bluuebunny/crossref_metadata_2025 huggingface dataset:
Gaia’s detectability of black hole–main sequence star binaries formed in open clusters
Authors: Shikauchi Minori , Kumamoto Jun , Tanikawa Ataru , Fujii Michiko S
Published: March 2020

Black hole–main sequence star (BH–MS) binaries are one of the targets of future data releases of the astrometric satellite Gaia. They are supposed to be formed in two main sites: a galactic field and star clusters. However, previous work has never predicted the number of BH–MS binaries originating in the latter sites. In this paper we estimate the number of BH–MS binaries formed in open clusters and detectable with Gaia based on the results of N-body simulations. By considering interstellar extinction in the Milky Way and observational constraints, we predict that ∼10 BH–MS binaries are observable. We also find that chemical abundance patterns of companion MSs will help us to identify the origin of the binaries as star clusters. Such MSs are not polluted by outflows of the BH progenitors, such as stellar winds and supernova ejecta. Chemical anomalies might be a good test to confirm the origin of binaries with relatively less massive MSs (≲5 M⊙), short orbital periods (∼1.5 yr), and higher eccentricities (e ≳0.1).
Productive performance and cost benefits of feeding wistar albino rats with processed tropical sickle pod (Senna obtusifolia) leaf meal-based diets
Authors: Augustine Clement , Khobe Dishi , Madugu Altine J , Babakiri Yahaya , Joel Isa , John Tiva , Igwebuike Joseph U , Ibrahim Asabe
Published: March 2020

A feeding trial was conducted for 28 d to evaluate the effects of feeding albino rats with processed Senna obtusifolia leaf meal (SOLM) based diets. Five experimental diets were compounded to contain 0% and 20% each of the sun-dried, boiled, fresh fermented, boiled fermented SOLM-based diets designated as T1, T2, T3, T4, and T5, respectively. A total of 90 young albino rats with initial weight of 13.52–14.48 g were randomly allocated to the dietary treatments in a completely randomized design with three replicates of six rats each. The result of the productive performance was not significantly (P > 0.05) different, except feed intake, which indicated significant (P < 0.05) variation. The highest total feed intake (365.40 g) was recorded in albino rats fed the control diet (0% SOLM) and 20% boiled and fermented SOLM (334.32 g). The overall weight gain among the albino rats fed the processed SOLM-based diets were not significantly (P > 0.05) different. Results on cost benefits revealed a reduction in feed cost per kilogram, cost of feed intake, and feed cost per kilogram body weight gain recorded in SOLM-based diets (T2–T5). Feed cost per kilogram was observed to reduce by 21.86, 20.79, 21.80, and 18.79 in T2–T5, respectively. It was concluded that the processed SOLM-based diets had enhanced the productive performance of albino rats. However, albino rats fed the boiled and fermented SOLM-based diet indicated better feed intake compared with the other groups of rats fed the other processed SOLM-based diets. On economic grounds, the use of processed SOLM as a feed ingredient for albino rats is cost effective because of the reduction in feed cost per kilogram of the SOLM-based diets and feed cost per kilogram body weight gain observed in albino rats fed SOLM-based diets and is, therefore, recommended for feeding albino rats.
Compression wood has a minor effect on the climate signal in tree-ring stable isotope records of montane Norway spruce
Authors: Janecka Karolina , Kaczka Ryszard J , Gärtner Holger , Harvey Jill E , Treydte Kerstin
Published: March 2020

Compression wood (CW) is a common tissue present in the trunk, branches and roots of mechanically stressed coniferous trees. Its main role is to increase the mechanical strength and regain the vertical orientation of a leaning stem. Compression wood is thought to influence the climate signal in different tree-ring measures. Hence trees containing CW are mostly excluded from tree-ring studies reconstructing past climate variability. There is a large gap of systematic work testing the potential effect of CW on the strength of the climate signal in different tree-ring parameters, especially stable isotope records. Here we test for the first time the effect of CW contained in montane Norway spruce (Picea abies L. Karst) on both δ13C and δ18O tree-ring cellulose records by analyzing compression and opposite wood radii from several disturbed trees together with samples from undisturbed reference trees. We selected four trees tilted by geomorphic processes that were felled by wind and four undisturbed reference trees in the Tatra Mountains, Poland. We qualitatively classified the strength of CW using wood cell anatomical characteristics (tracheid shape, cell wall thickness and presence of intercellular spaces). Then we developed tree-ring width and δ13C and δ18O chronologies from the CW radii, from the opposite radii of the tilted trees and from the reference radii. We tested the effect of CW on tree-ring cellulose δ13C and δ18O variability and on the climate signal strength. We found only minor differences in the means of δ13C and δ18O of compression (δ13C: −22.81‰, δ18O: 28.29‰), opposite (δ13C: −23.02‰; δ18O: 28.05‰) and reference (δ13C: −22.78‰; δ18O: 27.61‰) radii. The statistical relationships between climate variables, δ13C and δ18O, remained consistent among all chronologies. Our findings suggest that moderately tilted trees containing CW can be used to reconstruct past geomorphic activity and for stable isotope-based dendroclimatology.
Disentangling the effects of atmospheric CO2 and climate on intrinsic water-use efficiency in South Asian tropical moist forest trees
Authors: Rahman Mizanur , Islam Mahmuda , Gebrekirstos Aster , Bräuning Achim
Published: March 2020

Due to the increase in atmospheric CO2 concentrations, the ratio of carbon fixed by assimilation to water lost by transpiration through stomatal conductance (intrinsic water-use efficiency, iWUE) shows a long-term increasing trend globally. However, the drivers of short-term (inter-annual) variability in iWUE of tropical trees are poorly understood. We studied the inter-annual variability in iWUE of three South Asian tropical moist forest tree species (Chukrasia tabularis A.Juss., Toona ciliata M. Roem. and Lagerstroemia speciosa L.) derived from tree-ring stable carbon isotope ratio (δ13C) in response to variations of environmental conditions. We found a significantly decreasing trend in carbon discrimination (Δ13C) and an increasing trend in iWUE in all the three species, with a species-specific long-term trend in intercellular CO2 concentration (Ci). Growing season temperatures were the main driver of inter-annual variability of iWUE in C. tabularis and L. speciosa, whereas previous year temperatures determined the iWUE variability in T. ciliata. Vapor pressure deficit was linked with iWUE only in C. tabularis. Differences in shade tolerance, tree stature and canopy position might have caused this species-specific variation in iWUE response to climate. Linear mixed effect modeling successfully simulated iWUE variability, explaining 41–51% of the total variance varying with species. Commonality analysis revealed that temperatures had a dominant influence on the inter-annual iWUE variability (64–77%) over precipitation (7–22%) and atmospheric CO2 concentration (3–6%). However, the long-term variations in iWUE were explicitly determined by the atmospheric CO2 increase (83–94%). Our results suggest that the elevated CO2 and concomitant global warming might have detrimental effects on gas exchange and other physiological processes in South Asian tropical moist forest trees.
Matched Pairs Comparison of an Enhanced Recovery Pathway Versus Conventional Management on Opioid Exposure and Pain Control in Patients Undergoing Lung Surgery
Authors: Rice David , Rodriguez-Restrepo Andrea , Mena Gabriel , Cata Juan , Thall Peter , Milton Denai , Correa Arlene , Woodard TaCharra , Antonoff Mara , Hofstetter Wayne , Roth Jack , Sepesi Boris , Swisher Stephen , Walsh Garrett , Vaporciyan Ara , Mehran Reza
Published: March 2020

Objective:

The aim of this study was to assess the effect of an enhanced recovery after surgery (ERAS) pathway on pain and opioid use following lung resection.

Summary Background Data:

A major component ERAS pathways is opioid-sparing analgesia; however, the effect on postoperative pain and opioid use in patients undergoing lung resection is unknown.

Methods:

Following implementation of an ERAS pathway for lung resection, 123 consecutive patients were identified. Patients were propensity-matched 1:1 with a group of consecutive patients (n = 907) undergoing lung resection before ERAS. Differences regarding in-hospital opioid consumption, discharge prescribing of opioids, and postoperative pain scores were examined. Morphine milligram equivalents were separately calculated including and excluding tramadol as an opioid medication.

Results:

There were no significant differences between matched patients regarding age, sex, performance status, receipt of preoperative treatment, extent of lung resection, or operative approach. Epidural analgesia was used in 66% of controls and in none of the ERAS group (P < 0.001). The number of adjunct analgesics used postoperatively was greater in the ERAS group (median 3 vs 2, P < 0.001). There was a major reduction in morphine milligram equivalents in the ERAS group whether tramadol was included (median 14.2 vs 57.8, P < 0.001) or excluded (median 2.7 vs 57.8, P < 0.001) and regardless of surgical approach. Average daily pain scores were lower in the ERAS group (median 1.3 vs 1.8, P = 0.004); however, this difference was present only among patients undergoing thoracotomy. The proportion of patients who were prescribed discharge opioids varied whether tramadol was included (96% each group, P = 1.00) or excluded (39% vs 80%, P < 0.001) in the analysis.

Conclusions:

Implementation of an ERAS pathway was associated with effective post-operative analgesia, major reductions in in-hospital consumption of opioids, and reduced pain, compared to conventional management.
Inducible Left Ventricular Outflow Tract Obstruction in Patients Undergoing Liver Transplantation: Prevalence, Predictors, and Association With Cardiovascular Events
Authors: Cailes Benjamin , Koshy Anoop N. , Gow Paul , Weinberg Laurence , Srivastava Piyush , Testro Adam , Peverelle Matthew , Ko Jefferson , Salehi Hamid , Jones Elizabeth F. , Calafiore Paul , Farouque Omar
Published: March 2020

Background.

Inducible left ventricular outflow tract obstruction (LVOTO) is often encountered in liver transplantation (LT) candidates during cardiac workup. While the impact of LVOTO on adverse cardiovascular hemodynamics is well reported, it is unclear whether it predisposes to perioperative cardiovascular complications.

Methods.

Consecutive patients with end-stage liver disease undergoing dobutamine stress echocardiography (DSE) were evaluated at an LT center between 2010 and 2017. Perioperative major adverse cardiovascular events (MACEs) at 30 days and all-cause death were recorded from a prospectively maintained LT database.

Results.

We evaluated 560 patients who underwent DSE during LT workup, with LVOTO identified in 24.3% (n = 136). Of these, 309 patients progressed to transplant. Patients with LVOTO demonstrated a lower peak systolic blood pressure (SBP) and an overall reduction in SBP on DSE. A total of 85 MACEs were recorded in 72 patients (23.3%) including 3 deaths, 19 cases of heart failure, 11 cardiac arrests, 8 acute coronary syndromes, and 44 arrhythmias. MACE occurred in 15/64 patients (23.4%) with LVOTO and 57/245 (23.3%) without (P = 0.92). There was an increased risk of perioperative cardiac arrest in patients with LVOTO (7.4% versus 2.4%, P = 0.04). Intraoperatively, patients with LVOTO required higher doses of vasopressors (P = 0.01) and received greater volumes of fluid (10.5 ± 8.1 versus 8.4 ± 6.4 L, P = 0.03).

Conclusions.

Patients with end-stage liver disease and LVOTO demonstrate a reduction in SBP during physiological stress that may translate to hemodynamic instability during LT. LVOTO was not associated with an increased rate of perioperative MACE or death.
Myriapod haemocyanin: the first three-dimensional reconstruction ofScolopendra subspinipesand preliminary structural analysis ofS. viridicornis
Authors: Riciluca K. C. T. , Borges A. C. , Mello J. F. R. , de Oliveira U. C. , Serdan D. C. , Florez-Ariza A. , Chaparro E. , Nishiyama M. Y. , Cassago A. , Junqueira-de-Azevedo I. L. M. , van Heel M. , Silva P. I. , Portugal R. V.
Published: March 2020

Haemocyanins (Hcs) are copper-containing, respiratory proteins that occur in the haemolymph of many arthropod species. Here, we report the presence of Hcs in the chilopode Myriapoda, demonstrating that these proteins are more widespread among the Arthropoda than previously thought. The analysis of transcriptome ofS. subspinipes subpinipesreveals the presence of two distinct subunits of Hc, where the signal peptide is present, and six of prophenoloxidase (PPO), where the signal peptide is absent, in the 75 kDa range. Size exclusion chromatography profiles indicate different quaternary organization for Hc of both species, which was corroborated by TEM analysis:S. viridicornisHc is a 6 × 6-mer andS. subspinipesHc is a 3 × 6-mer, which resembles the half-structure of the 6 × 6-mer but also includes the presence of phenoloxidases, since the 1 × 6-mer quaternary organization is commonly associated with hexamers of PPO. Studies with Chelicerata showed that PPO activity are exclusively associated with the Hcs. This study indicates thatScolopendramay have different proteins playing oxygen transport (Hc) and PO function, both following the hexameric oligomerization observed in Hcs.
The effect of preregistration on trust in empirical research findings: results of a registered report
Authors: Field Sarahanne M. , Wagenmakers E.-J. , Kiers Henk A. L. , Hoekstra Rink , Ernst Anja F. , van Ravenzwaaij Don
Published: March 2020

The crisis of confidence has undermined the trust that researchers place in the findings of their peers. In order to increase trust in research, initiatives such as preregistration have been suggested, which aim to prevent various questionable research practices. As it stands, however, no empirical evidence exists that preregistration does increase perceptions of trust. The picture may be complicated by a researcher's familiarity with the author of the study, regardless of the preregistration status of the research. This registered report presents an empirical assessment of the extent to which preregistration increases the trust of 209 active academics in the reported outcomes, and how familiarity with another researcher influences that trust. Contrary to our expectations, we report ambiguous Bayes factors and conclude that we do not have strong evidence towards answering our research questions. Our findings are presented along with evidence that our manipulations were ineffective for many participants, leading to the exclusion of 68% of complete datasets, and an underpowered design as a consequence. We discuss other limitations and confounds which may explain why the findings of the study deviate from a previously conducted pilot study. We reflect on the benefits of using the registered report submission format in light of our results. The OSF page for this registered report and its pilot can be found here:
http://dx.doi.org/10.17605/OSF.IO/B3K75
.
Controlled release of basic fibroblast growth factor from a peptide biomaterial for bone regeneration
Authors: Zhao WeiKang , Li Yuling , Zhou Ao , Chen Xiaojun , Li Kai , Chen Sinan , Qiao Bo , Jiang Dianming
Published: March 2020

Self-assembled peptide scaffolds based on D-RADA16 are an important matrix for controlled drug release and three-dimensional cell culture. In this work, D-RADA16 peptide hydrogels were coated on artificial bone composed of nano-hydroxyapatite/polyamide 66 (nHA/PA66) to obtain a porous drug-releasing structure for treating bone defects. The developed materials were characterized via transmission electron microscopy and scanning electron microscopy. The proliferation and adhesion of bone mesenchymal stem cells (BMSCs) were examined by confocal laser microscopy and CCK-8 experiments. The osteogenic ability of the porous materials towards bone BMSCs was examined
in vitro
by staining with Alizarin Red S and alkaline phosphatase, and bioactivity was evaluated
in vivo
. The results revealed that nHA/PA66/D-RADA16/bFGF reduces the degradation rate of D-RADA16 hydrogels and prolongs sustained release of bFGF, which would promote BMSCs proliferation, adhesion and osteogenesis
in vitro
and bone repair
in vivo
. Thus, it deserves more attention and is worthy of further research.
Genetic evidence further elucidates the history and extent of badger introductions from Great Britain into Ireland
Authors: Allen Adrian , Guerrero Jimena , Byrne Andrew , Lavery John , Presho Eleanor , Courcier Emily , O'Keeffe James , Fogarty Ursula , Delahay Richard , Wilson Gavin , Newman Chris , Buesching Christina , Silk Matthew , O'Meara Denise , Skuce Robin , Biek Roman , McDonald Robbie A.
Published: March 2020

The colonization of Ireland by mammals has been the subject of extensive study using genetic methods and forms a central problem in understanding the phylogeography of European mammals after the Last Glacial Maximum. Ireland exhibits a depauperate mammal fauna relative to Great Britain and continental Europe, and a range of natural and anthropogenic processes have given rise to its modern fauna. Previous Europe-wide surveys of the European badger (Meles meles) have found conflicting microsatellite and mitochondrial DNA evidence in Irish populations, suggesting Irish badgers have arisen from admixture between human imported British and Scandinavian animals. The extent and history of contact between British and Irish badger populations remains unclear. We use comprehensive genetic data from Great Britain and Ireland to demonstrate that badgers in Ireland's northeastern and southeastern counties are genetically similar to contemporary British populations. Simulation analyses suggest this admixed population arose in Ireland 600–700 (CI 100–2600) years before present most likely through introduction of British badgers by people. These findings add to our knowledge of the complex colonization history of Ireland by mammals and the central role of humans in facilitating it.
Differential impact of severe drought on infant mortality in two sympatric neotropical primates
Authors: Campos Fernando A. , Kalbitzer Urs , Melin Amanda D. , Hogan Jeremy D. , Cheves Saul E. , Murillo-Chacon Evin , Guadamuz Adrián , Myers Monica S. , Schaffner Colleen M. , Jack Katharine M. , Aureli Filippo , Fedigan Linda M.
Published: March 2020

Extreme climate events can have important consequences for the dynamics of natural populations, and severe droughts are predicted to become more common and intense due to climate change. We analysed infant mortality in relation to drought in two primate species (white-faced capuchins,
Cebus capucinus imitator,
and Geoffroy's spider monkeys,
Ateles geoffroyi
) in a tropical dry forest in northwestern Costa Rica. Our survival analyses combine several rare and valuable long-term datasets, including long-term primate life-history, landscape-scale fruit abundance, food-tree mortality, and climate conditions. Infant capuchins showed a threshold mortality response to drought, with exceptionally high mortality during a period of intense drought, but not during periods of moderate water shortage. By contrast, spider monkey females stopped reproducing during severe drought, and the mortality of infant spider monkeys peaked later during a period of low fruit abundance and high food-tree mortality linked to the drought. These divergent patterns implicate differing physiology, behaviour or associated factors in shaping species-specific drought responses. Our findings link predictions about the Earth's changing climate to environmental influences on primate mortality risk and thereby improve our understanding of how the increasing severity and frequency of droughts will affect the dynamics and conservation of wild primates.
Microstructure-sensitive critical plastic strain energy density criterion for fatigue life prediction across various loading regimes
Authors: Bandyopadhyay Ritwik , Prithivirajan Veerappan , Peralta Alonso D. , Sangid Michael D.
Published: March 2020

In the present work, we postulate that a critical value of the stored plastic strain energy density (SPSED) is associated with fatigue failure in metals and is independent of the applied load. Unlike the classical approach of estimating the (homogenized) SPSED as the cumulative area enclosed within the macroscopic stress–strain hysteresis loops, we use crystal plasticity finite element simulations to compute the (local) SPSED at each material point within polycrystalline aggregates of a nickel-based superalloy. A Bayesian inference method is used to calibrate the critical SPSED, which is subsequently used to predict fatigue lives at nine different strain ranges, including strain ratios of 0.05 and −1, using nine statistically equivalent microstructures. For each strain range, the predicted lives from all simulated microstructures follow a lognormal distribution. Moreover, for a given strain ratio, the predicted scatter is seen to be increasing with decreasing strain amplitude; this is indicative of the scatter observed in the fatigue experiments. Finally, the lognormal mean lives at each strain range are in good agreement with the experimental evidence. Since the critical SPSED captures the experimental data with reasonable accuracy across various loading regimes, it is hypothesized to be a material property and sufficient to predict the fatigue life.
Underwater caustics disrupt prey detection by a reef fish
Authors: Matchette S. R. , Cuthill I. C. , Cheney K. L. , Marshall N. J. , Scott-Samuel N. E.
Published: March 2020

Natural habitats contain dynamic elements, such as varying local illumination. Can such features mitigate the salience of organism movement? Dynamic illumination is particularly prevalent in coral reefs, where patterns known as ‘water caustics’ play chaotically in the shallows. In behavioural experiments with a wild-caught reef fish, the Picasso triggerfish (
Rhinecanthus aculeatus
), we demonstrate that the presence of dynamic water caustics negatively affects the detection of moving prey items, as measured by attack latency, relative to static water caustic controls. Manipulating two further features of water caustics (sharpness and scale) implies that the masking effect should be most effective in shallow water: scenes with fine scale and sharp water caustics induce the longest attack latencies. Due to the direct impact upon foraging efficiency, we expect the presence of dynamic water caustics to influence decisions about habitat choice and foraging by wild prey and predators.
Positive correlations in species functional contributions drive the response of multifunctionality to biodiversity loss
Authors: Heilpern Sebastian A. , Anujan Krishna , Osuri Anand , Naeem Shahid
Published: March 2020

Changes in biodiversity can severely affect ecosystem functioning, but the impacts of species loss on an ecosystem's ability to sustain multiple functions remain unclear. When considering individual functions, the impacts of biodiversity loss depend on correlations between species functional contributions and their extinction probabilities. When considering multiple functions, the impacts of biodiversity loss depend on correlations between species contributions to individual functions. However, how correlations between extinction probabilities and functional contributions determine the impact of biodiversity loss on multifunctionality (MF) is not well understood. Here, we use biodiversity loss simulations to examine the influence of correlations among multiple functions and extinction probabilities on the diversity–MF relationship. In contrast with random extinction, we find that the response of MF to biodiversity loss is influenced by the absence of positive correlations between species functional contributions, rather than by negative correlations. Communities with a high number of pairwise positive correlations in functional contributions achieve higher levels of MF, but are also less resilient to extinction. This work implies that understanding how species extinction probabilities correlate with their contribution to MF can help identify the degree to which MF will change with ongoing biodiversity loss and target conservation efforts to maximize MF resiliency.
Division of labour promotes the spread of information in colony emigrations by the ant
Temnothorax rugatulus
Authors: Valentini Gabriele , Masuda Naoki , Shaffer Zachary , Hanson Jake R. , Sasaki Takao , Walker Sara Imari , Pavlic Theodore P. , Pratt Stephen C.
Published: March 2020

The fitness of group-living animals often depends on how well members share information needed for collective decision-making. Theoretical studies have shown that collective choices can emerge in a homogeneous group of individuals following identical rules, but real animals show much evidence for heterogeneity in the degree and nature of their contribution to group decisions. In social insects, for example, the transmission and processing of information is influenced by a well-organized division of labour. Studies that accurately quantify how this behavioural heterogeneity affects the spread of information among group members are still lacking. In this paper, we look at nest choices during colony emigrations of the ant
Temnothorax rugatulus
and quantify the degree of behavioural heterogeneity of workers. Using clustering methods and network analysis, we identify and characterize four behavioural castes of workers—primary, secondary, passive and wandering—covering distinct roles in the spread of information during an emigration. This detailed characterization of the contribution of each worker can improve models of collective decision-making in this species and promises a deeper understanding of behavioural variation at the colony level.
Pseudomonas kitaguniensis sp. nov., a pathogen causing bacterial rot of Welsh onion in Japan
Authors: Sawada Hiroyuki , Fujikawa Takashi , Nishiwaki Yoshie , Horita Harukuni
Published: March 2020

Five Gram-reaction-negative, aerobic, motile with one to three polar flagella, rod-shaped bacterial strains, MAFF 212408T, MAFF 212409, MAFF 212410, MAFF 301498 and MAFF 730085, were isolated from diseased Welsh onion (Allium fistulosumL.) in Japan. Analysis of their 16S rRNA gene sequences showed that they belong to the genusPseudomonaswith the highest similarity toPseudomonas extremaustralis14-3T(99.86 %),Pseudomonas antarcticaCMS 35T(99.79 %) andPseudomonas poaeDSM 14936T(99.72%). The genomic DNA G+C content was 59.5 mol% and the major fatty acids (>5 %) were summed feature 3, C16 : 0, summed feature 8 and C12 : 02-OH. Multilocus sequence analysis using therpoD,gyrBandrpoBgene sequences and phylogenomic analysis based on the 90 core genes demonstrated that the strains are members of theP. fluorescenssubgroup, but are distant from all closely related species. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analysis confirmed low genomic relatedness to their closest relatives [below the recommended thresholds of 95 % (ANI) and 70 % (dDDH) for prokaryotic species delineation]. The strains were characterized by using API 20NE and Biolog GEN III tests, and inoculation tests in Welsh onion, showing that they are phenotypically differentiated from their closest relatives. Based on the genetic and phenotypic evidence, the strains should be classified as representing a novel species, for which the namePseudomonas kitaguniensissp. nov. is proposed. The type strain is MAFF 212408T(=ICMP 23530T).
Defining metrics for whole-genome sequence analysis of MRSA in clinical practice
Authors: Raven Kathy E. , Blane Beth , Kumar Narender , Leek Danielle , Bragin Eugene , Coll Francesc , Parkhill Julian , Peacock Sharon J.
Published: March 2020

Bacterial sequencing will become increasingly adopted in routine microbiology laboratories. Here, we report the findings of a technical evaluation of almost 800 clinical methicillin-resistant

Staphylococcus aureus

(MRSA) isolates, in which we sought to define key quality metrics to support MRSA sequencing in clinical practice. We evaluated the accuracy of mapping to a generic reference versus clonal complex (CC)-specific mapping, which is more computationally challenging. Focusing on isolates that were genetically related (<50 single nucleotide polymorphisms (SNPs)) and belonged to prevalent sequence types, concordance between these methods was 99.5 %. We use MRSA MPROS0386 to control for base calling accuracy by the sequencer, and used multiple repeat sequences of the control to define a permitted range of SNPs different to the mapping reference for this control (equating to 3 standard deviations from the mean). Repeat sequences of the control were also used to demonstrate that SNP calling was most accurate across differing coverage depths (above 35×, the lowest depth in our study) when the depth required to call a SNP as present was at least 4−8×. Using 786 MRSA sequences, we defined a robust measure for mec gene detection to reduce false-positives arising from contamination, which was no greater than 2 standard deviations below the average depth of coverage across the genome. Sequencing from bacteria harvested from clinical plates runs an increased risk of contamination with the same or different species, and we defined a cut-off of 30 heterozygous sites >50 bp apart to identify same-species contamination for MRSA. These metrics were combined into a quality-control (QC) flowchart to determine whether sequence runs and individual clinical isolates passed QC, which could be adapted by future automated analysis systems to enable rapid hands-off sequence analysis by clinical laboratories.
Identification of genes required for the fitness of Streptococcus equi subsp. equi in whole equine blood and hydrogen peroxide
Authors: Charbonneau Amelia R. L. , Taylor Emma , Mitchell Catriona J. , Robinson Carl , Cain Amy K. , Leigh James A. , Maskell Duncan J. , Waller Andrew S.
Published: March 2020

The availability of next-generation sequencing techniques provides an unprecedented opportunity for the assignment of gene function.Streptococcus equisubspeciesequiis the causative agent of strangles in horses, one of the most prevalent and important diseases of equids worldwide. However, the live attenuated vaccines that are utilized to control this disease cause adverse reactions in some animals. Here, we employ transposon-directed insertion-site sequencing (TraDIS) to identify genes that are required for the fitness ofS. equiin whole equine blood or in the presence of H2O2to model selective pressures exerted by the equine immune response during infection. We report the fitness values of 1503 and 1471 genes, representing 94.5 and 92.5 % of non-essential genes inS. equi, following incubation in whole blood and in the presence of H2O2, respectively. Of these genes, 36 and 15 were identified as being important to the fitness ofS. equiin whole blood or H2O2, respectively, with 14 genes being important in both conditions. Allelic replacement mutants were generated to validate the fitness results. Our data identify genes that are important forS. equito resist aspects of the immune responsein vitro, which can be exploited for the development of safer live attenuated vaccines to prevent strangles.
Syndromic detectability of haemorrhagic fever outbreaks
Authors: Glennon Emma E. , Jephcott Freya L. , Oti Alexandra , Carlson Colin J. , Bustos Carillo Fausto A. , Hranac C. Reed , Parker Edyth , Wood James L. N. , Restif Olivier
Published: March 2020

Late detection of emerging viral transmission allows outbreaks to spread uncontrolled, the devastating consequences of which are exemplified by recent epidemics of Ebola virus disease. Especially challenging in places with sparse healthcare, limited diagnostic capacity, and public health infrastructure, syndromes with overlapping febrile presentations easily evade early detection. There is a clear need for evidence-based and context-dependent tools to make syndromic surveillance more efficient. Using published data on symptom presentation and incidence of 21 febrile syndromes, we develop a novel algorithm for aetiological identification of case clusters and demonstrate its ability to identify outbreaks of dengue, malaria, typhoid fever, and meningococcal disease based on clinical data from past outbreaks. We then apply the same algorithm to simulated outbreaks to systematically estimate the syndromic detectability of outbreaks of all 21 syndromes. We show that while most rare haemorrhagic fevers are clinically distinct from most endemic fevers in sub-Saharan Africa, VHF detectability is limited even under conditions of perfect syndromic surveillance. Furthermore, even large clusters (20+ cases) of filoviral diseases cannot be routinely distinguished by the clinical criteria present in their case definitions alone; we show that simple syndromic case definitions are insensitive to rare fevers across most of the region. We map the estimated detectability of Ebola virus disease across sub-Saharan Africa, based on geospatially mapped estimates of malaria, dengue, and other fevers with overlapping syndromes. We demonstrate “hidden hotspots” where Ebola virus is likely to spill over from wildlife and also transmit undetected for many cases. Such places may represent both the locations of past unobserved outbreaks and potential future origins for larger epidemics. Finally, we consider the implications of these results for improved locally relevant syndromic surveillance and the consequences of syndemics and under-resourced health infrastructure for infectious disease emergence.
The SARS-CoV-2 epidemic outbreak: a review of plausible scenarios of containment and mitigation for Mexico
Authors: Acuña-Zegarra Manuel Adrian , Comas-García Andreu , Hernández-Vargas Esteban , Santana-Cibrian Mario , Velasco-Hernandez Jorge X.
Published: March 2020

We present here several variants of a mathematical model to explore three main issues related to SARS-CoV-2 spread in scenarios similar to those present in Mexico and elsewhere in Latin America. We explore the consequences for travel inside a given region, in this case Mexico, particularly focusing on airplane transportation but attempting to give a gross approximation to terrestrial movement since this is the main form of population movement across geographical areas in the country; then we proceed to study the effect of behavioral changes required to lower transmission by lowering the contact rate and infection probability and lastly, we explore the consequences of disease spread in a population subject to social isolation.These models are not suitable for predictive purposes although some rough predictions can be extracted from them. They are presented as a tool that can serve to explore plausible scenarios of spread and impact, effectiveness and consequences of contention and mitigation policies. Given the early stage at which the epidemic is at the date of writing in Mexico, we hope these ideas can be helpful for the understanding of the importance of isolation, social distancing and screening of the general population.

Key findings

We have estimated the parameters of the epidemic curve (growth rate, carrying capacity and dispersion) as well as a first estimate of the basic reproduction number for Mexico.

We provide expected trends of epidemic outbreaks depending upon of the number of imported cases per day arriving to a large airport. We illustrate this trends with data from Mexico City airport.

We provide expected trends of disease dispersal depending upon of the number of exported cases per day either by airplane or bus. We illustrate this trends with data from Mexico City.

We evaluate the effect of behavioral change to reduce the contact rate and compare diverse scenarios that evaluate the timing of initial enforcement of behavior, time horizon in which to diminish the contact rate and the proportion of people under isolation.

We evaluate the effect of social isolation by itself with respect to two main parameters: the starting time for the enforcement of control measures, and the learning time to achieve the desired contact rate reduction. We stress the importance of quick and direct actions to isolate and reduce contact rate simultaneously.
A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production
Authors: Bhadra Sanchita , Maranhao Andre C. , Ellington Andrew D.
Published: March 2020

Given the scale of the ongoing COVID-19 pandemic, the need for reliable, scalable testing, and the likelihood of reagent shortages, especially in resource-poor settings, we have developed a RT-qPCR assay that relies on an alternative to conventional viral reverse transcriptases, a thermostable reverse transcriptase / DNA polymerase (RTX)1. Here we show that RTX performs comparably to the other assays sanctioned by the CDC and validated in kit format. We demonstrate two modes of RTX use – (i) dye-based RT-qPCR assays that require only RTX polymerase, and (ii) TaqMan RT-qPCR assays that use a combination of RTX and Taq DNA polymerases (as the RTX exonuclease does not degrade a TaqMan probe). We also provide straightforward recipes for the purification of this alternative reagent. We anticipate that in low resource or point-of-need settings researchers could obtain the available constructs from Addgene or our lab and begin to develop their own assays, within whatever regulatory framework exists for them.

We lay out protocols for dye-based and TaqMan probe-based assays, in order to best compare with ‘gold standard’ reagents. These protocols should form the basis of further modifications that can simplify the assay to the use of overexpressing cells themselves as reagents.

Developing dye-based and TaqMan probe-based RT-qPCR assays with RTX
Temporally-precise basolateral amygdala activation is required for the formation of taste memories in gustatory cortex
Authors: Arieli Elor , Gerbi Ron , Shein-Idelson Mark , Moran Anan
Published: March 2020

Learning to associate malaise with the intake of novel food is critical for survival. Since food poisoning may take hours to affect, animals developed brain circuits to transform the current novel taste experience into a taste memory trace (TMT) and bridge this time lag. Ample studies showed that the basolateral amygdala (BLA), the nucleus basalis magnocellularis (NBM) and the gustatory cortex (GC) are involved in TMT formation and taste-malaise association. However, how dynamic activity across these brain regions during novel taste experience promotes the formation of these memories is currently unknown. We used the conditioned taste aversion (CTA) learning paradigm in combination with short-term optogenetics and electrophysiological recording in rats to test the hypothesis that temporally specific activation of BLA projection neurons is essential for TMT formation in the GC, and consequently CTA. We found that late-epoch (LE, >800ms), but not the early epoch (EE, 200-700ms), BLA activation during novel taste experience is essential for normal CTA, for early c-Fos expression in the GC (a marker of TMT formation) and for the subsequent changes in GC ensemble palatability coding. Interestingly, BLA activity was not required for intact taste identity or palatability perceptions. We further show that BLA-LE information is transmitted to GC through the BLA→NBM pathway where it affects the formation of taste memories. These results expose the dependence of long-term memory formation on specific temporal windows during sensory responses and the distributed circuits supporting this dependence.

Significance

Consumption of a novel taste may result in malaise and poses a threat to animals. Since the effects of poisoning appear only hours after consumption, animals must store the novel taste’s information in memory until they associate it with its value (nutritious or poisonous). Here we elucidate the neuronal activity patterns and circuits that support the processing and creation of novel-taste memories in rats. Our results show that specific patterns of temporal activation in the basolateral amygdala transmitted across brain areas are important for formation of taste memory and taste-malaise association. These findings may shed light on long-term activity-to-memory transformation in other sensory modalities.
Flocked swab might be one main reason causing the high false-negative rate in COVID-19 screening----the advantages of a novel silicone swab
Authors: Zhou Jianye , Bai Zhongtian , Liu Xiaoping , Guo Yaqiong , Jiang Nan , Li Xiaodong , Zhang Xiaohui , Li Zhiqiang , Li Yonghong , Ma Zhongren , Zhao Jin
Published: March 2020

RNA testing using RT-PCR can provide direct evidence for diagnoses of COVID-19 which has brought unexpected disasters and changes to our human society. However, the absorption of cotton swab for RNA lysates may lead to a low concentration of detectable RNA, which might be one of the main reasons for the unstable positive detecting rate. We designed and manufactured a kind of silicone swab with concave-convex structure, and further compared the effects of silicone and cotton swab on RNA extraction. Principal component analysis and Paired Wilcoxcon test suggested that a higher RNA concentration and A260/A280 would be obtained using silicone swab. The results indicated that our silicone swab had a more excellent ability to sample than the cotton swab, characterized by the higher quantity and quality of extracted RNA. Thus, we advised that the current cotton swabs need to be improved urgently in COVID-19 diagnoses and the process of “sample collection” and “sample pre-processing” must be standardized and emphasized.

Highlights

The current cotton swabs need to be improved urgently in COVID-19 screening.
Depth and turbidity affectin situpumping activity of the Mediterranean spongeChondrosia reniformis(Nardo, 1847)
Authors: Gokalp Mert , Kuehnhold Holger , de Goeij Jasper M. , Osinga Ronald
Published: March 2020

Effects of depth and turbidity on thein situpumping activity of the Mediterranean spongeChondrosia reniformis(Nardo, 1847) were characterized by measuring osculum diameter, oscular outflow velocity, osculum density per sponge and sponge surface area at different locations around the Bodrum peninsula (Turkey). Outflow velocity was measured using a new method based on video analysis of neutrally buoyant particles moving in the exhalant stream of sponge oscula, which yielded results that were in good comparison to other studies. Using the new method, it was shown that forC. reniformis, oscular outflow had a location-dependent, in most cases positive relationship with oscular size: bigger oscules process more water per cm2of osculum surface. Turbidity and depth both affected sponge pumping in a negative way, but for the locations tested, the effect of depth was more profound than the effect of turbidity. Depth affected all parameters investigated except sponge size, whereas turbidity only affected specific pumping rates normalized to sponge surface area. Deep water sponges had clearly smaller oscula than shallow water sponges, but partially compensated for this lower pumping potential by showing a higher osculum density. Both increasing turbidity and increasing depth considerably decreased volumetric pumping rates ofC. reniformis. These findings have important implications for selecting sites for mariculture of this species.
Inhibition of the αv integrin-TGF-β axis improves natural killer cell function against glioblastoma stem cells
Authors: Shaim Hila , Sanabria Mayra Hernandez , Basar Rafet , Wang Fang , Daher May , Zamler Daniel , Gumin Joy , Gabrusiewicz Konrad , Miao Qi , Dou Jinzhuang , Alsuliman Abdullah , Kerbauy Lucila Nassif , Acharya Sunil , Mohanty Vakul , Banerjee Pinaki , Mendt Mayela , Li Sufang , Lu Junjun , Wei Jun , Fowlkes Natalie Wall , Gokdemir Elif , Ensley Emily L. , Kaplan Mecit , Uprety Nadima , Kassab Cynthia , Li Li , Ozcan Gonca , Shen Yifei , Gilbert April L. , Bdiwi Mustafa , Cortes Ana Karen Nunez , Liu Enli , Yu Jun , Imahashi Nobuhiko , Muniz-Feliciano Luis , Hu Jian , Draetta Giulio , Marin David , Yu Dihua , Mielke Stephan , Eyrich Matthias , Champlin Richard , Chen Ken , Lang Frederick F. , Shpall Elizabeth , Heimberger Amy , Rezvani Katayoun
Published: March 2020

Glioblastoma, the most aggressive brain cancer, often recurs because glioblastoma stem cells (GSCs) are resistant to all standard therapies. Here, we show that patient-derived GSCs, but not normal astrocytes, are highly sensitive to lysis by healthy allogeneic natural killer (NK) cellsin vitro. In contrast, single cell analysis of autologous, tissue infiltrating NK cells isolated from surgical samples of high-grade glioblastoma patient tumors using mass cytometry and single cell RNA sequencing revealed an abnormal phenotype associated with impaired lytic function compared with peripheral blood NK cells from GBM patients or healthy donors. This immunosuppression was attributed to an integrin-TGF-β mechanism, activated by direct cell-cell contact between GSCs and NK cells. Treatment of GSC-engrafted mice with allogeneic NK cells in combination with inhibitors of integrin or TGF-β signaling, or withTGF-β receptor 2gene-edited NK cells prevented GSC-induced NK cell dysfunction and tumor growth. Collectively, our findings reveal a novel mechanism of NK cell immune evasion by GSCs and implicate the integrin-TGF-β axis as a useful therapeutic target to eliminate GSCs in this devastating tumor.
Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples
Authors: Eis-Hübinger Anna M. , Hönemann Mario , Wenzel Jürgen J. , Berger Annemarie , Widra Marek , Schmidt Barbara , Aldabbagh Souhaib , Marx Benjamin , Streeck Hendrik , Ciesek Sandra , Liebert Uwe. G. , Huzly Daniela , Hengel Hartmut , Panning Marcus
Published: March 2020

We report a laboratory-based surveillance for SARS-CoV-2 using minipools of respiratory samples submitted for routine diagnostics. We tested a total of 70 minipools resembling 700 samples shortly before the upsurge of cases in Germany. We identified one SARS-CoV-2 positive patient. Our approach proved its concept, is easily adaptable and resource-saving.
Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling
Authors: Beilsten-Edmands James , Winter Graeme , Gildea Richard , Parkhurst James , Waterman David , Evans Gwyndaf
Published: March 2020

In processing X-ray diffraction data, the intensities obtained from integration of the diffraction images must be corrected for experimental effects in order to place all intensities on a common scale both within and between data collections. Scaling corrects for effects such as changes in sample illumination, absorption and, to some extent, global radiation damage that cause the measured intensities of symmetry-equivalent observations to differ throughout a data set. This necessarily requires a prior evaluation of the point-group symmetry of the crystal. This paper describes and evaluates the scaling algorithms implemented within the DIALS data-processing package and demonstrates the effectiveness and key features of the implementation on example macromolecular crystallographic rotation data. In particular, the scaling algorithms enable new workflows for the scaling of multi-crystal or multi-sweep data sets, providing the analysis required to support current trends towards collecting data from ever-smaller samples. In addition, the implementation of a free-set validation method is discussed, which allows the quantification of the suitability of scaling-model and algorithm choices.