Miracle-dz/UniFAR-FTUs huggingface dataset:
Field Theoretic Approaches To Early Universe

This thesis compiles the results of six works which deal with - inflationary model building and estimation of cosmological parameters from various field theoretic setup, quantification of reheating temperature, studies of leptogenesis in braneworld and estimation of primordial non-Gaussianity from ${\cal N}=1$ supergravity using $\delta N$ formalism. We start our discussion with exploring the possibility of MSSM inflation in the light of recent observed data from various D -flat directions using the saddle and inflection point techniques. The effective inflaton potential around saddle point and inflection point have been utilized in estimating the observable parameters and confronting them with WMAP7 and Planck dataset. Next we explore the possibility of inflation from the five dimensional ${\cal N} = 2$ supergravity setup by deriving the effective potential in the context of RS like braneworld model and DBI Galileon. After deriving an four dimensional effective potential, we obtain the inflationary observables from both the scenarios and confront them with the WMAP data. Further we fit the CMB angular power spectra from TT anisotropy and other polarization data obtained from WMAP. Further, we discuss the non-trivial features of reheating from supergravity inspired braneworld model, where the results are to some extent different from that of the usual low energy GR counterpart, because of the modified Friedmann equations in this setup. We explicitly derive the analytical expressions for the reheating temperature and further solve the evolution equation of the number density of thermal gravitino which results in the gravitino abundance. Finally, we study the primordial local type of non-Gaussian features using $\delta N$ formalism for a generic class of sub-Planckian models dominated by the Hubble-induced corrections within ${\cal N} = 1$ supergravity framework.
Zener tunneling in semiconducting nanotube and graphene nanoribbon p−n junctions

A theory is developed for interband tunneling in semiconducting carbon nanotube and graphene nanoribbon p−n junction diodes. Characteristic length and energy scales that dictate the tunneling probabilities and currents are evaluated. By comparing the Zener tunneling processes in these structures to traditional Group IV and III–V semiconductors, it is proved that for identical bandgaps, carbon-based one-dimensional (1D) structures have higher tunneling currents. The high tunneling current magnitudes for 1D carbon structures suggest the distinct feasibility of high-performance tunneling-based field-effect transistors.
A Systematic Analysis of Fe II Emission in Quasars: Evidence for Inflow to the Central Black Hole

Broad Fe II emission is a prominent feature of the optical and ultraviolet spectra of quasars. We report on a systematical investigation of optical Fe II emission in a large sample of 4037 z < 0.8 quasars selected from the Sloan Digital Sky Survey. We have developed and tested a detailed line-fitting technique, taking into account the complex continuum and narrow and broad emission-line spectra. Our primary goal is to quantify the velocity broadening and velocity shift of the Fe II spectrum in order to constrain the location of the Fe II-emitting region and its relation to the broad-line region. We find that the majority of quasars show Fe II emission that is redshifted, typically by ~400 km s−1, but up to 2000 km s−1, with respect to the systemic velocity of the narrow-line region or of the conventional broad-line region as traced by the Hβ line. Moreover, the line width of Fe II is significantly narrower than that of the broad component of Hβ. We show that the magnitude of the Fe II redshift correlates inversely with the Eddington ratio, and that there is a tendency for sources with redshifted Fe II emission to show red asymmetry in the Hβ line. These characteristics strongly suggest that Fe II originates from a location different from, and most likely exterior to, the region that produces most of Hβ. The Fe II-emitting zone traces a portion of the broad-line region of intermediate velocities whose dynamics may be dominated by infall.
CosTaL: An Accurate and Scalable Graph-Based Clustering Algorithm for High-Dimensional Single-Cell Data Analysis

With the aim of analyzing large-sized multidimensional single-cell datasets, we are describing our method for Cosine-based Tanimoto similarity-refined graph for community detection using Leiden’s algorithm (CosTaL). As a graph-based clustering method, CosTaL transforms the cells with high-dimensional features into a weighted k-nearest-neighbor (kNN) graph. The cells are represented by the vertices of the graph, while an edge between two vertices in the graph represents the close relatedness between the two similar cells. Specifically, CosTaL builds an exact kNN graph using cosine similarity and uses the Tanimoto coefficient as the refining strategy to re-weight the edges in order to improve the effectiveness of clustering. We demonstrate that CosTaL generally achieves equivalent or higher effectiveness scores on seven benchmark cytometry datasets and six single-cell RNA-sequencing datasets using six different evaluation metrics, compared with other state-of-the-art graph-based clustering methods, including PhenoGraph, Scanpy, and PARC. CosTaL is also the most efficient algorithm on large datasets, suggesting that CosTaL generally has better scalability than the other methods, which is beneficial for large-scale analysis.
Effects of lactate, super-GDF9, and low oxygen tension during bi-phasic in vitro maturation on the bioenergetic profiles of mouse cumulus–oocyte complex

Abstract In vitro maturation (IVM) is an alternative assisted reproductive technology with reduced hormone-related side effects and treatment burden compared to conventional IVF. Capacitation (CAPA)-IVM is a bi-phasic IVM system with improved clinical outcomes compared to standard monophasic IVM. Yet, CAPA-IVM efficiency compared to conventional IVF is still suboptimal in terms of producing utilizable blastocysts. Previously, we have shown that CAPA-IVM leads to a precocious increase in cumulus cell (CC) glycolytic activity during cytoplasmic maturation. In the current study, considering the fundamental importance of CCs for oocyte maturation and cumulus–oocyte complex (COC) microenvironment, we further analyzed the bioenergetic profiles of maturing CAPA-IVM COCs. Through a multi-step approach, we (i) explored mitochondrial function of the in vivo and CAPA-IVM matured COCs through real-time metabolic analysis with Seahorse analyzer, and to improve COC metabolism (ii) supplemented the culture media with lactate and/or super-GDF9 (an engineered form of growth differentiation factor 9) and (iii) reduced culture oxygen tension. Our results indicated that the pre-IVM step is delicate and prone to culture-related disruptions. Lactate and/or superGDF9 supplementations failed to eliminate pre-IVM-induced stress on COC glucose metabolism and mitochondrial respiration. However, when performing pre-IVM culture under 5% oxygen tension, CAPA-IVM COCs showed similar bioenergetic profiles compared to in vivo matured counterparts. This is the first study providing real-time metabolic analysis of the COCs from a bi-phasic IVM system. The currently used analytical approach provides the quantitative measures and the rational basis to further improve IVM culture requirements. Summary Sentence Culture-inflicted disturbances on cumulus–oocyte complex glucose metabolism and mitochondrial respiration can be normalized when culturing under low oxygen (5%) tension during pre-IVM. Graphical Abstract
The curious case of the companion: evidence for cold accretion onto a dwarf satellite near the isolated elliptical NGC 7796

Context. The isolated elliptical (IE) NGC 7796 is accompanied by an interesting early-type dwarf galaxy, named NGC 7796-DW1. It exhibits a tidal tail, very boxy isophotes, and multiple nuclei or regions (A, B, and C) that are bluer than the bulk population of the galaxy, indicating a younger age. These properties are suggestive of a dwarf–dwarf merger remnant. Aims. Dwarf–dwarf mergers are poorly understood, but may have a high importance for dwarf galaxy evolution. We want to investigate the properties of the dwarf galaxy and its components to find more evidence for a dwarf–dwarf merger or for alternative formation scenarios. Methods. We use the Multi-Unit Spectroscopic Explorer (MUSE) at the VLT to investigate NGC 7796-DW1. We extract characteristic spectra to which we apply the STARLIGHT population synthesis software to obtain ages and metallicities of the various population components of the galaxy. This permits us to isolate the emission lines for which fluxes and flux ratios can be measured and to which strong-line diagnostic tools can be applied. Results. The galaxy’s main body is old and metal-poor. A surprising result is the extended line emission in the galaxy, forming a ring-like structure with a projected diameter of 2.2 kpc. The line ratios fall into the regime of HII-regions, although OB-stellar populations cannot be identified by spectral signatures. The low Hα surface brightnesses indicate unresolved star-forming substructures, which means that broad-band colours are not reliable age or metallicity indicators. Nucleus A is a relatively old (7 Gyr or older) and metalpoor super star cluster, most probably the nucleus of the dwarf, now displaced. The star-forming regions B and C show younger and distinctly more metal-rich components. The emission line ratios of regions B and C indicate an almost solar oxygen abundance, if compared with radiation models of HII regions. Oxygen abundances from empirical calibrations point to only half-solar. The ring-like Hα-structure does not exhibit signs of rotation or orbital movements. Conclusions. NGC 7796-DW1 occupies a particular role in the group of transition-type galaxies with respect to its origin and current evolutionary state, being the companion of an IE. The dwarf–dwarf merger scenario is excluded because of the missing metal-rich merger component. A viable alternative is gas accretion from a reservoir of cold, metal-rich gas. NGC 7796 has to provide this gas within its X-ray bright halo. As illustrated by NGC 7796-DW1, cold accretion may be a general solution to the problem of extended star formation histories in transition dwarf galaxies.
Germinal Centers Convergent Evolution and B-cell Recirculation in Human Lymph Nodes

Germinal centers (GCs) are specialized compartments within the secondary lymphoid organs where B cells proliferate, differentiate, and mutate their antibody genes in response to the presence of foreign antigens. They play a central role in generating an effective immune response against infectious pathogens, and failures in their regulating mechanisms can lead to the development of autoimmune diseases and cancer. While previous works study experimental systems of the immune response with mouse models that are immunized with specific antigens, our study focuses on a real life situation, with an ongoing GC response in a human lymph node (LN) involving multiple asynchronized GCs reacting simultaneously to unknown antigens. We combined laser capture microdissection (LCM) of individual GCs from human LN with next-generation repertoire sequencing (Rep-seq) to characterize individual GCs as distinct evolutionary spaces. In line with well-characterized GC responses in mice, elicited by immunization with model antigens such as NP-CGG, we observe a relatively low sequence similarity, as well as heterogeneous clonal diversity across individual GCs from the same human LN. We identify shared clones in several individual GCs, and phylogenetic tree analysis combined with paratope modeling suggest the re-engagement and rediversification of B cell clones across GCs as well as expanded clones exhibiting shared antigen responses across distinct GCs, indicating convergent evolution of the GCs. Finally, our study allows for the characterization of non-functional clones, where frequencies of V(D)J or SHM induced stop codons are quantified.
AGN Feedback in Galaxy Groups: A Detailed Study of X-Ray Features and Diffuse Radio Emission in IC 1262

This paper reports a systematic search of X-ray cavities, density jumps, and shocks in the intergalactic environment of the galaxy group IC 1262 using Chandra, GMRT, and Very Large Array archival observations. The X-ray imaging analysis reveals a pair of X-ray cavities to the north and south of the X-ray peak, at projected distances of 6.48 kpc and 6.30 kpc respectively. Total mechanical power contained in both of these cavities is found to be ∼12.37 × 1042 erg s−1, and compares well with the X-ray luminosity, within the cooling radius, measured to be ∼3.29 × 1042 erg s−1, suggesting that the mechanical power injected by the central AGN efficiently balances the radiative loss. We detect a previously unknown X-ray cavity at the position of the southern radio lobe in the intra-group medium and find a loop of excess X-ray emission extending ∼100 kpc southwest from the central galaxy. The X-ray cavity at the position of the southern radio lobe probably represents a first generation X-ray cavity. Two surface brightness edges are evident to the west and northeast of the center of this group. The radio galaxy at the core of the IC 1262 group is a rare low-redshift ultra-steep radio galaxy, its spectral index being α ∼ −1.73 (including the central AGN) and α ∼ −2.08 (excluding the central AGN). We detect a radio phoenix embedded within the southern radio lobe, for the first time in a poor group, with a spectral index (α ≤ −1.92). The spectral index distribution across the phoenix steepens with increasing distance from its intensity peak.
The homeodomain transcriptional regulator DVE-1 directs a program for synapse elimination during circuit remodeling

An important step in brain development is the remodeling of juvenile neural circuits to establish mature connectivity. The elimination of juvenile synapses is a critical step in this process; however, the molecular mechanisms directing synapse elimination activities and their timing are not fully understood. We identify here a conserved transcriptional regulator, DVE-1, that shares homology with mammalian special AT-rich sequence-binding (SATB) family members and directs the elimination of juvenile synaptic inputs onto remodeling C. elegans GABAergic neurons. Dorsally localized juvenile acetylcholine receptor clusters and apposing presynaptic sites are eliminated during maturation of wild type GABAergic neurons but persist into adulthood in dve-1 mutants. The persistence of juvenile synapses in dve-1 mutants does not impede synaptic growth during GABAergic remodeling and therefore produces heightened motor connectivity and a turning bias during movement. DVE-1 is localized to GABAergic nuclei prior to and during remodeling and DVE-1 nuclear localization is required for synapse elimination to proceed, consistent with DVE-1’s function as a transcriptional regulator. Pathway analysis of DVE-1 targets and proteasome inhibitor experiments implicate transcriptional control of the ubiquitin-proteasome system in synapse elimination. Together, our findings demonstrate a new role for a SATB family member in the control of synapse elimination during circuit remodeling through transcriptional regulation of ubiquitin-proteasome signaling. Contributions Summary KDA generated strains, transgenic lines, molecular constructs, confocal microscopy images and analysis, performed optogenetic behavioral experiments, photoconversion experiments, modencode ChIP-seq analysis and pathway analysis. SR performed all calcium imaging experiments/analysis and conducted single worm tracking. KB performed all Bortezomib inhibitor experiments and analysis. CL generated most vectors and constructs. JR assisted with generation of CRISPR/Cas9 generated strains. WA and MR assisted with aldicarb behavioral assay. DO assisted with EMS screen and isolation of dve-1 mutant. CB and MD aided in CloudMap bioinformatic analysis of the uf171 mutant. MMF and KDA designed and interpreted results of all experiments and wrote the manuscript.
Gac Is a Transcriptional Repressor of the Lyme Disease Spirochete’s OspC Virulence-Associated Surface Protein

Borrelia burgdorferi sensu lato requires its surface-exposed OspC protein in order to establish infection in humans and other vertebrate hosts. Bacteria that either do not produce OspC during transmission or fail to repress OspC after infection is established are rapidly cleared by the host. ABSTRACT The OspC outer-surface lipoprotein is essential for the Lyme disease spirochete’s initial phase of vertebrate infection. Bacteria within the midguts of unfed ticks do not express OspC but produce high levels when ticks begin to ingest blood. Lyme disease spirochetes cease production of OspC within 1 to 2 weeks of vertebrate infection, and bacteria that fail to downregulate OspC are cleared by host antibodies. Thus, tight regulation of OspC levels is critical for survival of Lyme borreliae and, therefore, an attractive target for development of novel treatment strategies. Previous studies determined that a DNA region 5′ of the ospC promoter, the ospC operator, is required for control of OspC production. Hypothesizing that the ospC operator may bind a regulatory factor, DNA affinity pulldown was performed and identified binding by the Gac protein. Gac is encoded by the C-terminal domain of the gyrA open reading frame from an internal promoter, ribosome-binding site, and initiation codon. Our analyses determined that Gac exhibits a greater affinity for ospC operator and promoter DNAs than for other tested borrelial sequences. In vitro and in vivo analyses demonstrated that Gac is a transcriptional repressor of ospC. These results constitute a substantial advance to our understanding of the mechanisms by which the Lyme disease spirochete controls production of OspC. IMPORTANCE Borrelia burgdorferi sensu lato requires its surface-exposed OspC protein in order to establish infection in humans and other vertebrate hosts. Bacteria that either do not produce OspC during transmission or fail to repress OspC after infection is established are rapidly cleared by the host. Herein, we identified a borrelial protein, Gac, that exhibits preferential affinity to the ospC promoter and 5′ adjacent DNA. A combination of biochemical analyses and investigations of genetically manipulated bacteria demonstrated that Gac is a transcriptional repressor of ospC. This is a substantial advance toward understanding how the Lyme disease spirochete controls production of the essential OspC virulence factor and identifies a novel target for preventative and curative therapies.
First-principles predictions of low-energy phases of multiferroic BiFeO 3

We used first-principles methods to perform a systematic search for potentially-stable phases of multiferroic BiFeO3. We considered a simulation cell compatible with the atomic distortions that are most common among perovskite oxides, and found a large number of local minima of the energy within 100 meV/f.u. of the ferroelectric ground state. We discuss the variety of low-symmetry structures discovered, as well as the implications of these findings as regards current experimental (e.g., on thin films displaying {\em super-tetragonal} phases) and theoretical (on models for BiFeO3's structural phase transitions) work on this compound.
GOODS-HERSCHEL MEASUREMENTS OF THE DUST ATTENUATION OF TYPICAL STAR-FORMING GALAXIES AT HIGH REDSHIFT: OBSERVATIONS OF ULTRAVIOLET-SELECTED GALAXIES AT z ∼ 2

We take advantage of the sensitivity and resolution of the Herschel Space Observatory at 100 and 160 μm to directly image the thermal dust emission and investigate the infrared luminosities (LIR) and dust obscuration of typical star-forming (L*) galaxies at high redshift. Our sample consists of 146 UV-selected galaxies with spectroscopic redshifts 1.5 ⩽ zspec < 2.6 in the GOODS-North field. Supplemented with deep Very Large Array and Spitzer imaging, we construct median stacks at the positions of these galaxies at 24, 100, and 160 μm, and 1.4 GHz. The comparison between these stacked fluxes and a variety of dust templates and calibrations implies that typical star-forming galaxies with UV luminosities LUV ≳ 1010 L☉ at z ∼ 2 are luminous infrared galaxies with a median LIR = (2.2 ± 0.3) × 1011 L☉. Their median ratio of LIR to rest-frame 8 μm luminosity (L8) is LIR/L8 = 8.9 ± 1.3 and is ≈80% larger than that found for most star-forming galaxies at z ≲ 2. This apparent redshift evolution in the LIR/L8 ratio may be tied to the trend of larger infrared luminosity surface density for z ≳ 2 galaxies relative to those at lower redshift. Typical galaxies at 1.5 ⩽ z < 2.6 have a median dust obscuration LIR/LUV = 7.1 ± 1.1, which corresponds to a dust correction factor, required to recover the bolometric star formation rate (SFR) from the unobscured UV SFR, of 5.2 ± 0.6. This result is similar to that inferred from previous investigations of the UV, Hα, 24 μm, radio, and X-ray properties of the same galaxies studied here. Stacking in bins of UV slope (β) implies that L* galaxies with redder spectral slopes are also dustier and that the correlation between β and dustiness is similar to that found for local starburst galaxies. Hence, the rest-frame ≃ 30 and 50 μm fluxes validate on average the use of the local UV attenuation curve to recover the dust attenuation of typical star-forming galaxies at high redshift. In the simplest interpretation, the agreement between the local and high-redshift UV attenuation curves suggests a similarity in the dust production and stellar and dust geometries of starburst galaxies over the last 10 billion years.
Transient Rayleigh–Bénard–Marangoni convection due to evaporation: a linear non-normal stability analysis

The convective instability in a plane liquid layer with time-dependent temperature profile is investigated by means of a general method suitable for linear stability analysis of an unsteady basic flow. The method is based on a non-normal approach, and predicts the onset of instability, critical wavenumber and time. The method is applied to transient Rayleigh–Bénard–Marangoni convection due to cooling by evaporation. Numerical results as well as theoretical scalings for the critical parameters as function of the Biot number are presented for the limiting cases of purely buoyancy-driven and purely surface-tension-driven convection. Critical parameters from calculations are in good agreement with those from experiments on drying polymer solutions, where the surface cooling is induced by solvent evaporation.