Miracle-dz/UniFAR-FTUs huggingface dataset:
A Search for Extraplanar Dust in Nearby Edge-on Spirals

We present high-resolution (0.″6 to ∼ 1.″0) BV images of 12 edge-on spiral galaxies observed with the WIYN 3.5 m telescope. These images were obtained to search for extraplanar (|z| > 0.4 kpc) absorbing dust structures similar to those previously found in NGC 891 (Howk & Savage). Many of these galaxies have been previously searched for diffuse ionized gas at high z. Our imaged galaxies include a sample of seven massive L*-like spiral galaxies within D ≲ 25 Mpc that have inclinations i ≳ 87° from the plane of the sky. We find that five of these seven systems show extraplanar dust, visible as highly structured absorbing clouds against the background stellar light of the galaxies. These dust structures lie at heights |z| ≳ 0.4 kpc, which should be above most of the thin disk molecular material in these galaxies. The more prominent structures are estimated to have associated gas masses ≳105 M⊙; the implied potential energies are ≳1052 ergs. All of the galaxies in our sample that show detectable Hα emission at large z also show extraplanar dust structures. None of those galaxies for which extraplanar Hα searches were negative show evidence for extensive high-z dust. The existence of extraplanar dust is a common property of massive spiral galaxies. We discuss several mechanisms for shaping the observed dust features. We emphasize in this discussion the possibility that these dusty clouds represent the dense phase of a multiphase medium at high z in spiral galaxies. In a few cases interactions with close galaxy companions could be responsible for the high-z dust, either through dynamical stripping or triggered star formation. We can rule out warps as the source of the observed high-z dust. Flaring gas layers seem an unlikely source of the observed material but cannot be ruled out at this time, except for those features that clearly connect to energetic processes in the disk. The correlation between high-z dust and extraplanar Hα emission may simply suggest that both trace the high-z interstellar medium in its various forms (or phases), the existence of which may ultimately be driven by vigorous star formation in the underlying disk. The absorption produced by high-z dust and associated gas in spiral galaxies must be accounted for when studying extraplanar emission from spiral galaxies over much of the electromagnetic spectrum.
Saving and Income Smoothing in Côte d'Ivoire

This paper is concerned with the extent to which farmers and other households in Cote d'lvoire save and dis-save in order to make their consumption smoother than their incomes. I attempt to test a strict form of inter-temporal smoothing, that consumption follows the permanent income hypothesis, by which consumption is equal to the annuity value of the sum of assets and the present discounted value of current and expected future labour income. The extent to which households in LDCs can and do smooth their incomes is still a matter of debate. Especially in rural areas, formal credit markets are imperfect or absent, and it has sometimes been argued that poor and ill-educated people find it inherently difficult to make good inter-temporal choices. Yet many important policy issues hang on the issue.
Changes in Plasma Homocyst(e)ine in the Acute Phase After Stroke

Background and Purpose—; Elevated plasma homocyst(e)ine [H(e)] concentration has been associated with an increased risk of stroke. Although the literature suggests that H(e) increases from the acute to the convalescent phase after a stroke, it is not known whether H(e) changes within the acute period. Methods—; A prospective, multicenter study was conducted to examine changes in H(e) during the 2 weeks after an incident stroke. Blood samples were collected at days 1, 3, 5, 7, and between 10 and 14 days after the stroke. Results—; Seventy-six participants (51 men) were enrolled from 9 sites from February 1997 through June 1998. Mean age was 65.6 years, and subjects had at least two H(e) measurements. The estimated mean H(e) level at baseline was 11.3±0.5 &mgr;mol/L, which increased consistently to a mean of 12.0±0.05, 12.4±0.5, 13.3±0.5, and 13.7±0.7 &mgr;mol/L at days 3, 5, 7, and 10 to 14, respectively. The magnitude of the change in H(e) was not affected by age, sex, smoking status, alcohol use, history of hypertension or diabetes, or Rankin Scale Score. Conclusions—; These data suggest that the clinical interpretation of H(e) after stroke and the eligibility for clinical trials assessing treatment for elevated H(e) levels require an adjustment in time since stroke to properly interpret the observed H(e) levels.
Tuning the band structure of carbon nanotubes

The experiments presented in this thesis show that carbon nanotube (NT) electronic structure can be tuned by mechanical stretching and by magnetic fields. These fascinating electromechanical and magnetic effects are quantified using electrical transport techniques. Nanotubes are thin, hollow cylinders made entirely from carbon atoms. The electron wavestates of a NT are quantized into one-dimensional (1-D) subbands, with each subband corresponding to a different wrapping mode. The 1-D subbands in a NT come in degenerate pairs due to the clockwise/counterclockwise (CW/CCW) symmetry of the wrapping modes. Electron transport though a NT occurs in the pair of subbands with electron states nearest the Fermi level. This pair of subbands can be metallic or semiconducting depending on NT diameter and chirality. To investigate the electromechanical properties of NTs, electrical transport measurements are combined with in-situ atomic force microscopy (AFM) manipulation. Nanotubes suspended over trenches are stretched by pushing with an AFM tip. Electrical measurements taken during stretching reveal dramatic changes in electronic structure near the Fermi level. It is shown that stretching can open a bandgap in metallic subbands and modify the bandgap of semiconducting subbands. These measurements are consistent with theoretical work which predicts that bandgap changes can range between ±100 meV per 1% strain, depending on NT chirality, and that stretching does not break the degeneracy between subband pairs. Significant changes in electronic structure are also found in magnetic field experiments. Because CW and CCW electron orbitals have opposite magnetic moments, a magnetic field is expected to break the degeneracy between NT subbands. Breaking of subband degeneracy is measured by detecting the charge carriers that are thermally activated across the NT bandgaps, and by measuring the energy shifts of individual electron states in a NT quantum dot. Both techniques show that electron states near the NT bandgaps have large magnetic moments along the NT axis. The measured magnitudes and directions of orbital magnetic moments are consistent with theoretical predictions and are an order of magnitude larger than the Bohr magneton. iv ACKNOWLEDGMENTS Many people have helped me complete this thesis. My advisor, Paul, has been a fantastic mentor and teacher, opening my eyes to new ideas at every step. Thank you for patiently sharing all you know about science and how to communicate science. Thank you, also, for knowing when to push me – I'm grateful I was able to experience the fun of discovery that follows long hours of …
Analysis of the Initiating Events in HIV-1 Particle Assembly and Genome Packaging

HIV-1 Gag drives a number of events during the genesis of virions and is the only viral protein required for the assembly of virus-like particles in vitro and in cells. Although a reasonable understanding of the processes that accompany the later stages of HIV-1 assembly has accrued, events that occur at the initiation of assembly are less well defined. In this regard, important uncertainties include where in the cell Gag first multimerizes and interacts with the viral RNA, and whether Gag-RNA interaction requires or induces Gag multimerization in a living cell. To address these questions, we developed assays in which protein crosslinking and RNA/protein co-immunoprecipitation were coupled with membrane flotation analyses in transfected or infected cells. We found that interaction between Gag and viral RNA occurred in the cytoplasm and was independent of the ability of Gag to localize to the plasma membrane. However, Gag:RNA binding was stabilized by the C-terminal domain (CTD) of capsid (CA), which participates in Gag-Gag interactions. We also found that Gag was present as monomers and low-order multimers (e.g. dimers) but did not form higher-order multimers in the cytoplasm. Rather, high-order multimers formed only at the plasma membrane and required the presence of a membrane-binding signal, but not a Gag domain (the CA-CTD) that is essential for complete particle assembly. Finally, sequential RNA-immunoprecipitation assays indicated that at least a fraction of Gag molecules can form multimers on viral genomes in the cytoplasm. Taken together, our results suggest that HIV-1 particle assembly is initiated by the interaction between Gag and viral RNA in the cytoplasm and that this initial Gag-RNA encounter involves Gag monomers or low order multimers. These interactions per se do not induce or require high-order Gag multimerization in the cytoplasm. Instead, membrane interactions are necessary for higher order Gag multimerization and subsequent particle assembly in cells.
Late Diagnosis of Anorectal Malformations in Children

Anorectal malformations (ARM) include a wide spectrum of congenital defects of the anus, anal canal and rectum, which are often associated with congenital anomalies of other organ systems. They appear with different clinical presentations ranging from simple imperforate anal membrane to very complex defects. They are usually detected immediately after birth or early at neonatal age, but some patients with the milder defects are diagnosed at a later age. Objectives: The aim of this study is to analyze the incidence of patients with ARM diagnosed after neonatal period, clinical features and consequences of delayed diagnosis. Materials and Methods: Since 2010 we performed a combined retrospective and prospective analysis of a total of 76 patients with anorectal malformations, diagnosed and treated at our clinic between 2005 and 2014. We analyzed patients’ age at the time of diagnosis, sex, type of defect, associated anomalies and postoperative functional outcome. Results: 18 patients with ARM (23.68%) were diagnosed beyond the neonatal period. Of them 11 were female (61.11%) and 7 male patients (38.89%). The earliest diagnosed patient was a male of three months of age, while the latest diagnosed patient was a female of 8.5 years of age. All patients had low type anomalies, presented with anal stenosis (16), perineal fistula (1) and vestibular fistula (1). Six patients (33.33%) were also diagnosed with associated anomalies. Conclusion: High incidence of delayed diagnosis of ARM highlights the importance of a careful, comprehensive clinical examination of the perineum of newborns. All patients with severe and chronic constipation must be evaluated for eventually missed diagnosis of low type anorectal malformations.
Th1 T Cell-Driven Autoimmune Hepatitis Populations and Provides Protection against Stromal TIMP3 Regulates Liver Lymphocyte

Lymphocyte inﬁltration into epithelial tissues and proinﬂammatory cytokine release are key steps in autoimmune disease. Although cell-autonomous roles of lymphocytes are well studied in autoimmunity, much less is understood about the stromal factors that dictate immune cell function. Tissue inhibitor of metalloproteinases 3 (TIMP3) controls systemic cytokine bioavailability and signaling by inhibiting the ectodomain shedding of cytokines and their receptors. The role of TIMP3 in cytokine biology is emerging; however, its contribution to cellular immunology remains unknown. In this study, we show that TIMP3 produced by the hepatic stroma regulates the basal lymphocyte populations in the liver and prevents autoimmune hepatitis. TIMP3 deﬁciency in mice led to spontaneous accumulation and activation of hepatic CD4 + , CD8 + , and NKT cells. Treatment with Con A in a model of polyclonal T lymphocyte activation resulted in a greatly enhanced Th1 cytokine response and acute liver failure, which mechanistically depended on TNF signaling. Bone marrow chimeras demonstrated that TIMP3 derived from the stromal rather than hematopoietic compartment provided protection against autoimmunity. Finally, we identiﬁed hepatocytes as the major source of Timp3 in a resting liver, whereas signiﬁcant Timp3 gene transcription was induced by hepatic stellate cells in the inﬂamed liver. These results uncover metalloproteinase inhibitors as critical stromal factors in regulating cellular immunity during autoimmune hepatitis. The Journal of Immunology , 2012, 188: 000–000.
Mechanism-Based Competitive Binding Model to Investigate the Effect of Neonatal Fc Receptor Binding Affinity on the Pharmacokinetic of Humanized Anti-VEGF Monoclonal IgG1 Antibody in Cynomolgus Monkey

The quantitative relationship between neonatal Fc receptor (FcRn) binding affinity at both acidic and physiological pH and the pharmacokinetics of protein engineered FcRn IgG1 variants has not yet been reported. Our objective was to develop a quantitatively mechanism-based competitive binding model to describe the effects of FcRn binding affinity at acidic and physiological pH on the pharmacokinetics of anti-VEGF IgG1 antibodies when both endogenous and exogenous antibodies are competing for the same FcRn. Pharmacokinetic (PK) and FcRn binding data from five Fc variants of humanized anti-VEGF IgG1 monoclonal antibodies with wide range of FcRn binding affinity were used for the analysis. Sixty-seven anti-VEGF IgG1 antibody-treated animals and 25 control animals with simulated endogenous IgG levels were used to develop the final model. A hybrid iterative two stages and Monte Carlo parametric expectation-maximization method was used to obtain the final model parameters estimates. The final model well described the observed PK data. Quantitative FcRn binding affinity-pharmacokinetics relationships was constructed to provide important biological insights in better understanding of the FcRn binding effect on pharmacokinetics of anti-VEGF IgG1 antibodies in cynomolgus monkeys and served as an important model-based drug discovery platform to guide the design and development of the future generation of anti-VEGF or other therapeutic IgG1 antibodies.
Application of Micro-Computed Tomography With Iodine Staining to Cardiac Imaging, Segmentation, and Computational Model Development

Micro-computed tomography (micro-CT) has been widely used to generate high-resolution 3-D tissue images from small animals nondestructively, especially for mineralized skeletal tissues. However, its application to the analysis of soft cardiovascular tissues has been limited by poor inter-tissue contrast. Recent ex vivo studies have shown that contrast between muscular and connective tissue in micro-CT images can be enhanced by staining with iodine. In the present study, we apply this novel technique for imaging of cardiovascular structures in canine hearts. We optimize the method to obtain high-resolution X-ray micro-CT images of the canine atria and its distinctive regions-including the Bachmann's bundle, atrioventricular node, pulmonary arteries and veins-with clear inter-tissue contrast. The imaging results are used to reconstruct and segment the detailed 3-D geometry of the atria. Structure tensor analysis shows that the arrangement of atrial fibers can also be characterized using the enhanced micro-CT images, as iodine preferentially accumulates within the muscular fibers rather than in connective tissues. This novel technique can be particularly useful in nondestructive imaging of 3-D cardiac architectures from large animals and humans, due to the combination of relatively high speed ( ~ 1 h/per scan of the large canine heart) and high voxel resolution (36 μm) provided. In summary, contrast micro-CT facilitates fast and nondestructive imaging and segmenting of detailed 3-D cardiovascular geometries, as well as measuring fiber orientation, which are crucial in constructing biophysically detailed computational cardiac models.
Fast computation of the L1-principal component of real-valued data

Recently, Markopoulos et al. [1], [2] presented an optimal algorithm that computes the L1 maximum-projection principal component of any set of N real-valued data vectors of dimension D with complexity polynomial in N, O(ND). Still, moderate to high values of the data dimension D and/or data record size N may render the optimal algorithm unsuitable for practical implementation due to its exponential in D complexity. In this paper, we present for the first time in the literature a fast greedy single-bit-flipping conditionally optimal iterative algorithm for the computation of the L1 principal component with complexity O(N3). Detailed numerical studies are carried out demonstrating the effectiveness of the developed algorithm with applications to the general field of data dimensionality reduction and direction-of-arrival estimation.
Abrogation of Viral Interleukin-6 (vIL-6)-Induced Signaling by Intracellular Retention and Neutralization of vIL-6 with an Anti-vIL-6 Single-Chain Antibody Selected by Phage Display

ABSTRACT Human herpesvirus 8 (HHV-8) encodes several putative oncogenes, which are homologues to cellular host genes known to function in cell cycle regulation, control of apoptosis, and cytokine signaling. Viral interleukin (vIL-6) is believed to play an important role in the pathogenesis of Kaposi's sarcoma as well as primary effusion lymphoma and multicentric Castleman's disease. Therefore, vIL-6 is a promising target for novel therapies directed against HHV-8-associated diseases. By phage display screening of human synthetic antibody libraries, we have selected a specific recombinant antibody, called monoclonal anti-vIL-6 (MAV), binding to vIL-6. The epitope recognized by MAV was localized on the top of the D helix of the vIL-6 protein, which is a part of receptor binding site III. Consequently, MAV specifically inhibits vIL-6-mediated growth of the primary effusion lymphoma-derived cell line BCBL-1 and blocks STAT3 phosphorylation in the human hepatoma cell line HepG2. Since it was previously found that vIL-6 can also induce signals from within the cell, presumably within the endoplasmic reticulum, we fused the recombinant antibody MAV with the endoplasmic retention sequence KDEL (MAV-KDEL). As a result, COS-7 cells expressing MAV-KDEL and synthesizing vIL-6 ceased to secrete the cytokine. Moreover, we observed that vIL-6 that was bound to MAV-KDEL and retained in the endoplasmic reticulum did not induce STAT3 phosphorylation in HepG2 cells. We conclude that the activity of the intracellularly retained vIL-6 protein is neutralized by MAV-KDEL. Our results might represent a novel therapeutic strategy to neutralize virally encoded growth factors or oncogenes.
Hyperosmotic stress strongly potentiates serum response factor (SRF)‐dependent transcriptional activity in ehrlich lettré ascites cells through a mechanism involving p38 mitogen‐activated protein kinase

Long‐term osmotic stress results in altered gene transcription, however, with the exception of the TonE/TonEBP system, the underlying mechanisms are poorly understood. We previously showed that upon osmotic shrinkage of Ehrlich Lettré Ascites (ELA) fibroblasts, the MEK1‐ERK1/2 pathway is transiently inhibited while p38 MAPK is activated, in turn impacting on cell survival (Pedersen et al., 2007, Cell Physiol Biochem 20: 735–750). Here, we show that downstream of these kinases, two transcription factors with major roles in control of cell proliferation and death, serum response factor (SRF) and cAMP response element‐binding protein (CREB) are differentially regulated in ELA cells. SRF Ser103 phosphorylation and SRF‐dependent transcriptional activity were strongly augmented 5–30 min and 24 h, respectively, after hyperosmotic stress (50% increase in extracellular ionic strength), in a p38 MAPK‐dependent manner. In contrast, CREB Ser133 was transiently dephosphorylated upon osmotic shrinkage. The ERK1/2 effector ribosomal S kinase (RSK) and the ERK1/2‐ and p38 MAPK effector mitogen‐ stress‐activated protein kinase 1 (MSK1) both phosphorylate CREB at Ser133. RSK and MSK1 were dephosphorylated within 5 min of shrinkage. MSK1 phosphorylation recovered within 30 min in a p38‐MAPK‐dependent manner. CREB was transiently dephosphorylated after shrinkage in a manner exacerbated by p38 MAPK inhibition or MSK1 knockdown, but unaffected by inhibition of RSK. In conclusion, in ELA cells, hyperosmotic stress activates SRF in a p38 MAPK‐dependent manner and transiently inactivates CREB, likely due to MSK1 inactivation. We suggest that these events contribute to shrinkage‐induced changes in gene transcription and death/survival balance. J. Cell. Physiol. 226: 2857–2868, 2011. © 2011 Wiley‐Liss, Inc.
Deviations in Birth Rates with Respect to the Day of the Week and the Month for a 100 Year Period Regarding Social and Medical Aspects in Explaining Models

During the last hundred years the birth rates on Sundays changed dramatically with a neutral point around 1955. Modern birth regulation is considered as the main reason for that. Medical backgrounds for this situation were discussed in the 1970s. Prior to that no analysis has relevant case numbers. The time from conception to birth measured in days is divisable by 7. The time of conception is relevant in relation to social aspects. Conception rates can be determined under the assumption that we can split up the population in a low and a high risk share. This consideration principally leads to an instable problem on a discrete cyclic space. But using some limiting considerations we get a numerically stable solution with feasible characteristics. For observing long time changes we need a relevant smoothing operator. In numerical calculations we look for a quadratic minimum solution or alternatively a linear program. For the discussion of inequality the concept of Shannon entropy as well as and Lorenz curve and Gini coefficient are relevant.
Nudging the obese: a UK–US consideration

Abstract Over recent years, nudge policies have become increasingly popular (if somewhat confused) internationally. This article attempts to clarify what a nudge entails, and critically summarises some of the nudge policies that have been proposed to motivate weight loss in the United Kingdom and the United States. Despite the fact that most of the evidence on nudge-related policy has so far been produced in the United States, and that the leading nudge champions are American, the United Kingdom, at least with respect to considering policy interventions of this kind at the national level, appears to be relatively advanced. That said, nudge interventions remain of marginal practical import everywhere, and are never going to solve completely the obesity problem. Nonetheless, even a marginal effect may extend and improve many lives, a result that would satisfy most behavioural economists.