bluuebunny/crossref_metadata_2025 huggingface dataset:
Earthquake source properties from analysis of dynamic ruptures and far-field seismic waves in a damage-breakage model
Authors: Kurzon Ittai , Lyakhovsky Vladimir , Ben-Zion Yehuda
Published: October 2020

We present results on earthquake source properties using simulations of dynamic rupture and radiated seismic waves in a continuum damage-breakage rheological model. The source properties are derived by (1) calculation of source parameters directly from the simulated ruptures and (2) observational processing of the far-field radiated waves. The seismic potency, moment, damage-related source term, rupture velocity and effective rigidity are estimated directly from the simulated sources, while the radiation pattern, dominant frequency, directivity, rupture velocity and seismic potency are calculated through analysis of the radiated waves. The potencies calculated directly from the sources are used to validate those estimated by wave analysis. The effective rigidity at the rupture zone during failure is about four times smaller than that of the intact surrounding rocks. Rupture velocity can be estimated by far-field measurements for sources with unidirectional ruptures with prominent rupture directivity. The dominant frequencies for P and S waves $f_d^S/f_d^P$ reflect clearly the rupture duration and have a ratio in the range 0.87–1.12. Seismic potencies obtained through processing the P or S waves have an overall ±15 per cent difference from the source reference values. The calculated values of the coefficient ${\rm{\kappa }}$, relating rupture length to corner or dominant frequency, have strong dependency on the source geometry. Using a strain-rate dependent ${\rm{\kappa }}$, we obtain much weaker dependencies of strain-drop on the dominant frequencies, $\Delta {\rm{\varepsilon }} \propto {( {{f_d}} )^{3/4}}$, than the classical cube-dependency between stress drop and corner frequency, and corresponding weak dependency of average slip on dominant frequency, ${\rm{\bar{D}}} \propto {( {{f_d}} )^{1/2}}$. The obtained analysis procedure and relations can be used to reduce the uncertainty of source properties derived from far-field seismic waves.
Mitral valve surgery after a failed MitraClip procedure
Authors: Melillo Francesco , Baldetti Luca , Beneduce Alessandro , Agricola Eustachio , Margonato Alberto , Godino Cosmo
Published: October 2020

OBJECTIVES

Among patients undergoing transcatheter mitral valve repair with the MitraClip device, a relevant proportion (2–6%) requires open mitral valve surgery within 1 year after unsuccessful clip implantation. The goal of this review is to pool data from different reports to provide a comprehensive overview of mitral valve surgery outcomes after the MitraClip procedure and estimate in-hospital and follow-up mortality.

METHODS

All published clinical studies reporting on surgical intervention for a failed MitraClip procedure were evaluated for inclusion in this meta-analysis. The primary study outcome was in-hospital mortality. Secondary outcomes were in-hospital adverse events and follow-up mortality. Pooled estimate rates and 95% confidence intervals (CIs) of study outcomes were calculated using a DerSimionian–Laird binary random-effects model. To assess heterogeneity across studies, we used the Cochrane Q statistic to compute I2 values.

RESULTS

Overall, 20 reports were included, comprising 172 patients. Mean age was 70.5 years (95% CI 67.2–73.7 years). The underlying mitral valve disease was functional mitral regurgitation in 50% and degenerative mitral regurgitation in 49% of cases. The indication for surgery was persistent or recurrent mitral regurgitation (grade >2) in 93% of patients, whereas 6% of patients presented with mitral stenosis. At the time of the operation, 80% of patients presented in New York Heart Association functional class III–IV. Despite favourable intraoperative results, in-hospital mortality was 15%. The rate of periprocedural cerebrovascular accidents was 6%. At a mean follow-up of 12 months, all-cause death was 26.5%. Mitral valve replacement was most commonly required because the possibility of valve repair was jeopardized, likely due to severe valve injury after clip implantation.

CONCLUSIONS

Surgical intervention after failed transcatheter mitral valve intervention is burdened by high in-hospital and 1-year mortality, which reflects reflecting the high-risk baseline profile of the patients. Mitral valve replacement is usually required due to leaflet injury.
Solid Ergodicity and Orbit Equivalence Rigidity for Coinduced Actions
Authors: Drimbe Daniel
Published: October 2020

We prove that the solid ergodicity property is stable with respect to taking coinduction for a fairly large class of coinduced action. More precisely, assume that $\Sigma <\Gamma $ are countable groups such that $g\Sigma g^{-1}\cap \Sigma $ is finite for any $g\in \Gamma \setminus \Sigma $. Then any measure preserving action $\Sigma \curvearrowright X_0$ gives rise to a solidly ergodic equivalence relation if and only if the equivalence relation of the associated coinduced action $\Gamma \curvearrowright X$ is solidly ergodic. We also obtain orbit equivalence rigidity for such actions by showing that the orbit equivalence relation of a rigid or compact measure preserving action $\Sigma \curvearrowright X_0$ of a property (T) group is “remembered” by the orbit equivalence relation of $\Gamma \curvearrowright X$.
Influence of Strongyloides stercoralis Coinfection on the Presentation, Pathogenesis, and Outcome of Tuberculous Meningitis
Authors: Donovan Joseph , Tram Trinh Thi Bich , Phu Nguyen Hoan , Hiep Nguyen Thi Thu , Van Vu Thi Thu , Mui Dang Thi Hong , Ny Nguyen Thi Han , Nghia Ho Dang Trung , Hanh Nguyen Ho Hong , Tan Le Van , Thuong Nguyen Thuy Thuong , Thwaites Guy E
Published: October 2020

Background

Helminth infections may modulate the inflammatory response to Mycobacterium tuberculosis and influence disease presentation and outcome. Strongyloides stercoralis is common among populations with high tuberculosis prevalence. Our aim was to determine whether S. stercoralis coinfection influenced clinical presentation, cerebrospinal fluid (CSF) inflammation, and outcome from tuberculous meningitis (TBM).

Methods

From June 2017 to December 2019, 668 Vietnamese adults with TBM, enrolled in the ACT HIV or LAST ACT trials (NCT03092817 and NCT03100786), underwent pretreatment S. stercoralis testing by serology, stool microscopy, and/or stool polymerase chain reaction. Comparisons of pretreatment TBM severity, CSF inflammation (including cytokines), and 3-month clinical end points were performed in groups with or without active S. stercoralis infection.

Results

Overall, 9.4% participants (63 of 668) tested positive for S. stercoralis. Active S. stercoralis infection was significantly associated with reduced pretreatment CSF neutrophil counts (median [interquartile range], 3/μL [0–25/μL] vs 14 /μL [1–83/μL]; P = .04), and with reduced CSF interferon ɣ, interleukin 2, and tumor necrosis factor α concentrations (11.4 vs 56.0 pg/mL [P = .01], 33.1 vs 54.5 pg/mL [P = .03], and 4.5 vs 11.9 pg/mL [P = .02], respectively), compared with uninfected participants. Neurological complications by 3 months were significantly reduced in participants with active S. stercoralis infection compared with uninfected participants (3.8% [1 of 26] vs 30.0% [33 of 110], respectively; P = .01).

Conclusions

S. stercoralis coinfection may modulate the intracerebral inflammatory response to M. tuberculosis and improve TBM clinical outcomes.
Transmission Dynamics and Microevolution of Neisseria meningitidis During Carriage and Invasive Disease in High School Students in Georgia and Maryland, 2006–2007
Authors: Mustapha Mustapha M , Marsh Jane W , Shutt Kathleen A , Schlackman Jessica , Ezeonwuka Chinelo , Farley Monica M , Stephens David S , Wang Xin , Van Tyne Daria , Harrison Lee H
Published: October 2020

Background

The mechanisms by which Neisseria meningitidis cause persistent human carriage and transition from carriage to invasive disease have not been fully elucidated.

Methods

Georgia and Maryland high school students were sampled for pharyngeal carriage of N. meningitidis during the 2006–2007 school year. A total of 321 isolates from 188 carriers and all 67 invasive disease isolates collected during the same time and from the same geographic region underwent whole-genome sequencing. Core-genome multilocus sequence typing was used to compare allelic profiles, and direct read mapping was used to study strain evolution.

Results

Among 188 N. meningitidis culture–positive students, 98 (52.1%) were N. meningitidis culture positive at 2 or 3 samplings. Most students who were positive at >1 sampling (98%) had persistence of a single strain. More than a third of students carried isolates that were highly genetically related to isolates from other students in the same school, and occasional transmission within the same county was also evident. The major pilin subunit gene, pilE, was the most variable gene, and no carrier had identical pilE sequences at different time points.

Conclusion

We found strong evidence of local meningococcal transmission at both the school and county levels. Allelic variation within genes encoding bacterial surface structures, particularly pilE, was common.
Carbapenemase-producing Enterobacterales causing secondary infections during the COVID-19 crisis at a New York City hospital
Authors: Gomez-Simmonds Angela , Annavajhala Medini K , McConville Thomas H , Dietz Donald E , Shoucri Sherif M , Laracy Justin C , Rozenberg Felix D , Nelson Brian , Greendyke William G , Furuya E Yoko , Whittier Susan , Uhlemann Anne-Catrin
Published: October 2020

Background

Patients with COVID-19 may be at increased risk for secondary bacterial infections with MDR pathogens, including carbapenemase-producing Enterobacterales (CPE).

Objectives

We sought to rapidly investigate the clinical characteristics, population structure and mechanisms of resistance of CPE causing secondary infections in patients with COVID-19.

Methods

We retrospectively identified CPE clinical isolates collected from patients testing positive for SARS-CoV-2 between March and April 2020 at our medical centre in New York City. Available isolates underwent nanopore sequencing for rapid genotyping, antibiotic resistance gene detection and phylogenetic analysis.

Results

We identified 31 CPE isolates from 13 patients, including 27 Klebsiella pneumoniae and 4 Enterobacter cloacae complex isolates. Most patients (11/13) had a positive respiratory culture and 7/13 developed bacteraemia; treatment failure was common. Twenty isolates were available for WGS. Most K. pneumoniae (16/17) belonged to ST258 and encoded KPC (15 KPC-2; 1 KPC-3); one ST70 isolate encoded KPC-2. E. cloacae isolates belonged to ST270 and encoded NDM-1. Nanopore sequencing enabled identification of at least four distinct ST258 lineages in COVID-19 patients, which were validated by Illumina sequencing data.

Conclusions

While CPE prevalence has declined substantially in New York City in recent years, increased detection in patients with COVID-19 may signal a re-emergence of these highly resistant pathogens in the wake of the global pandemic. Increased surveillance and antimicrobial stewardship efforts, as well as identification of optimal treatment approaches for CPE, will be needed to mitigate their future impact.
Towards clinical data-driven eligibility criteria optimization for interventional COVID-19 clinical trials
Authors: Kim Jae Hyun , Ta Casey N , Liu Cong , Sung Cynthia , Butler Alex M , Stewart Latoya A , Ena Lyudmila , Rogers James R , Lee Junghwan , Ostropolets Anna , Ryan Patrick B , Liu Hao , Lee Shing M , Elkind Mitchell S V , Weng Chunhua
Published: October 2020

Objective

This research aims to evaluate the impact of eligibility criteria on recruitment and observable clinical outcomes of COVID-19 clinical trials using electronic health record (EHR) data.

Materials and Methods

On June 18, 2020, we identified frequently used eligibility criteria from all the interventional COVID-19 trials in ClinicalTrials.gov (n = 288), including age, pregnancy, oxygen saturation, alanine/aspartate aminotransferase, platelets, and estimated glomerular filtration rate. We applied the frequently used criteria to the EHR data of COVID-19 patients in Columbia University Irving Medical Center (CUIMC) (March 2020–June 2020) and evaluated their impact on patient accrual and the occurrence of a composite endpoint of mechanical ventilation, tracheostomy, and in-hospital death.

Results

There were 3251 patients diagnosed with COVID-19 from the CUIMC EHR included in the analysis. The median follow-up period was 10 days (interquartile range 4–28 days). The composite events occurred in 18.1% (n = 587) of the COVID-19 cohort during the follow-up. In a hypothetical trial with common eligibility criteria, 33.6% (690/2051) were eligible among patients with evaluable data and 22.2% (153/690) had the composite event.

Discussion

By adjusting the thresholds of common eligibility criteria based on the characteristics of COVID-19 patients, we could observe more composite events from fewer patients.

Conclusions

This research demonstrated the potential of using the EHR data of COVID-19 patients to inform the selection of eligibility criteria and their thresholds, supporting data-driven optimization of participant selection towards improved statistical power of COVID-19 trials.
House Fly (Diptera: Muscidae): Biology, Pest Status, Current Management Prospects, and Research Needs
Authors: Geden C J , Nayduch D , Scott J G , Burgess E R , Gerry A C , Kaufman P E , Thomson J , Pickens V , Machtinger E T
Published: October 2020

The house fly, Musca domestica L. (Diptera: Muscidae), is a global pest of humans and animals that carries scores of pathogens and costs up to $1 billion per year in the United States alone. Information is reviewed on recognition, distribution, biology, dispersal, and associations with microbes. Particular challenges of managing flies in different animal systems are discussed for swine, poultry, dairy cattle, beef feedlot, and equine operations. Effective fly management requires diligent monitoring and integration of cultural control, especially manure management, with mechanical control, traps, conservation or augmentative biological control, and judicious use of insecticides. House fly is notorious for developing insecticide resistance and its resistance status is summarized as of August 2020. Several critical research needs are identified. Monitoring systems and nuisance/action thresholds need improvement. Faster-killing strains and better formulations are needed to integrate pathogens into Integrated Pest management (IPM) programs. The use of parasitoids remains an inexact science with many questions remaining about species selection and release rates. New attractants are needed for use in traps and attract-and-infect/kill strategies. Screening of new active ingredients for toxicity should continue, including a rigorous assessment of essential oils and other botanicals. Rising global temperatures may affect the balance of the fly with natural enemies. An understanding of the fly microbiome may reveal unknown vulnerabilities, and much remains to be learned about how flies acquire, retain, and transmit human and animal pathogens. System-specific research is also needed to tailor fly IPM programs to individual animal systems, especially in organic and free-range animal production.
Validity of measuring psoas muscle mass index for assessing sarcopenia in patients with gynecological cancer
Authors: Yamada Ryutaro , Todo Yukiharu , Kurosu Hiroyuki , Minowa Kaoru , Tsuruta Tomohiko , Minobe Shinichiro , Matsumiya Hiroko , Kato Hidenori , Mori Yoichi , Osanai Toshihisa
Published: October 2020

Objective

The current study evaluated the performance of psoas muscle mass measurement for detecting low skeletal muscle mass quantity.

Methods

A sample of 82 consecutive patients with gynecological cancers was examined using computed tomography and dual energy X-ray absorptiometric scan before treatment. Skeletal muscle mass index was measured by dual energy X-ray absorptiometric scan and its cut-off value was set at 5.40 kg/m2 for detecting low skeletal muscle mass. Psoas muscle mass index was manually measured with cross-sectional computed tomography imaging at the level of L3 by six evaluators.

Results

Low skeletal muscle mass index was identified in 23 (28.0%) patients. Two-way analysis of variance confirmed a significant main effect of skeletal muscle mass index on mean psoas muscle mass index values (P < 0.0001). A receiver operating characteristic curve obtained from a total of 492 psoas muscle mass index data points gathered from six evaluators produced an area under the curve value of 0.697 (95% confidence interval 0.649–0.744) and a cut-off value of 3.52 cm2/m2, with sensitivity of 79.0% and specificity of 59.6%. Using the cut-off value, the kappa coefficient for evaluating diagnostic agreement between skeletal muscle mass index (low vs. normal) and psoas muscle mass index (low vs. normal) was 0.308 (95% confidence interval 0.225–0.392), suggesting poor agreement. Fleiss’ kappa produced a coefficient of 0.418 (95% confidence interval 0.362–0.473), suggesting moderate agreement.

Conclusions

Although relevance between skeletal muscle mass index and psoas muscle mass index was confirmed, intensity of relevance between them was weak. Psoas muscle mass index measurement should be subordinated to skeletal muscle mass index measurement for detection of low skeletal muscle mass.
Patient-Reported Outcomes in Clinical Trials Leading to Cancer Immunotherapy Drug Approvals From 2011 to 2018: A Systematic Review
Authors: Safa Houssein , Tamil Monica , Spiess Philippe E , Manley Brandon , Pow-Sang Julio , Gilbert Scott M , Safa Firas , Gonzalez Brian D , Oswald Laura B , Semaan Adele , Diab Adi , Chahoud Jad
Published: October 2020

Background

Patient-reported outcomes (PROs) promote patient centeredness in clinical trials; however, in the field of rapidly emerging and clinically impressive immunotherapy, data on PROs are limited.

Methods

We systematically identified all immunotherapy approvals from 2011 through 2018 and assessed the analytic tools and reporting quality of associated PRO reports. For randomized clinical trials (RCTs), we developed a novel 24-point scoring scale: the PRO Endpoints Analysis Score based on 24 criteria derived from the recommendations of the Setting International Standards in Analyzing Patient-Reported Outcomes and Quality of Life Endpoints Data Consortium.

Results

We assessed 44 trial publications supporting 42 immunotherapy approvals. PROs were published for 21 of the 44 (47.7%) trial publications. Twenty-three trials (52.3%) were RCTs and 21 (47.7%) pertained to single-arm trials. The median time between primary clinical outcomes publications and their corresponding secondary PRO publications was 19 months (interquartile range = 9-29 months). Of the 21 PRO reports, 4 (19.0%) reported a specific hypothesis, and most (85.7%) used descriptive statistics. Three (3 of 21 [14.3%]) studies performed a control for type I error. As for RCTs, 14 of 23 (60.9%) published PRO data, including 13 (56.5%) that published a secondary dedicated manuscript. One-half of these 14 trials scored less than 13 points on the 24-point PRO Endpoints Analysis Score. The mean score was 12.71 (range = 5-17, SD = 3.71), and none met all the recommendations of the Setting International Standards in Analyzing Patient-Reported Outcomes and Quality of Life Endpoints Data Consortium.

Conclusions

Suboptimal reporting of PROs occurs regularly in cancer immunotherapy trials. Increased efforts are needed to maximize the value of these data in cancer immunotherapy development and approval.
PRKCA D463H Mutation in Chordoid Glioma of the Third Ventricle: A Cohort of 16 Cases, Including Two Cases Harboring BRAFV600E Mutation
Authors: Yao Kun , Duan Zejun , Du Zunguo , Fan Xiaolong , Qu Yanming , Zhang Mingshan , Wang Yin , Liu Hailong , Sun Lingyan , Qi Xueling
Published: October 2020

Chordoid gliomas (CG) of the third ventricle are characterized by chordoid and glial features, but the extent of histological variations across CG is not fully understood. Herein, we report 16 consecutive cases of CG. All 16 patients had histories of headache and vision loss; their median age was 41.7 years at the surgery. Histological examination revealed typical features of CG, including cords of epithelioid cells within the mucinous stroma and lymphoplasmacytic infiltration. Two cases exhibited atypical histological features including histiocyte-like cells. PRKCA mutation was found in 14 cases, including the 2 with histiocytic features. BRAFV600E mutation was found only in the 2 cases with histiocytic features. The patients underwent gross total tumor resection without radiotherapy or chemotherapy. Three patients died between 1 and 4 months postsurgery. Only one had a recurrence. Eleven were alive at the most recent follow-up (range: 2–58 months). These data indicate that PRKCA mutation was a good diagnostic marker for CG and additionally suggest that histiocyte-like features can be present in CG in association with BRAF mutations.
On the compressive nature of turbulence driven by ionizing feedback in the pillars of the Carina Nebula
Authors: Menon Shyam H , Federrath Christoph , Klaassen Pamela , Kuiper Rolf , Reiter Megan
Published: October 2020

The ionizing radiation of massive stars sculpts the surrounding neutral gas into pillar-like structures. Direct signatures of star formation through outflows and jets are observed in these structures, typically at their tips. Recent numerical simulations have suggested that this star formation could potentially be triggered by photoionizing radiation, driving compressive modes of turbulence in the pillars. In this study, we use recent high-resolution ALMA observations of 12CO, 13CO, and C18O, J = 2 − 1 emission to test this hypothesis for pillars in the Carina Nebula. We analyse column density and intensity-weighted velocity maps, and subtract any large-scale bulk motions in the plane of the sky to isolate the turbulent motions. We then reconstruct the dominant turbulence driving mode in the pillars, by computing the turbulence driving parameter b, characterized by the relation $\sigma _{\rho /\rho _0} = b \mathcal {M}$ between the standard deviation of the density contrast $\sigma _{\rho /\rho _0}$ (with gas density ρ and its average ρ0) and the turbulent Mach number $\mathcal {M}$. We find values of b ∼ 0.7–1.0 for most of the pillars, suggesting that predominantly compressive modes of turbulence are driven in the pillars by the ionizing radiation from nearby massive stars. We find that this range of b values can produce star formation rates in the pillars that are a factor ∼3 greater than with b ∼ 0.5, a typical average value of b for spiral-arm molecular clouds. Our results provide further evidence for the potential triggering of star formation in pillars through compressive turbulent motions.
Inferring the dark matter velocity anisotropy to the cluster edge
Authors: Svensmark Jacob , Hansen Steen H , Martizzi Davide , Moore Ben , Tessier Romaine
Published: October 2020

Dark matter (DM) dominates the properties of large cosmological structures such as galaxy clusters, and the mass profiles of the DM have been inferred for these equilibrated structures for years by using cluster X-ray surface brightnesses and temperatures. A new method has been proposed, which should allow us to infer a dynamical property of the DM, namely the velocity anisotropy. For the gas, a similar velocity anisotropy is zero due to frequent collisions; however, the collisionless nature of DM allows it to be non-trivial. Numerical simulations have for years found non-zero and radially varying DM velocity anisotropies. Here we employ the method proposed by Hansen & Piffaretti, and developed by Høst et al. to infer the DM velocity anisotropy in the bright galaxy cluster Perseus, to near five times the radii previously obtained. We find the DM velocity anisotropy to be consistent with the results of numerical simulations, however, still with large error bars. At half the virial radius, we find the DM velocity anisotropy to be non-zero at 1.7$\, \sigma$, lending support to the collisionless nature of DM.
Implications of baryon–dark matter interaction on IGM temperature and tSZ effect with magnetic field
Authors: Pandey Arun Kumar , Malik Sunil , Seshadri T R
Published: October 2020

We show that the combined effect of cosmic magnetic field and a possible non-standard interaction between baryons and dark matter (DM) has interesting consequences on the thermal Sunyaev−Zel’dovich (tSZ) effect depending on the temperature and the ionization state of the intergalactic medium. The drag force between the baryons and DM due to the relative velocity between them, and their temperature difference results in heat transfer between these two species. At the same time, the ambipolar diffusion and the decaying magnetic turbulence tends to heat up the baryons. This interplay of these two processes give rise to different evolution histories of the thermal and ionization state of the universe and hence influences the cosmic microwave background (CMB) spectrum at small scales through the tSZ effect. In this work, we have computed the evolution of the temperature, ionization fraction, and the y-parameter of the CMB for different strengths of the magnetic field and the interaction cross-section. We note that the y-parameter can be significantly enhanced with the inclusion of magnetic field and baryon–DM interaction as compared to the case when these are absent. The enhancement depends on the strength of the magnetic field.
Brightest cluster galaxies: the centre can(not?) hold
Authors: De Propris Roberto , West Michael J , Andrade-Santos Felipe , Ragone-Figueroa Cinthia , Rasia Elena , Forman William , Jones Christine , Kipper Rain , Borgani Stefano , Lambas Diego García , Romashkova Elena A , Patra Kishore C
Published: October 2020

We explore the persistence of the alignment of brightest cluster galaxies (BCGs) with their local environment. We find that a significant fraction of BCGs do not coincide with the centroid of the X-ray gas distribution and/or show peculiar velocities (they are not at rest with respect to the cluster mean). Despite this, we find that BCGs are generally aligned with the cluster mass distribution even when they have significant offsets from the X-ray centre and significant peculiar velocities. The large offsets are not consistent with simple theoretical models. To account for these observations BCGs must undergo mergers preferentially along their major axis, the main infall direction. Such BCGs may be oscillating within the cluster potential after having been displaced by mergers or collisions, or the dark matter halo itself may not yet be relaxed.
A new estimator of resolved molecular gas in nearby galaxies
Authors: Chown Ryan , Li Cheng , Parker Laura , Wilson Christine D , Li Niu , Gao Yang
Published: October 2020

A relationship between dust-reprocessed light from recent star formation and the amount of star-forming gas in a galaxy produces a correlation between Wide-field Infrared Survey Explorer (WISE) 12 μm emission and CO line emission. Here, we explore this correlation on kiloparsec scales with CO(1–0) maps from EDGE–CALIFA matched in resolution to WISE 12 μm images. We find strong CO-12 μm correlations within each galaxy and we show that the scatter in the global CO-12 μm correlation is largely driven by differences from galaxy to galaxy. The correlation is stronger than that between star formation rate and H2 surface densities [Σ(H2)]. We explore multivariable regression to predict Σ(H2) in star-forming pixels using the WISE 12 μm data combined with global and resolved galaxy properties, and provide the fit parameters for the best estimators. We find that Σ(H2) estimators that include $\Sigma (\mathrm{12\:\mu m})$ are able to predict Σ(H2) more accurately than estimators that include resolved optical properties instead of $\Sigma (\mathrm{12\:\mu m})$. These results suggest that 12 μm emission and H2 as traced by CO emission are physically connected at kiloparsec scales. This may be due to a connection between polycyclic aromatic hydrocarbon emission and the presence of H2. The best single-property estimator is $\log \frac{\Sigma (\mathrm{H_2})}{\mathrm{M_\odot \:pc^{-2}}} = (0.48 \pm 0.01) + (0.71 \pm 0.01)\log \frac{\Sigma (\mathrm{12\:\mu m})}{\mathrm{L_\odot \:pc^{-2}}}$. This correlation can be used to efficiently estimate Σ(H2) down to at least 1 M⊙ pc−2 in star-forming regions within nearby galaxies.
Stellar velocity dispersion and dynamical mass of the ultra diffuse galaxy NGC 5846_UDG1 from the keck cosmic web imager
Authors: Forbes Duncan A , Gannon Jonah S , Romanowsky Aaron J , Alabi Adebusola , Brodie Jean P , Couch Warrick J , Ferré-Mateu Anna
Published: October 2020

The ultra diffuse galaxy in the NGC 5846 group (NGC 5846_UDG1) was shown to have a large number of globular cluster (GC) candidates from deep imaging as part of the VEGAS survey. Recently, Müller et al. published a velocity dispersion, based on a dozen of its GCs. Within their quoted uncertainties, the resulting dynamical mass allowed for either a dark matter free or a dark-matter-dominated galaxy. Here, we present spectra from KCWI that reconfirms membership of the NGC 5846 group and reveals a stellar velocity dispersion for UDG1 of σGC = 17 ± 2 km s−1. Our dynamical mass, with a reduced uncertainty, indicates a very high contribution of dark matter within the effective radius. We also derive an enclosed mass from the locations and motions of the GCs using the tracer mass estimator, finding a similar mass inferred from our stellar velocity dispersion. We find no evidence that the galaxy is rotating and is thus likely pressure supported. The number of confirmed GCs, and the total number inferred for the system (∼45), suggests a total halo mass of ∼2 × 1011 M⊙. A cored mass profile is favoured when compared to our dynamical mass. Given its stellar mass of 1.1 × 108 M⊙, NGC 5846_UDG1 appears to be an ultra diffuse galaxy with a dwarf-like stellar mass and an overly massive halo.
DAYENU: a simple filter of smooth foregrounds for intensity mapping power spectra
Authors: Ewall-Wice Aaron , Kern Nicholas , Dillon Joshua S , Liu Adrian , Parsons Aaron , Singh Saurabh , Lanman Adam , Plante Paul La , Fagnoni Nicolas , Acedo Eloy de Lera , DeBoer David R , Nunhokee Chuneeta , Bull Philip , Chang Tzu-Ching , Lazio T Joseph W , Aguirre James , Weinberg Sean
Published: October 2020

We introduce DPSS Approximate lazY filtEriNg of foregroUnds (dayenu), a linear, spectral filter for H i intensity mapping that achieves the desirable foreground mitigation and error minimization properties of inverse co-variance weighting with minimal modelling of the underlying data. Beyond 21-cm power-spectrum estimation, our filter is suitable for any analysis where high dynamic-range removal of spectrally smooth foregrounds in irregularly (or regularly) sampled data is required, something required by many other intensity mapping techniques. Our filtering matrix is diagonalized by Discrete Prolate Spheroidal Sequences which are an optimal basis to model band-limited foregrounds in 21-cm intensity mapping experiments in the sense that they maximally concentrate power within a finite region of Fourier space. We show that dayenu enables the access of large-scale line-of-sight modes that are inaccessible to tapered discrete Fourier transform estimators. Since these modes have the largest SNRs,dayenu significantly increases the sensitivity of 21-cm analyses over tapered Fourier transforms. Slight modifications allow us to use dayenu as a linear replacement for iterative delay clean ing (dayenurest). We refer readers to the Code section at the end of this paper for links to examples and code.
AtMAD: Arabidopsis thaliana multi-omics association database
Authors: Lan Yiheng , Sun Ruikun , Ouyang Jian , Ding Wubing , Kim Min-Jun , Wu Jun , Li Yuhua , Shi Tieliu
Published: October 2020

Integration analysis of multi-omics data provides a comprehensive landscape for understanding biological systems and mechanisms. The abundance of high-quality multi-omics data (genomics, transcriptomics, methylomics and phenomics) for the model organism Arabidopsis thaliana enables scientists to study the genetic mechanism of many biological processes. However, no resource is available to provide comprehensive and systematic multi-omics associations for Arabidopsis. Here, we developed an Arabidopsis thaliana Multi-omics Association Database (AtMAD, http://www.megabionet.org/atmad), a public repository for large-scale measurements of associations between genome, transcriptome, methylome, pathway and phenotype in Arabidopsis, designed for facilitating identification of eQTL, emQTL, Pathway-mQTL, Phenotype-pathway, GWAS, TWAS and EWAS. Candidate variants/methylations/genes were identified in AtMAD for specific phenotypes or biological processes, many of them are supported by experimental evidence. Based on the multi-omics association strategy, we have identified 11 796 cis-eQTLs and 10 119 trans-eQTLs. Among them, 68 837 environment-eQTL associations and 149 622 GWAS-eQTL associations were identified and stored in AtMAD. For expression–methylation quantitative trait loci (emQTL), we identified 265 776 emQTLs and 122 344 pathway-mQTLs. For TWAS and EWAS, we obtained 62 754 significant phenotype-gene associations and 3 993 379 significant phenotype-methylation associations, respectively. Overall, the multi-omics associated network in AtMAD will provide new insights into exploring biological mechanisms of plants at multi-omics levels.
RJunBase: a database of RNA splice junctions in human normal and cancerous tissues
Authors: Li Qin , Lai Hongyan , Li Yuchen , Chen Bing , Chen Siyuan , Li Yan , Huang Zhaohui , Meng Zhiqiang , Wang Peng , Hu Zhixiang , Huang Shenglin
Published: October 2020

Splicing is an essential step of RNA processing for multi-exon genes, in which introns are removed from a precursor RNA, thereby producing mature RNAs containing splice junctions. Here, we develope the RJunBase (www.RJunBase.org), a web-accessible database of three types of RNA splice junctions (linear, back-splice, and fusion junctions) that are derived from RNA-seq data of non-cancerous and cancerous tissues. The RJunBase aims to integrate and characterize all RNA splice junctions of both healthy or pathological human cells and tissues. This new database facilitates the visualization of the gene-level splicing pattern and the junction-level expression profile, as well as the demonstration of unannotated and tumor-specific junctions. The first release of RJunBase contains 682 017 linear junctions, 225 949 back-splice junctions and 34 733 fusion junctions across 18 084 non-cancerous and 11 540 cancerous samples. RJunBase can aid researchers in discovering new splicing-associated targets and provide insights into the identification and assessment of potential neoepitopes for cancer treatment.
Biophysical analysis ofPseudomonas-phage PaP3 small terminase suggests a mechanism for sequence-specific DNA-binding by lateral interdigitation
Authors: Niazi Marzia , Florio Tyler J , Yang Ruoyu , Lokareddy Ravi K , Swanson Nicholas A , Gillilan Richard E , Cingolani Gino
Published: October 2020

The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.
Relationship between measured and prescribed dialysate sodium in haemodialysis: a systematic review and meta-analysis
Authors: Ng Jack Kit-Chung , Smyth , Brendan , Marshall , Mark R , Kang , Amy , Pinter , Jule , Bassi , Abhinav , Krishnasamy , Rathika , Rossignol , Patrick , Rocco , Michael V , Li , Zuo , Jha , Vivekanand , Hawley Carmel M , Kerr , Peter G , DI Tanna , Gian Luca , Woodward , Mark , Jardine and Meg ,   The RESOLVE Steering Committee
Published: October 2020

Background

Dialysate sodium (DNa) prescription policy differs between haemodialysis (HD) units, and the optimal DNa remains uncertain. We sought to summarize the evidence on the agreement between prescribed and delivered DNa, and whether the relationship varied according to prescribed DNa.

Methods

We searched MEDLINE and PubMed from inception to 26 February 2020 for studies reporting measured and prescribed DNa. We analysed results reported in aggregate with random-effects meta-analysis. We analysed results reported by individual sample, using mixed-effects Bland–Altman analysis and linear regression. Pre-specified subgroup analyses included method of sodium measurement, dialysis machine manufacturer and proportioning method.

Results

Seven studies, representing 908 dialysate samples from 10 HD facilities (range 16–133 samples), were identified. All but one were single-centre studies. Studies were of low to moderate quality. Overall, there was no statistically significant difference between measured and prescribed DNa {mean difference = 0.73 mmol/L [95% confidence interval (CI) −1.12 to 2.58; P = 0.44]} but variability across studies was substantial (I2 = 99.3%). Among individually reported samples (n = 295), measured DNa was higher than prescribed DNa by 1.96 mmol/L (95% CI 0.23–3.69) and the 95% limits of agreement ranged from −3.97 to 7.88 mmol/L. Regression analysis confirmed a strong relationship between prescribed and measured DNa, with a slope close to 1:1 (β = 1.16, 95% CI 1.06–1.27; P < 0.0001).

Conclusions

A limited number of studies suggest that, on average, prescribed and measured DNa are similar. However, between- and within-study differences were large. Further consideration of the precision of delivered DNa is required to inform rational prescribing.
Postacute COVID-19: An Overview and Approach to Classification
Authors: Amenta Eva M , Spallone Amy , Rodriguez-Barradas Maria C , El Sahly Hana M , Atmar Robert L , Kulkarni Prathit A
Published: October 2020

As the coronavirus disease 2019 (COVID-19) pandemic has progressed, a large volume of literature has developed delineating the clinical manifestations of acute infection. Recent reports have also started to describe persistent symptoms extending beyond the period of initial illness or hospitalization. Anecdotes of different signs and symptoms occurring after acute infection have also arisen in the lay press. Here we describe the current existing medical literature on the emerging concept of postacute COVID-19 and suggest an approach to classifying different manifestations of the syndrome. We also review long-term clinical manifestations observed in patients who recovered from infection due to other epidemic coronaviruses and briefly discuss potential mechanisms driving the phenomenon of postacute COVID-19.
Ethics and Natural Philosophy in Empedocles
Authors: Palmer John
Published: October 2020

“Ethics and Natural Philosophy in Empedocles” demonstrates how the broad features of Plato’s naturalistic ethics are prefigured in the integration of ethics and natural philosophy in Empedocles, while at the same time emphasizing the distinctive features of Empedocles’ conception. Empedocles’ doctrine of metempsychosis, the basis for a universal prohibition against killing other living creatures and consequent imperatives for self-purification, is itself grounded in the more general idea at the heart of his cosmology that no mortal thing is either born from, or passes away into, total nothingness. The chapter explores the deep connection between the birth, destruction, and rebirth of the elements and the wandering of the daimones or spirits, with whom Empedocles identifies his reincarnated self, all of which are subject to the lamentable influence of cosmic Strife as well as the more positive influence of cosmic Love that he advocates.
Volume of Line Bundles via Valuation Vectors (Different from Okounkov Bodies)
Authors: Braunling O
Published: October 2020

Up to a factor 1/n!, the volume of a big line bundle agrees with the Euclidean volume of its Okounkov body. The latter is the convex hull of top rank valuation vectors of sections, all with respect to a single flag. In this paper, we give a new volume formula, valid in the ample cone. It is also based on top rank valuation vectors, but mixes data coming from several different flags.
Anakinra for colchicine refractory familial Mediterranean fever: a cohort of 44 patients
Authors: Marko Limor , Shemer Asaf , Lidar Merav , Grossman Chagai , Druyan Amit , Livneh Avi , Kivity Shaye
Published: October 2020

Objective

FMF is an autoinflammatory disease of genetic origin. Colchicine is the mainstay of treatment for the prevention of attacks and long-term complications but 5–10% of FMF patients are resistant to colchicine therapy. The aim of our study was to investigate the real-life safety and efficacy of anakinra in a cohort of patients with colchicine-resistant FMF.

Methods

In this retrospective study, patients treated with anakinra for colchicine-resistant FMF between 2010 and 2018 were identified using the computerized database of Sheba Medical Center and enrolled in the study. Data from structured clinical files were analysed to evaluate the efficacy and safety outcomes. To assess efficacy, we used the Global Assessment Score (GAS), a measure comprised of three different domains: number of attacks per month, duration of attacks and number of sites involved in the attacks. Reported adverse events were compiled.

Results

A total of 44 patients (24 female) were treated with anakinra. Of these patients, 75% were homozygous for the M649V mutation. The mean duration of treatment was 18 months. The GAS decreased significantly from 6.6 (IQR 5.3–7.8) before treatment to 2 (IQR 0–4.2) while on treatment (P < 0.001). During anakinra treatment, six hospitalizations were reported (three due to related adverse effects). In addition, 11 patients suffered from injection site reactions (5 ceased treatment). Twelve patients reported mild side effects.

Conclusion

Treatment with anakinra is beneficial for the majority of colchicine-resistant FMF patients and is relatively safe.
A framework for open policy analysis
Authors: Hoces de la Guardia Fernando , Grant Sean , Miguel Edward
Published: October 2020

The evidence-based policy movement promotes the use of empirical evidence to inform policy decision-making. While several social science disciplines are undergoing a ‘credibility revolution’ focused on openness and replication, policy analysis has yet to systematically embrace transparency and reproducibility. We argue that policy analysis should adopt the open research practices increasingly espoused in related disciplines to advance the credibility of evidence-based policy making. We first discuss the importance of evidence-based policy in an era of increasing disagreement about facts, analysis, and expertise. We present a novel framework for ‘open’ policy analysis (OPA) and how to achieve it, focusing on examples of recent policy analyses that have incorporated open research practices such as transparent reporting, open data, and code sharing. We conclude with recommendations on how key stakeholders in evidence-based policy can make OPA the norm and thus safeguard trust in using empirical evidence to inform important public policy decisions.
A multicentric knowledge-attitude-practice survey in the community about antimicrobial use and resistance in India
Authors: Chatterjee Suparna , Hazra Avijit , Chakraverty Raja , Shafiq Nusrat , Pathak Ashish , Trivedi Niyati , Sadasivam Balakrishnan , Kakkar Ashish Kumar , Jhaj Ratinder , Kaul Rajni , Kshirsagar Nilima
Published: October 2020

Background

To address the reasons for inappropriate use of antimicrobials, it is important to understand the knowledge, attitude and practices (KAP) of all pertinent stakeholders. This multicentric survey is aimed at understanding the KAP quotients of the community regarding antimicrobial use and antimicrobial resistance (AMR), as such information is lacking in India.

Methods

A cross-sectional survey was conducted by face-to-face interviews across five centers in India using a validated, field-tested questionnaire incorporating KAP domain questions. Scores were appropriately assigned to the questions.

Results

The mean (SD) age of the respondents was 35.2 (12.61) y and 62% had a graduate or higher level of education. The median (IQR) KAP scores were 10 (8–12), 5 (3–5) and 2 (2–3) out of a maximum of 18, 5 and 6, respectively. Higher educational and socioeconomic levels were associated with better attitude scores, but knowledge levels were comparable. Correlations between KAP scores were poor.

Conclusions

This study reveals that laypeople have appropriate knowledge and attitude regarding antibiotic use and AMR to some degree but there are important lacunae and practices are often wanting. These issues need to be addressed in sustained public awareness and motivation campaigns to improve the rational use of antibiotics in India.
Recognizing and treating autosomal dominant polycystic kidney disease
Authors: Uko Chigozie G.
Published: October 2020

Autosomal dominant polycystic kidney disease causes chronic kidney disease and end-stage renal disease. Mechanisms include cyst production, multiplication, and enlargement leading to increased kidney size, and ultimately kidney failure. Although there is no known cure, NPs are uniquely positioned to help patients manage their symptoms and delay onset of kidney failure and need for dialysis.
A 3-way Cross-over Study of Pregabalin, Placebo, and the Histamine 3 Receptor Inverse Agonist AZD5213 in Combination With Pregabalin in Patients With Painful Diabetic Neuropathy and Good Pain-reporting Ability
Authors: Alexander Robert C. , Raudibaugh Karen , Spierings Egilius L.H. , Katz Nathaniel
Published: October 2020

Objectives:

In this study, patients with painful diabetic neuropathy were trained using an experimental pain paradigm in an attempt to enroll a subset of patients who are “pain connoisseurs” and therefore more able to discriminate between active and placebo treatments.

Methods:

AZD5213, a novel histamine H3 receptor inverse agonist+pregabalin, pregabalin, and placebo were then tested in a 3-period cross-over.

Results:

The study did not provide any evidence of clinical efficacy for AZD5213 when combined with pregabalin in the treatment of painful diabetic neuropathy.

Discussion:

The training of study patients in pain reporting and subsequent enrichment with good pain reporters also did not enable the robust detection of the efficacy of pregabalin relative to placebo in a small sample size. Further work is required before recommending the use of “connoisseur” patients in future neuropathic pain studies.