bluuebunny/crossref_metadata_2025 huggingface dataset:
Factors Associated With Candida auris Colonization and Transmission in Skilled Nursing Facilities With Ventilator Units, New York, 2016–2018
Authors: Rossow John , Ostrowsky Belinda , Adams Eleanor , Greenko Jane , McDonald Robert , Vallabhaneni Snigdha , Forsberg Kaitlin , Perez Stephen , Lucas Todd , Alroy Karen A , Jacobs Slifka Kara , Walters Maroya , Jackson Brendan R , Quinn Monica , Chaturvedi Sudha , Blog Debra ,   New York Candida auris Investigation Workgroup, Southwick Karen , Denis Ronald Jean , Erazo Richard , Fernandez Rafael , Bucher Coralie , Leach Lynn , Zhu Yan , Lutterloh Emily
Published: September 2020

Background

Candida auris is an emerging, multidrug-resistant yeast that spreads in healthcare settings. People colonized with C. auris can transmit this pathogen and are at risk for invasive infections. New York State (NYS) has the largest US burden (>500 colonized and infected people); many colonized individuals are mechanically ventilated or have tracheostomy, and are residents of ventilator-capable skilled nursing facilities (vSNF). We evaluated the factors associated with C. auris colonization among vSNF residents to inform prevention interventions.

Methods

During 2016–2018, the NYS Department of Health conducted point prevalence surveys (PPS) to detect C. auris colonization among residents of vSNFs. In a case-control investigation, we defined a case as C. auris colonization in a resident, and identified up to 4 residents with negative swabs during the same PPS as controls. We abstracted data from medical records on patient facility transfers, antimicrobial use, and medical history.

Results

We included 60 cases and 218 controls identified from 6 vSNFs. After controlling for potential confounders, the following characteristics were associated with C. auris colonization: being on a ventilator (adjusted odds ratio [aOR], 5.9; 95% confidence interval [CI], 2.3–15.4), receiving carbapenem antibiotics in the prior 90 days (aOR, 3.5; 95% CI, 1.6–7.6), having ≥1 acute care hospital visit in the prior 6 months (aOR, 4.2; 95% CI, 1.9–9.6), and receiving systemic fluconazole in the prior 90 days (aOR, 6.0; 95% CI, 1.6–22.6).

Conclusions

Targeted screening of patients in vSNFs with the above risk factors for C. auris can help identify colonized patients and facilitate the implementation of infection control measures. Antimicrobial stewardship may be an important factor in the prevention of C. auris colonization.
Population Trends of the Sugarcane Borer (Lepidoptera: Crambidae) in Louisiana Sugarcane
Authors: Wilson B E , White W H , Richard R T , Johnson R M
Published: September 2020

The sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), is the primary pest of sugarcane, Saccharum spp., in Louisiana. Spring populations are not considered economically damaging, but quantifying infestations can provide an indication of the spatial and temporal character of the damaging summer populations. Statewide surveys quantified the density of sugarcane tillers killed by D. saccharalis (deadhearts) from sugarcane fields across the state in spring from 2003 to 2020. Deadheart density varied greatly among years with a high of 1,318/ha in 2003 to a low of 0/ha in 2018. Linear regressions of the 3-yr rolling average showed declines in spring D. saccharalis populations and the percentage of acreage treated with insecticides over 17 yr. Weather factors including minimum winter temperatures and average spring temperatures were poor predictors of D. saccharalis populations. Only total precipitation in the month of April was positively correlated with numbers of deadhearts per hectare. Results suggest overwintering mortality is not a key factor influencing populations of the first generation of D. saccharalis in Louisiana. Total precipitation in the month of July was positively associated with percentage of treated acreage. Spring deadheart density was directly related to percentage of acreage treated with insecticides during the summer. Quantifying first-generation D. saccharalis populations by recording deadheart density can aid in predicting pest pressure later in the growing season.
Extracorporeal life support rewarming rate is associated with survival with good neurological outcome in accidental hypothermia
Authors: Saczkowski Richard , Kuzak Nick , Grunau Brian , Schulze Costas
Published: September 2020

OBJECTIVES

Favourable outcomes have been demonstrated after extracorporeal life support (ECLS) facilitated rewarming for severe accidental hypothermia. The clinical impact of varying rewarming rates however is unclear. We sought to quantify the change in the probability of good neurological outcome with ECLS rewarming rate and identify the optimal rewarming rate threshold.

METHODS

We performed a secondary analysis of the International ACcidental Hypothermia Extracorporeal Life Support Collaborators, an individual patient data data set (n = 658) for ECLS-assisted rewarming for accidental hypothermia. The independent variable of interest was rewarming rate. The primary outcome was survival with good neurological status. We applied an adjusted marginal effects model to quantify the probability of good neurological outcome over clinically observed rewarming rates. We examined strata defined by sex, initial potassium level and history of asphyxiation.

RESULTS

Of 658 cases, the median age and initial core temperature were 36 years (22–55) and 24.5°C (22.1–26.2) respectively; 190 (29%) were female, and 547 (83%) had a non-perfusing initial cardiac rhythm. The mean rewarming rate was 7.0°C/h. The median ECLS duration was 5.8 h (range: 0.5–158 h). The overall survival was 46% (n = 303/658), and good neurological outcome was 40% (n = 265/658). The median intensive care unit and hospital length of stay was 5 days (range: 1–35 days) and 18 days (range: 1–106 days), respectively. Marginal effects analysis demonstrated a 1.9% decrease in the probability of survival with good neurological outcome for each 1°C/h increase in rewarming. Across the reported range of rewarming rates (0.05–30.8°C/h), the probability of good neurological outcome declined from 49.6% to 4.1% for an average patient. The relationship was similar within various subgroups. The optimal cut-off threshold for the rate of rewarming to distinguish between a good and poor neurological outcome was ≤5.0°C/h.

CONCLUSIONS

Among cases with severe accidental hypothermia treated with ECLS, slower rewarming rates are associated with improved survival with good neurological outcomes. Slow rewarming, at rates ≤5.0°C/h, may improve clinical outcomes.
Interdisciplinary management of acute ischaemic stroke: Current evidence training requirements for endovascular stroke treatment: Position Paper from the ESC Council on Stroke and the European Association for Percutaneous Cardiovascular Interventions with the support of the European Board of Neurointervention
Authors: Nardai Sandor , Lanzer Peter , Abelson Mark , Baumbach Andreas , Doehner Wolfram , Hopkins L Nelson , Kovac Jan , Meuwissen Martijn , Roffi Marco , Sievert Horst , Skrypnik Dmitry , Sulzenko Jakub , van Zwam Wim , Gruber Andreas , Ribo Marc , Cognard Christophe , Szikora Istvan , Flodmark Olof , Widimsky Petr
Published: September 2020

This ESC Council on Stroke/EAPCI/EBNI position paper summarizes recommendations for training of cardiologists in endovascular treatment of acute ischaemic stroke. Interventional cardiologists adequately trained to perform endovascular stroke interventions could complement stroke teams to provide the 24/7 on call duty and thus to increase timely access of stroke patients to endovascular treatment. The training requirements for interventional cardiologists to perform endovascular therapy are described in details and should be based on two main principles: (i) patient safety cannot be compromised, (ii) proper training of interventional cardiologists should be under supervision of and guaranteed by a qualified neurointerventionist and within the setting of a stroke team. Interdisciplinary cooperation based on common standards and professional consensus is the key to the quality improvement in stroke treatment.
Anatomical-based percutaneous left stellate ganglion block in patients with drug-refractory electrical storm and structural heart disease: a single-centre case series
Authors: Savastano Simone , Dusi Veronica , Baldi Enrico , Rordorf Roberto , Sanzo Antonio , Camporotondo Rita , Fracchia Rosa , Compagnoni Sara , Frigerio Laura , Oltrona Visconti Luigi , De Ferrari Gaetano Maria
Published: September 2020

Aims

The adoption of percutaneous stellate ganglion blockade for the treatment of drug-refractory electrical storm (ES) has been increasingly reported; however, the time of onset of the anti-arrhythmic effects, the safety of a purely anatomical approach in conscious patients and the additional benefit of repeated procedures remain unclear.

Methods and results

This study included consecutive patients undergoing percutaneous left stellate ganglion blockade (PLSGB) in our centre for drug-refractory ES. Lidocaine, bupivacaine, or a combination of both were injected in the vicinity of the left stellate ganglion. Overall, 18 PLSGBs were performed in 11 patients (age 69 ± 13 years; 63.6% men, left ventricular ejection fraction 31.6 ± 16%). Seven patients received only one PLSGB; three underwent two procedures and one required three PLSGB and two continuous infusions to control ventricular arrhythmias (VAs). All PLSGBs were performed with an anatomical approach; lidocaine, alone, or in combination was used in 77.7% of the procedures. The median burden of VAs 1 h after each block was zero compared with five in the hour before (P < 0.001); 83% of the patients were free from VAs; the efficacy at 24 h increased with repeated blocks. The anti-arrhythmic efficacy of PLSGB was not related to anisocoria. No procedure-related complications were reported.

Conclusion

Anatomical-based PLSGB is a safe and rapidly effective treatment for refractory ES; repeated blocks provide additional benefits. Percutaneous left stellate ganglion blockade should be considered for stabilizing patients to allow further ES management.
Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome
Authors: Kinnunen-Grubb Marta , Sapkota Rumakanta , Vignola Marta , Nunes Inês Marques , Nicolaisen Mogens
Published: September 2020

Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history.
Network Modeling of Assisted Living Facility Residents’ Attendance at Programmed Group Activities: Proximity and Social Contextual Correlates of Attendance
Authors: Mauldin Rebecca L , Wong Carin , Fernandez Jason , Fujimoto Kayo
Published: September 2020

Background and Objectives

Social engagement, including participation in group activities, supports older adults’ mental and physical health. However, many residents of assisted living facilities do not participate in their facility’s programmed group activities. Explaining residents’ attendance at group activities is complex; attendance is associated with a confluence of individual-level and contextual factors. The aim of this study was to assess the effects of multilevel factors on attendance, including residents’ proximity to activity location and the potential for one resident’s attendance to depend on other residents’ attendance.

Research Design and Methods

We used bipartite exponential random graph models to examine the attendance of 35 residents at 563 programmed group activities. We simultaneously modeled the effects of the geospatial distance from a resident’s apartment to the activity and the tendency for residents to attend activities with similar groups of other residents (i.e., shared attendance) on the likelihood of attendance, while controlling for individual-level factors (demographic and health indicators) and activity popularity.

Results

Greater distance was associated with a reduced likelihood of attendance (p < .001) and residents tended to attend activities with similar subsets of other residents (p < .001).

Discussion and Implications

Findings suggest that greater distance to group activities may be a barrier to attendance. Implications include facility design, placement of activities and apartments, and mobility-related strategies to increase activity participation. It is also important to recognize that participation in activities is dependent on social context. We recommend that proximity to activities and social contextual factors be considered in future examinations of attendance at group activities.
Construction of a chromosome-scale long-read reference genome assembly for potato
Authors: Pham Gina M , Hamilton John P , Wood Joshua C , Burke Joseph T , Zhao Hainan , Vaillancourt Brieanne , Ou Shujun , Jiang Jiming , Buell C Robin
Published: September 2020

Background

Worldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1–3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short-read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at minimal cost.

Findings

Here, we present an updated version of the DM1–3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes.

Conclusions

Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.
Time-lapse CSEM: how important is survey repeatability?
Authors: Shantsev Daniil V , Nerland Elias A , Gelius Leiv-J
Published: September 2020

An important concern for time-lapse studies using the controlled-source electromagnetic (CSEM) method is repeatability of acquisition parameters for the base and monitoring surveys. We consider a challenging case when variations in source and receiver positions, conductivity of seawater, etc. will lead to differences in the recorded EM fields that exceed EM response due to production-induced changes in the reservoir resistivity. We show that even in that case, 4-D response can often be clearly resolved if the base and monitor EM data sets are inverted to produce 3-D resistivity distributions. More precisely, for a synthetic model of the Snøhvit gas field, changes in the inverted resistivity maps caused by such non-repeatability will be at least 10 times smaller than the time-lapse differences in the reservoir resistivity. By contrast, measurement errors and poor knowledge of background resistivity may reduce the resolution of 4-D CSEM to a much stronger degree. Analysis of field CSEM data from the Wisting oil field supports our conclusion about strongly relaxed repeatability requirements when 4-D effects are established by examining inverted resistivity volumes rather than by looking at raw EM data.
Application of the theory of planned behavior to predict smoking intentions: cross-cultural comparison of Kenyan and American young adults
Authors: Lu Yu , Shin YoungJu , Gitau Mary W , Njoroge Margaret W , Gitau Peter , Temple Jeff R
Published: September 2020

Despite well-established research on the applications of the theory of planned behavior (TPB) in the American culture, TPB has not been fully tested in the Kenyan culture. This study compared the applications of TPB in predicting smoking intentions (i.e., future and weekend smoking intentions) of Kenyan and American young adults. Data were collected from 252 Kenyans and 227 Americans. The Kenyan participants consisted of 41.7% females with a mean age of 25 years (SD = 4.81). The American participants (49.3% females) had an average age of 19 years (SD = 1.30). Multi-group path analysis was performed to test the equivalence of a TPB-based mediation model in Kenyans and Americans. Significant differences of TPB application were detected. In the American model, smoking consequence beliefs were indirectly associated with smoking intentions through attitudes whereas neither direct nor indirect effects of smoking consequence beliefs were detected in the Kenyan model. Instead, normative beliefs indirectly associated with future and weekend smoking intentions through attitudes and subjective norms in the Kenyan model. Despite some overlapping paths, there were cultural variations on specific associations among TPB constructs between Kenyans and Americans. Cultural adaptations may be needed when applying TPB in the Kenyan cultural context.
Safety of Ustekinumab in Inflammatory Bowel Disease: Pooled Safety Analysis of Results from Phase 2/3 Studies
Authors: Sandborn William J , Feagan Brian G , Danese Silvio , O’Brien Christopher D , Ott Elyssa , Marano Colleen , Baker Thomas , Zhou Yiying , Volger Sheri , Tikhonov Ilia , Gasink Christopher , Sands Bruce E , Ghosh Subrata
Published: September 2020

Background

Ustekinumab is currently approved globally in Crohn’s disease (CD) and psoriatic diseases. Recent phase 3 data demonstrate safety/efficacy in ulcerative colitis (UC). Crohn’s disease and UC phase 3 programs had similar study designs, facilitating integrated safety analyses.

Methods

Data from 6 ustekinumab phase 2/3 CD and UC studies were pooled, and safety was evaluated through 1 year. Patients received 1 placebo or ustekinumab (generally 130 mg or ~6 mg/kg) intravenous induction, then subcutaneous (90 mg) maintenance every 8/12 weeks. Analyses incorporated all patients who received ≥1 ustekinumab dose. Safety outcomes are presented as percentages of patients (induction) and as number of patients with events per 100 patient-years of follow-up (through 1 year). For key safety events, 95% confidence intervals (CIs) are provided, as appropriate. Hazard ratios with 95% CIs from time-to-event analyses for serious adverse events and serious infections were also performed.

Results

Through 1 year, 2574 patients received ustekinumab (1733 patient-years of follow-up). The number of patients with adverse events per 100 patient-years (placebo 165.99 [95% CI, 155.81–176.67] vs ustekinumab 118.32 [95% CI, 113.25–123.55]), serious AEs (27.50 [95% CI, 23.45–32.04] vs 21.23 [95% CI, 19.12–23.51]), infections (80.31 [95% CI, 73.28–87.84] vs 64.32 [95% CI, 60.60–68.21]), serious infections (5.53 [95% CI, 3.81–7.77] vs 5.02 [95% CI, 4.02–6.19]), and malignancies excluding nonmelanoma skin cancer (0.17 [95% CI, 0.00–0.93] vs 0.40 [95% CI, 0.16–0.83]) were similar between placebo and ustekinumab.

Conclusions

The safety profile of ustekinumab across the pooled inflammatory bowel disease population through 1 year was favorable and generally comparable to placebo. These data are consistent with the established safety profile of ustekinumab across indications.

ClinicalTrials.gov numbers

NCT00265122; NCT00771667; NCT01369329; NCT01369342; NCT01369355; NCT02407236.
Current understandings of the relationship between extracellular vesicles and cilia
Authors: Ikegami Koji , Ijaz Faryal
Published: September 2020

Mammalian cells have a tiny hair-like protrusion on their surface called a primary cilium. Primary cilia are thought to be the antennae for the cells, receiving signals from the environment. In some studies, extracellular vesicles (EVs) were found attached to the surface of the primary cilium. An idea for the phenomenon is that the primary cilium is the receptor for receiving the EVs. Meanwhile, a unicellular organism, Chlamydomonas, which has two long cilia, usually called flagella, release EVs termed ectosomes from the surface of the flagella. Accumulating evidence suggests that the primary cilium also functions as the ‘emitter’ of EVs. Physiological and pathological impacts are also elucidated for the release of EVs from primary cilia. However, the roles of released cilia-derived EVs remain to be clarified. This review introduces the historical background of the relationship between EVs and cilia, and recent progresses in the research field.
Management of Pear Psylla (Hemiptera: Psyllidae) Using Reflective Plastic Mulch
Authors: Nottingham Louis B , Beers Elizabeth H
Published: September 2020

Pear psylla, Cacopsylla pyricola (Förster), has remained the most challenging pest of commercial pears in Washington and Oregon, the top producers of pears in the United States. The lack of effective integrated pest management tactics for this pest has been a major barrier to effective management. In this study, we examined the potential for reflective plastic mulch affixed beneath pear trees to suppress pear psylla. In 2017 and 2018, single pear tree (cv. Bartlett) plots of reflective plastic mulch, black plastic mulch, and no mulch (check) were established in a research orchard to compare their effects on pear psylla. Arthropods were sampled every 7–14 d from March through late summer. In both years, reflective mulch plots had significantly fewer pear psylla adults, eggs, and nymphs of the first generation compared with black plastic and check plots. However, later generations of psylla were not suppressed by reflective mulch. Semi-field tests were conducted in 2019 and 2020 using uniformly pruned potted pear trees on either reflective plastic mulch or grass to determine whether summerform adults were tolerant to reflected light from mulch, or if shading from vegetative growth negated the effect of the mulch. In both years, significantly fewer summerform adults and eggs were found in reflective mulch plots, suggesting that shading, rather than summerform tolerance, reduced effects from reflective mulch in the summer. This study demonstrates the potential for reflective mulch to suppress pear psylla and justifies future examination as part of a season-long management program.
Complexity of finite-variable fragments of products withK
Authors: Rybakov Mikhail , Shkatov Dmitry
Published: September 2020

We show that products and expanding relativized products of propositional modal logics where one component is the minimal monomodal logic K are polynomial-time reducible to their single-variable fragments. Therefore, the known lower-bound complexity and undecidability results for such logics are extended to their single-variable fragments. Similar results are obtained for products where one component is a polymodal logic with a K-style modality; these include products with propositional dynamic logics.
The impact of episodic outflow feedback on stellar multiplicity and the star formation efficiency
Authors: Rohde P F , Walch S , Clarke S D , Seifried D , Whitworth A P , Klepitko A
Published: September 2020

The accretion of material on to young protostars is accompanied by the launching of outflows. Observations show that accretion, and therefore also outflows, are episodic. However, the effects of episodic outflow feedback on the core scale are not well understood. We have performed 88 smoothed particle hydrodynamic simulations of turbulent dense $1 \, {{\mathrm{M}}}_{\odot }$ cores to study the influence of episodic outflow feedback on the stellar multiplicity and the star formation efficiency (SFE). Protostars are represented by sink particles, which use a subgrid model to capture stellar evolution, inner-disc evolution, episodic accretion, and the launching of outflows. By comparing simulations with and without episodic outflow feedback, we show that simulations with outflow feedback reproduce the binary statistics of young stellar populations, including the relative proportions of singles, binaries, triples, etc. and the high incidence of twin binaries with q ≥ 0.95; simulations without outflow feedback do not. Entrainment factors (the ratio between total outflowing mass and initially ejected mass) are typically ∼7 ± 2, but can be much higher if the total mass of stars formed in a core is low and/or outflow episodes are infrequent. By decreasing both the mean mass of the stars formed and the number of stars formed, outflow feedback reduces the SFE by about a factor of 2 (as compared with simulations that do not include outflow feedback).
Planet migration, resonant locking, and accretion streams in PDS 70: comparing models and data
Authors: Toci Claudia , Lodato Giuseppe , Christiaens Valentin , Fedele Davide , Pinte Christophe , Price Daniel J , Testi Leonardo
Published: September 2020

The disc surrounding PDS 70, with two directly imaged embedded giant planets, is an ideal laboratory to study planet–disc interaction. We present 3D smoothed particle hydrodynamics simulations of the system. In our simulations, planets, which are free to migrate and accrete mass, end up in a locked resonant configuration that is dynamically stable. We show that features observed at infrared (scattered light) and millimetre (thermal continuum) wavelengths are naturally explained by the accretion stream on to the outer planet, without requiring a circumplanetary disc around Planet c. We post-processed our near-infrared synthetic images in order to account for observational biases known to affect high-contrast images. Our successful reproduction of the observations indicates that planet–disc dynamical interactions alone are sufficient to explain the observations of PDS 70.
Supernovae and their host galaxies – VII. The diversity of Type Ia supernova progenitors
Authors: Hakobyan A A , Barkhudaryan L V , Karapetyan A G , Gevorgyan M H , Mamon G A , Kunth D , Adibekyan V , Turatto M
Published: September 2020

We present an analysis of the light curve (LC) decline rates (Δm15) of 407 normal and peculiar supernovae (SNe) Ia and global parameters of their host galaxies. As previously known, there is a significant correlation between the Δm15 of normal SNe Ia and global ages (morphologies, colours, and masses) of their hosts. On average, those normal SNe Ia that are in galaxies from the Red Sequence (early-type, massive, old hosts) have faster declining LCs in comparison with those from the Blue Cloud (late-type, less massive, younger hosts) of the colour–mass diagram. The observed correlations between the Δm15 of normal SNe Ia and hosts’ parameters appear to be due to the superposition of at least two distinct populations of faster and slower declining normal SNe Ia from older and younger stellar components. We show, for the first time, that the Δm15 of 91bg- and 91T-like SNe is independent of host morphology and colour. The distribution of hosts on the colour–mass diagram confirms the known tendency for 91bg-like SNe to occur in globally red/old galaxies, while 91T-like events prefer blue/younger hosts. On average, the youngest global ages of 02cx-like SNe hosts and their positions in the colour–mass diagram hint that these events likely originate from young population, but they differ from 91T-like events in the LC decline rate. Finally, we discuss the possible explosion channels and present our favoured SN Ia models that have the potential to explain the observed SN–host relations.
Encounters involving planetary systems in birth environments: the significant role of binaries
Authors: Li Daohai , Mustill Alexander J , Davies Melvyn B
Published: September 2020

Most stars form in a clustered environment. Both single and binary stars will sometimes encounter planetary systems in such crowded environments. Encounter rates for binaries may be larger than for single stars, even for binary fractions as low as 10–20 per cent. In this work, we investigate scatterings between a Sun–Jupiter pair and both binary and single stars as in young clusters. We first perform a set of simulations of encounters involving wide ranges of binaries and single stars, finding that wider binaries have larger cross-sections for the planet’s ejection. Secondly, we consider such scatterings in a realistic population, drawing parameters for the binaries and single stars from the observed population. The scattering outcomes are diverse, including ejection, capture/exchange, and collision. The binaries are more effective than single stars by a factor of several or more in causing the planet’s ejection and collision. Hence, in a cluster, as long as the binary fraction is larger than about 10 per cent, the binaries will dominate the scatterings in terms of these two outcomes. For an open cluster of a stellar density 50 pc−3, a lifetime 100 Myr, and a binary fraction 0.5, we estimate that Jupiters of the order of 1 per cent are ejected, 0.1 per cent collide with a star, 0.1 per cent change ownership, and 10 per cent of the Sun–Jupiter pairs acquire a stellar companion during scatterings. These companions are typically thousands of au distant and in half of the cases (so 5 per cent of all Sun–Jupiter pairs), they can excite the planet’s orbit through Kozai–Lidov mechanism before being stripped by later encounters. Our result suggests that the Solar system may have once had a companion in its birth cluster.
Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications
Authors: Prodanov Timofey , Bansal Vikas
Published: September 2020

The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read aligners and leverages paralogous sequence variants (PSVs)—sequence differences between paralogous sequences—to distinguish between multiple alignment locations. On simulated datasets, DuploMap increased the percentage of correctly mapped reads with high confidence for multiple long-read aligners including Minimap2 (74.3–90.6%) and BLASR (82.9–90.7%) while maintaining high precision. Across multiple whole-genome long-read datasets, DuploMap aligned an additional 8–21% of the reads in segmental duplications with high confidence relative to Minimap2. Using DuploMap-aligned PacBio circular consensus sequencing reads, an additional 8.9 Mb of DNA sequence was mappable, variant calling achieved a higher F1 score and 14 713 additional variants supported by linked-read data were identified. Finally, we demonstrate that a significant fraction of PSVs in segmental duplications overlaps with variants and adversely impacts short-read variant calling.
Senescence-activated enhancer landscape orchestrates the senescence-associated secretory phenotype in murine fibroblasts
Authors: Guan Yiting , Zhang Chao , Lyu Guoliang , Huang Xiaoke , Zhang Xuebin , Zhuang Tenghan , Jia Lumeng , Zhang Lijun , Zhang Chen , Li Cheng , Tao Wei
Published: September 2020

The three-dimensional configuration of the chromatin architecture is known to be crucial for alterations in the transcriptional network; however, the underlying mechanisms of epigenetic control of senescence-related gene expression by modulating the chromatin architecture remain unknown. Here, we demonstrate frequent chromosomal compartment switching during mouse embryonic fibroblasts (MEFs) replicative senescence as characterized by senescence-inactivated (SIAEs) and -activated enhancers (SAEs) in topologically associated domains (TADs). Mechanistically, SAEs are closely correlated with senescence-associated secretory phenotype (SASP) genes, which are a key transcriptional feature of an aging microenvironment that contributes to tumor progression, aging acceleration, and immunoinflammatory responses. Moreover, SAEs can positively regulate robust changes in SASP expression. The transcription factor CCAAT/enhancer binding protein α (C/EBPα) is capable of enhancing SAE activity, which accelerates the emergence of SAEs flanking SASPs and the secretion of downstream factors, contributing to the progression of senescence. Our results provide novel insight into the TAD-related control of SASP gene expression by revealing hierarchical roles of the chromatin architecture, transcription factors, and enhancer activity in the regulation of cellular senescence.
Direct measurement of protein–protein interactions by FLIM-FRET at UV laser-induced DNA damage sites in living cells
Authors: Kaufmann Tanja , Herbert Sébastien , Hackl Benjamin , Besold Johanna Maria , Schramek Christopher , Gotzmann Josef , Elsayad Kareem , Slade Dea
Published: September 2020

Protein–protein interactions are essential to ensure timely and precise recruitment of chromatin remodellers and repair factors to DNA damage sites. Conventional analyses of protein–protein interactions at a population level may mask the complexity of interaction dynamics, highlighting the need for a method that enables quantification of DNA damage-dependent interactions at a single-cell level. To this end, we integrated a pulsed UV laser on a confocal fluorescence lifetime imaging (FLIM) microscope to induce localized DNA damage. To quantify protein–protein interactions in live cells, we measured Förster resonance energy transfer (FRET) between mEGFP- and mCherry-tagged proteins, based on the fluorescence lifetime reduction of the mEGFP donor protein. The UV-FLIM-FRET system offers a unique combination of real-time and single-cell quantification of DNA damage-dependent interactions, and can distinguish between direct protein–protein interactions, as opposed to those mediated by chromatin proximity. Using the UV-FLIM-FRET system, we show the dynamic changes in the interaction between poly(ADP-ribose) polymerase 1, amplified in liver cancer 1, X-ray repair cross-complementing protein 1 and tripartite motif containing 33 after DNA damage. This new set-up complements the toolset for studying DNA damage response by providing single-cell quantitative and dynamic information about protein–protein interactions at DNA damage sites.
DockCoV2: a drug database against SARS-CoV-2
Authors: Chen Ting-Fu , Chang Yu-Chuan , Hsiao Yi , Lee Ko-Han , Hsiao Yu-Chun , Lin Yu-Hsiang , Tu Yi-Chin Ethan , Huang Hsuan-Cheng , Chen Chien-Yu , Juan Hsueh-Fen
Published: September 2020

The current state of the COVID-19 pandemic is a global health crisis. To fight the novel coronavirus, one of the best-known ways is to block enzymes essential for virus replication. Currently, we know that the SARS-CoV-2 virus encodes about 29 proteins such as spike protein, 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), Papain-like protease (PLpro), and nucleocapsid (N) protein. SARS-CoV-2 uses human angiotensin-converting enzyme 2 (ACE2) for viral entry and transmembrane serine protease family member II (TMPRSS2) for spike protein priming. Thus in order to speed up the discovery of potential drugs, we develop DockCoV2, a drug database for SARS-CoV-2. DockCoV2 focuses on predicting the binding affinity of FDA-approved and Taiwan National Health Insurance (NHI) drugs with the seven proteins mentioned above. This database contains a total of 3,109 drugs. DockCoV2 is easy to use and search against, is well cross-linked to external databases, and provides the state-of-the-art prediction results in one site. Users can download their drug-protein docking data of interest and examine additional drug-related information on DockCoV2. Furthermore, DockCoV2 provides experimental information to help users understand which drugs have already been reported to be effective against MERS or SARS-CoV. DockCoV2 is available at https://covirus.cc/drugs/.
Adding Physical Impairment to Risk Stratification Improved Outcome Prediction in Low Back Pain
Authors: Beneciuk Jason M , George Steven Z
Published: September 2020

Objective

Identifying subgroups of low back pain (LBP) has the potential to improve prediction of clinical outcomes. Risk stratification is one such strategy that identifies similar characteristics indicative of a common clinical outcome trajectory. The purpose of this study was to determine if an empirically derived subgrouping approach based on physical impairment measures improves information provided from the STarT Back Tool (SBT).

Methods

At baseline in this secondary analysis of a cohort study, patients (N = 144) receiving physical therapy for LBP completed the SBT and tests (active lumbar flexion, extension, lateral bending, and passive straight-leg raise) from a validated physical impairment index. Clinical outcomes were assessed at 4 weeks and included the Numerical Pain Rating Scale and Oswestry Disability Index. Exploratory hierarchical agglomerative cluster analysis identified empirically derived subgroups based on physical impairment measures. Independent samples t testing and chi-square analysis were used to assess baseline subgroup differences in demographic and clinical measures. Spearman rho correlation coefficient was used to assess baseline SBT risk and impairment subgroup relationships, and a 3-way mixed-model ANOVA was used to assessed SBT risk and impairment subgroup relationships with clinical outcomes at 4 weeks.

Results

Two physical impairment-based subgroups emerged from cluster analysis: (1) low-risk impairment (n = 119, 81.5%), characterized by greater lumbar mobility; and (2) high-risk impairment (n = 25, 17.1%), characterized by less lumbar mobility. A weak, positive relationship was observed between baseline SBT risk and impairment subgroups (rs = .170). An impairment-by-SBT risk-by-time interaction effect was observed for Oswestry Disability Index scores but not for Numerical Pain Rating Scale scores at 4 weeks.

Conclusions

Physical impairment subgroups were not redundant with SBT risk categories and could improve prediction of 4-week LBP disability outcomes. Physical impairment subgroups did not improve the prediction of 4-week pain intensity scores.

Impact

Subgroups based on physical impairment and psychosocial risk could lead to better prediction of LBP disability outcomes and eventually allow for treatment options tailored to physical and psychosocial risk.
Dr Fossile’s Crocodile: Science and the ‘Oriental Chronotope’ in Eighteenth-Century Literature
Authors: Risling Matthew
Published: September 2020

This article explores eighteenth-century questions surrounding the spatiotemporal nature of the field we now call ‘science’. Today’s commonplace notion of ‘modern Western science’ assumes conceptual binaries that do not map onto eighteenth-century discourses. The article focuses on two works by the so-called Scriblerians—Three Hours after Marriage (1717), and Memoirs of Martinus Scriblerus (1714, pub. 1741)—which satirize the much-maligned Dr John Woodward and, ostensibly, the philosophical mode he represented. Though these texts are satirical, the article does not posit a clash of cultures. Instead, it examines a set of tropes, shared by numerous authors at various purposes, which inflected science with the narratological space-time of the ancient Orient. This ‘Oriental chronotope’ (in Bakhtinian terms) speaks to the complex space that science occupied in emerging narratives of Western modernity. The Eastern artefacts featured in these works, and their shared themes of dubious reproduction, establish an unlikely affinity with Thomas Sprat’s History of the Royal Society (1667), which offers the new sciences as a dialectic between the ancient and modern worlds.
Differences in clinical characteristics of IgG4-related disease across age groups: a prospective study of 737 patients
Authors: Lu Hui , Teng Fei , Zhang Panpan , Fei Yunyun , Peng Linyi , Zhou Jiaxin , Wang Mu , Liu Xiaowei , Zhu Liang , Wang Liwen , Luo Xuan , Liu Zheng , Li Jieqiong , Zhao Yan , Zhang Wen , Zeng Xiaofeng
Published: September 2020

Objective

The aim of this study was to compare the clinical characteristics of IgG4-related disease (IgG4-RD) among different age groups.

Methods

We conducted a prospective study of 737 patients who were newly diagnosed with IgG4-RD and compared detailed demographic features, organ involvements, laboratory tests, treatments and outcomes across age groups. The patients were divided into five groups according to their age at diagnosis: ≤39, 40–49, 50–59, 60–69 and ≥70 years. The clinical characteristics of paediatric patients were also described.

Results

Sex ratio, disease duration, allergy history and clinical symptoms were significantly different across age groups. Besides, the proportions of superficial organ involvement (lacrimal gland and sinus) decreased with age, while the proportions of internal organ involvement (pancreas, biliary tract, retroperitoneal tissue, lung and prostate) increased with age, which was more prominent in male patients. Mikulicz’s disease was the most common manifestation (70%) in paediatric IgG4-RD patients. Multiple Cox analysis identified that age ≤56 years at diagnosis was an independent risk factor of relapse.

Conclusion

We revealed the impact of age on clinical characteristics of IgG4-RD, which indicated that different management might be required among different age groups.
Smoke Chemistry, In Vitro Cytotoxicity, and Genotoxicity Demonstrates Enhanced Toxicity of Cigarillos Compared With Cigarettes
Authors: Crosby Lynn , Yucesoy Berran , Leggett Carmine , Tu Zheng , Belinsky Steven A , McDonald Jake , Leng Shuguang , Wu Guodong , Irshad Hammad , Valerio Luis G , Rosenfeldt Hans
Published: September 2020

There has been limited toxicity testing of cigarillos, including comparison to cigarettes. This study compared the smoke chemistry and the cytotoxic and genotoxic potential of 10 conventional cigarettes and 10 cigarillos based on the greatest market share. Whole smoke and total particulate matter (TPM) were generated using the Canadian Intense and International Organization for Standardization puffing protocols. Tobacco-specific nitrosamines, carbonyls, and polycyclic aromatic hydrocarbons were measured using gas chromatography-mass spectrometry. TPM smoke extracts were used for the in vitro assays. Cytotoxicity was assessed in human bronchial epithelial continuously cultured cell line cells using the neutral red uptake assay. Genotoxic potential was assessed using the micronucleus (human lung adenocarcinoma continuously cultured cell line cells), Ames, and thymidine kinase assays. TPM from all cigarillos tested was more cytotoxic than cigarettes. Micronucleus formation was significantly greater for cigarillos compared with cigarettes at the highest dose of TPM, with or without rat liver S9 fraction. In the Ames test +S9, both tobacco products exhibited significant dose-dependent increases in mutation frequency, indicating metabolic activation is required for genotoxicity. In the thymidine kinase assay +S9, cigarillos showed a significantly enhanced mutation frequency although both tobacco products were positive. The levels of all measured polycyclic aromatic hydrocarbons, tobacco-specific nitrosamines, and carbonyls (except acrolein) were significantly greater in cigarillos than cigarettes. The Canadian Intense puffing protocol demonstrated increased smoke constituent levels compared with International Organization for Standardization. Even though the gas vapor phase was not tested, the results of this study showed that under the tested conditions the investigated cigarillos showed greater toxicity than comparator cigarettes. This study found that there is significantly greater toxicity in the tested U.S. marketed cigarillos than cigarettes for tobacco constituent levels, cytotoxicity, and genotoxicity. These findings are important for understanding the human health toxicity from the use of cigarillos relative to cigarettes and for building upon knowledge regarding harm from cigarillos to inform risk mitigation strategies.
Development of a Telemedicine Neurological Examination for Spine Surgery
Authors: Goyal Dhruv K.C. , Divi Srikanth N. , Schroeder Gregory D. , Pfeifer Ryan , Canseco Jose A. , Bowles Daniel R. , Nicholson Kristen J. , Patel Parthik D. , Reyes Ariana A. , Radcliff Kristen E. , Kurd Mark F. , Woods Barrett I. , Kaye Ian David , Rihn Jeffrey A. , Anderson David Greg , Hilibrand Alan S. , Kepler Christopher K. , Harrop James S. , Vaccaro Alexander R.
Published: September 2020

Study Design:

This was a prospective cohort study.

Objective:

The objective of this study was to design and test a novel spine neurological examination adapted for telemedicine.

Summary of Background Data:

Telemedicine is a rapidly evolving technology associated with numerous potential benefits for health care, especially in the modern era of value-based care. To date, no studies have assessed whether.

Methods:

Twenty-one healthy controls and 20 patients with cervical or lumbar spinal disease (D) were prospectively enrolled. Each patient underwent a telemedicine neurological examination as well as a traditional in-person neurological examination administered by a fellowship trained spine surgeon and a physiatrist. Both the telemedicine and in-person tests consisted of motor, sensory, and special test components. Scores were compared via univariate analysis and secondary qualitative outcomes, including responses from a satisfaction survey, were obtained upon completion of the trial.

Results:

Of the 20 patients in the D group, 9 patients had cervical disease and 11 patients had lumbar disease. Comparing healthy control with the D group, there were no significant differences with respect to all motor scores, most sensory scores, and all special tests. There was a high rate of satisfaction among the cohort with 92.7% of participants feeling “very satisfied” with the overall experience.

Conclusions:

This study presents the development of a viable neurological spine examination adapted for telemedicine. The findings in this study suggest that patients have comparable motor, sensory, and special test scores with telemedicine as with a traditional in-person examination administered by an experienced clinician, as well as reporting a high rate of satisfaction among participants. To our knowledge, this is the first telemedicine neurological examination for spine surgery. Further studies are warranted to validate these findings.