pseudogap state: d-wave symmetry, lattice, and low-dimensional effects

We investigate the behavior of the superconducting transition temperature within a previously developed BCS-Bose Einstein crossover picture. This picture, based on a decoupling scheme of Kadanoff and Martin, further extended by Patton, can be used to derive a simple form for the superconducting transition temperature in the presence of a pseudogap. We extend previous work which addressed the case of s-wave pairing in jellium, to explore the solutions for T_c as a function of variable coupling in more physically relevant situations. We thereby ascertain the effects of reduced dimensionality, periodic lattices and a d-wave pairing interaction. Implications for the cuprate superconductors are discussed.Comment: REVTeX, 11 pages, 6 EPS figures included, Replace with published versio

The Nonlinear Meissner Effect in Unconventional Superconductors

We examine the long-wavelength current response in anisotropic superconductors and show how the field-dependence of the Meissner penetration length can be used to detect the structure of the order parameter. Nodes in the excitation gap lead to a nonlinear current-velocity constitutive equation at low temperatures which is distinct for each symmetry class of the order parameter. The effective Meissner penetration length is linear in $H$ and exhibits a characteristic anisotropy for fields in the $ab$-plane that is determined by the positions of the nodes in momentum space. The nonlinear current-velocity relation also leads to an intrinsic magnetic torque for in-plane fields that are not parallel to a nodal or antinodal direction. The torque scales as $H^3$ for $T\rightarrow 0$ and has a characteristic angular dependence. We analyze the effects of thermal excitations, impurity scattering and geometry on the current response of a $d_{x^2-y^2}$ superconductor, and discuss our results in light of recent measurements of the low-temperature penetration length and in-plane magnetization of single-crystals of $YBa_2Cu_3O_{7-\delta}$ and $LuBa_2Cu_3O_{7-\delta}$.Comment: 30 pages, RevTeX file with 16 postscript figures. Submitted to Phys. Rev.

Infrared Conductivity in Layered dd-wave Superconductors

We calculate the infrared conductivity of a stack of coupled, two-dimensional superconducting planes within the Fermi liquid theory of superconductivity. We include the effects of random scattering processes and show that the presence of even a small concentration of resonant impurities, in a $d$-wave superconductor, has an important effect on both the in-plane and $c$-axis transport properties, which could serve as signatures for $d$-wave pairing.Comment: 18 pages in a RevTex (3.0) file plus 5 postscript figures (uuencoded). Replaced with minor changes as it will appear in the Physical Review B {\bf 52} issue 1 Oct. 199

Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays

Zebrafish (Danio rerio) is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula) revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html)

Role of Van Hove Singularities and Momentum Space Structure in High-Temperature Superconductivity

There is a great deal of interest in attributing the high critical temperatures of the cuprates to either the proximity of the Fermi level to a van Hove singularity or to structure of the superconducting pairing potential in momentum space far from the Fermi surface. We examine these ideas by calculating the critical temperature Tc for model Einstein-phonon- and spin-fluctuation-mediated superconductors within both the standard, Fermi-surface-restricted Eliashberg theory and the exact mean field theory, which accounts for the full momentum structure of the pairing potential and the energy dependence of the density of states. By using two models of spin-fluctuation-mediated pairing in the cuprates, we demonstrate that our results are independent of the details of the dynamical susceptibility, which is taken to be the pairing potential. We also compare these two models against available neutron scattering data, since these data provide the most direct constraints on the susceptibility. We conclude that the van Hove singularity does not drastically alter Tc from its value when the density of states is constant and that the effect of momentum structure is significant but secondary in importance to that of the energy dependence in the density of states.Comment: 23 pages, 6 figures upon request, revtex version 2, vHs-

Pairing fluctuations and pseudogaps in the attractive Hubbard model

The two-dimensional attractive Hubbard model is studied in the weak to intermediate coupling regime by employing a non-perturbative approach. It is first shown that this approach is in quantitative agreement with Monte Carlo calculations for both single-particle and two-particle quantities. Both the density of states and the single-particle spectral weight show a pseudogap at the Fermi energy below some characteristic temperature T*, also in good agreement with quantum Monte Carlo calculations. The pseudogap is caused by critical pairing fluctuations in the low-temperature renormalized classical regime $\omega < T$ of the two-dimensional system. With increasing temperature the spectral weight fills in the pseudogap instead of closing it and the pseudogap appears earlier in the density of states than in the spectral function. Small temperature changes around T* can modify the spectral weight over frequency scales much larger than temperature. Several qualitative results for the s-wave case should remain true for d-wave superconductors.Comment: 20 pages, 12 figure

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000

Genomewide Expression Profiling in the Zebrafish Embryo Identifies Target Genes Regulated by Hedgehog Signaling During Vertebrate Development

Hedgehog proteins play critical roles in organizing the embryonic development of animals, largely through modulation of target gene expression. Little is currently known, however, about the kinds and numbers of genes whose expression is controlled, directly or indirectly, by Hedgehog activity. Using techniques to globally repress or activate Hedgehog signaling in zebrafish embryos followed by microarray-based expression profiling, we have discovered a cohort of genes whose expression responds significantly to loss or gain of Hedgehog function. We have confirmed the Hedgehog responsiveness of a representative set of these genes with whole-mount in situ hybridization as well as real time PCR. In addition, we show that the consensus Gli-binding motif is enriched within the putative regulatory elements of a sizeable proportion of genes that showed positive regulation in our assay, indicating that their expression is directly induced by Hedgehog. Finally, we provide evidence that the Hedgehog-dependent spatially restricted transcription of one such gene, nkx2.9, is indeed mediated by Gli1 through a single Gli recognition site located within an evolutionarily conserved enhancer fragment. Taken together, this study represents the first comprehensive survey of target genes regulated by the Hedgehog pathway during vertebrate development. Our data also demonstrate for the first time the functionality of the Gli-binding motif in the control of Hedgehog signaling-induced gene expression in the zebrafish embryo

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

Maternally deposited mRNAs direct early development before the initiation of zygotic transcription during mid-blastula transition (MBT). To study mechanisms regulating this developmental event in zebrafish, we applied mRNA deep sequencing technology and generated comprehensive information and valuable resources on transcriptome dynamics during early embryonic (egg to early gastrulation) stages. Genome-wide transcriptome analysis documented at least 8000 maternal genes and identified the earliest cohort of zygotic transcripts. We determined expression levels of maternal and zygotic transcripts with the highest resolution possible using mRNA-seq and clustered them based on their expression pattern. We unravel delayed polyadenylation in a large cohort of maternal transcripts prior to the MBT for the first time in zebrafish. Blocking polyadenylation of these transcripts confirms their role in regulating development from the MBT onward. Our study also identified a large number of novel transcribed regions in annotated and unannotated regions of the genome, which will facilitate reannotation of the zebrafish genome. We also identified splice variants with an estimated frequency of 50%–60%. Taken together, our data constitute a useful genomic information and valuable transcriptome resource for gene discovery and for understanding the mechanisms of early embryogenesis in zebrafish