Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects

Motivation

Meta-analysis is essential to combine the results of genome-wide association studies (GWASs). Recent large-scale meta-analyses have combined studies of different ethnicities, environments and even studies of different related phenotypes. These differences between studies can manifest as effect size heterogeneity. We previously developed a modified random effects model (RE2) that can achieve higher power to detect heterogeneous effects than the commonly used fixed effects model (FE). However, RE2 cannot perform meta-analysis of correlated statistics, which are found in recent research designs, and the identified variants often overlap with those found by FE.

Results

Here, we propose RE2C, which increases the power of RE2 in two ways. First, we generalized the likelihood model to account for correlations of statistics to achieve optimal power, using an optimization technique based on spectral decomposition for efficient parameter estimation. Second, we designed a novel statistic to focus on the heterogeneous effects that FE cannot detect, thereby, increasing the power to identify new associations. We developed an efficient and accurate p-value approximation procedure using analytical decomposition of the statistic. In simulations, RE2C achieved a dramatic increase in power compared with the decoupling approach (71% vs. 21%) when the statistics were correlated. Even when the statistics are uncorrelated, RE2C achieves a modest increase in power. Applications to real genetic data supported the utility of RE2C. RE2C is highly efficient and can meta-analyze one hundred GWASs in one day.

Availability and implementation

The software is freely available at http://software.buhmhan.com/RE2C.

Supplementary information

Supplementary data are available at Bioinformatics online.

Severe Asthma Phenotypes Classified by Site of Airway Involvement and Remodeling via Chest CT Scan

OBJECTIVES

This study aimed to establish a system that can classify severe asthma on the basis of airway remodeling patterns visualizedusing computed tomography (CT) images and to evaluate the clinical characteristics of individual image-based subtypes.

METHODS

Chest CT images from severe asthma patients were retrospectively evaluated to classify phenotypes by site of airway involvement and remodeling. The association between radiologic subtypes and clinical characteristics was assessed.

RESULTS

Of 91 patients with severe asthma, 74 (81.3%) exhibited abnormal radiologic findings, including bronchial wall thickening (BT), mucus plugging (MP), and bronchiectasis (BE). The severity of BT and the extent of MP were independently associated with peripheral blood eosinophil count (P=.012, r2=0.112) and sputum eosinophil count (P=.022, r2=0.090), respectively. The large-to-medium airway remodeling type, which showed diffuse BT combined with MP and BE, accounted for 44% of patients and revealed higher peripheral blood eosinophil counts than other types. In the small airway remodeling type, which accounted for 6.6% of patients, we observed a higher rate of fixed airflow obstruction, along with a predominance of males and smokers and more frequent use of controller medication than other phenotypes. In 26% of patients with severe asthma, no prominent airway remodeling was observed (near-normal type); the near-normal type required oral corticosteroids less frequently than the large-to-medium airway and small airway remodeling types.

CONCLUSIONS

Depending on the site of airway involvement and remodeling pattern, 3 different structural types can be distinguished in chest CT findings from patients with severe asthma. Remodeling in large-to-medium sized airways revealed an association with systemic eosinophilic inflammation in patients with severe asthma.

Identification of pyruvate kinase as a novel allergen in whiteleg shrimp (Litopenaeus vannamei) by specific-IgE present in patients with shrimp allergy

Food allergy is one of the most important health issues worldwide. In Taiwan, current literature suggests shrimps and crabs are the most common causes of food allergy, and are frequently associated with acute allergic reactions such as urticaria, atopic dermatitis, and asthma. However, knowledge regarding the shrimp allergens remains limited. Thus, there is an urgent need to establish comprehensive information for elucidating underlying triggers for food allergy. In this study, whiteleg shrimp (Litopenaeus vannamei) was used to evaluate the IgE-binding properties of various shrimp proteins to 7 allergic patients' sera by western blot. A 63 kDa protein was found in raw and cooked shrimp bound to specific-IgEs in 7 and 4 patients' sera, respectively. This protein was further identified as pyruvate kinase based on the proteomic mass spectrometry. This study identifies an important shrimp allergen unique to Taiwan and further testing and prevention measures might be implemented in the allergen analysis.

Defective formyl peptide receptor 2/3 and annexin A1 expressions associated with M2a polarization of blood immune cells in patients with chronic obstructive pulmonary disease

Background

Controversy exists in previous studies on macrophage M1/M2 polarization in chronic obstructive pulmonary disease (COPD). We hypothesized that formyl peptide receptor (FPR), a marker of efferocytosis and mediator of M1/M2 polarization, may be involved in the development of COPD.

Methods

We examined FPR 1/2/3 expressions of blood M1/M2a monocyte, neutrophil, natural killer (NK) cell, NK T cell, T helper (Th) cell, and T cytotoxic (Tc) cell by flowcytometry method in 40 patients with cigarette smoking-related COPD and 16 healthy non-smokers. Serum levels of five FPR ligands were measured by ELISA method.

Results

The COPD patients had lower M2a percentage and higher percentages of NK, NK T, Th, and Tc cells than the healthy non-smokers. FPR2 expressions on Th/Tc cells, FPR3 expressions of M1, M2a, NK, NK T, Th, and Tc cells, and serum annexin A1 (an endogenous FPR2 ligand) levels were all decreased in the COPD patients as compared with that in the healthy non-smokers. FPR1 expression on neutrophil was increased in the COPD patient with a high MMRC dyspnea scale, while FPR2 expression on neutrophil and annexin A1 were both decreased in the COPD patients with a history of frequent moderate exacerbation (≥ 2 events in the past 1 year). In 10 COPD patients whose blood samples were collected again after 1-year treatment, M2a percentage, FPR3 expressions of M1/NK/Th cells, FPR2 expression on Th cell, and FPR1 expression on neutrophil were all reversed to normal, in parallel with partial improvement in small airway dysfunction.

Conclusions

Our findings provide evidence for defective FPR2/3 and annexin A1 expressions that, associated with decreased M2a polarization, might be involved in the development of cigarette smoking induced persistent airflow limitation in COPD.

GW170817: Implications for the Stochastic Gravitational-Wave Background from Compact Binary Coalescences

The LIGO Scientific and Virgo Collaborations have announced the event GW170817, the first detection of gravitational waves from the coalescence of two neutron stars. The merger rate of binary neutron stars estimated from this event suggests that distant, unresolvable binary neutron stars create a significant astrophysical stochastic gravitational-wave background. The binary neutron star component will add to the contribution from binary black holes, increasing the amplitude of the total astrophysical background relative to previous expectations. In the Advanced LIGO-Virgo frequency band most sensitive to stochastic backgrounds (near 25 Hz), we predict a total astrophysical background with amplitude Ω_{GW}(f=25  Hz)=1.8_{-1.3}^{+2.7}×10^{-9} with 90% confidence, compared with Ω_{GW}(f=25  Hz)=1.1_{-0.7}^{+1.2}×10^{-9} from binary black holes alone. Assuming the most probable rate for compact binary mergers, we find that the total background may be detectable with a signal-to-noise-ratio of 3 after 40 months of total observation time, based on the expected timeline for Advanced LIGO and Virgo to reach their design sensitivity.

Split-graft liver transplantation from an adult donor with an unrecognized UCD to a pediatric and adult recipient

We report the outcomes of an adult and pediatric split liver transplant from an adult male donor who died due to an unrecognized UCD, OTC deficiency. Recognizing inborn errors of metabolism can be challenging, especially in adult centers where such disorders are rarely encountered. Shortage of donors for liver transplantation has led to procedures to maximize donor utilization, such as split and live donor grafts. The cause of death should be ascertained before accepting a cadaveric donor organ.

Orbital-anisotropic electronic structure in the nonmagnetic state of BaFe2(As1-xP x )2 superconductors

High-temperature superconductivity in iron-pnictides/chalcogenides arises in balance with several electronic and lattice instabilities. Beside the antiferromagnetic order, the orbital anisotropy between Fe 3d xz and 3d yz occurs near the orthorhombic structural transition in several parent compounds. However, the extent of the survival of orbital anisotropy against the ion-substitution remains to be established. Here we report the composition (x) and temperature (T) dependences of the orbital anisotropy in the electronic structure of a BaFe2(As1-xP x )2 system by using angle-resolved photoemission spectroscopy. In the low-x regime, the orbital anisotropy starts to evolve on cooling from high temperatures above both antiferromagnetic and orthorhombic transitions. By increasing x, it is gradually suppressed and survives in the optimally doped regime. We find that the in-plane orbital anisotropy persists in a large area of the nonmagnetic phase, including the superconducting dome. These results suggest that the rotational symmetry-broken electronic state acts as the stage for superconductivity in BaFe2(As1-xP x )2.

First Search for Nontensorial Gravitational Waves from Known Pulsars

We present results from the first directed search for nontensorial gravitational waves. While general relativity allows for tensorial (plus and cross) modes only, a generic metric theory may, in principle, predict waves with up to six different polarizations. This analysis is sensitive to continuous signals of scalar, vector, or tensor polarizations, and does not rely on any specific theory of gravity. After searching data from the first observation run of the advanced LIGO detectors for signals at twice the rotational frequency of 200 known pulsars, we find no evidence of gravitational waves of any polarization. We report the first upper limits for scalar and vector strains, finding values comparable in magnitude to previously published limits for tensor strain. Our results may be translated into constraints on specific alternative theories of gravity.

Hepatic Portal Venous Gas in a Patient with Penetrating Injuries

Hepatic portal venous gas (HPVG) refers to the branching area of low attenuation extending to within 2 cm of the liver capsule in computed tomography scan. The most common causes of HPVG are mesenteric ischaemia in adults and necrotising enterocolitis in infants. HPVG in trauma patients is mostly reported in cases of blunt abdominal trauma. We present a deceased patient who had chest and abdominal wall penetrating injuries with concomitant hypovolemic shock. A computed tomography scan revealed HPVG and pulmonary artery air emboli. The mechanism of the presentation of HPVG in this patient and the possible cause of death would be discussed. (Hong Kong j.emerg.med. 2013;20:382-384)

The Academic Contribution of Emergency Departments in Taiwan: Data on Scientific Publications, 1992-2011

Introduction

This study aimed to evaluate the academic contribution of emergency departments (EDs) in Taiwan by analysing scientific publications during the past 20 years.

Methods

This was an observational study. All data were collected from the 2010 Journal Citation Reports (JCR) and the SciVerse Scopus database. Three groups of publications were enrolled: (1) publications from Taiwan EDs in emergency medicine (EM) journals; (2) publications from Taiwan EDs in non-EM journals; (3) publications from Taiwan who were not affiliated with EDs in EM journals. We collected data regarding the name and category of the journal, the publication year, the publication type, and the number of citations for further analysis.

Results

A total of 475 publications affiliated with Taiwan EDs appeared in EM journals and 735 appeared in non-EM journals. A total of 389 publications in EM journals affiliated with departments other than EM. The number of publications showed an increasing trend (all p-value <0.001). The number of publications from Taiwan EDs in EM and non-EM journals changed in opposite directions since 2008. Researches from Taiwan EDs were published in 68 categories of journals in addition to EM. Publications in non-EM journals were more frequently cited than were the publications in EM journals.

conclusions

During the past 20 years, the academic contribution of EDs in Taiwan has increased substantially. The bidirectional change in publication numbers since 2008 constitutes a milestone in the development of EM in Taiwan, and improvements are evident in the quality, quantity, and breadth of research. (Hong Kong j.emerg.med. 2016;23:28-34)

Cyclin D1 promoter -56 and -54bp CpG un-methylation predicts invasive progression in arsenic-induced Bowen's disease

BACKGROUND

Patients with arsenic-induced Bowen's disease (As-BD) are at risk of developing invasive cancers in the skin, lung, and urinary bladder. However, a longitudinal follow-up study on the association between As-BD and invasive cancers is still lacking.

OBJECTIVES

This study aims to investigate the underlying molecular mechanisms of this malignant progression in the skin and internal organs.

METHODS

This is a biopsy-based follow-up study. We tested the DNA histograms, Cyclin D1 (CCND1) protein expression and CCND1 promoter DNA methylation in 40 pathologically confirmed specimens from As-BD patients to correlate with individual's invasive cancer occurrence in the 5-year follow-up.

RESULTS

Flow cytometric DNA histogram analysis of skin specimens showed aneuploid (n=15), G2/M arrest (n=22), and normal (n=3) DNA histograms. No patients with normal DNA histograms developed invasive cancers, whereas 13 developed invasive cancers in the aneuploid group and 2 developed invasive cancers in the G2/M arrest group. The aneuploid group showed a high risk of invasive cancer development. In all assessed aneuploid specimens, the CCND1 promoter hypomethylation was observed. Statistically, percentage of un-methylation more than 55.85% among 17 detected CpG sites showed extremely high predictive power in the occurrence of invasive arsenical cancers. Furthermore, the un-methylation at -56 and -54bp CpG sites was statistically significantly associated with invasive arsenical cancer development (p=1.29×10^-5).

CONCLUSIONS

As-BD lesions showing an aneuploid DNA histogram had a high risk of invasive cancer development. Un-methyaltion at -56 and -54bp CpG in the CCND1 promoter serves as a predictor for invasive progression in As-BD patients.

Control of Chiral Magnetism Through Electric Fields in Multiferroic Compounds above the Long-Range Multiferroic Transition

Polarized neutron scattering experiments reveal that type-II multiferroics allow for controlling the spin chirality by external electric fields even in the absence of long-range multiferroic order. In the two prototype compounds TbMnO_{3} and MnWO_{4}, chiral magnetism associated with soft overdamped electromagnons can be observed above the long-range multiferroic transition temperature T_{MF}, and it is possible to control it through an electric field. While MnWO_{4} exhibits chiral correlations only in a tiny temperature interval above T_{MF}, in TbMnO_{3} chiral magnetism can be observed over several kelvin up to the lock-in transition, which is well separated from T_{MF}.

GW170817: Observation of Gravitational Waves from a Binary Neutron Star Inspiral

On August 17, 2017 at 12∶41:04 UTC the Advanced LIGO and Advanced Virgo gravitational-wave detectors made their first observation of a binary neutron star inspiral. The signal, GW170817, was detected with a combined signal-to-noise ratio of 32.4 and a false-alarm-rate estimate of less than one per 8.0×10^{4}  years. We infer the component masses of the binary to be between 0.86 and 2.26  M_{⊙}, in agreement with masses of known neutron stars. Restricting the component spins to the range inferred in binary neutron stars, we find the component masses to be in the range 1.17-1.60  M_{⊙}, with the total mass of the system 2.74_{-0.01}^{+0.04}M_{⊙}. The source was localized within a sky region of 28  deg^{2} (90% probability) and had a luminosity distance of 40_{-14}^{+8}  Mpc, the closest and most precisely localized gravitational-wave signal yet. The association with the γ-ray burst GRB 170817A, detected by Fermi-GBM 1.7 s after the coalescence, corroborates the hypothesis of a neutron star merger and provides the first direct evidence of a link between these mergers and short γ-ray bursts. Subsequent identification of transient counterparts across the electromagnetic spectrum in the same location further supports the interpretation of this event as a neutron star merger. This unprecedented joint gravitational and electromagnetic observation provides insight into astrophysics, dense matter, gravitation, and cosmology.

GW170814: A Three-Detector Observation of Gravitational Waves from a Binary Black Hole Coalescence

On August 14, 2017 at 10∶30:43 UTC, the Advanced Virgo detector and the two Advanced LIGO detectors coherently observed a transient gravitational-wave signal produced by the coalescence of two stellar mass black holes, with a false-alarm rate of ≲1 in 27 000 years. The signal was observed with a three-detector network matched-filter signal-to-noise ratio of 18. The inferred masses of the initial black holes are 30.5_{-3.0}^{+5.7}M_{⊙} and 25.3_{-4.2}^{+2.8}M_{⊙} (at the 90% credible level). The luminosity distance of the source is 540_{-210}^{+130}  Mpc, corresponding to a redshift of z=0.11_{-0.04}^{+0.03}. A network of three detectors improves the sky localization of the source, reducing the area of the 90% credible region from 1160   deg^{2} using only the two LIGO detectors to 60  deg^{2} using all three detectors. For the first time, we can test the nature of gravitational-wave polarizations from the antenna response of the LIGO-Virgo network, thus enabling a new class of phenomenological tests of gravity.

Cutaneous sarcoidosis: A retrospective case series and a hospital-based case-control study in Taiwan

Sarcoidosis is a systemic granulomatous disorder of unknown etiology often involving skin. Studies on cutaneous sarcoidosis and comorbidities are limited. This study is aimed to describe the clinical features of cutaneous sarcoidosis diagnosed in our hospital and to determine the relationships between cutaneous sarcoidosis and comorbidities.This retrospective study evaluates patients with cutaneous sarcoidosis in a tertiary center in Taiwan from 1996 to 2015. The records of 38 patients with cutaneous sarcoidosis were reviewed for clinical characteristics and evaluated by analysis of variance. A 1:4 case-control analysis was conducted with 152 age- and sex-matched controls who underwent biopsy for other benign skin tumors.The male to female ratio was 1:4.4. The average age at diagnosis was 51.7 years. Female patients were on average 13.9 years older than male patients. The correlation of age with gender was statistically significant (P = .037). The most common cutaneous lesions were plaques (47.4%) and confined to the face (71.1%). Of the 38 patients, 26.3% had diabetes mellitus. Age over 40 (P = .014) and female (P = .014) were associated with facial involvement. In the case-control study, a higher percentage of patients with cutaneous sarcoidosis than of control subjects had diabetes mellitus (P = .001), hearing loss (P = .031) and eye diseases (P = .047).The present study demonstrates a striking female predominance and high proportions of facial involvement. Diabetes mellitus, hearing loss, and eye diseases may be associated with Taiwanese patients with cutaneous sarcoidosis.

Anisotropic resonance modes emerging in an antiferromagnetic superconducting state

Two strong arguments in favor of magnetically driven unconventional superconductivity arise from the coexistence and closeness of superconducting and magnetically ordered phases on the one hand, and from the emergence of magnetic spin-resonance modes at the superconducting transition on the other hand. Combining these two arguments one may ask about the nature of superconducting spin-resonance modes occurring in an antiferromagnetic state. This problem can be studied in underdoped BaFe₂ As₂, for which the local coexistence of large moment antiferromagnetism and superconductivity is well established by local probes. However, polarized neutron scattering experiments are required to identify the nature of the resonance modes. In the normal state of Co underdoped BaFe₂ As₂ the antiferromagnetic order results in broad magnetic gaps opening in all three spin directions that are reminiscent of the magnetic response in the parent compound. In the superconducting state two distinct anisotropic resonance excitations emerge, but in contrast to numerous studies on optimum and over-doped BaFe₂ As₂ there is no isotropic resonance excitation. The two anisotropic resonance modes appearing within the antiferromagnetic phase are attributed to a band selective superconducting state, in which longitudinal magnetic excitations are gapped by antiferromagnetic order with sizable moment.

Poly(ε-caprolactone) nanocapsule carriers with sustained drug release: single dose for long-term glaucoma treatment

Glaucoma is an eye-related disease accompanied by highly elevated intraocular pressure (IOP), which causes damage to the optic nerve and results in vision loss and even blindness. Although the treatment of glaucoma with eye drops may reduce the IOP, eye drops have some limitations, such as poor patient compliance and short duration. To develop drug carriers that facilitate the sustained and long-term release of drugs for glaucoma therapy, we synthesized poly(ε-caprolactone) nanoparticles (PCL NPs) capable of loading pilocarpine, a widely used drug for the treatment of dry eye and glaucoma. We prepared two types of PCL NPs, namely, nanospheres (NSs), which are solid spheres capable of harboring the drug in their solid mass, and nanocapsules (NCs), which are hollow spherical structures for encapsulating the drug. The influence of the vesicular structure of PCL NPs on the drug loading efficiencies and release was investigated. The loading of pilocarpine in the PCL NCs was approximately 3 times higher than that in the PCL NSs. In addition, pilocarpine-loaded PCL NCs (PILO-PCL NCs) exhibited a sustained drug release profile. Effective pharmacological responses (i.e., IOP reduction and pupillary constriction) were observed in rabbits intracamerally treated with pilocarpine-loaded PCL NPs. Moreover, the PILO-PCL NCs show long-term therapeutic ability in alleviating ocular hypertension-induced corneal and retinal injuries under physiological conditions, even after 42 days. The results of in vivo studies also reveal that the PCL NCs are advantageous for the treatment of chronic ocular hypertension in glaucomatous eyes.

Bioengineered keratocyte spheroids fabricated on chitosan coatings enhance tissue repair in a rabbit corneal stromal defect model

Cultivated cell spheroid transplantation is widely studied as a means of facilitating tissue regeneration. Chitosan biomaterial has been shown to promote keratocyte aggregation and multicellular spheroid formation. This study provides further evidence on application of bioengineered keratocyte spheroids for corneal stromal tissue engineering. In an allogeneic rabbit model of stromal destruction caused by bacterial keratitis, the corneas were intrastromally injected with isolated keratocyte suspensions or aggregated spheroid grafts at same cell number. Results of clinical observations and histological examinations on postoperative day 14 showed that when an antibiotic eye drop is only medication for inhibiting bacterial growth, permanent damage to stroma occurs, leading to disorganization of collagen lamellae and tissue structure as well as loss of corneal transparency and visual function. Intrastromal grafting of keratocytes provided additional benefits to overcome drawbacks of limited disease treatment performance associated with topically applied antibiotics. In particular, as compared to their cell suspension counterparts, bioengineered keratocyte spheroids had higher ability to preserve cellular phenotype, secrete collagen matrix, and enhance graft retention, suggesting excellent repair capability for managing stromal tissue defect and alleviating corneal haze/oedema. In summary, the findings emphasize the role of keratocyte configuration (i.e., two-dimensional monolayer or three-dimensional spheroid) in determining therapeutic potency of cellular allografts for stromal tissue reconstruction. Transplantation of keratocyte spheroids cultured on chitosan substrates may represent a promising strategy for corneal stromal repair.

Genomic Alterations and Outcomes with VEGF-Targeted Therapy in Patients with Clear Cell Renal Cell Carcinoma

Background: Mutations in VHL, PBRM1, SETD2, BAP1, and KDM5C are common in clear cell renal cell carcinoma (ccRCC), and presence of certain mutations has been associated with outcomes in patients with non-metastatic disease. Limited information is available regarding the correlation between genomic alterations and outcomes in patients with metastatic disease, including response to VEGF-targeted therapy.

Objective: To explore correlations between mutational profiles and cancer-specific outcomes, including response to standard VEGF-targeted agents, in patients with metastatic cc RCC.

Methods: A retrospective review of 105 patients with metastatic ccRCC who had received systemic therapy and had targeted next-generation sequencing of tumors was conducted. Genomic alterations were correlated to outcomes, including overall survival and time to treatment failure to VEGF-targeted therapy.

Results: The most frequent mutations were detected in VHL (83%), PBRM1 (51%), SETD2 (35%), BAP1 (24%), KDM5C (16%), and TERT (14%). Time to treatment failure with VEGF-targeted therapy differed significantly by PBRM1 mutation status (p = 0.01, median 12.0 months for MT versus 6.9 months for WT) and BAP1 mutation status (p = 0.01, median 6.4 months for MT versus 11.0 months for WT). Shorter overall survival was associated with TERT mutations (p = 0.03, median 29.6 months for MT versus 52.6 months for WT) or BAP1 mutations (p = 0.02, median 28.7 months for MT versus not reached for WT).

Conclusions: Genomic alterations in ccRCC tumors have prognostic implications in patients with metastatic disease. BAP1 and TERT promoter mutations may be present in higher frequency than previously thought, and based on this data, deserve further study for their association with poor prognosis.

Inflammatory and Noninflammatory Itch: Implications in Pathophysiology-Directed Treatments

Itch is the main chief complaint in patients visiting dermatologic clinics and has the ability to deeply impair life quality. Itch results from activation of cutaneous nerve endings by noxious stimuli such as inflammatory mediators, neurotransmitters and neuropeptides, causing itch signal transduction from peripheral skin, through the spinal cord and thalamus, to the brain cortex. Primarily noninflammatory diseases, such as uremic pruritus, cause itch through certain pruritogens in the skin. In inflammatory skin diseases, atopic dermatitis (AD) is the prototypic disease causing intensive itch by aberrant skin inflammation and epidermal barrier disruption. Recent understanding of disease susceptibility, severity markers, and mechanisms have helped to develop targeted therapy for itch in AD, including monoclonal antibodies against IL-4, IL-13, thymic stromal lymphopoietin (TSLP), IgE and IL-31. Promising effects have been observed in some of them. In this review, we summarized targeted therapies for inflammatory itch in AD and for managing abnormal itch transductions in other common itching skin diseases.

Assessment of DNA Ploidy in the ProMisE molecular subgroups of endometrial cancer

OBJECTIVE

We sought to determine whether DNA ploidy correlates with the four molecular subgroups of endometrial carcinoma (EC) as determined using ProMisE (Proactive Molecular Risk Classifier for Endometrial Cancer).

METHODS

90 cases of EC previously characterized by clinicopathological parameters, outcomes, and ProMisE molecular subgroup (POLE EDM, MMR-D, p53 wt or p53 abn) were assessed for DNA ploidy using image cytometry. Associations of ploidy with traditional clinicopathological parameters were also tested.

RESULTS

Abnormal DNA ploidy status differed amongst the ProMisE groups (p<0.001) and was found in 80.9% (17/21) of p53 abn, 37.0% (10/27) of p53 wt, 28.6% (4/14) of POLE EDM and 14.3% (4/28) of MMR-D. Abnormal DNA content was significantly associated with lower BMI (p=0.034) and grade 3 tumors (p=0.001). In the entire cohort, abnormal DNA content was significantly associated with worse progression free survival (p=0.0094) but not disease specific survival (p=0.249) or overall survival (p=0.187). When examining ploidy within each of the ProMisE groups, abnormal DNA content correlated with worse overall survival (p=0.041) and progression free survival (p=0.011) in the MMR-D group. No statistically significant relationship was seen in the remaining 3 groups.

CONCLUSION

Abnormal DNA ploidy status did correlate with the molecular subgroups of EC; abnormal DNA content was seen in the large majority of p53 abn cases. Abnormal ploidy however was also seen in smaller numbers in the p53 wt, POLE EDM and MMR-D groups; therefore abnormal DNA content was not a specific marker for any one molecular group. The addition of ploidy to the ProMisE molecular categories conferred additional prognostic value within the MMR-D group, which merits further study.

GW170104: Observation of a 50-Solar-Mass Binary Black Hole Coalescence at Redshift 0.2

We describe the observation of GW170104, a gravitational-wave signal produced by the coalescence of a pair of stellar-mass black holes. The signal was measured on January 4, 2017 at 10∶11:58.6 UTC by the twin advanced detectors of the Laser Interferometer Gravitational-Wave Observatory during their second observing run, with a network signal-to-noise ratio of 13 and a false alarm rate less than 1 in 70 000 years. The inferred component black hole masses are 31.2_{-6.0}^{+8.4}M_{⊙} and 19.4_{-5.9}^{+5.3}M_{⊙} (at the 90% credible level). The black hole spins are best constrained through measurement of the effective inspiral spin parameter, a mass-weighted combination of the spin components perpendicular to the orbital plane, χ_{eff}=-0.12_{-0.30}^{+0.21}. This result implies that spin configurations with both component spins positively aligned with the orbital angular momentum are disfavored. The source luminosity distance is 880_{-390}^{+450}  Mpc corresponding to a redshift of z=0.18_{-0.07}^{+0.08}. We constrain the magnitude of modifications to the gravitational-wave dispersion relation and perform null tests of general relativity. Assuming that gravitons are dispersed in vacuum like massive particles, we bound the graviton mass to m_{g}≤7.7×10^{-23}  eV/c^{2}. In all cases, we find that GW170104 is consistent with general relativity.

Which creatinine-based estimated glomerular filtration rate equation best predicts all-cause mortality in Chinese subjects with type 2 diabetes?

AIM

In Chinese, ethnicity-based and/or diabetes specific modifications of the Modification of Diet in Renal Disease (MDRD) and the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations have been developed for determining estimated glomerular filtrate rate (eGFR). This study aimed to compare the performance of five different creatinine-based eGFR equations in predicting all-cause mortality among Chinese subjects with type 2 diabetes (T2DM).

METHODS

A total of 6739 Chinese subjects with T2DM were included. Their eGFR was calculated using the MDRD, CKD-EPI, their respective modified equations for Chinese, and the diabetes specific CKD-EPI Chinese T2DM equations. Multiple Cox regression analysis was used to evaluate the associations of eGFR with all-cause mortality. C-statistics, net reclassification index (NRI) and integrated discrimination index (IDI) were applied to assess the discrimination and reclassification of each eGFR equation in predicting mortality outcome.

RESULTS

Over a follow-up of 5.7years, the incidence of all-cause mortality was 12.9% (N=867). The CKD-EPI equation discriminated all-cause mortality better than the MDRD equation (C-statistics: 0.714 vs. 0.689, p<0.0001), and Chinese modification of their respective equations did not improve discrimination. Among the five eGFR equations evaluated, the CKD-EPI Chinese T2DM equation provided the best discrimination in predicting all-cause mortality among Chinese subjects with T2DM, and was the only equation providing a significantly positive NRI and IDI relative to the CKD-EPI equation.

CONCLUSIONS

Among Chinese subjects with T2DM, our findings suggested that the CKD-EPI Chinese T2DM equation best predicted all-cause mortality, and relative to the CKD-EPI equation, conferred improved discrimination and reclassification.

Upper Limits on the Stochastic Gravitational-Wave Background from Advanced LIGO's First Observing Run

A wide variety of astrophysical and cosmological sources are expected to contribute to a stochastic gravitational-wave background. Following the observations of GW150914 and GW151226, the rate and mass of coalescing binary black holes appear to be greater than many previous expectations. As a result, the stochastic background from unresolved compact binary coalescences is expected to be particularly loud. We perform a search for the isotropic stochastic gravitational-wave background using data from Advanced Laser Interferometer Gravitational Wave Observatory's (aLIGO) first observing run. The data display no evidence of a stochastic gravitational-wave signal. We constrain the dimensionless energy density of gravitational waves to be Ω_{0}<1.7×10^{-7} with 95% confidence, assuming a flat energy density spectrum in the most sensitive part of the LIGO band (20-86 Hz). This is a factor of ∼33 times more sensitive than previous measurements. We also constrain arbitrary power-law spectra. Finally, we investigate the implications of this search for the background of binary black holes using an astrophysical model for the background.

Directional Limits on Persistent Gravitational Waves from Advanced LIGO's First Observing Run

We employ gravitational-wave radiometry to map the stochastic gravitational wave background expected from a variety of contributing mechanisms and test the assumption of isotropy using data from the Advanced Laser Interferometer Gravitational Wave Observatory's (aLIGO) first observing run. We also search for persistent gravitational waves from point sources with only minimal assumptions over the 20-1726 Hz frequency band. Finding no evidence of gravitational waves from either point sources or a stochastic background, we set limits at 90% confidence. For broadband point sources, we report upper limits on the gravitational wave energy flux per unit frequency in the range F_{α,Θ}(f)<(0.1-56)×10^{-8}    erg cm^{-2} s^{-1} Hz^{-1}(f/25  Hz)^{α-1} depending on the sky location Θ and the spectral power index α. For extended sources, we report upper limits on the fractional gravitational wave energy density required to close the Universe of Ω(f,Θ)<(0.39-7.6)×10^{-8}  sr^{-1}(f/25  Hz)^{α} depending on Θ and α. Directed searches for narrowband gravitational waves from astrophysically interesting objects (Scorpius X-1, Supernova 1987 A, and the Galactic Center) yield median frequency-dependent limits on strain amplitude of h_{0}<(6.7,5.5,  and  7.0)×10^{-25}, respectively, at the most sensitive detector frequencies between 130-175 Hz. This represents a mean improvement of a factor of 2 across the band compared to previous searches of this kind for these sky locations, considering the different quantities of strain constrained in each case.

Cutaneous manifestations of subcutaneous and systemic fungal infections in tropical regions: a retrospective study from a referral center in southern Taiwan

BACKGROUND

Deep cutaneous fungal infections, including subcutaneous mycoses and systemic fungal infection with cutaneous involvement, cause significant morbidity and mortality in light of increasing immunocompromised patients and global warming. Although a few studies reviewed deep fungal infections in temperate regions, a relevant study in tropical regions is lacking. We evaluated features of deep cutaneous fungal infections in southern Taiwan among the tropical regions.

METHODS

We retrospectively reviewed all histopathological specimens with deep cutaneous fungal infections in a single referral center from 2001 to 2014 and successfully identified 23 cases. Medical chart review revealed patient demographic data, clinical presentation, underlying disease, microbiological culture reports, and treatment outcomes.

RESULTS

The average patient age was 52 years. Fourteen cases had primary subcutaneous mycoses, and nine had systemic mycoses. Fifteen patients were immunocompromised, including hematological malignancies. Acquired immune deficiency syndrome (AIDS) and long-term steroid use were most commonly associated with deep fungal infections. The positive culture growth rate was 63%. Fonsecaea sp. was most frequently identified by tissue culture. Aspergillosis, mucormycosis, and disseminated cryptococcosis were particularly fatal.

CONCLUSIONS

Diabetes and long-term steroid use appear as major risk factors for advanced mycoses in this region. Rapid diagnosis with skin biopsy and tissue culture along with appropriate treatment of deep cutaneous fungal infection are necessary.

Effects of essential oil (blended and single essential oils) on anti-biofilm formation of Salmonella and Escherichia coli

Background

Biofilms were the third-dimensional structure in the solid surface of bacteria. Bacterial biofilms were difficult to control by host defenses and antibiotic therapies. Escherichia coli (E. coli) and Salmonella were popular pathogenic bacteria that live in human and animal intestines. Essential oils are aromatic oily liquids from plant materials and well known for their antibacterial activities.

Method

This study was conducted to determine effect of essential oil on anti-biological biofilm formation of E. coli and Salmonella strains in in vitro experiment. Two kinds of bacterial strains were separated from 0.2 g pig feces. Bacterial strains were distributed in 24 plates per treatment and each plates as a replication. The sample was coated with a Bacterial biofilm formation was.

Result

Photographic result, Escherichia coli (E. coli) and Salmonella bacteria colony surface were thick smooth surface in control. However, colony surface in blended and single essential oil treatment has shown crack surface layer compared with colony surfaces in control.

Conclusion

In conclusion, this study could confirm that essential oils have some interesting effect on anti-biofilm formation of E. coli and Salmonella strains from pig feces.

Successful Management of New-Onset Diabetes Mellitus and Obesity With the Use of Laparoscopic Sleeve Gastrectomy After Kidney Transplantation-A Case Report

In kidney transplantation, obesity is associated with poorer graft survival and patient survival. Bariatric surgery may provide benefit for these patients, not only by inducing weight loss, but also via reduction of diabetes. We report a case of morbid obesity, poorly controlled new-onset diabetes mellitus, and gout after kidney transplantation that was treated with laparoscopic sleeve gastrectomy 3 years after kidney transplantation. After 1 year of follow-up, 76% excessive body weight loss was attained. No complications were noted. The operation also provided total remission of diabetes and gout as well as good graft survival. Based on our experience, laparoscopic sleeve gastrectomy may be a feasible treatment for obese patients after renal transplantation to help resolve obesity and control new-onset diabetes. However, the timing of operation and the long-term potential for graft and patient survivals with this operation require further study.

Gelatin-functionalized mesoporous silica nanoparticles with sustained release properties for intracameral pharmacotherapy of glaucoma

Herein, pilocarpine-loaded gelatin-covered mesoporous silica nanoparticles (denoted as p/GM) were intracamerally administrated into the anterior chamber for the reduction of intraocular pressure (IOP).

Lifetime Increased Risk of Adult Onset Atopic Dermatitis in Adolescent and Adult Patients with Food Allergy

Food allergy can result in life-threatening anaphylaxis. Atopic dermatitis (AD) causes intense itching and impaired quality of life. Previous studies have shown that patients with classical early-onset AD tend to develop food allergy and that 10% of adults with food allergies have concomitant AD. However, it is not known whether late-onset food allergy leads to adult-onset AD, a recently recognized disease entity. Using an initial cohort of one-million subjects, this study retrospectively followed-up 2851 patients with food allergy (age > 12 years) for 14 years and compared them with 11,404 matched controls. While 2.8% (81) of the 2851 food allergy patients developed AD, only 2.0% (227) of the 11,404 controls developed AD. Multivariate regression analysis showed that food allergy patients were more likely to develop AD (adjusted hazard ratio = 2.49, p < 0.0001). Controls had a 1.99% risk of developing AD, while food allergy patients had a significantly higher risk (7.18% and 3.46% for patients with ≥3 and <3 food allergy claims, respectively) of developing adult-onset AD. This is the first study to describe the chronological and dose-dependent associations between food allergy in adolescence and the development of adult-onset AD.

Water as neutral oral contrast agent in abdominopelvic CT: comparing effectiveness with Gastrografin in the same patient

INTRODUCTION

Positive oral contrast is no longer deemed necessary for abdominopelvic computed tomography (CT) scans. Studies have shown water to be an equally effective oral contrast agent. However, to our knowledge no study has compared effectiveness between gastrografin and water in the same patient, which will provide a more objective evaluation of the two oral contrast agents. We aim to make a head-to-head comparison of water as neutral oral contrast (OC) against gastrografin as positive OC for abdominopelvic CT scans in the same patient.

METHODS

A retrospective review of 206 abdominopelvic CT scans of 103 patients was performed. The scans were reviewed in consensus by two blinded radiologists. The ability to visualise each abdominopelvic organ, contrastassociated artefacts and small bowel wall delineation, was qualitatively scored on a 5-point scale. Each patient had two sets of scores, one with water and another with gastrografin as OC. Paired scores from the two OCs were evaluated by Wilcoxon signed rank test to determine any significant difference in performance between the two OCs for visualisation of abdominopelvic anatomy on CT.

RESULTS

There was significantly better delineation of duodenal wall (p<0.001) and overall visualisation of the duodenum (p=0.011) using water as OC compared to gastrografin. No statistically significant differences were demonstrated between water and gastrografin for visualisation of the rest of the abdominopelvic organs, walldelineation of the rest small bowel and contrast-associated artefacts.

CONCLUSIONS

Water can be used in place of gastrografin as oral contrast in abdominopelvic CT without compromising visualization of abdominopelvic organs.

Cumulative arsenic exposure is associated with fungal infections: Two cohort studies based on southwestern and northeastern basins in Taiwan

Long-term arsenic exposure results in atherosclerosis and cancers, along with aberrant immune responses. Animal-based and epidemiological studies indicate that arsenic exposure increases susceptibility to viral and bacterial infections. This study aimed to assess whether arsenic exposure is associated with the development of fungal infection, which is substantially attributed to as a cause of aberrant immunity. Based on two well-established cohorts from two basins in southwestern (SW; high arsenic area) and northeastern (NE; low arsenic area) Taiwan (n=297 and 2738, respectively), the arsenic exposure in well water was estimated using HPLC-ICP-MS. Fungal infections were defined via clinical and mycological assessments (PCR of fungal 18S rRNA) of nail samples. Individuals in SW cohort with cumulative arsenic exposure >10,000μg/L∗years had a higher risk of developing fungal infections (OR=1.57, 95% CI=1.08-1.92) after adjusting for diabetes and occupation. In NE cohort, female sex, alcohol consumption, and chronic kidney diseases were associated with toenail infections. In contrast, fingernail infections (OR=1.33, 95% CI=1.05-1.68) were highly associated with arsenic exposure in a dose-dependent manner. We are the first to report palmar and plantar hyperkeratosis upon low arsenic exposure in 3.9% and 6.7% individuals, respectively. This is the first large-scale study showing arsenic exposure is associated with fungal infections in a dose-dependent manner.

Melt volume flow rate and melt flow rate of kenaf fibre reinforced Floreon/magnesium hydroxide biocomposites

A study of the melt volume flow rate (MVR) and the melt flow rate (MFR) of kenaf fibre (KF) reinforced Floreon (FLO) and magnesium hydroxide (MH) biocomposites under different temperatures (160-180 °C) and weight loadings (2.16, 5, 10 kg) is presented in this paper. FLO has the lowest values of MFR and MVR. The increment of the melt flow properties (MVR and MFR) has been found for KF or MH insertion due to the hydrolytic degradation of the polylactic acid in FLO. Deterioration of the entanglement density at high temperature, shear thinning and wall slip velocity were the possible causes for the higher melt flow properties. Increasing the KF loadings caused the higher melt flow properties while the higher MH contents created stronger bonding for higher macromolecular chain flow resistance, hence lower melt flow properties were recorded. However, the complicated melt flow behaviour of the KF reinforced FLO/MH biocomposites was found in this study. The high probability of KF-KF and KF-MH collisions was expected and there were more collisions for higher fibre and filler loading causing lower melt flow properties.

Progression of Idiopathic Eruptive Macular Pigmentation in a Girl from Childhood to Adolescence: Case Report and Literature Review

A 14-year-old girl developed brownish round macules and patches over the face, trunk, and proximal limbs with extensive progression since she was 7 years old. Electron microscopy examination revealed an increase in the number and maturity of melanosomes in basal and suprabasal keratinocytes, although the number of melanocytes was within the normal range. A diagnosis of idiopathic eruptive macular pigmentation was made. We describe the unusual disease progression of this case of idiopathic eruptive macular pigmentation, which was thought to be self-limited.

Characterization of transient noise in Advanced LIGO relevant to gravitational wave signal GW150914

On September 14, 2015, a gravitational wave signal from a coalescing black hole binary system was observed by the Advanced LIGO detectors. This paper describes the transient noise backgrounds used to determine the significance of the event (designated GW150914) and presents the results of investigations into potential correlated or uncorrelated sources of transient noise in the detectors around the time of the event. The detectors were operating nominally at the time of GW150914. We have ruled out environmental influences and non-Gaussian instrument noise at either LIGO detector as the cause of the observed gravitational wave signal.

Critical role of duplex ultrasonography for the advanced management of a venous malformation

Objectives: Duplex ultrasonography was assessed for its advanced role as a contemporary guide for the safer management of venous malformation (VM) at the lower extremities through a comparison study with matching magnetic resonance imaging (MRI) and/or ascending phlebography findings.

Methods: A retrospective review of 50 patients with a VM in the lower extremities was performed using the duplex scan findings on the initial diagnosis and the subsequent follow-up assessment of the treatment response. The screening findings of deep vein thrombosis (DVT) development following ethanol sclerotherapy on 40 patients were also included. A marginal vein (lateral embryonal) compression test was also performed on 10 patients, who were candidates for a resection preoperatively, in order to assess its value in predicting the response to the subsequent resection. The duplex scan findings were compared with the available ascending phlebography results in 38 patients, and also with the MRI findings available for all 50 patients.

Results: The duplex scan on the 50 patients confirmed the existence of a normal deep vein system in the lower extremities in 43 patients as the true-positive test findings. One false-negative test finding was subsequently confirmed by an angiographic evaluation. The duplex scan also confirmed the absence of a normal deep vein system in four patients as a true-negative test. MRI subsequently confirmed two false-positive findings in one patient, and angiography confirmed two false-positive findings in another (sensitivity − 97.8%, specificity − 66.7%, positive predictive value − 95.6%, and negative predictive value − 80%). Among a total of 40 patients who received ethanol sclerotherapy, the duplex scan identified DVT in three patients, and also screened out properly in 37 patients through a total of 185 ethanol sclerotherapy sessions. The compression test predicted the surgical outcome successfully in the majority (7/8). The duplex scan appears to have comparable reliability to MRI and/or angiography for diagnosing and managing VM.

Conclusions: The duplex scan can provide the critical haemodynamic information of both the deep venous system and VM lesions quite effectively with the cost-effectiveness of a non-invasive test. In particular, the duplex scan is an excellent test for the safe management of VM of the lower extremity, including the early detection of DVT through multi-session ethanol sclerotherapy.

GW151226: Observation of Gravitational Waves from a 22-Solar-Mass Binary Black Hole Coalescence

We report the observation of a gravitational-wave signal produced by the coalescence of two stellar-mass black holes. The signal, GW151226, was observed by the twin detectors of the Laser Interferometer Gravitational-Wave Observatory (LIGO) on December 26, 2015 at 03:38:53 UTC. The signal was initially identified within 70 s by an online matched-filter search targeting binary coalescences. Subsequent off-line analyses recovered GW151226 with a network signal-to-noise ratio of 13 and a significance greater than 5σ. The signal persisted in the LIGO frequency band for approximately 1 s, increasing in frequency and amplitude over about 55 cycles from 35 to 450 Hz, and reached a peak gravitational strain of 3.4_{-0.9}^{+0.7}×10^{-22}. The inferred source-frame initial black hole masses are 14.2_{-3.7}^{+8.3}M_{⊙} and 7.5_{-2.3}^{+2.3}M_{⊙}, and the final black hole mass is 20.8_{-1.7}^{+6.1}M_{⊙}. We find that at least one of the component black holes has spin greater than 0.2. This source is located at a luminosity distance of 440_{-190}^{+180}  Mpc corresponding to a redshift of 0.09_{-0.04}^{+0.03}. All uncertainties define a 90% credible interval. This second gravitational-wave observation provides improved constraints on stellar populations and on deviations from general relativity.