Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria

Transcriptional regulators recognize specific DNA sequences. Because these sequences are embedded in the background of genomic DNA, it is hard to identify the key cis-regulatory elements that determine disparate patterns of gene expression. The detection of the intra- and inter-species differences among these sequences is crucial for understanding the molecular basis of both differential gene expression and evolution. Here, we address this problem by investigating the target promoters controlled by the DNA-binding PhoP protein, which governs virulence and Mg2+ homeostasis in several bacterial species. PhoP is particularly interesting; it is highly conserved in different gamma/enterobacteria, regulating not only ancestral genes but also governing the expression of dozens of horizontally acquired genes that differ from species to species. Our approach consists of decomposing the DNA binding site sequences for a given regulator into families of motifs (i.e., termed submotifs) using a machine learning method inspired by the “Divide & Conquer” strategy. By partitioning a motif into sub-patterns, computational advantages for classification were produced, resulting in the discovery of new members of a regulon, and alleviating the problem of distinguishing functional sites in chromatin immunoprecipitation and DNA microarray genome-wide analysis. Moreover, we found that certain partitions were useful in revealing biological properties of binding site sequences, including modular gains and losses of PhoP binding sites through evolutionary turnover events, as well as conservation in distant species. The high conservation of PhoP submotifs within gamma/enterobacteria, as well as the regulatory protein that recognizes them, suggests that the major cause of divergence between related species is not due to the binding sites, as was previously suggested for other regulators. Instead, the divergence may be attributed to the fast evolution of orthologous target genes and/or the promoter architectures resulting from the interaction of those binding sites with the RNA polymerase

Kilonova Luminosity Function Constraints Based on Zwicky Transient Facility Searches for 13 Neutron Star Merger Triggers during O3

We present a systematic search for optical counterparts to 13 gravitational wave (GW) triggers involving at least one neutron star during LIGO/Virgo's third observing run (O3). We searched binary neutron star (BNS) and neutron star black hole (NSBH) merger localizations with the Zwicky Transient Facility (ZTF) and undertook follow-up with the Global Relay of Observatories Watching Transients Happen (GROWTH) collaboration. The GW triggers had a median localization area of 4480 deg², a median distance of 267 Mpc, and false-alarm rates ranging from 1.5 to 10⁻²⁵ yr⁻¹. The ZTF coverage in the g and r bands had a median enclosed probability of 39%, median depth of 20.8 mag, and median time lag between merger and the start of observations of 1.5 hr. The O3 follow-up by the GROWTH team comprised 340 UltraViolet/Optical/InfraRed (UVOIR) photometric points, 64 OIR spectra, and three radio images using 17 different telescopes. We find no promising kilonovae (radioactivity-powered counterparts), and we show how to convert the upper limits to constrain the underlying kilonova luminosity function. Initially, we assume that all GW triggers are bona fide astrophysical events regardless of false-alarm rate and that kilonovae accompanying BNS and NSBH mergers are drawn from a common population; later, we relax these assumptions. Assuming that all kilonovae are at least as luminous as the discovery magnitude of GW170817 (−16.1 mag), we calculate that our joint probability of detecting zero kilonovae is only 4.2%. If we assume that all kilonovae are brighter than −16.6 mag (the extrapolated peak magnitude of GW170817) and fade at a rate of 1 mag day⁻¹ (similar to GW170817), the joint probability of zero detections is 7%. If we separate the NSBH and BNS populations based on the online classifications, the joint probability of zero detections, assuming all kilonovae are brighter than −16.6 mag, is 9.7% for NSBH and 7.9% for BNS mergers. Moreover, no more than 10⁻⁴, or φ > 30° to be consistent with our limits. We look forward to searches in the fourth GW observing run; even 17 neutron star mergers with only 50% coverage to a depth of −16 mag would constrain the maximum fraction of bright kilonovae to <25%

GROWTH on S190425z: Searching Thousands of Square Degrees to Identify an Optical or Infrared Counterpart to a Binary Neutron Star Merger with the Zwicky Transient Facility and Palomar Gattini-IR

The third observing run by LVC has brought the discovery of many compact binary coalescences. Following the detection of the first binary neutron star merger in this run (LIGO/Virgo S190425z), we performed a dedicated follow-up campaign with the Zwicky Transient Facility (ZTF) and Palomar Gattini-IR telescopes. The initial skymap of this single-detector gravitational wave (GW) trigger spanned most of the sky observable from Palomar Observatory. Covering 8000 deg2 of the initial skymap over the next two nights, corresponding to 46% integrated probability, ZTF system achieved a depth of ≈21 m AB in g- and r-bands. Palomar Gattini-IR covered 2200 square degrees in J-band to a depth of 15.5 mag, including 32% integrated probability based on the initial skymap. The revised skymap issued the following day reduced these numbers to 21% for the ZTF and 19% for Palomar Gattini-IR. We narrowed 338,646 ZTF transient "alerts" over the first two nights of observations to 15 candidate counterparts. Two candidates, ZTF19aarykkb and ZTF19aarzaod, were particularly compelling given that their location, distance, and age were consistent with the GW event, and their early optical light curves were photometrically consistent with that of kilonovae. These two candidates were spectroscopically classified as young core-collapse supernovae. The remaining candidates were ruled out as supernovae. Palomar Gattini-IR did not identify any viable candidates with multiple detections only after merger time. We demonstrate that even with single-detector GW events localized to thousands of square degrees, systematic kilonova discovery is feasible

GROWTH on GW190425: Searching thousands of square degrees to identify an optical or infrared counterpart to a binary neutron star merger with the Zwicky Transient Facility and Palomar Gattini IR

The beginning of the third observing run by the network of gravitational-wave detectors has brought the discovery of many compact binary coalescences. Prompted by the detection of the first binary neutron star merger in this run (GW190425 / LIGO/Virgo S190425z), we performed a dedicated follow-up campaign with the Zwicky Transient Facility (ZTF) and Palomar Gattini-IR telescopes. As it was a single gravitational-wave detector discovery, the initial skymap spanned most of the sky observable from Palomar Observatory, the site of both instruments. Covering 8000 deg$^2$ of the inner 99\% of the initial skymap over the next two nights, corresponding to an integrated probability of 46\%, the ZTF system achieved a depth of $\approx$\,21 $m_\textrm{AB}$ in $g$- and $r$-bands. Palomar Gattini-IR covered a total of 2200 square degrees in $J$-band to a depth of 15.5\,mag, including 32\% of the integrated probability based on the initial sky map. However, the revised skymap issued the following day reduced these numbers to 21\% for the Zwicky Transient Facility and 19\% for Palomar Gattini-IR. Out of the 338,646 ZTF transient "alerts" over the first two nights of observations, we narrowed this list to 15 candidate counterparts. Two candidates, ZTF19aarykkb and ZTF19aarzaod were particularly compelling given that their location, distance, and age were consistent with the gravitational-wave event, and their early optical lightcurves were photometrically consistent with that of kilonovae. These two candidates were spectroscopically classified as young core-collapse supernovae. The remaining candidates were photometrically or spectroscopically ruled-out as supernovae. Palomar Gattini-IR identified one fast evolving infrared transient after the merger, PGIR19bn, which was later spectroscopically classified as an M-dwarf flare. [abridged

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Letter to the Editor

Background Diabetic retinopathy (DR) is of the sight threatening ocular diseases having public health implications in India because an estimated 57 million people in India may be diabetic by 2025. This study highlights the prevalence of DR in type 2 diabetics among a small population in Chennai in relation to various risk factors.     Method The cross sectional study was done on 203 patients, as a part of the monthly screening camp conducted by “Sankara Nethralaya , Chennai”, for the patients of Kilpauk Medical College Hospital. A detailed history including risk factors like age ,sex , duration of diabetes , smoking ,alcohol ,Ischaemic heart disease(IHD), Oral Hypoglycaemic Drugs(OHA) , Insulin was taken followed by measurement of blood pressure and examination of Eye including Visual acuity , Intraocular pressure , Anterior chamber examination and Optic Fundoscopy .Statistical analysis was done by SPSS using Binary logistics Regression method.       ResultsOf the 203 patients, 146(71.9%) were females.136 (67%) people had awareness about DR. The prevalence rate of DR is 13.8% (28) in which Moderate NPDR had the maximum incidence with 5.9%. Prevalence is more in the 5th - 6th decades of life with 5.9% having DR.  DR increases with the duration of diabetes. Men were at a slightly higher risk (14% males v/s 13.6% females) though not statistically significant. There was no increased risk among hypertensives, IHD patients, smokers, alcoholics and no significant relationship with treatment history.       Conclusion Though the awareness about the disease of 67% is encouraging, incidence rate of 13.8% of diabetic retinopathy in a small population is alarming. Higher number of woman in the study could have influenced the results. This triggers the need for studies with higher sample size to assess various risk factors and mass screening programs.   Word count: 287   Key Words Diabetic Retinopathy, prevalence, risk factors

Baseline results indicate poor glycemic control and delay in initiation and optimization of insulin therapy: results from the improving management practices and clinical outcomes in type 2 diabetes study

Introduction: Improving management practices and clinical outcomes in type 2 diabetes (IMPACT), was a prospective, open-label, 26- week, comparative, multi-center study to compare efficacy and safety of the Indian insulin guideline (IIG) group versus routine clinical practice (RCP) group in patients with type 2 diabetes. Materials and Methods: A total of 20,653 patients from 885 centers across India were enrolled and treated with premixed insulin therapy as per IIG or routine care. Results: Most of the participating centers (81.7%) reported following a diabetes guideline in their practice routinely but only 20.4% targeted HbA1c <7%. Very few of the physicians (2.7%) reported that most of their patients (>75%) achieved an HbA1c <7%. Most of the physicians (39.8%) also agreed that only 10-25% of the patients agree to start insulin therapy at the first counseling. Mean duration of diabetes before initiating insulin in patients using oral anti-diabetic drugs (OADs) was 7 years, indicating a delay in initiating insulin therapy. The difference in mean daily dose of insulin at initiation vs. at 26 weeks was only 0.8 U (25.8 ± 11.3 at initiation compared to 26.6 ± 9.5, respectively, p = ns) suggesting lack of treatment optimization. Weekly titration till achieving HbA1c <7% was done in 51.1% of the patients and only 8.9% performed self-titration. Conclusion: Baseline glycemic control in these patients was poor and reflects a delay in initiating insulin therapy. Data also reflect a lack of optimization of insulin doses