bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity of putative ericoid mycorrhizal fungi increases with soil age and progressive phosphorus limitation across a 4.1-million-year chronosequence
Authors: Leopold Devin R , Peay Kabir G , Vitousek Peter M , Fukami Tadashi
Published: January 2021

Ericaceous plants rely on ericoid mycorrhizal fungi for nutrient acquisition. However, the factors that affect the composition and structure of fungal communities associated with the roots of ericaceous plants remain largely unknown. Here, we use a 4.1-million-year (myr) soil chronosequence in Hawaii to test the hypothesis that changes in nutrient availability with soil age determine the diversity and species composition of fungi associated with ericoid roots. We sampled roots of a native Hawaiian plant, Vaccinium calycinum, and used DNA metabarcoding to quantify changes in fungal diversity and community composition. We also used a fertilization experiment at the youngest and oldest sites to assess the importance of nutrient limitation. We found an increase in diversity and a clear pattern of species turnover across the chronosequence, driven largely by putative ericoid mycorrhizal fungi. Fertilization with nitrogen at the youngest site and phosphorus at the oldest site reduced fungal diversity, suggesting a direct role of nutrient limitation. Our results also reveal the presence of novel fungal species associated with Hawaiian Ericaceae and suggest a greater importance of phosphorus availability for communities of ericoid mycorrhizal fungi than is generally assumed.
Genome assemblies for two Neotropical trees: Jacaranda copaia and Handroanthus guayacan
Authors: Burley John T , Kellner James R , Hubbell Stephen P , Faircloth Brant C
Published: January 2021

The lack of genomic resources for tropical canopy trees is impeding several research avenues in tropical forest biology. We present genome assemblies for two Neotropical hardwood species, Jacaranda copaia and Handroanthus (formerly Tabebuia) guayacan, that are model systems for research on tropical tree demography and flowering phenology. For each species, we combined Illumina short-read data with in vitro proximity-ligation (Chicago) libraries to generate an assembly. For Jacaranda copaia, we obtained 104X physical coverage and produced an assembly with N50/N90 scaffold lengths of 1.020/0.277 Mbp. For H. guayacan, we obtained 129X coverage and produced an assembly with N50/N90 scaffold lengths of 0.795/0.165 Mbp. J. copaia and H. guayacan assemblies contained 95.8% and 87.9% of benchmarking orthologs, although they constituted only 77.1% and 66.7% of the estimated genome sizes of 799 and 512 Mbp, respectively. These differences were potentially due to high repetitive sequence content (>59.31% and 45.59%) and high heterozygosity (0.5% and 0.8%) in each species. Finally, we compared each new assembly to a previously sequenced genome for Handroanthus impetiginosus using whole-genome alignment. This analysis indicated extensive gene duplication in H. impetiginosus since its divergence from H. guayacan.
Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon
Authors: Christensen Kris A , Le Luyer Jérémy , Chan Michelle T T , Rondeau Eric B , Koop Ben F , Bernatchez Louis , Devlin Robert H
Published: January 2021

Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to measure gene transcription and whole-genome bisulfite sequencing to measure gene methylation in liver tissue. Gene ontology (GO) term analysis revealed stress as an important biological process potentially influencing growth rate GxE interactions. While few genes with transcription differences also had methylation differences, in promoter or gene regions, many genes were differentially methylated between tank and stream environments. A GO term analysis of differentially methylated genes between tank and stream environments revealed increased methylation in the stream environment of more than 95% of the differentially methylated genes, many with biological processes unrelated to liver function. The lower nutritional condition of the stream environment may cause increased negative regulation of genes less vital for liver tissue function than when fish are reared in tanks with unlimited food availability. These data show a large effect of rearing environment both on gene expression and methylation, but it is less clear that the detected epigenetic marks are responsible for the observed altered growth and physiological responses.
Continental-Scale Gene Flow Prevents Allopatric Divergence of Pelagic Freshwater Bacteria
Authors: Hoetzinger Matthias , Pitt Alexandra , Huemer Andrea , Hahn Martin W
Published: January 2021

Allopatric divergence is one of the principal mechanisms for speciation of macro-organisms. Microbes by comparison are assumed to disperse more freely and to be less limited by dispersal barriers. However, thermophilic prokaryotes restricted to geothermal springs have shown clear signals of geographic isolation, but robust studies on this topic for microbes with less strict habitat requirements are scarce. Furthermore, it has only recently been recognized that homologous recombination among conspecific individuals provides species coherence in a wide range of prokaryotes. Recombination barriers thus may define prokaryotic species boundaries, yet, the extent to which geographic distance between populations gives rise to such barriers is an open question. Here, we investigated gene flow and population structure in a widespread species of pelagic freshwater bacteria, Polynucleobacter paneuropaeus. Through comparative genomics of 113 conspecific strains isolated from freshwater lakes and ponds located across a North–South range of more than 3,000 km, we were able to reconstruct past gene flow events. The species turned out to be highly recombinogenic as indicated by significant signs of gene transfer and extensive genome mosaicism. Although genomic differences increased with spatial distance on a regional scale (<170 km), such correlations were mostly absent on larger scales up to 3,400 km. We conclude that allopatric divergence in European P. paneuropaeus is minor, and that effective gene flow across the sampled geographic range in combination with a high recombination efficacy maintains species coherence.
Multi-scale assessment of distribution and density of procellariiform seabirds within the Northern Antarctic Peninsula marine ecosystem
Authors: Warwick-Evans V , A Santora J , Waggitt J J , Trathan P N
Published: January 2021

The Antarctic Peninsula is one of the most rapidly warming regions on earth, and it is likely that the abundance and distribution of marine predators will change as a result.Procellariiform seabirds are highly mobile predators, which target specific habitat characteristics associated with underlying distributions of prey and areas of increased prey availability. We use ship surveys and hurdle models, to estimate the summer distribution and relative density of 11 seabird species within the northern Antarctic Peninsula marine ecosystem. Models differed among species; however, sea surface temperature and depth were frequently associated with seabird occurrence and had the greatest explanatory power across many species. Null models based on observation data were better at predicting seabird density than models that included environmental covariates. This suggests that the main driver of distribution patterns is the broad-scale habitat features, and fine-scale aggregations within these ranges are harder to predict. Our seabird distribution models reflect known habitat associations, species hotspots, and community organization relative to oceanic and coastal marine processes. Application of species distribution models will benefit the assessments of critical habitat and potential responses to climate change and anthropogenic disturbance, which will provide insight into how species may change in polar ecosystems.
Human Monoclonal Antibody Cocktail for the Treatment or Prophylaxis of Middle East Respiratory Syndrome Coronavirus
Authors: Sivapalasingam Sumathi , Saviolakis George A , Kulcsar Kirsten , Nakamura Aya , Conrad Thomas , Hassanein Mohamed , Sumner Giane , Elango Chinnasamy , Kamal Mohamed A , Eng Simon , Kyratsous Christos A , Musser Bret J , Frieman Matthew , Kantrowitz Joel , Weinreich David M , Yancopoulos George , Stahl Neil , Lipsich Leah
Published: January 2021

Background

REGN3048 and REGN3051 are human monoclonal antibodies (mAb) targeting the spike glycoprotein on the Middle East respiratory syndrome coronavirus (MERS-CoV), which binds to the receptor dipeptidyl peptidase-4 (DPP4) and is necessary for infection of susceptible cells.

Methods

Preclinical study: REGN3048, REGN3051 and isotype immunoglobulin G (IgG) were administered to humanized DPP4 (huDPP4) mice 1 day prior to and 1 day after infection with MERS-CoV (Jordan strain). Virus titers and lung pathology were assessed. Phase 1 study: healthy adults received the combined mAb (n = 36) or placebo (n = 12) and followed for 121 days. Six dose levels were studied. Strict safety criteria were met prior to dose escalation.

Results

Preclinical study: REGN3048 plus REGN3051, prophylactically or therapeutically, was substantially more effective for reducing viral titer, lung inflammation, and pathology in huDPP4 mice compared with control antibodies and to each antibody monotherapy. Phase 1 study: REGN3048 plus REGN3051 was well tolerated with no dose-limiting adverse events, deaths, serious adverse events, or infusion reactions. Each mAb displayed pharmacokinetics expected of human IgG1 antibodies; it was not immunogenic.

Conclusions

REGN3048 and REGN3051 in combination were well tolerated. The clinical and preclinical data support further development for the treatment or prophylaxis of MERS-CoV infection.
The 49th Annual Meeting of the Japanese Society for Immunology: COVID-19 and Immunity
Authors: Shinkura Reiko , Kang Sujin , Arase Hisashi , Toyama-Sorimachi Noriko
Published: January 2021

Meeting Report: COVID-19 and Immunity
Technical Note: Coccygeal vein catheterization for sampling of reproductive tract-derived products from the uterine–ovarian drainage
Authors: Reese Sydney T , Franco Gessica A , Oliveira Filho Ramiro V , Cooke Reinaldo F , Smith Michael F , Pohler Ky G
Published: January 2021

Blood sample collection from the caudal vena cava at the site of uterine–ovarian drainage provides a more exact evaluation of the concentration and pattern of secretion of uterine or ovarian secreted products for studies of reproductive processes in cyclic and pregnant cattle compared with samples collected from general circulation. This paper describes a thorough and updated procedure for cannulating the coccygeal vein into the caudal vena cava for the collection of serial blood samples at or near the site of uterine–ovarian drainage. Concentrations of progesterone were quantified in cows of different reproductive tract sizes with an active corpus luteum to assess the distance for proper catheter placement compared with circulating concentrations collected from the jugular vein. This procedure has a low risk for side effects, can be used effectively in pregnant animals with no major consequence to the viability of the pregnancy, and provides means for frequent collections up to 12 d.
A cost-minimization analysis of measures against metallic dental restorations for head and neck radiotherapy
Authors: Katsura Kouji , Soga Yoshihiko , Zenda Sadatomo , Nishi Hiromi , Soga Marie , Usubuchi Masatoshi , Mitsunaga Sachiyo , Tomizuka Ken , Konishi Tetsuhito , Yatsuoka Wakako , Ueno Takao , Aragaki Tadanobu , Hayashi Takafumi
Published: January 2021

The aim of this study was to compare the estimated public medical care cost of measures to address metallic dental restorations (MDRs) for head and neck radiotherapy using high-energy mega-voltage X-rays. This was considered a first step to clarify which MDR measure was more cost-effective. We estimated the medical care cost of radiotherapy for two representative MDR measures: (i) with MDR removal or (ii) without MDR removal (non-MDR removal) using magnetic resonance imaging and a spacer. A total of 5520 patients received head and neck radiation therapy in 2018. The mean number of MDRs per person was 4.1 dental crowns and 1.3 dental bridges. The mean cost per person was estimated to be 121 720 yen for MDR removal and 54 940 yen for non-MDR removal. Therefore, the difference in total public medical care cost between MDR removal and non-MDR removal was estimated to be 303 268 800 yen. Our results suggested that non-MDR removal would be more cost-effective than MDR removal for head and neck radiotherapy. In the future, a national survey and cost-effectiveness analysis via a multicenter study are necessary; these investigations should include various outcomes such as the rate of local control, status of oral mucositis, frequency of hospital visits and efforts of the medical professionals.
Pediatric Thoracic Trauma Mortality in Iraq and Afghanistan Compared to the United States National Trauma Data Bank
Authors: Keneally Ryan J , Meyers Brittney A , Shields Cynthia H , Ricca Robert , Creamer Kevin M
Published: January 2021

Introduction

The authors compared pediatric thoracic patients in the Joint Theatre Trauma Registry (JTTR) to those in the National Trauma Data Bank (NTDB) to assess differences in patient mortality rates and mortality risk accounting for age, injury patterns, and injury severity.

Materials and Methods

Patients less than 19 years of age with thoracic trauma were identified in both the JTTR and NTDB. Multiple logistic regression, χ2, Student’s t-test, or Mann-Whitney U test were used as indicated to compare the two groups.

Results

Pediatric thoracic trauma patients seen in Iraq and Afghanistan (n = 955) had a significantly higher mortality rate (15.1 vs. 6.0%, P <.01) than those in the NTDB (n = 9085). After controlling for covariates between the JTTR and the NTDB, there was no difference in mortality (odds ratio for mortality for U.S. patients was 0.74, 95% CI 0.52-1.06, P = .10). The patients seen in Iraq or Afghanistan were significantly younger (8 years old, interquartile ratio (IQR) 2-13 vs. 15, IQR 10-17, P <.01) had greater severity of injuries (injury severity score 17, IQR 12-26 vs. 12, IQR 8-22, P <.01), had significantly more head injuries (29 vs. 14%, P <.01), and over half were exposed to a blast.

Discussion

Pediatric patients with thoracic trauma in Iraq and Afghanistan in the JTTR had similar mortality rates compared to the civilian population in the NTDB after accounting for confounding covariates. These findings indicate that deployed military medical professionals are providing comparable quality of care in extremely challenging circumstances. This information has important implications for military preparedness, medical training, and casualty care.
The wide upper main sequence and main-sequence turnoff of the ∼ 800 Myr old star cluster NGC 1831
Authors: Correnti Matteo , Goudfrooij Paul , Bellini Andrea , Girardi Leo
Published: January 2021

We present the analysis of the colour–magnitude diagram (CMD) morphology of the ∼800 Myr old star cluster NGC 1831 in the Large Magellanic Cloud, exploiting deep, high-resolution photometry obtained using the Wide Field Camera 3 onboard the Hubble Space Telescope. We perform a simultaneous analysis of the wide upper main sequence and main-sequence turn-off observed in the cluster, to verify whether these features are due to an extended star formation or a range of stellar rotation rates, or a combination of these two effects. Comparing the observed CMD with Monte Carlo simulations of synthetic stellar populations, we derive that the morphology of NGC 1831 can be fully explained in the context of the rotation velocity scenario, under the assumption of a bimodal distribution for the rotating stars, with ∼40 per cent of stars being slow rotators (Ω/Ωcrit < 0.5) and the remaining ∼60 per cent being fast rotators (Ω/Ωcrit > 0.9). We derive the dynamical properties of the cluster, calculating the present cluster mass and escape velocity, and predicting their past evolution starting at an age of 10 Myr. We find that NGC 1831 has an escape velocity vesc = 18.4 km s−1 at an age of 10 Myr, above the previously suggested threshold of 15 km s−1 below which the cluster cannot retain the material needed to create second-generation stars. These results, combined with those obtained from the CMD morphology analysis, indicate that for the clusters whose morphology cannot be easily explained only in the context of the rotation velocity scenario, the threshold limit should be at least ∼20 km s−1.
Limits on mass outflow from optical tidal disruption events
Authors: Matsumoto Tatsuya , Piran Tsvi
Published: January 2021

The discovery of optical/UV (ultraviolet) tidal disruption events (TDEs) was surprising. The expectation was that, upon returning to the pericentre, the stellar-debris stream will form a compact disc that will emit soft X-rays. Indeed, the first TDEs were discovered in this energy band. A common explanation for the optical/UV events is that surrounding optically thick matter reprocesses the disc’s X-ray emission and emits it from a large photosphere. If accretion follows the super-Eddington mass infall rate, it would inevitably result in an energetic outflow, providing naturally the reprocessing matter. We describe here a new method to estimate, using the observed luminosity and temperature, the mass and energy of outflows from optical transients. When applying this method to a sample of supernovae, our estimates are consistent with a more detailed hydrodynamic modelling. For the current sample of a few dozen optical TDEs, the observed luminosity and temperature imply outflows that are significantly more massive than typical stellar masses, posing a problem to this common reprocessing picture.
GAMA/XXL: X-ray point sources in low-luminosity galaxies in the GAMA G02/XXL-N field
Authors: Nwaokoro E , Phillipps S , Young A J , Baldry I , Bongiorno A , Bremer M N , Brown M J I , Chiappetti L , De Propris R , Driver S P , Elyiv A , Fotopoulou S , Giles P A , Hopkins A M , Maughan B , McGee S , Pacaud F , Pierre M , Plionis M , Poggianti B M , Vignali C
Published: January 2021

Relatively few X-ray sources are known that have low-mass galaxies as hosts. This is an important restriction on studies of active galactic nuclei (AGNs), hence black holes, and of X-ray binaries (XRBs) in low-mass galaxies; addressing it requires very large samples of both galaxies and X-ray sources. Here, we have matched the X-ray point sources found in the XXL-N field of the XXL survey (with an X-ray flux limit of ∼6 × 10−15 erg s−1 cm−2 in the [0.5–2] keV band) to galaxies with redshifts from the Galaxy And Mass Assembly (GAMA) G02 survey field (down to a magnitude limit r = 19.8) in order to search for AGNs and XRBs in GAMA galaxies, particularly those of low optical luminosity or stellar mass (fainter than Mr = −19 or $M_* \lesssim 10^{9.5}\, \mathrm{M}_{\odot }$). Out of a total of 1200 low-mass galaxies in the overlap region, we find a total of 28 potential X-ray source hosts, though this includes possible background contaminants. From a combination of photometry (optical and infrared colours), positional information, and optical spectra, we deduce that most of the ≃20 X-ray sources genuinely in low-mass galaxies are high-mass X-ray binaries in star-forming galaxies. None of the matched sources in a low-mass galaxy has a BPT classification as an AGN, and even ignoring this requirement, none passes both criteria of close match between the X-ray source position and optical galaxy centre (separation ≤3 arcsec) and high [O iii] line luminosity (above 1040.3 erg s−1).
Submillimetre galaxies in cosmological hydrodynamical simulations – an opportunity for constraining feedback models
Authors: Hayward Christopher C , Sparre Martin , Chapman Scott C , Hernquist Lars , Nelson Dylan , Pakmor Rüdiger , Pillepich Annalisa , Springel Volker , Torrey Paul , Vogelsberger Mark , Weinberger Rainer
Published: January 2021

Submillimetre galaxies (SMGs) have long posed a challenge for theorists, and self-consistently reproducing the properties of the SMG population in a large-volume cosmological hydrodynamical simulation has not yet been achieved. We use a scaling relation derived from previous simulations plus radiative transfer calculations to predict the submm flux densities of simulated SMGs drawn from cosmological simulations from the Illustris and IllustrisTNG projects based on the simulated galaxies’ star formation rates (SFRs) and dust masses, and compare the predicted number counts with observations. We find that the predicted SMG number counts based on IllustrisTNG are significantly less than observed (more than 1 dex at S850 ≳ 4 mJy). The simulation from the original Illustris project yields more SMGs than IllustrisTNG: the predicted counts are consistent with those observed at both S850 ≲ 5 mJy and S850 ≳ 9 mJy and only a factor of ∼2 lower than those observed at intermediate flux densities. The redshift distribution of SMGs with S850 > 3 mJy in IllustrisTNG is consistent with the observed distribution, whereas the Illustris redshift distribution peaks at significantly lower redshift (1.5 versus 2.8). We demonstrate that IllustrisTNG hosts fewer SMGs than Illustris because in the former, high-mass ($M_{\star }\sim 10^{11} \, \text{M}_{\odot }$) z ∼ 2–3 galaxies have lower dust masses and SFRs than in Illustris owing to differences in the subgrid models for stellar and/or active galactic nucleus feedback between the two simulations (we unfortunately cannot isolate the specific cause(s) post hoc). Our results demonstrate that because our method enables predicting SMG number counts in post-processing with a negligible computational expense, SMGs can provide useful constraints for tuning subgrid models in future large-volume cosmological simulations.
Flat rotation curves of z ∼ 1 star-forming galaxies
Authors: Sharma Gauri , Salucci Paolo , Harrison C M , van de Ven Glenn , Lapi Andrea
Published: January 2021

We investigate the shape of the rotation curves (RCs) of z ∼ 1 star-forming galaxies (SFGs) and compare them with local SFGs. For this purpose, we have used 344 galaxies from the K-band Multi-Object Spectrograph (KMOS) for Redshift One Spectroscopic Survey (KROSS). This sample covers the redshift range 0.57 ≤ z ≤ 1.04, the effective radii 0.69 ≤ Re [kpc] ≤ 7.76, and the stellar masses 8.7 ≤ log (M* [M⊙]) ≤ 11.32. Using 3DBAROLO, we extract the H α kinematic maps and corresponding RCs. The main advantage of 3DBAROLO is that it incorporates the beam smearing in the 3D observational space, which provide us with the intrinsic rotation velocity even in the low spatial resolution data. We have corrected the RCs for pressure support, which seems to be a more dominant effect than beam smearing in high-z galaxies. Only a combination of the three techniques (3D-kinematic modelling + 3D-beam smearing correction + pressure gradient correction) yields the intrinsic RC of an individual galaxy. Further, we present the co-added and binned RCs constructed out of 256 high-quality objects. We do not see any change in the shape of RCs with respect to the local SFGs. Moreover, we notice a significant evolution in the stellar-disc length (RD) of the galaxies as a function of their circular velocity. Therefore, we conclude that the stellar disc of SFGs evolves over cosmic time (from z ∼ 1) while the total mass stays constant (within ∼20 kpc).
The CRISPR ancillary effector Can2 is a dual-specificity nuclease potentiating type III CRISPR defence
Authors: Zhu Wenlong , McQuarrie Stuart , Grüschow Sabine , McMahon Stephen A , Graham Shirley , Gloster Tracey M , White Malcolm F
Published: January 2021

Cells and organisms have a wide range of mechanisms to defend against infection by viruses and other mobile genetic elements (MGE). Type III CRISPR systems detect foreign RNA and typically generate cyclic oligoadenylate (cOA) second messengers that bind to ancillary proteins with CARF (CRISPR associated Rossman fold) domains. This results in the activation of fused effector domains for antiviral defence. The best characterised CARF family effectors are the Csm6/Csx1 ribonucleases and DNA nickase Can1. Here we investigate a widely distributed CARF family effector with a nuclease domain, which we name Can2 (CRISPR ancillary nuclease 2). Can2 is activated by cyclic tetra-adenylate (cA4) and displays both DNase and RNase activity, providing effective immunity against plasmid transformation and bacteriophage infection in Escherichia coli. The structure of Can2 in complex with cA4 suggests a mechanism for the cA4-mediated activation of the enzyme, whereby an active site cleft is exposed on binding the activator. These findings extend our understanding of type III CRISPR cOA signalling and effector function.
Droplet digital PCR-based detection of circulating tumor DNA from pediatric high grade and diffuse midline glioma patients
Authors: Izquierdo Elisa , Proszek Paula , Pericoli Giulia , Temelso Sara , Clarke Matthew , Carvalho Diana M , Mackay Alan , Marshall Lynley V , Carceller Fernando , Hargrave Darren , Lannering Birgitta , Pavelka Zdenek , Bailey Simon , Entz-Werle Natacha , Grill Jacques , Vassal Gilles , Rodriguez Daniel , Morgan Paul S , Jaspan Tim , Mastronuzzi Angela , Vinci Mara , Hubank Michael , Jones Chris
Published: January 2021

Background

The use of liquid biopsy is of potential high importance for children with high grade (HGG) and diffuse midline gliomas (DMG), particularly where surgical procedures are limited, and invasive biopsy sampling not without risk. To date, however, the evidence that detection of cell-free DNA (cfDNA) or circulating tumor DNA (ctDNA) could provide useful information for these patients has been limited, or contradictory.

Methods

We optimized droplet digital PCR (ddPCR) assays for the detection of common somatic mutations observed in pediatric HGG/DMG, and applied them to liquid biopsies from plasma, serum, cerebrospinal fluid (CSF), and cystic fluid collected from 32 patients.

Results

Although detectable in all biomaterial types, ctDNA presented at significantly higher levels in CSF compared to plasma and/or serum. When applied to a cohort of 127 plasma specimens from 41 patients collected from 2011 to 2018 as part of a randomized clinical trial in pediatric non-brainstem HGG/DMG, ctDNA profiling by ddPCR was of limited use due to the small volumes (mean = 0.49 mL) available. In anecdotal cases where sufficient material was available, cfDNA concentration correlated with disease progression in two examples each of poor response in H3F3A_K27M-mutant DMG, and longer survival times in hemispheric BRAF_V600E-mutant cases.

Conclusion

Tumor-specific DNA alterations are more readily detected in CSF than plasma. Although we demonstrate the potential of the approach to assessing tumor burden, our results highlight the necessity for adequate sample collection and approach to improve detection if plasma samples are to be used.
CovidNeuroOnc: A UK multicenter, prospective cohort study of the impact of the COVID-19 pandemic on the neuro-oncology service
Authors: Fountain Daniel M , Piper Rory J , Poon Michael T C , Solomou Georgios , Brennan Paul M , Chowdhury Yasir A , Colombo Francesca , Elmoslemany Tarek , Ewbank Frederick G , Grundy Paul L , Hasan Md T , Hilling Molly , Hutchinson Peter J , Karabatsou Konstantina , Kolias Angelos G , McSorley Nathan J , Millward Christopher P , Phang Isaac , Plaha Puneet , Price Stephen J , Rominiyi Ola , Sage William , Shumon Syed , Silva Ines L , Smith Stuart J , Surash Surash , Thomson Simon , Lau Jun Y , Watts Colin , Jenkinson Michael D ,   British Neurosurgical Trainee Research Collaborative (BNTRC), Al-Tamimi Yahia , Alalade Andrew F , Albanese Erminia , Bailey Matthew , Brodbelt Andrew R , Chalmers Anthony , Chan Huan Wee , Coope David J , Cundliffe Sarah , D'Urso Pietro I , Entwistle Helen , Evans Rhiannon M , Fielding Rebecca , Gkolemis Christos , Hammerbeck-Ward Charlotte , Jeyaretna D Sanjeeva , King Andrew T , Laurente Raphael M , Leggate James , Lewis Rachel , Maclean Jillian , McBain Catherine , McKenna Grainne S , Molloy Elizabeth , Pathmanaban Omar N , Patkar Pradnya , Powell James , Rutherford Scott A , Santarius Thomas , Sinha Saurabh , Sitaraman Murugan , Solth Anna , Thakur Bhaskar , Wadeson Andrea , Wykes Victoria , Zafar Muhammed R
Published: January 2021

Background

The COVID-19 pandemic has profoundly affected cancer services. Our objective was to determine the effect of the COVID-19 pandemic on decision making and the resulting outcomes for patients with newly diagnosed or recurrent intracranial tumors.

Methods

We performed a multicenter prospective study of all adult patients discussed in weekly neuro-oncology and skull base multidisciplinary team meetings who had a newly diagnosed or recurrent intracranial (excluding pituitary) tumor between 01 April and 31 May 2020. All patients had at least 30-day follow-up data. Descriptive statistical reporting was used.

Results

There were 1357 referrals for newly diagnosed or recurrent intracranial tumors across 15 neuro-oncology centers. Of centers with all intracranial tumors, a change in initial management was reported in 8.6% of cases (n = 104/1210). Decisions to change the management plan reduced over time from a peak of 19% referrals at the start of the study to 0% by the end of the study period. Changes in management were reported in 16% (n = 75/466) of cases previously recommended for surgery and 28% of cases previously recommended for chemotherapy (n = 20/72). The reported SARS-CoV-2 infection rate was similar in surgical and non-surgical patients (2.6% vs. 2.4%, P > .9).

Conclusions

Disruption to neuro-oncology services in the UK caused by the COVID-19 pandemic was most marked in the first month, affecting all diagnoses. Patients considered for chemotherapy were most affected. In those recommended surgical treatment this was successfully completed. Longer-term outcome data will evaluate oncological treatments received by these patients and overall survival.
Self-assembly-induced luminescence of Eu3+-complexes and application in bioimaging
Authors: Su Ping-Ru , Wang Tao , Zhou Pan-Pan , Yang Xiao-Xi , Feng Xiao-Xia , Zhang Mei-Na , Liang Li-Juan , Tang Yu , Yan Chun-Hua
Published: January 2021

Design and engineering of highly efficient emitting materials with assembly-induced luminescence, such as room-temperature phosphorescence (RTP) and aggregation-induced emission (AIE), have stimulated extensive efforts. Here, we propose a new strategy to obtain size-controlled Eu3+-complex nanoparticles (Eu-NPs) with self-assembly-induced luminescence (SAIL) characteristics without encapsulation or hybridization. Compared with previous RTP or AIE materials, the SAIL phenomena of increased luminescence intensity and lifetime in aqueous solution for the proposed Eu-NPs are due to the combined effect of self-assembly in confining the molecular motion and shielding the water quenching. As proof of concept, we also show that this system can be further applied in bioimaging, temperature measurement and HClO sensing. The SAIL activity of the rare-earth (RE) system proposed here offers a further step forward on the roadmap for the development of RE light conversion systems and their integration in bioimaging and therapy applications.
Rifampicin Mono-Resistant Tuberculosis—A Review of an Uncommon But Growing Challenge for Global Tuberculosis Control
Authors: Malenfant Jason H , Brewer Timothy F
Published: January 2021

Tuberculosis (TB) remains the leading cause of death by an infectious pathogen worldwide, and drug-resistant TB is a critical and rising obstacle to global control efforts. Most scientific studies and global TB efforts have focused on multidrug-resistant TB (MDR-TB), meaning isolates resistant to both isoniazid (INH) and rifampicin (RIF). Newer diagnostic tests are resulting in an increasing awareness of RIF-resistant TB in addition to MDR disease. To date, RIF resistance has been assumed to be synonymous with MDR-TB, but this approach may expose TB patients with RIF mono-resistance disease to unnecessarily long and toxic treatment regimens. We review what is currently known about RIF mono-resistant TB, its history and epidemiology, mechanisms of RIF resistance, available diagnostic techniques, treatment outcomes reported globally, and future directions for combatting this disease.
HIV-1 Infection Does Not Change Disease Course or Inflammatory Pattern of SARS-CoV-2-Infected Patients Presenting at a Large Urban Medical Center in New York City
Authors: Laracy Justin , Zucker Jason , Castor Delivette , McMahon Donald J , Guo Tai Wei , Yan Michael , Shalev Noga , Scherer Matthew , Gordon Peter , Sobieszczyk Magdalena , Yin Michael T
Published: January 2021

Background

The clinical impact of coronavirus disease 2019 (COVID-19) among people with HIV (PWH) remains unclear. In this retrospective cohort study of COVID-19, we compared clinical outcomes and laboratory parameters among PWH and controls.

Methods

Sixty-eight PWH diagnosed with COVID-19 were matched 1:4 to patients without known HIV diagnosis, drawn from a study population of all patients who were diagnosed with COVID-19 at an academic urban hospital. The primary outcome was death/discharge to hospice within 30 days of hospital presentation.

Results

PWH were more likely to be admitted from the emergency department than patients without HIV (91% vs 71%; P = .001). We observed no statistically significant difference between admitted PWH and patients without HIV in terms of 30-day mortality rate (19% vs 13%, respectively) or mechanical ventilation rate (18% vs 20%, respectively). PWH had higher erythrocyte sedimentation rates than controls on admission but did not differ in other inflammatory marker levels or nasopharyngeal/oropharyngeal severe acute respiratory syndrome coronavirus 2 viral load estimated by reverse transcriptase polymerase chain reaction cycle thresholds.

Conclusions

HIV infection status was associated with a higher admission rate; however, among hospitalized patients, PWH did not differ from HIV-uninfected controls by rate of mechanical ventilation or death/discharge to hospice.
Stewards enquiry: challenging a professional trustee’s remuneration
Authors: Bueno Emily , Steen Peter
Published: January 2021

This article examines how a professional trustee charging remuneration to the trust is approached in respect of non-charitable trusts. It reminds the reader of the legal basis on which a professional trustee is able to charge for its fees, considers certain specific features of a professional trustee’s remuneration and examines the general approach of the courts to assessing a professional trustee’s charges. It also looks at the relative advantages and disadvantages of investigating a professional trustee’s charges before or after the resignation of a trustee and the winding up of a trust.
Meta-analysis of the effect of glycerin inclusion in dairy cattle diet on milk fatty acid profile
Authors: Torres Rodrigo N S , Bertoco João P A , de Arruda Maria C G , Rodrigues Julia L , Coelho Larissa M , Paschoaloto Josimari R , de Almeida Júnior Gercílio A , Ezequiel Jane M B , Almeida Marco T C
Published: January 2021

The use of glycerin in diets for dairy cows initially emerged as an alternative for the prevention and control of ketosis. However, despite some controversy, there are still several studies associating glycerin with increases in daily milk yield, with possible changes in its constituents. Therefore, the objective of this study was to evaluate, using a meta-analysis approach, the effect of glycerin inclusion in dairy cow diets on milk fatty acid. Twenty-two peer-reviewed publications with 66 treatment means were included in data set. The effect of glycerin inclusion in diet (treatment) were evaluated using random-effect models to examine the weighted mean differences (WMD) between a control diet (without glycerin in the diet) and the treatment diet. Heterogeneity was explored by meta-regression and subgroup analysis performed for: genetic type; days in milk; experimental period; glycerin in diet; glycerin type and concentrate in diet. Inclusion of glycerin in the diet increased the digestibility of dry matter and protein, as well as ruminal propionate. It did not affect dry matter intake (P = 0.351) and milk yield (P = 0.730). The effect of glycerin inclusion on the milk fat yield is dependent on the genetic group, in which Holstein (WMD = −0.04 kg/d; P = 0.010) and Holstein-crossbreed (WMD = −0.10 kg/d; P < 0.0001) cows produced less fat in milk compared to Jersey cows, when glycerin was included in the diets. Glycine inclusions of up to 100 g/kg in the diet of dairy cows did not negatively affect milk production and composition. However, inclusions above 150 g/kg of glycerin in the diet reduced the concentration of fat, and of unsaturated, monounsaturated, polyunsaturated fatty acids and conjugated linoleic acid (CLA C18: 2 cis-9 and trans-11) in milk. The results reported in our meta-analysis does not demonstrate the effectiveness of glycerin in improving the composition of milk and a group of fatty acids of importance for human health such as C18: 2 cis-9, trans-11 CLA.
Seasonal dynamics of non-structural carbon pools and their relationship to growth in two boreal conifer tree species
Authors: Schoonmaker A L , Hillabrand R M , Lieffers V J , Chow P S , Landhäusser S M
Published: January 2021

In an attempt to comprehensively study the dynamics of non-structural carbon compounds (NCCs), we measured the seasonal changes of soluble sugars, starch, lipids and sugar alcohols in the leaves, branches, stem and roots of the fast-growing Pinus contorta (Loudon) (pine) and slow-growing Picea glauca (Moench) Voss (spruce) trees growing in a boreal climate. In addition to measuring the seasonal concentrations of these compounds, the relative contribution of these compounds to the total NCC pool within the organs of trees (~8 m tall) was estimated and compared across different phenological and growth stages. Both species showed large seasonal shifts from starch to sugars from spring to fall in nearly all organs and tissues; most likely an adaptation to the cold winters. For both species, the total fluctuation of sugar + starch across the year (i.e., the difference between the minimum and maximum observed across collection times) was estimated to be between 1.6 and 1.8 kg for all NCCs. The fluctuation, however, was 1.40 times greater than the minimum reserves in pine, while only 0.72 times the minimum reserves in spruce. By tissue type, NCC fluctuations were greatest in the roots of both species. Roots showed a large build-up of reserves in late spring, but these reserves were depleted over summer and fall. Storage reserves in needles and branches declined over the summer, and this decline may be linked to the sink strength of the stem during diameter growth. Some notable highlights of this holistic study: a late winter build-up of sugars in the stem xylem of both species, but especially spruce; and an increase in sugar alcohols in the bark of spruce in very late winter, which could indicate mobilization to support early growth in spring and high lipid reserves in the bark of pine, which appeared not to be impacted by seasonal changes between summer and winter. Collectively, these observations point toward a more conservative NCC reserve strategy in spruce compared with pine, which is consistent with its stress tolerance and greater longevity.
Alternate primers for whole-genome SARS-CoV-2 sequencing
Authors: Cotten Matthew , Lule Bugembe Dan , Kaleebu Pontiano , V.T. Phan My
Published: January 2021

As the world is struggling to control the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is an urgency to develop effective control measures. Essential information is encoded in the virus genome sequence with accurate and complete SARS-CoV-2 sequences essential for tracking the movement and evolution of the virus and for guiding efforts to develop vaccines and antiviral drugs. While there is unprecedented SARS-CoV-2 sequencing efforts globally, approximately 19 to 43 per cent of the genomes generated monthly are gapped, reducing their information content. The current study documents the genome gap frequencies and their positions in the currently available data and provides an alternative primer set and a sequencing scheme to help improve the quality and coverage of the genomes.
Prediction of Late-Onset Sepsis in Preterm Infants Using Monitoring Signals and Machine Learning
Authors: Cabrera-Quiros Laura , Kommers Deedee , Wolvers Maria K. , Oosterwijk Laurien , Arents Niek , van der Sluijs-Bens Jacqueline , Cottaar Eduardus J. E. , Andriessen Peter , van Pul Carola
Published: January 2021

Objectives:

Prediction of late-onset sepsis (onset beyond day 3 of life) in preterm infants, based on multiple patient monitoring signals 24 hours before onset.

Design:

Continuous high-resolution electrocardiogram and respiration (chest impedance) data from the monitoring signals were extracted and used to create time-interval features representing heart rate variability, respiration, and body motion. For each infant with a blood culture-proven late-onset sepsis, a Cultures, Resuscitation, and Antibiotics Started Here moment was defined. The Cultures, Resuscitation, and Antibiotics Started Here moment served as an anchor point for the prediction analysis. In the group with controls (C), an “equivalent crash moment” was calculated as anchor point, based on comparable gestational and postnatal age. Three common machine learning approaches (logistic regressor, naive Bayes, and nearest mean classifier) were used to binary classify samples of late-onset sepsis from C. For training and evaluation of the three classifiers, a leave-k-subjects-out cross-validation was used.

Setting:

Level III neonatal ICU.

Patients:

The patient population consisted of 32 premature infants with sepsis and 32 age-matched control patients.

Interventions:

No interventions were performed.

Measurements and Main Results:

For the interval features representing heart rate variability, respiration, and body motion, differences between late-onset sepsis and C were visible up to 5 hours preceding the Cultures, Resuscitation, and Antibiotics Started Here moment. Using a combination of all features, classification of late-onset sepsis and C showed a mean accuracy of 0.79 ± 0.12 and mean precision rate of 0.82 ± 0.18 3 hours before the onset of sepsis.

Conclusions:

Information from routine patient monitoring can be used to predict sepsis. Specifically, this study shows that a combination of electrocardiogram-based, respiration-based, and motion-based features enables the prediction of late-onset sepsis hours before the clinical crash moment.
Immunophenotypic Differences in Tumor-Infiltrating Lymphocytes and Neovascularization Between Primary Cutaneous Melanoma With and Without Metastasis: An Immunohistochemical Study of 80 Cases
Authors: Salgüero Irene , Roustán Gaston , Requena Luis , Suárez Dolores , García-Fresnadillo Diego , Redondo José Ignacio , Nájera Laura
Published: January 2021

The prognostic implications of the immunophenotype of the tumor-infiltrating lymphocytes (TILs) in primary cutaneous melanoma are well known. In recent years, the study of this immunophenotype has also resulted in immunotherapeutic consequences. The aims of this study were to characterize the subpopulations of TILs in primary cutaneous melanoma, in cases with and without metastasis, as well as the neovascularization associated with the primary neoplasm, and its influence on the development of metastasis. To this end, the immunophenotype of TILs and the neovascularization of 80 patients with primary cutaneous melanoma (40 each with metastatic and non-metastatic melanoma) were analyzed by immunohistochemistry for CD3, CD4, CD8, FOXP3, PD-1, CD31, and D2-40 antibodies. We found that higher frequencies of TILs with brisk pattern, and CD4+, CD8+, and CD20+ cells in TILs, and a lower frequency of CD31+ vessels were histopathological features associated with better prognosis in primary cutaneous melanoma. Our results support the notion that the immunohistochemical study of TILs and neovascularization in primary cutaneous melanoma may be helpful tools for identifying patients at increased risk of metastasis development.
Long-Term Outcome of Femtosecond Laser–Assisted Keratopigmentation: Using Intacs Channels for Precise Pigment Deposition Within the Cornea
Authors: Yin Han Y. , Walter Keith A.
Published: January 2021

Purpose:

To describe a long-term outcome of a new technique using the femtosecond laser to assist with keratopigmentation (corneal tattooing).

Method:

Nineteen eyes of 18 patients with a history of significant visual disability related to iris defects underwent femtosecond laser–assisted keratopigmentation (FAK) for functional restoration of their visual disabilities. Postoperative visual acuity and symptomatic resolution were collected during their postoperative visits.

Results:

After FAK surgery, all patients had improvement in their previous visual-related symptoms. Eighteen of 19 eyes (94%) had improvement in their best-corrected Snellen visual acuity. Eight of 19 eyes (42%) had at least 1 line improvement, 8 of 19 eyes (42%) had at least 2 lines of improvement, and 2 of 19 eyes (10%) had at least 3 lines improvement. The average follow-up period was approximately 60 months.

Conclusions:

The FAK technique offers a long-term effective and safe technique for visual disabilities and improves visual acuity in patients with various traumatic iris defects.
Anterior Chamber Versus Ciliary Sulcus Ahmed Glaucoma Valve Tube Placement: Longitudinal Evaluation of Corneal Endothelial Cell Profiles
Authors: Godinho Gonçalo , Barbosa-Breda Joao , Oliveira-Ferreira Cláudia , Madeira Carolina , Melo António , Falcão-Reis Fernando , Estrela-Silva Sérgio
Published: January 2021

Précis:

An Ahmed glaucoma valve (AGV) tube in the ciliary sulcus (CS) is safer for the endothelium. At 4 years of follow-up, there was a significant decrease in endothelial cell count only with anterior chamber (AC) placement.

Purpose:

Corneal endothelium (CE) damage is one of the most feared long-term complications that can result from glaucoma drainage devices. Nonetheless, there is a lack of studies evaluating longitudinal changes in CE cells. This study aims to compare CE changes after AGV implantation in eyes with AC or CS tube placement.

Materials and Methods:

This was a retrospective, nonrandomized, longitudinal study of pseudophakic eyes with open-angle glaucoma and medically uncontrolled intraocular pressure that received an AGV. Eyes with additional glaucoma surgeries performed during follow-up were excluded. The main outcome measure was endothelial cell density (ECD), which was evaluated 1 year±2 months and 4 years±2 months postoperatively. The average endothelial cell size (AS) and the distance from the tube tip to the cornea were also evaluated.

Results:

Twenty-six eyes from 26 patients, with a mean age of 73±10 years, were included. The tube was placed in the AC in 15 eyes and in the CS in 11 eyes. The eyes with tube placement in the AC showed a significant AS increase (P=0.007) and ECD decrease (P=0.034), whereas eyes with tube placement in the CS had no significant AS (P=0.575) or ECD (P=0.445) change. In the eyes with tube placement in the AC, there was no correlation between DTC and ECD (P=0.260) or AS (P=0.428) changes.

Conclusions:

Tube placement in the AC seems to lead to significant CE cell loss over time, compared with tube placement in the CS.