Solution to the generalized lattice point and related problems to disjunctive programming

Issued as Pre-prints [1-5], Progress reports [1-2], Final summary report, and Final technical report, Project no. E-24-67

Dust SEDs in the era of Herschel and Planck: a Hierarchical Bayesian fitting technique

We present a hierarchical Bayesian method for fitting infrared spectral energy distributions (SEDs) of dust emission to observed fluxes. Under the standard assumption of optically thin single temperature (T) sources the dust SED as represented by a power--law modified black body is subject to a strong degeneracy between T and the spectral index beta. The traditional non-hierarchical approaches, typically based on chi-square minimization, are severely limited by this degeneracy, as it produces an artificial anti-correlation between T and beta even with modest levels of observational noise. The hierarchical Bayesian method rigorously and self-consistently treats measurement uncertainties, including calibration and noise, resulting in more precise SED fits. As a result, the Bayesian fits do not produce any spurious anti-correlations between the SED parameters due to measurement uncertainty. We demonstrate that the Bayesian method is substantially more accurate than the chi-square fit in recovering the SED parameters, as well as the correlations between them. As an illustration, we apply our method to Herschel and sub millimeter ground-based observations of the star-forming Bok globule CB244. This source is a small, nearby molecular cloud containing a single low-mass protostar and a starless core. We find that T and beta are weakly positively correlated -- in contradiction with the chi-square fits, which indicate a T-beta anti-correlation from the same data-set. Additionally, in comparison to the chi-square fits the Bayesian SED parameter estimates exhibit a reduced range in values.Comment: 20 pages, 9 figures, ApJ format, revised version matches ApJ-accepted versio

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli

AbstractEscherichia coli that are capable of causing human disease are often classified into pathogenic variants (pathovars) based on their virulence gene content. However, disease-associated hybrid E. coli, containing unique combinations of multiple canonical virulence factors have also been described. Such was the case of the E. coli O104:H4 outbreak in 2011, which caused significant morbidity and mortality. Among the pathovars of diarrheagenic E. coli that cause significant human disease are the enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC). In the current study we use comparative genomics, transcriptomics, and functional studies to characterize isolates that contain virulence factors of both EPEC and ETEC. Based on phylogenomic analysis, these hybrid isolates are more genomically-related to EPEC, but appear to have acquired ETEC virulence genes. Global transcriptional analysis using RNA sequencing, demonstrated that the EPEC and ETEC virulence genes of these hybrid isolates were differentially-expressed under virulence-inducing laboratory conditions, similar to reference isolates. Immunoblot assays further verified that the virulence gene products were produced and that the T3SS effector EspB of EPEC, and heat-labile toxin of ETEC were secreted. These findings document the existence and virulence potential of an E. coli pathovar hybrid that blurs the distinction between E. coli pathovars.</jats:p

A case of Guillain-Barre syndrome presenting at third trimester of pregnancy complicated with pre-eclampsia and acute kidney injury

Guillain-Barre syndrome (GBS) is immune mediated injury of the peripheral nerves. This condition can affect any individuals with some trigger. Here the disease affected the lady in her last trimester of pregnancy which was complicated with pre-eclampsia and acute kidney injury. Later she recovered by multimodal treatment approach, with a prolonged intensive care unit stay. Currently she and her baby are stable with frequent follow up. This case highlights the fact that GBS can affect any trimester of pregnancy and her pregnancy could be a trigger. Further, treatment approach involves multiple specialties including internal medicine, nephrologist, neurologist, physiotherapist and psychiatrist

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.

As sequencing read length has increased, researchers have quickly adopted longer reads for their experiments. Here, we examine 14 pathogen or host-pathogen differential gene expression data sets to assess whether using longer reads is warranted. A variety of data sets was used to assess what genomic attributes might affect the outcome of differential gene expression analysis including: gene density, operons, gene length, number of introns/exons and intron length. No genome attribute was found to influence the data in principal components analysis, hierarchical clustering with bootstrap support, or regression analyses of pairwise comparisons that were undertaken on the same reads, looking at all combinations of paired and unpaired reads trimmed to 36, 54, 72 and 101 bp. Read pairing had the greatest effect when there was little variation in the samples from different conditions or in their replicates (e.g. little differential gene expression). But overall, 54 and 72 bp reads were typically most similar. Given differences in costs and mapping percentages, we recommend 54 bp reads for organisms with no or few introns and 72 bp reads for all others. In a third of the data sets, read pairing had absolutely no effect, despite paired reads having twice as much data. Therefore, single-end reads seem robust for differential-expression analyses, but in eukaryotes paired-end reads are likely desired to analyse splice variants and should be preferred for data sets that are acquired with the intent to be community resources that might be used in secondary data analyses

A questionnaire based survey to evaluate the usage pattern of carbapenems for sepsis management in intensive care unit

Background: Sepsis remains one of the most common critical illnesses for patients to be admitted to an intensive care unit (ICU) and has very high associated morbidity and mortality ranging from 18 to 50%. It is a well-known fact that early goal directed therapy with broad spectrum antibiotics, IV fluids and other supportive therapies improve outcome. The current study was done to know the importance of carbapenems in the management of sepsis focusing on perceived use and the clinical outcome in real time setting in tertiary care hospitals.Methods: A structured questionnaire designed to collect information on the perceived use of carbapenems, the clinical outcome, response period for clinical cure and combination antibiotic therapy preferred with carbapenem was circulated among 50 clinicians in tertiary care hospitals and nursing homes in and around Mangalore between January 2015 to March 2015.Results: Majority of doctors (>80%) felt that carbapenems a broad spectrum antibiotic administration provided good clinical improvement in hospital infections along with improvement in blood cell count and bacteriological cure.Conclusions: Our study provides an important insight regarding the knowledge, practice pattern and clinical outcome through the use of carbapenem in Sepsis management in ICU’s around Mangalore. The experience of practice patterns and clinical outcomes with carbapenem shared by doctors through this survey is similar to that in other studies

Distribution and mass of diffuse and dense CO gas in the Milky Way

This is the final version of the article. Available from American Astronomical Society and IOP Publishing via the DOI in this record.Emission from carbon monoxide (CO) is ubiquitously used as a tracer of dense star-forming molecular clouds. There is, however, growing evidence that a significant fraction of CO emission originates from diffuse molecular gas. Quantifying the contribution of diffuse CO-emitting gas is vital for understanding the relation between molecular gas and star formation. We examine the Galactic distribution of two CO-emitting gas components, a high column density component detected in 13CO and 12CO, and a low column density component detected in 12CO, but not in 13CO. The “diffuse” and “dense” components are identified using a combination of smoothing, masking, and erosion/dilation procedures, making use of three large-scale 12CO and 13CO surveys of the inner and outer Milky Way. The diffuse component, which globally represents 25% (1.5 × 108M⊙) of the total molecular gas mass (6.5 × {10}8 M⊙), is more extended perpendicular to the Galactic plane. The fraction of diffuse gas increases from ∼10%–20% at a galactocentric radius of 3–4 kpc to 50% at 15 kpc, and increases with decreasing surface density. In the inner Galaxy, a yet denser component traced by CS emission represents 14% of the total molecular gas mass traced by 12CO emission. Only 14% of the molecular gas mass traced by 12CO emission is identified as part of molecular clouds in 13CO surveys by cloud identification algorithms. This study indicates that CO emission not only traces star-forming clouds, but also a significant diffuse molecular ISM component.R.S. and R.S.K. acknowledge support from the Deutsche Forschungsgemeinschaft (DFG) for funding through the SPP 1573 “The Physics of the Interstellar Medium” as well as via SFB 881 “The Milky Way System” (sub-projects B12, and B8). R.S.K. also receives funding from the European Research Council under the European Communitys Seventh Framework Program (FP7/2007-2013) via the ERC Advanced Grant “STARLIGHT” (project number 339177)

Accuracy of core mass estimates in simulated observations of dust emission

We study the reliability of mass estimates obtained for molecular cloud cores using sub-millimetre and infrared dust emission. We use magnetohydrodynamic simulations and radiative transfer to produce synthetic observations with spatial resolution and noise levels typical of Herschel surveys. We estimate dust colour temperatures using different pairs of intensities, calculate column densities and compare the estimated masses with the true values. We compare these results to the case when all five Herschel wavelengths are available. We investigate the effects of spatial variations of dust properties and the influence of embedded heating sources. Wrong assumptions of dust opacity and its spectral index beta can cause significant systematic errors in mass estimates. These are mainly multiplicative and leave the slope of the mass spectrum intact, unless cores with very high optical depth are included. Temperature variations bias colour temperature estimates and, in quiescent cores with optical depths higher than for normal stable cores, masses can be underestimated by up to one order of magnitude. When heated by internal radiation sources the observations recover the true mass spectra. The shape, although not the position, of the mass spectrum is reliable against observational errors and biases introduced in the analysis. This changes only if the cores have optical depths much higher than expected for basic hydrostatic equilibrium conditions. Observations underestimate the value of beta whenever there are temperature variations along the line of sight. A bias can also be observed when the true beta varies with wavelength. Internal heating sources produce an inverse correlation between colour temperature and beta that may be difficult to separate from any intrinsic beta(T) relation of the dust grains. This suggests caution when interpreting the observed mass spectra and the spectral indices.Comment: Revised version, 17 pages, 17 figures, submitted to A&

Myocardial injury associated with coronavirus disease 2019 in pregnancy.

OBJECTIVE:Coronavirus disease 2019 (COVID-19) is associated with cardiac injury1-3 and bradycardia4 in the non-pregnant population. The incidence of these complications in pregnancy is unknown. The objective of this study was to determine the rate of abnormal serum cardiac biomarkers or bradycardia among pregnant and immediately postpartum women admitted for treatment of severe or critical COVID-19 in a large integrated health system in New York. STUDY DESIGN:This is a retrospective review of all pregnant and immediately postpartum women hospitalized for COVID-19 at 7 hospitals within Northwell Health, the largest academic health system in New York state, from March 1 to April 30, 2020. Women who tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by polymerase chain reaction (PCR) assay and who met the National Institute of Health (NIH) criteria for severe or critical illness5 were included. Women with a positive PCR test who were admitted for a reason other than treatment of COVID-19 (eg, labor) were excluded. The Northwell Health Institutional Review Board approved the study as minimal-risk research using data collected for routine clinical practice and waived the requirement for informed consent. Clinical records were manually reviewed. Data collected included demographics, medical comorbidities, pregnancy characteristics, laboratory and imaging results, medications administered, and clinical outcomes. Laboratory and imaging studies were ordered at the discretion of the attending physician. The primary outcomes evaluated were elevated cardiac troponins (I, T, or high sensitivity), elevated brain natriuretic peptide (BNP), bradycardia (defined as \u3c 60 beats per minute, bpm), and maternal heart rate (HR) nadir. Descriptive statistics were used to characterize the data. RESULTS:A total of 31 women met inclusion criteria; 20 (65%) had cardiac biomarkers measured during hospitalization (Table). Cardiac troponins and BNP were elevated in 22% (n=4/18) and 30% (n=3/10) of these patients, respectively. Four patients had transthoracic echocardiograms performed and all were reported as normal. No patients had preexisting cardiovascular disease or hypertension. Two maternal mortalities in this cohort were previously reported;6 both patients had elevated cardiac troponins and one also had an elevated BNP. The nadir HR ranged from 30-92 bpm and bradycardia occurred in one-third of patients (n=10/31). Half of women with elevated troponin and three-fourths of women with elevated BNP had an episode of bradycardia recorded during their hospital course. CONCLUSION:Myocardial injury as demonstrated by abnormal cardiac biomarkers and bradycardia may be common among pregnant women with severe or critical COVID-19. In this study, one-fifth of patients who had troponin levels measured were found to have elevations (one-eighth of the overall study population). Among patients who had brain natriuretic peptide levels measured, 30% were elevated (10% of the overall study population). One third of women had bradycardia. This study is limited by a small sample size. Laboratory testing and imaging was not uniform due to the retrospective nature of the study. Sampling bias was unavoidable because the decision to measure cardiac markers or perform imaging studies was made by the patient\u27s care team, based on clinical presentation rather than a formal protocol. Few studies have evaluated the risk of cardiac injury or arrhythmia among pregnant women with COVID-19. It is also unknown whether there are long-term sequelae that affect maternal health or future pregnancy outcomes. This is an important area of focus for future research

Phase diagram of neutron-rich nuclear matter and its impact on astrophysics

Dense matter as it can be found in core-collapse supernovae and neutron stars is expected to exhibit different phase transitions which impact the matter composition and equation of state, with important consequences on the dynamics of core-collapse supernova explosion and on the structure of neutron stars. In this paper we will address the specific phenomenology of two of such transitions, namely the crust-core solid-liquid transition at sub-saturation density, and the possible strange transition at super-saturation density in the presence of hyperonic degrees of freedom. Concerning the neutron star crust-core phase transition at zero and finite temperature, it will be shown that, as a consequence of the presence of long-range Coulomb interactions, the equivalence of statistical ensembles is violated and a clusterized phase is expected which is not accessible in the grand-canonical ensemble. A specific quasi-particle model will be introduced to illustrate this anomalous thermodynamics and some quantitative results relevant for the supernova dynamics will be shown. The opening of hyperonic degrees of freedom at higher densities corresponding to the neutron stars core modifies the equation of state. The general characteristics and order of phase transitions in this regime will be analyzed in the framework of a self-consistent mean-field approach.Comment: Invited Talk given at the 11th International Conference on Nucleus-Nucleus Collisions (NN2012), San Antonio, Texas, USA, May 27-June 1, 2012. To appear in the NN2012 Proceedings in Journal of Physics: Conference Series (JPCS