bluuebunny/crossref_metadata_2025 huggingface dataset:
The trade-off between mobility and vaccination for COVID-19 control: a metapopulation modelling approach
Authors: Saldaña Fernando , Velasco-Hernández Jorge X.
Published: June 2021

November 2020 received a string of encouraging results from leading vaccine developers raising hopes for the imminent availability of an effective and safe vaccine against the SARS-CoV-2. In the present work, we discuss the theoretical impact of introducing a vaccine across a range of scenarios. In particular, we investigate how vaccination coverage, efficacy and delivery time affect the control of the transmission dynamics in comparison to mobility restrictions. The analysis is based on a metapopulation epidemic model structured by risk. We perform a global sensitivity analysis using the Sobol method. Our analysis suggest that the reduction of mobility among patches plays a significant role in the mitigation of the disease close to the effect of immunization coverage of 30% achieved in four months. Moreover, for an immunization coverage between 20% and 50% achieved in the first half of 2021 with a vaccine efficacy between 70% and 95%, the percentage reduction in the total number of SARS-CoV-2 infections is between 30% and 50% by the end of 2021 in comparison with the no vaccination scenario.
The N250 event-related potential as an index of face familiarity: a replication study
Authors: Sommer Werner , Stapor Katarzyna , Kończak Grzegorz , Kotowski Krzysztof , Fabian Piotr , Ochab Jeremi , Bereś Anna , Ślusarczyk Grażyna
Published: June 2021

The neural correlates of face individuation—the acquisition of memory representations for novel faces—have been studied only in coarse detail and disregarding individual differences between learners. In their seminal study, Tanaka
et al
. (Tanaka
et al.
2006
J. Cogn. Neurosci.
18
, 1488–1497. (
doi:10.1162/jocn.2006.18.9.1488
)) required the identification of a particular novel face across 70 trials and found that the N250 component in the EEG event-related potentials became more negative from the first to the second half of the experiment, where it reached a similar amplitude as a well-known face. We were unable to directly replicate this finding in our study when we used the original split of trials. However, when we applied a different split of trials we observed very similar changes in N250 amplitude. We conclude that the N250 component is indeed sensitive to the build-up of a robust representation of a face in memory; the time course of this process appears to vary as a function of variables that may be determined in future research.
Preparation of autoxidative water-reducible alkyd resins from waste polyethylene terephthalate
Authors: Ouyang Siming , Xie Yuqing , Fu Wangxing , Ding Yongbo , Shen Liang
Published: June 2021

In this paper, the waste polyethylene terephthalate (PET) was glycolysed by trimethylolpropane with zinc acetate as catalyst. The effects of different content glycolysis product of waste PET on the appearance, viscosity, particle size and molecular weight of autoxidative water-reducible alkyd resins and the corresponding film adhesion, flexibility, impact resistance, gloss, hardness and chemical resistance were studied. Meanwhile, experimental results were compared with commercial water-reducible alkyd and water-reducible alkyd without the glycolysis product of waste PET. The results show that the maximum concentration of PET in autoxidative water-reducible alkyd resins can reach 8.5 wt%, and the molecular weight, particle size and viscosity of water-reducible alkyd resin do not change much with the increase of PET concentration. The introduction of PET resulted in the viscosity of water-reducible alkyd resins being greater than that of water-reducible alkyd resin without PET; this is mainly because PET contains harder terephthalic acid monomer units. However, the particle size of water-reducible alkyd resins with waste PET is significantly lower than that of the water-reducible alkyd resin without PET; this is due to PET-free water-reducible alkyd resin containing more pentaerythritol with greater steric hindrance. In addition, the hardness of the water-reducible alkyd resin paint film (PET content is 8.5%) reaches 1H, which is higher than the hardness (HB) of the water-reducible alkyd resin paint film without PET and the commercial alkyd resin paint film, while the physical properties and chemical resistance of the former are comparable to those of the latter two kinds of paint films. Therefore, the use of waste PET in water-borne coatings systems not only reduces the cost of coatings, but also opens up a new market for recycled PET, which may contribute a promising method for management of waste PET.
On the propagation of waves in the atmosphere
Authors: Constantin Adrian , Johnson Robin S.
Published: June 2021

The leading-order equations governing the unsteady dynamics of large-scale
atmospheric motions are derived,
via
a systematic asymptotic
approach based on the thin-shell approximation applied to the ellipsoidal model
of the Earth’s geoid. We present some solutions of this single set of
equations that capture properties of specific atmospheric flows, using field
data to choose models for the heat sources that drive the motion. In particular,
we describe standing-waves solutions, waves propagating towards the Equator,
equatorially trapped waves and we discuss the African Easterly Jet/Waves. This
work aims to show the benefits of a systematic analysis based on the governing
equations of fluid dynamics.
Dynamical landscape and multistability of a climate model
Authors: Margazoglou Georgios , Grafke Tobias , Laio Alessandro , Lucarini Valerio
Published: June 2021

We apply two independent data analysis methodologies to locate stable climate states in an intermediate complexity climate model and analyse their interplay. First, drawing from the theory of quasi-potentials, and viewing the state space as an energy landscape with valleys and mountain ridges, we infer the relative likelihood of the identified multistable climate states and investigate the most likely transition trajectories as well as the expected transition times between them. Second, harnessing techniques from data science, and specifically manifold learning, we characterize the data landscape of the simulation output to find climate states and basin boundaries within a fully agnostic and unsupervised framework. Both approaches show remarkable agreement, and reveal, apart from the well known warm and snowball earth states, a third intermediate stable state in one of the two versions of PLASIM, the climate model used in this study. The combination of our approaches allows to identify how the negative feedback of ocean heat transport and entropy production via the hydrological cycle drastically change the topography of the dynamical landscape of Earth’s climate.
Selection and evaluation of spherical acquisition trajectories for industrial computed tomography
Authors: Bauer Fabian , Goldammer Matthias , Grosse Christian U.
Published: June 2021

In conventional industrial computed tomography, the source–detector system rotates in equiangular steps in-plane relative to the part of investigation. While being by far the most frequently used acquisition trajectory today, this method has several drawbacks like the formation of cone beam artefacts or limited usability in case of geometrical restrictions. In such cases, the usage of alternative spherical trajectories can be beneficial to improve image quality and defect visibility. While investigations have been performed to relate the influence of the trajectory choice in the typical metrological case of a high number of available projections, so far barely any work has been done for the case of few source–detector poses, which is more relevant in the field of non-destructive testing. In this work, we provide an overview of quantitative metrics that can be used to assess the image quality of reconstructed computed tomography volumes, discuss their advantages and drawbacks and propose a framework to investigate the performance of several non-standard trajectories with respect to previously defined regions of interest. Inspired by pseudorandom sampling methods for Monte–Carlo-algorithms, we also suggest an entirely new trajectory design, the low-discrepancy spherical trajectory, which extends the concept of equiangular planar trajectories into three dimensions and can be used for benchmarking and comparison with other spherical trajectories. Last, we use an optimization method to calculate task-specific acquisition trajectories and relate their performance to other spherical designs.
A modified two-process Knox test for investigating the relationship between law enforcement opioid seizures and overdoses
Authors: Mohler G. , Mishra S. , Ray B. , Magee L. , Huynh P. , Canada M. , O’Donnell D. , Flaxman S.
Published: June 2021

Recent research has shown an association between monthly law enforcement drug seizure events and accidental drug overdose deaths using cross-sectional data in a single state, whereby increased seizures correlated with more deaths. In this study, we conduct statistical analysis of street-level data on law enforcement drug seizures, along with street-level data on fatal and non-fatal overdose events, to determine possible micro-level causal associations between opioid-related drug seizures and overdoses. For this purpose, we introduce a novel, modified two-process Knox test that controls for self-excitation to measure clustering of overdoses nearby in space and time following law enforcement seizures. We observe a small, but statistically significant (
p
 < 0.001), effect of 17.7 excess non-fatal overdoses per 1000 law enforcement seizures within three weeks and 250 m of a seizure. We discuss the potential causal mechanism for this association along with policy implications.
Invariant analysis, exact solutions and conservation laws of (2+1)-dimensional time fractional Navier–Stokes equations
Authors: Cheng Xiaoyu , Wang Lizhen
Published: June 2021

In this paper, we investigate the exact solutions and conservation laws of (2 + 1)-dimensional time fractional Navier–Stokes equations (TFNSE). Specifically, Lie symmetries and corresponding one-dimensional optimal system for TFNSE in Riemann–Liouville sense are obtained. Then, based on the admitted symmetries and optimal system, we reduce these equations to one-dimensional equations or (1 + 1)-dimensional fractional partial differential equations (PDEs) with the help of Erdélyi–Kober fractional differential operator and compound variable transformation. In addition, we solve the reduced PDEs applying power series expansion method and invariant subspace method, respectively. Furthermore, the conservation laws of TFNSE are derived using new Noether theorem.
Long-term study shows that increasing body size in response to warmer summers is associated with a higher mortality risk in a long-lived bat species
Authors: Mundinger Carolin , Scheuerlein Alexander , Kerth Gerald
Published: June 2021

Change in body size is one of the universal responses to global warming, with most species becoming smaller. While small size in most species corresponds to low individual fitness, small species typically show high population growth rates in cross-species comparisons. It is unclear, therefore, how climate-induced changes in body size ultimately affect population persistence. Unravelling the relationship between body size, ambient temperature and individual survival is especially important for the conservation of endangered long-lived mammals such as bats. Using an individual-based 24-year dataset from four free-ranging Bechstein's bat colonies (
Myotis bechsteinii
), we show for the first time a link between warmer summer temperatures, larger body sizes and increased mortality risk. Our data reveal a crucial time window in June–July, when juveniles grow to larger body sizes in warmer conditions. Body size is also affected by colony size, with larger colonies raising larger offspring. At the same time, larger bats have higher mortality risks throughout their lives. Our results highlight the importance of understanding the link between warmer weather and body size as a fitness-relevant trait for predicting species-specific extinction risks as consequences of global warming.
The Goldilocks effect: female geladas in mid-sized groups have higher fitness
Authors: Tinsley Johnson Elizabeth , Feder Jacob A. , Bergman Thore J. , Lu Amy , Snyder-Mackler Noah , Beehner Jacinta C.
Published: June 2021

The cost–benefit ratio of group living is thought to vary with group size: individuals in ‘optimally sized’ groups should have higher fitness than individuals in groups that are either too large or too small. However, the relationship between group size and individual fitness has been difficult to establish for long-lived species where the number of groups studied is typically quite low. Here, we present evidence for optimal group size that maximizes female fitness in a population of geladas (Theropithecus gelada). Drawing on 14 years of demographic data, we found that females in small groups experienced the highest death rates, while females in mid-sized groups exhibited the highest reproductive performance. This group size effect on female reproductive performance was largely explained by variation in infant mortality (and, in particular, by infanticide from immigrant males) but not by variation in reproductive rates. Taken together, females in mid-sized groups are projected to attain optimal fitness due to conspecific infanticide and, potentially, predation. Our findings provide insight into how and why group size shapes fitness in long-lived species.
Organizational Readiness for the Implementation of a Three-Month Short-Course TB Preventive Therapy Regimen (3HP) in Four Health Care Facilities in Zimbabwe in 2020: A Mixed Methods Study
Authors: Chisare Dorothy T. , Zinyama-Gutsire Rutendo B.L. , Chasela Charles
Published: June 2021

Background

Tuberculosis preventive therapy (TPT) for latent TB infection has had limited success in Zimbabwe. The country plans to roll-out the three-month short-course TPT regimen (3HP) to address the implementation lag and poor uptake of the 6-9-month regimens. The study measured the level of organizational readiness while identifying barriers and facilitators to implement 3HP in four health facilities in Zimbabwe.

Methods

A convergent, parallel mixed-methods approach was used to collect data from four primary healthcare clinics in Bulawayo and Harare Metropolitan provinces, Zimbabwe. Twenty healthcare providers completed a 35-item, self-administered questionnaire designed on a 5-point Likert scale and developed from the Weiner organizational readiness model. Nine of the providers and five TB program managers took part in 20-30 minute individual semi-structured key-informant interviews. Median scores with interquartile ranges were calculated wherein a score of 3.3 or greater indicated readiness. Differences between facilities were assessed using a Kruskal-Wallis rank test. Qualitative data on barriers and facilitators were transcribed and analyzed using a framework approach.

Results

Readiness to implement 3HP across the four facilities was positive with a score of 3.8(IQR 3.3-4.1). The difference between the best 4.0(IQR 3.8-4.2) and worst-performing facility 3.2(IQR 2.7-3.3) was 0.8 and statistically significant (p=0.039). The low facility score was due to poor contextual factors 2.5(IQR 2.0-3.3), task demands 2.6(IQR 2.3-2.9), and resource availability 2.1(IQR 1.5-2.5) scores. Key organizational readiness facilitators included healthcare provider and management buy-in; community willingness to generate demand for 3HP; strong collective capability through task-shifting, alignment with existing primary healthcare programs, perceived benefits, and need for 3HP. Barriers were negative past TPT experiences, suboptimal programmatic monitoring, inconsistent health provider remuneration, inadequate staffing, added workload, and an erratic supply chain across facilities. The organizational communication gap prompts the slow program implementation culture.

Conclusions

The varied scores between facilities suggest distinct underlying conditions for readiness. Healthcare provider motivation is temporary based on the inconsistent resource supply, absence of TPT-specific monitoring and evaluation, and daily contextual challenges in facilities that must be addressed. Similar research is necessary for countries yet to implement 3HP to optimize the design or revision of delivery strategies and increase uptake of TPT.
Prevalence of Fetal Alcohol Spectrum Disorder (FASD) in Greater Manchester, UK: an active case ascertainment study
Authors: McCarthy Robyn , Mukherjee Raja A.S. , Fleming Kate M. , Green Jonathan , Clayton-Smith Jill , Price Alan D. , Allely Clare S. , Cook Penny A.
Published: June 2021

Background

Despite high levels of prenatal alcohol exposure in the UK, evidence on the prevalence of fetal alcohol spectrum disorders (FASD) is lacking. This paper reports on FASD prevalence in a small sample of children in primary school.

Methods

A two-phase active case ascertainment study was conducted in three mainstream primary schools in Greater Manchester, UK. Schools were located in areas that ranged from relatively deprived to relatively affluent. Initial screening of children aged 8-9 years used pre-specified criteria for elevated FASD risk (small for age; special educational needs; currently/previously in care; significant social/emotional/mental health symptoms). Screen positive children were invited for detailed ascertainment of FASD using gold standard measures including medical history, facial dysmorphology, neurological impairment, executive function and behavioural difficulties.

Results

Of 220 eligible children, 50 (23%) screened positive and 12% (26/220) proceeded to phase-two assessment. Twenty had a developmental disorder, of which, four had FASD and four were assessed as possible FASD. The crude prevalence rate of FASD in these schools was 1.8% (95%CI: 1.0%,3.4%) and when including possible cases was 3.6% (2.1%,6.3%). None of these children had previously identified with a developmental diagnosis.

Conclusions

FASD was found to be common in these schools, but limitations to the sampling restrict inferences to a population prevalence. Most of these children’s needs had not previously been identified.
The impact of three progressively introduced interventions on second wave daily COVID-19 case numbers in Melbourne, Australia
Authors: Saul Allan , Scott Nick , Spelman Tim , Crabb Brendan S. , Hellard Margaret
Published: June 2021

Background

The city of Melbourne, Australia experienced two waves of the COVID-19 epidemic peaking, the first in March and a more substantial wave in July 2020. During the second wave, a series of control measure were progressively introduced that initially slowed the growth of the epidemic then resulted in decreasing cases until there was no detectable local transmission.

Methods

To determine the relative efficacy of the progressively introduced intervention measures, we modelled the second wave as a series of exponential growth and decay curves. We used a linear regression of the log of daily cases vs time, using a four-segment linear spline model corresponding to implementation of the three successive major public health measures. The primary model used all reported cases between 14 June and 15 September then compared the projection of the model with observed cases predict future case trajectory up until the 31 October to assess the use of exponential models in projecting the future course and planning future interventions. The main outcome measures were the exponential daily growth constants, analysis of residuals and estimates of the 95% confidence intervals for the expected case distributions, comparison of predicted daily cases.

Results

The exponential growth/decay constants in the primary analysis were: 0.122 (s.e. 0.004), 0.035 (s.e. 0.005), -0.037 (s.e. 0.011), and -0.069 (s.e. 0.003) for the initial growth rate, Stage 3, stage 3 + compulsory masks and Stage 4, respectively. Extrapolation of the regression model from the 14 September to the 31 October matched the decline in observed cases over this period.

Conclusions

The four-segment exponential model provided an excellent fit of the observed reported case data and predicted the day-to-day range of expected cases. The extrapolated regression accurately predicted the decline leading to epidemic control in Melbourne.
A Systematic Review of COVID - 19 Induced Myocarditis - Symptomatology, Prognosis, and Clinical Findings
Authors: Jaiswal Vikash , Nagpal Shavy , Labitag Christine Angela E. , Tayo Janelle , Patel Abhinav , Lo Kevin Bryan , Vijayan Rupalakshmi , Matos Wanessa F , Yaqoob Sadia , Panday Priyanka , Savani Saloni , Alnahas Zeinab , Bhatnagar Arushee , Diaz Yoandra , Dylewski John R.
Published: June 2021

Objective

With the advent of a novel coronavirus in December 2019, several case studies have reported its adversity on cardiac cells. We conducted a systematic review that describes the symptomatology, prognosis, and clinical findings of patients with COVID-19-related myocarditis.

Methods

Search engines including PubMed, Google Scholar, Cochrane Central, and Web of Science were queried for “SARS-CoV-2” or “COVID 19” and “myocarditis.” PRISMA guidelines were employed, and peer-reviewed journals in English related to COVID-19 were included.

Results

This systematic review included 22 studies and 37 patients. Eight patients (36%) were confirmed myocarditis, while the rest were possible myocarditis. Most patients had elevated cardiac biomarkers, including troponin, CRP, CK, CK-MB, and NT-pro BNP. Electrocardiogram results noted tachycardia (47%), left ventricular hypertrophy (50%), ST-segment alterations (41%), and T wave inversion (18%). Echocardiography presented reduced LVEF (77%), left ventricle abnormalities (34%), right ventricle aberrations (12%), and pericardial effusion (71%). Further, CMR showed reduced myocardial edema (75%), non-ischemic patterns (50%), and hypokinesis (26%). The mortality was significant at 25%.

Conclusions

Mortality associated with COVID-19 myocarditis appears significant but underestimated. Further studies are warranted to evaluate and quantify patients’ actual prognosis and outcomes with COVID-19 myocarditis.
Effect of 2021 Assembly Election in India on Covid-19 Transmission
Authors: Manik Souvik , Pal Sabyasachi , Mandal Manoj , Hazra Mangal
Published: June 2021

India is one of the countries in the world which is badly affected by the Covid-19 second wave. Assembly election in four states and a union territory of India was taken place during March-May 2021 when the Covid-19 second wave was close to its peak and affected a huge number of people. We studied the impact of assembly election on the effective contact rate and the effective reproduction number of Covid-19 using different epidemiological models like SIR, SIRD, and SEIR. We also modeled the effective reproduction number for all election-bound states using different mathematical functions. We separately studied the case of all election-bound states and found all the states shown a distinct increase in the effective contact rate and the effective reproduction number during the election-bound time and just after that compared to pre-election time. States, where elections were conducted in single-phase, showed less increase in the effective contact rate and the reproduction number. The election commission imposed extra measures from the first week of April 2021 to restrict big campaign rallies, meetings, and different political activities. The effective contact rate and the reproduction number showed a trend to decrease for few states due to the imposition of the restrictions. We also compared the effective contact rate, and the effective reproduction number of all election-bound states and the rest of India and found all the parameters related to the spread of virus for election-bound states are distinctly high compared to the rest of India.
Signatures of mast cell activation are associated with severe COVID-19
Authors: Tan Janessa , Anderson Danielle E. , Rathore Abhay P. S. , O’Neill Aled , Mantri Chinmay Kumar , Saron Wilfried A. A. , Lee Cheryl , Cui Chu Wern , Kang Adrian E. Z. , Foo Randy , Kalimuddin Shirin , Low Jenny G. , Ho Lena , Tambyah Paul , Burke Thomas W. , Woods Christopher W. , Chan Kuan Rong , Karhausen Jörn , John Ashley L. St.
Published: June 2021

Lung inflammation is a hallmark of Coronavirus disease 2019 (COVID-19) in severely ill patients and the pathophysiology of disease is thought to be immune-mediated. Mast cells (MCs) are polyfunctional immune cells present in the airways, where they respond to certain viruses and allergens, often promoting inflammation. We observed widespread degranulation of MCs during acute and unresolved airway inflammation in SARS-CoV-2-infected mice and non-human primates. In humans, transcriptional changes in patients requiring oxygen supplementation also implicated cells with a MC phenotype. MC activation in humans was confirmed, through detection of the MC-specific protease, chymase, levels of which were significantly correlated with disease severity. These results support the association of MC activation with severe COVID-19, suggesting potential strategies for intervention.
The impact of local vaccine coverage and recent incidence on measles transmission in France between 2009 and 2018
Authors: Robert Alexis , Kucharski Adam J. , Funk Sebastian
Published: June 2021

Background

Despite high levels of vaccine coverage, sub-national heterogeneity in immunity to measles can create pockets of susceptibility, which are hard to detect and may result in long-lasting outbreaks. The elimination status defined by the World Health Organization aims to identify countries where the virus is no longer circulating and can be verified after 36 months of interrupted transmission. However, since 2018, numerous countries have lost their elimination status soon after reaching it, showing that the indicators used to define elimination may not be predictive of lower risks of outbreaks.

Methods and Findings

We quantified the impact of local vaccine coverage and recent levels of incidence on the dynamics of measles in each French department between 2009 and 2018, using mathematical models based on the ‘Epidemic-Endemic’ regression framework. High values of local vaccine coverage were associated with fewer imported cases and lower risks of local transmissions. Regions that had recently reported high levels of incidence were also at a lower risk of local transmission, potentially due to additional immunity accumulated during these recent outbreaks. Therefore, all else being equal, the risk of local transmission was not lower in areas fulfilling the elimination criteria (i.e., low recent incidence). After fitting the models using daily case counts, we used the parameters’ estimates to simulate the effect of variations in the vaccine coverage and recent incidence on future transmission. A decrease of 3% in the three-year average vaccine uptake led to a five-fold increase in the number of cases simulated in a year on average.

Conclusions

Spatiotemporal variation in vaccine coverage because of disruption of routine immunisation programmes, or lower trust in vaccines, can lead to large increases in both local and cross regional transmission. The association found between local vaccine coverage and incidence suggests that, although regional vaccine uptake can be hard to collect and unreliable because of population movements, it can provide insights into the risks of imminent outbreak. Periods of low local measles incidence were not indicative of a decrease in the risks of local transmission. Therefore, the incidence indicator used to define the elimination status was not consistently associated with lower risks of measles outbreak in France. More detailed models of local immunity levels or subnational seroprevalence studies may yield better estimates of local risk of measles outbreaks.
Targeting the MYC interaction network in B-cell lymphoma via histone deacetylase 6 inhibition
Authors: Winkler René , Mägdefrau Ann-Sophie , Piskor Eva-Maria , Kleemann Markus , Beyer Mandy , Linke Kevin , Hansen Lisa , Schaffer Anna-Maria , Hoffmann Marina E. , Poepsel Simon , Heyd Florian , Beli Petra , Möröy Tarik , Mahboobi Siavosh , Krämer Oliver H. , Kosan Christian
Published: June 2021

Overexpression of MYC is a genuine cancer driver in lymphomas and related to poor prognosis. However, therapeutic targeting of the transcription factor MYC remains challenging. Here, we show that inhibition of the histone deacetylase 6 (HDAC6) using the HDAC6 inhibitor Marbostat-100 (M-100) reduces oncogenic MYC levels and prevents lymphomagenesis in a mouse model of MYC-induced aggressive B-cell lymphoma. M-100 specifically alters protein-protein interactions by switching the acetylation state of HDAC6 substrates, such as tubulin. Tubulin facilitates nuclear import of MYC, and MYC-dependent B-cell lymphoma cells rely on continuous import of MYC due to its high turn-over. Acetylation of tubulin impairs this mechanism and enables proteasomal degradation of MYC. M-100 targets almost exclusively B-cell lymphoma cells with high levels of MYC whereas non-tumor cells are not affected. M-100 induces massive apoptosis in human and murine MYC-overexpressing B-cell lymphoma cells. We identified the heat-shock protein DNAJA3 as an interactor of tubulin in an acetylation-dependent manner and overexpression of DNAJA3 resulted in a pronounced degradation of MYC. We propose a mechanism by which DNAJA3 associates with hyperacetylated tubulin in the cytoplasm to control MYC turnover. Taken together, our data demonstrate a beneficial role of HDAC6 inhibition in MYC-dependent B-cell lymphoma.
Characterization of SARS2 Nsp15 Nuclease Activity Reveals it’s Mad About U
Authors: Frazier Meredith N. , Dillard Lucas B. , Krahn Juno M. , Perera Lalith , Williams Jason G. , Wilson Isha M. , Stewart Zachary D. , Pillon Monica C. , Deterding Leesa J. , Borgnia Mario J. , Stanley Robin E.
Published: June 2021

Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and evade host immune defense systems. Previous structures of Nsp15 from across Coronaviridae revealed that Nsp15 assembles into a homo-hexamer and has a conserved active site similar to RNase A. Beyond a preference for cleaving RNA 3’ of uridines, it is unknown if Nsp15 has any additional substrate preferences. Here we used cryo-EM to capture structures of Nsp15 bound to RNA in pre- and post-cleavage states. The structures along with molecular dynamics and biochemical assays revealed critical residues involved in substrate specificity, nuclease activity, and oligomerization. Moreover, we determined how the sequence of the RNA substrate dictates cleavage and found that outside of polyU tracts, Nsp15 has a strong preference for purines 3’ of the cleaved uridine. This work advances our understanding of how Nsp15 recognizes and processes viral RNA and will aid in the development of new anti-viral therapeutics.
The human language system, including its inferior frontal component in ‘Broca’s area’, does not support music perception
Authors: Chen Xuanyi , Affourtit Josef , Ryskin Rachel , Regev Tamar I. , Norman-Haignere Samuel , Jouravlev Olessia , Malik-Moraleda Saima , Kean Hope , Varley Rosemary , Fedorenko Evelina
Published: June 2021

Language and music are two human-unique capacities whose relationship remains debated. Some have argued for overlap in processing mechanisms, especially for structure processing. Such claims often concern the inferior frontal component of the language system located within ‘Broca’s area’. However, others have failed to find overlap. Using a robust individual-subject fMRI approach, we examined the responses of language brain regions to music stimuli, and probed the musical abilities of individuals with severe aphasia. Across four experiments, we obtained a clear answer: music perception does not engage the language system, and judgments about music structure are possible even in the presence of severe damage to the language network. In particular, the language regions’ responses to music are generally low, often below the fixation baseline, and never exceed responses elicited by non-music auditory conditions, like animal sounds. Further, the language regions are not sensitive to music structure: they show low responses to intact and structure-scrambled music, and to melodies with vs. without structural violations. Finally, in line with past patient investigations, individuals with aphasia who cannot judge sentence grammaticality perform well on melody well-formedness judgments. Thus the mechanisms that process structure in language do not appear to process music, including music syntax.
Plasticity in intrinsic excitability of hypothalamic magnocellular neurosecretory neurons in late-pregnant and lactating rats
Authors: Perkinson Michael R. , Augustine Rachael A. , Bouwer Gregory T. , Brown Emily F. , Cheong Isaiah , Seymour Alexander J. , Fronius Martin , Brown Colin H.
Published: June 2021

Oxytocin and vasopressin secretion from the posterior pituitary gland are required for normal pregnancy and lactation. Oxytocin secretion is relatively low and constant under basal conditions but becomes pulsatile during birth and lactation to stimulate episodic contraction of the uterus for delivery of the fetus and milk ejection during suckling. Vasopressin secretion is maintained in pregnancy and lactation despite reduced osmolality (the principal stimulus for vasopressin secretion) to increase water retention to cope with the cardiovascular demands of pregnancy and lactation. Oxytocin and vasopressin secretion are determined by the action potential (spike) firing of magnocellular neurosecretory neurons of the hypothalamic supraoptic and paraventricular nucleus. In addition to synaptic input activity, spike firing depends on intrinsic excitability conferred by the suite of channels expressed by the neurons. Therefore, we analysed oxytocin and vasopressin neuron activity in anaesthetised non-pregnant, late-pregnant and lactating rats to test the hypothesis that intrinsic excitability of oxytocin and vasopressin neurons is increased in late pregnancy and lactation to promote oxytocin and vasopressin secretion required for successful pregnancy and lactation. Hazard analysis of spike firing revealed a higher incidence of post-spike hyperexcitability immediately following each spike in oxytocin neurons, but not in vasopressin neurons, in late pregnancy and lactation, which is expected to facilitate high frequency firing during bursts. Despite lower osmolality in late-pregnant and lactating rats, vasopressin neuron activity was not different between non-pregnant, late-pregnant and lactating rats, and blockade of osmosensitive ΔN-TRPV1 channels inhibited vasopressin neurons to a similar extent in non-pregnant, late-pregnant and lactating rats. Furthermore, supraoptic nucleus ΔN-TRPV1 mRNA expression was not different between non-pregnant and late-pregnant rats, suggesting that enhanced activity of ΔN-TRPV1 channels might maintain vasopressin neuron activity to increase water retention during pregnancy and lactation.
SARS-CoV-2 cell-to-cell spread occurs rapidly and is insensitive to antibody neutralization
Authors: Jackson Laurelle , Rodel Hylton , Hwa Shi-Hsia , Cele Sandile , Ganga Yashica , Tegally Houriiyah , Bernstein Mallory , Giandhari Jennifer ,   COMMIT-KZN Team, Gosnell Bernadett I. , Khan Khadija , Hanekom Willem , Karim Farina , de Oliveira Tulio , Moosa Mahomed-Yunus S. , Sigal Alex
Published: June 2021

Viruses increase the efficiency of close-range transmission between cells by manipulating cellular physiology and behavior, and SARS-CoV-2 uses cell fusion as one mechanism for cell-to-cell spread. Here we visualized infection using time-lapse microscopy of a human lung cell line and used live virus neutralization to determine the sensitivity of SARS-CoV-2 cell-to-cell spread to neutralizing antibodies. SARS-CoV-2 infection rapidly led to cell fusion, forming multinucleated cells with clustered nuclei which started to be detected at 6h post-infection. To compare sensitivity of cell-to-cell spread to neutralization, we infected either with cell-free virus or with single infected cells expressing on their surface the SARS-CoV-2 spike protein. We tested two variants of SARS-CoV-2: B.1.117 containing only the D614G substitution, and the escape variant B.1.351. We used the much smaller area of single infected cells relative to infection foci to exclude any input infected cells which did not lead to transmission. The monoclonal antibody and convalescent plasma we tested neutralized cell-free SARS-CoV-2, with the exception of B.1.351 virus, which was poorly neutralized with plasma from non-B.1.351 infections. In contrast, cell-to-cell spread of SARS-CoV-2 showed no sensitivity to monoclonal antibody or convalescent plasma neutralization. These observations suggest that, once cells are infected, SARS-CoV-2 may be more difficult to neutralize in cell types and anatomical compartments permissive for cell-to-cell spread.
Transcriptome analysis of developmental stages of cocoa pod borer, Conopomorpha cramerella: A polyphagous insect pest of economic importance in Southeast Asia
Authors: Tan Chia Lock , Kasran Rosmin , Lee Wei Wei , Leong Wai Mun
Published: June 2021

The cocoa pod borer, Conopomorpha cramerella (Snellen) is a serious pest in cocoa plantations in Southeast Asia. It causes significant losses in the crop. Unfortunately, genetic resources for this insect is extremely scarce. To improve these resources, we sequenced the transcriptome of C. cramerella representing the three stages of development, larva, pupa and adult moth using Illumina NovaSeq6000. Transcriptome assembly was performed by Trinity for all the samples. A total number of 147,356,088 high quality reads were obtained. Of these, 285,882 contigs were assembled. The mean contig size was 374 bp. Protein coding sequence (CDS) was extracted from the reconstructed transcripts by TransDecoder. Subsequently, BlastX and InterProScan were applied for homology search to make a prediction of the function of CDS in unigene. Additionally, we identified a number of genes that are involved in reproduction and development such as genes involved in general function processes in the insect. Genes found to be involved in reproduction such as porin, dsx, bol and fruitless were associated with sex determination, spermatogenesis and pheromone binding. Furthermore, transcriptome changes during development were analysed. There were 2,843 differentially expressed genes (DEG) detected between the larva and pupa samples. A total of 2,861 DEG were detected between adult and larva stage whereas between adult and pupa stage, 1,953 DEG were found. In conclusion, the transcriptomes could be a valuable genetic resource for identification of genes in C. cramerella and the study will provide putative targets for RNAi pest control.
Description of the sound diversity of two species of tuco-tucos (Ctenomys torquatusandCtenomys lami) in natural environment
Authors: Zaché Keila C. , Silveira Lucas Machado , Francescoli Gabriel , de Freitas Thales Renato Ochotorena
Published: June 2021

Sound signals can travel through long distances, becoming an important communication channel between animals that need to establish contact beyond the visual form. They can then be considered a relevant form of communication between species living in the underground environment.Ctenomys torquatusandCtenomys lamiare solitary subterranean rodents, thus demanding an improvement of the communicative channels, especially in territorial defense actions and meeting potential reproductive partners. This work was aimed to describe the variability of acoustic signals emitted byC. torquatusandC. lamiby analyzing the physical-morphological characteristics of the signals. The study was carried out in two populations, one of each species and was selected 14 individuals ofC. torquatusand 15C. lami.The acoustic signals were recorded in a natural environment, obtaining the sounds straight from the animal tunnels. A total of 1,380 signals were captured and analyzed, 786 fromC. torquatusand 594 fromC. lami.It was possible to characterize 5 different types of signals, emitted by both species. Most of the analyzed sequences presented low frequency, and many of these calls exhibited characteristics of long-range signals. It was verified a sharing of sound signals in both species, as regarding the acoustic parameters as the morphology of the analyzed spectrograms. For the first time, it was possible to have access to sound data emitted by direct subterranean rodents from their tunnels in the natural environment.
Theobroma grandiflorum breeding optimization based on repeatability, stability and adaptability information
Authors: Chaves Saulo Fabrício da Silva , Alves Rafael Moysés , Alves Rodrigo Silva , Sebbenn Alexandre Magno , de Resende Marcos Deon Vilela , Dias Luiz Antônio dos Santos
Published: June 2021

The cultivation of Theobroma grandiflorum in the Brazilian Amazon is mainly conducted by family farmers who use a range of different management strategies. Thus, breeding programs of the species must address the challenge of developing cultivars that are adapted to and stable in a variety of cultivation environments. In this context, this study aimed to estimate the optimum number of harvests for genetic selection of T. grandiflorum progenies and identify the most promising ones in terms of productivity, stability, and adaptability. The trials were implemented in three environments, using a randomized complete block design, with 25 full-sib progenies, five replications, and three plants per plot. The traits mean number of fruits/plant, mean fruit production/plant, and rate of infection with witches’ broom (Moniliophthora perniciosa) were evaluated over 11 harvests. The Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP) mixed model method was used to estimate genetic parameters and predict genetic values, which were then applied to assess stability and adaptability. The results show that there is genetic variability among the studied T. grandiflorum progenies and that accurate genetic selection aiming at recombination is effective after three harvests, for recombination, or eleven harvests for identification of recommended progenies. Six progenies were selected that met the requirements for productivity, stability, and adaptability to different cultivation environments. These results can be used to optimize and advance T. grandiflorum breeding programs.
Extraction, purification and anti-TMV effects of α (β)-2,7,11-cembratriene-4,6-diol from tobacco leaves
Authors: Feng Yongxin , Jia Haijiang , Guan Hui , Zhang Weidong , Zhou Yanbin , Liu Kaiyi , Wang Yuejing , Li Qiuli , Chen Weihua , Sohail Muhammad Aamir , Wang Jie , Huang Shen , Wei Jianyu
Published: June 2021

Background

Acetone ethanol extracts from tobacco leaves have antiviral activity against TMV, but the antiviral effects of their specialized metabolites have not been systematically studied yet, especially the underlying mechanism is still unexplored.

Results

The tobacco cembranoids α(β)-2,7,11-cembratriene-4,6-diol (α(β)-CBD) were extracted and purified with an effective and green protocol including innovatively added 5% phosphoric acid for elution, one time silica gel chromatographic column separation and impurity removal and further HPLC purification. The results of antiviral activities against tobacco mosaic virus (TMV) with the local lesion counting method showed that α(β)-CBD have in vivo higher protective effects of 73.2% and 71.6%, at 75.0 μM, respectively, than control agent Ningnanmycin (53.1%). Notably, The results of ELISA and and TMV-GFP fluorescent optical imaging assay indicated a obviously reduced viral protein and weaker GFP fluorescence signal and smaller infection area, which confirmed their anti-TMV activities at protein level. Furthermore, the enhanced production of SA and JA and the significantly increased transcription of of JA signaling pathway (COI1 and PDF1.2) and SA signaling pathway genes (PR1, NPR1 and EDS1) in treated plants further conformed that exogenously applied α(β)-CBD can effectively elicit the tobacco plant immunity against TMV.

Conclusions

The α(β)-CBD mainly stimulates disease resistance of tobacco plants to resist TMV and it can be used as bioagents to control TMV in the future.
Signal-based optical map alignment
Authors: Akdel Mehmet , van de Geest Henri , Schijlen Elio , van Rijswijck Irma M.H. , Smid Eddy J. , Sanchez-Perez Gabino , de Ridder Dick
Published: June 2021

In genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and detect structural variation. Originally a laborious manual process, Bionano Genomics platforms now offer high-throughput, automated optical mapping based on chips packed with nanochannels through which unwound DNA is guided and the fluorescent DNA backbone and specific restriction sites are recorded. Although the raw image data obtained is of high quality, the processing and assembly software accompanying the platforms is closed source and does not seem to make full use of data, labeling approximately half of the measured signals as unusable. Here we introduce two new software tools, independent of Bionano Genomics software, to extract and process molecules from raw images (OptiScan) and to perform molecule-to-molecule and molecule-to-reference alignments using a novel signal-based approach (OptiMap). We demonstrate that the molecules detected by OptiScan can yield better assemblies, and that the approach taken by OptiMap results in higher use of molecules from the raw data. These tools lay the foundation for a suite of open-source methods to process and analyze high-throughput optical mapping data. The Python implementations of the OptiTools are publicly available throughhttp://www.bif.wur.nl/.
Effect of white mulberry (Morus albas L.) On common carp performance, biological parameters, and blood picture
Authors: Abdulrahman Nasreen Mohi Alddin
Published: June 2021

This study has been done for evaluating the growth performance and health performance of Cyprinus carpio isoenergetic with isonitrogenous diets which contain three levels (0, 10, 15, gm of mulberry fruit powder, have been used for a period of 12 weeks. The effect of white mulberry (Morus albas L.) fruit powder on common carp, T2 was significantly higher than other treatments in each of growth performance and feed utilization parameters. the adding of white mulberry fruit powder significantly increased each of CBC counts in T2 of RBC and HCT%. The conrol was significantly higher in each of MCH, MCHC, MCV and Platelets count. Cholestrol, triglyceride and HDL were higher significantly in T2, LDL was significantly higher in control. The white mulberry (M. albas L.) fruit powder effect significantly in, GPT, GOT, in T2 and the CKI and blood suger were higher significantly in the control, the control was significantly higher in each of total protein, and albumin ratio. T2 was higher significantly in Intestine Length Index in both fish weigth and length, and both fish weigth without viscera and/ or head. No significant differences in each of Intestine Weight Index among treatments, blood Globulin ratio, Hemoglobin count and VLDL.