bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-objective waveform inversion of shallow seismic wavefields
Authors: Pan Yudi , Gao Lingli , Shigapov Renat
Published: November 2019

It has been increasingly popular to use shallow-seismic full-waveform inversion (FWI) to reconstruct near-surface structures. Conventional FWI tries to resolve the earth model by minimizing the difference between observed and synthetic seismic data using a certain criterion (conventionally, l2-norm of waveform difference). In this paper, we propose a multi-objective waveform inversion (MOWI) in which the similarity of data is quantified and minimized using multiple criteria simultaneously. By doing so, we expand the dimensionality of objective space as well as the mapping from data space to objective space, which provides MOWI higher freedom in exploring the model space compared to single-objective FWI. We combine three different scalar-valued objective functions into a vector-valued multi-objective function which measures the similarity of the waveform, the waveform envelope, and the amplitude spectra of the data, respectively. This multi-objective function takes not only trace-based waveform and wave packet similarity but also the dispersion characteristics of surface waves into account. Furthermore, the uncertainty in the inversion result could be estimated and analysed quantitatively by the variance of the optimal models. We propose a modified ϵ-constraint algorithm to solve the multi-objective optimization problem. Two synthetic examples are used to show the advantages of using MOWI compared to single-objective FWI. We also test the efficiency of MOWI by using two synthetic shallow-seismic examples, which confirm that MOWI can converge to a better result compared to the conventional single-objective FWI.
Depressed forehead scar: a case report and review of literature
Authors: Ozinko Mba O , Otei Otei O , Ekpo Rijami G , Isiwele Egi
Published: November 2019

Depressed forehead scars are not frequently reported in the literature in the West African sub-region. Although they are not commonly reported, few cases were managed and are to be documented. We had seen a case of depressed forehead scar which was due to post frontal avulsion injury of the forehead with an intact posterior table of the frontal bone. He complained of aesthetic and psychological problems of the scar on presentation. The scar revision was done with polymethylmethacrylate bone cement with simple wound closure based on patient’s choice after counseling. The treatment outcome was satisfactory. We intend to highlight the use of polymethylmethacrylate bone cement and simple wound closure as an option in the revision of depressed forehead scars as well as add a report to the volume of literature from the sub-region.
Epicardial and coronary vascular development
Authors: Cahill Thomas J. , Riley Paul R.
Published: November 2019

The coronary circulation is essential for human life. In embryonic development, abnormal formation of the coronary vasculature can cause death in utero or after birth. In adulthood, atherosclerosis of the coronary arteries is the commonest cause of death worldwide. The last decade has witnessed significant strides forward in our understanding of coronary development. Multiple sources of coronary endothelial cells have been identified using genetic tools for fate mapping. The epicardium, the outermost layer of the developing heart, has emerged as both a source of cell progenitors and key signalling mediators. Knowledge of the specific genes underlying formation, function, and heterogeneity of the epicardium is expanding. Significant challenges remain, however, in understanding the spatiotemporal signalling patterns required for organized migration, differentiation, and patterning of the vasculature. In addition, dissecting how coronary development is perturbed in patients with congenital coronary anomalies is a major ongoing focus of research.
Significant luminosity differences of two twin Type Ia supernovae
Authors: Foley Ryan J , Hoffmann Samantha L , Macri Lucas M , Riess Adam G , Brown Peter J , Filippenko Alexei V , Graham Melissa L , Milne Peter A
Published: November 2019

The Type Ia supernovae (SNe Ia) 2011by, hosted in NGC 3972, and 2011fe, hosted in M101, are optical ‘twins,’ having almost identical optical light-curve shapes, colours, and near-maximum-brightness spectra. However, SN 2011fe had significantly more ultraviolet (UV; 1600 < λ < 2500 Å) flux than SN 2011by before and at peak luminosity. Several theoretical models predict that SNe Ia with higher progenitor metallicity should (1) have additional UV opacity and thus lower UV flux; (2) have an essentially unchanged optical spectral-energy distribution; (3) have a similar optical light-curve shape; and (4) because of the excess neutrons, produce more stable Fe-group elements at the expense of radioactive 56Ni and thus have a lower peak luminosity. Following these predictions, Foley and Kirshner suggested that the difference in UV flux between SNe 2011by and 2011fe was the result of their progenitors having significantly different metallicities. They also measured a large, but insignificant, difference between the peak absolute magnitudes of the SNe (ΔMV, peak = 0.60 ± 0.36 mag), with SN 2011fe being more luminous. We present a new Cepheid-based distance to NGC 3972, substantially improving the precision of the distance measurement for SN 2011by. With these new data, we determine that the SNe have significantly different peak luminosities (ΔMV, peak = 0.335 ± 0.069 mag). Consequently, SN 2011fe produced 38 per cent more 56Ni than SN 2011by, consistent with predictions for progenitor metallicity differences for these SNe, although alternative models may also explain this difference. We discuss how progenitor metallicity differences can contribute to the intrinsic scatter for light-curve-shape-corrected SN luminosities, the use of ‘twin’ SNe for measuring distances, and implications for using SNe Ia for constraining cosmological parameters.
The spatial distribution of circumstellar material of the wind-fed system GX 301-2
Authors: Zheng Xueying , Liu Jiren , Gou Lijun
Published: November 2019

The distribution of the circumstellar material in systems of supergiant X-ray binaries (SgXBs) is complex and not well probed observationally. We report a detailed study of the spatial distribution of the Fe K α-emitting material in the wind-fed system GX 301-2, by measuring the time delay between the Fe K α line and the hard X-ray continuum (7.8–12 keV) using the cross-correlation method, based on XMM–Newton observation. We found that to obtain the true time delay, it is crucial to subtract the underlying continuum of the Fe K α line. The measured size of the Fe Kα-emitting region over the whole observation period is 40 ± 20 light-seconds. It is 5 times larger than the accretion radius estimated from a quasi-isotropic stellar wind, but consistent with the one estimated from a tidal stream, which could be the dominant mass-loss mechanism of GX 301-2 as inferred from the orbital distribution of the absorption column density previously. The measured time delay of the quiescent period is a little smaller than those of the flare periods, revealing the unsteady behaviour of the accretion flow in GX 301-2. Statistical and detailed temporal studies of the circumstellar material in SgXBs are expected for a large sample of SgXBs with future X-ray missions, such as Athena and eXTP.
Improving baryon acoustic oscillation measurement with the combination of cosmic voids and galaxies
Authors: Zhao Cheng , Chuang Chia-Hsun , Kitaura Francisco-Shu , Liang Yu , Pellejero-Ibanez Marcos , Tao Charling , Vargas-Magaña Mariana , Variu Andrei , Yepes Gustavo
Published: November 2019

We develop a methodology to optimize the measurement of baryon acoustic oscillation (BAO) from a given galaxy sample. In our previous work, we demonstrated that one can measure BAO from tracers in underdense regions (voids). In this study, we combine the overdense and underdense tracers (galaxies and voids) to obtain better constraints on the BAO scale. To this end, we modify the de-wiggled BAO model with an additional parameter to describe both the BAO peak and the underlying exclusion pattern of void 2PCFs. We show that after applying BAO reconstruction to galaxies, the BAO peak scale of both galaxies and voids are unbiased using the modified model. Furthermore, we use a new 2PCF estimator for a multitracer analysis with galaxies and voids. In simulations, the joint sample improves by about 10 per cent the constraint for the post-reconstruction BAO peak position compared to the result from galaxies alone, which is equivalent to an enlargement of the survey volume by 20 per cent. Applying this method to the BOSS DR12 data, we have an 18 per cent improvement for the low-z sample (0.2 < z < 0.5), but a worse constraint for the high-z sample (0.5 < z < 0.75), which is consistent with statistical fluctuations for the current survey volume. Future larger samples will give more robust improvements due to less statistical fluctuations.
Constraining the magnetic field structure in collisionless relativistic shocks with a radio afterglow polarization upper limit in GW 170817
Authors: Gill Ramandeep , Granot Jonathan
Published: November 2019

Gamma-ray burst (GRB) afterglow arises from a relativistic shock driven into the ambient medium, which generates tangled magnetic fields and accelerates relativistic electrons that radiate the observed synchrotron emission. In relativistic collisionless shocks the post-shock magnetic field $\boldsymbol {B}$ is produced by the two-stream and/or Weibel instabilities on plasma skin-depth scales (c/ωp), and is oriented predominantly within the shock plane (B⊥; transverse to the shock normal, $\hat{\boldsymbol {n}}_{\rm {sh}}$), and is often approximated to be completely within it ($B_\parallel \equiv \hat{\boldsymbol {n}}_{\rm {sh}}\, \cdot \, \boldsymbol {B}=0$). Current 2D/3D particle-in-cell simulations are limited to short time-scales and box sizes ≲104(c/ωp) ≪ R/Γsh much smaller than the shocked region’s comoving width, and hence cannot probe the asymptotic downstream $\boldsymbol {B}$ structure. We constrain the latter using the linear polarization upper limit, $\vert \Pi \vert \lt 12{{\ \rm per\ cent}}$, on the radio afterglow of GW $170817$ / GRB 170817A. Afterglow polarization depends on the jet’s angular structure, our viewing angle, and the $\boldsymbol {B}$ structure. In GW $170817$ / GRB 170817A the latter can be tightly constrained since the former two are well-constrained by its exquisite observations. We model $\boldsymbol {B}$ as an isotropic field in 3D that is stretched along $\hat{\boldsymbol {n}}_{\rm {sh}}$ by a factor ξ ≡ $B_\parallel $/B⊥, whose initial value ξf ≡ $B_\parallel,$f/B⊥, f describes the field that survives downstream on plasma scales ≪R/Γsh. We calculate Π(ξf) by integrating over the entire shocked volume for a Gaussian or power-law core-dominated structured jet, with a local Blandford-McKee self-similar radial profile (used for evolving ξ downstream). We find that independent of the exact jet structure, $\boldsymbol {B}$ has a finite, but initially sub-dominant, parallel component: 0.57 ≲ ξf ≲ 0.89, making it less anisotropic. While this motivates numerical studies of the asymptotic $\boldsymbol {B}$ structure in relativistic collisionless shocks, it may be consistent with turbulence amplified magnetic field.
Twenty Years of Wage Inequality in Latin America
Authors: Messina Julian , Silva Joana
Published: November 2019

This article documents an inverse U-shape in the evolution of wage inequality in Latin America since 1995, with a sharp reduction starting in 2002. The Gini coefficient of wages increased from 42 to 44 between 1995 and 2002 and declined to 39 by 2015. Between 2002 and 2015, the 90/10 log hourly earnings ratio decreased by 26 percent. The decline since 2002 was characterized by rising wages across the board, but especially at the bottom of the wage distribution in each country. Triggered by a rapid expansion of educational attainment, the wages of college and high school graduates fell relative to the wages of workers with only primary education. The premium for labor market experience also fell significantly. However, the compression of wages was not entirely driven by changes in the wage structure across skill groups. Two-thirds of the decline in the variance of wages took place within skill groups. Changes in the sectoral, occupational, and formal/informal composition of jobs matter for the process of reduction in inequality, but they do not fully account for the fall in within-skill variance. Evidence based on longitudinal matched employer-employee administrative data suggests that an important driver was falling wage dispersion across firms.
Clinicopathologic and Molecular Pathology of Collecting Duct Carcinoma and Related Renal Cell Carcinomas
Authors: Seo An Na , Yoon Ghilsuk , Ro Jae Y.
Published: November 2019

Collecting duct carcinoma (CDC) and related tumors [ie, renal medullary carcinoma (RMC)] are rare types of highly aggressive renal cell carcinomas (RCC) with poor prognosis. Because of the rarity and diagnostic uncertainty of them, their molecular pathology and significance have not yet been fully elucidated. CDC, RMC, fumarate hydratase–deficient RCC (including hereditary leiomyomatosis and RCC-associated RCC HLRCC-RCC), and recently reported anaplastic lymphoma kinase (ALK)-rearrangement RCC have significant morphologic overlaps, but they are separately distinct entities having different molecular pathway and clinical settings. CDC is more likely to occur in middle to old age population with immunoreactivity for PAX8 and integrase interactor-1 proteins (INI-1). Various chromosomal and genomic alterations have been reported with inconsistent results. In contrast, RMC is more likely to occur in younger patients with sickle cell trait. In RMC, loss of INI-1 expression and OCT3/4 expression are distinguished compared with other RCCs. Finally, ALK-rearrangement RCC seems to have 2 different clinical settings, one with sickle cell trait (VCL-ALK fusion) and the other without (other fusions such as TPM3-ALK, EML4-ALK, and STRN-ALK fusions). Interestingly, VCL-ALK fusion was found in pediatric patients with sickle cell trait, whereas other fusions were detected in adolescent or adult without sickle cell trait. Taken together, CDC and related tumors such as RMC, fumarate hydratase–deficient RCC (including hereditary leiomyomatosis and RCC-associated RCC), and ALK-rearrangement RCC are the distinct entities and their recognition is important for the development of future personalized therapeutic options. This review updates the clinicopathologic features of these tumors with overlapping morphology and outcome.
Perineural Pseudoinvasion: An Unusual Phenomenon in Nonmalignancies
Authors: Moghimi Mansour , Joukar Fatemeh , Salehi-Abargouei Amin , Mozayan Mohammad-Reza , Aryanfar Amir
Published: November 2019

Perineural invasion (PNI) is characterized as tumoral or nontumoral cells invading in or around the nerves. The neural invasion is considered as a histopathologic characteristic for malignancy and is considered a mechanism for its spread. Both of these patterns usually portend a poor prognosis and very often are markers to prompt additional treatment. There are also some nonmalignancies representing PNI, including benign neoplasms, mimicking lesions, and disorders, such as chronic pancreatitis and endometriosis. The previously recommended terms are PNI, spread, or infiltration. To distinguish PNI in malignancies from that in nonmalignancies, we propose the term “perineural pseudoinvasion” to convey their nonmalignant behavior. Despite the low prevalence, awareness of this benign pseudoinvasion is necessary to avoid aggressive treatment and its misdiagnosis with malignancies. We conducted a systematic search in PubMed and Scopus databases up to December 2015 to find articles reporting PNI in nonmalignancies. After screening, 63 articles were identified as relevant. There were also 2 review articles discussing PNI in nonmalignancies. We aim to present an overview of the perineural pseudoinvasion and to discuss the previously published review articles.
Comparative modelling of crack propagation in elastic–plastic materials using the meshfree local radial basis point interpolation method and eXtended finite-element method
Authors: Li Yazhe , Xu Nengxiong , Tu Jinzhi , Mei Gang
Published: November 2019

The modelling and understanding of crack propagation for elastic–plastic materials is critical in various engineering applications, such as safety analysis of concrete structures and stability analysis of rock slopes. In this paper, the local radial basis point interpolation method (LRPIM) combined with elastic–plastic theory and fracture mechanics is employed to analyse crack propagation in elastic–plastic materials. Crack propagation in elastic–plastic materials is compared using the LRPIM and eXtended finite-element method (XFEM). The comparative investigation indicates that: (i) the LRPIM results are close to the model test results, which indicates that it is feasible for analysing the crack growth of elastic–plastic materials; (ii) compared with the LRPIM, the XFEM results are closer to the experimental results, showing that the XFEM has higher accuracy and computational efficiency; and (iii) compared with the XFEM, when the LRPIM method is used to analyse crack propagation, the propagation path is not smooth enough, which can be explained as the crack tip stress and strain not being accurate enough and still needing further improvement.
Alternative pathways to α,β-unsaturated ketones via direct oxidative coupling transformation using Sr-doped LaCoO
3
perovskite catalyst
Authors: Trinh Khang H. , Doan Son H. , Huynh Tien V. , Tran Phuong H. , Pham Diep N. , Le Minh-Vien , Nguyen Tung T. , Phan Nam T. S.
Published: November 2019

A strontium-doped lanthanum cobaltite perovskite material was prepared, and used as a recyclable and effective heterogeneous catalyst for the direct oxidative coupling of alkenes with aromatic aldehydes to produce α,β-unsaturated ketones. The reaction afforded high yields in the presence of di-
tert
-butylperoxide as oxidant. Single oxides or salts of strontium, lanthanum and cobalt, and the undoped perovskite offered a lower catalytic activity than the strontium-doped perovskite. Benzaldehyde could be replaced by benzyl alcohol, dibenzyl ether, 2-oxo-2-phenylacetaldehyde, 2-bromoacetophenone or (dimethoxymethyl) benzene in the oxidative coupling reaction with alkenes. To our best knowledge, reactions between these starting materials with alkenes are new and unknown in the literature.
Neurofilaments as blood biomarkers at the preataxic and ataxic stage of spinocerebellar ataxia type 3: a cross-species analysis in humans and mice
Authors: Wilke Carlo , Haas Eva , Reetz Kathrin , Faber Jennifer , Garcia-Moreno Hector , Santana Magda M. , van de Warrenburg Bart , Hengel Holger , Lima Manuela , Filla Alessandro , Durr Alexandra , Melegh Bela , Masciullo Marcella , Infante Jon , Giunti Paola , Neumann Manuela , de Vries Jeroen , de Almeida Luis Pereira , Rakowicz Maria , Jacobi Heike , Schüle Rebecca , Kaeser Stephan A. , Kuhle Jens , Klockgether Thomas , Schöls Ludger ,   SCA3 neurofilament study group,   European Integrated Project on Spinocerebellar Ataxias (EuroSCA/RiSCA),   European Spinocerebellar Ataxia Type 3/Machado-Joseph Disease Initiative (ESMI), Barro Christian , Hübener-Schmid Jeannette , Synofzik Matthis
Published: November 2019

Spinocerebellar ataxia type 3 (SCA3) is a devastating multisystemic neurodegenerative disease for which targeted molecular therapies are coming into reach (e.g. antisense oligonucleotides). To pave the way for upcoming translational trials, easily accessible biomarkers in SCA3 are needed, particularly for subjects at the preataxic stage and cross-validated also in animal models. We hypothesised that serum neurofilaments might serve as blood biomarkers of disease progression in both human SCA3 and mouse models, expecting increased concentrations already at the preataxic stage. Serum neurofilament light (NfL) and phosphorylated neurofilament heavy (pNfH) levels were determined by ultra-sensitive single molecule array (Simoa) in cross-sectional samples of ataxic and preataxic SCA3 subjects and controls in two independent cohorts (ESMI cohort = cohort #1: n=160, EuroSCA/RiSCA cohort = cohort #2: n=89). Serum NfL and pNfH were also assessed in a 304Q SCA3 knock-in mouse model across presymptomatic and symptomatic disease stages (n=147). Ataxic SCA3 subjects showed increased serum NfL (p<0.001) and pNfH (p<0.001) levels in cohort #1, with NfL levels already increased in preataxic subjects (p<0.001). All these results were replicated in cohort #2 (all p<0.001). Cross-sectional NfL levels correlated with clinical disease severity (Scale for the Assessment and Rating of Ataxia [SARA]; r=0.43, p<0.001) and with longitudinal disease progression (annual SARA score change, ϱ=0.42, p=0.012). CAG count and age were significant predictors of individual NfL concentrations (each p<0.001). NfL levels in preataxic subjects increased with proximity to individual expected onset of ataxia (p<0.001), with significant elevations already 7.5 years before onset. Serum NfL and pNfH increases in SCA3 subjects were paralleled by similar changes in SCA3 knock-in mice, here also already starting at the presymptomatic stage and close to the onset of ataxin-3 protein increase. Serum concentrations of neurofilaments, particularly NfL, might provide easily accessible biomarkers of disease severity in both ataxic and preataxic SCA3 subjects and mice prior to conversion. Neurofilaments thus entail potential applications as progression, onset/proximity and treatment-response markers in both human and murine SCA3 trials.
Can we predict early 7-day readmissions using a standard 30-day hospital readmission risk prediction model?
Authors: Saleh Sameh N. , Makam Anil N. , Halm Ethan A. , Nguyen Oanh Kieu
Published: November 2019

Despite focus on preventing 30-day readmissions, early readmissions (within 7 days of discharge) may be more preventable than later readmissions (8-30 days). We assessed how well a previously validated 30-day readmission prediction model predicts 7-day readmissions. We re-derived model coefficients for the same predictors as in the original 30-day model to optimize prediction of 7-day readmissions. We compared model performance and compared differences in strength of model factors between the 7-day model to the 30-day model. While there was no substantial change in model performance between the original 30-day and the re-derived 7-day model, there was significant change in strength of predictors. Characteristics at discharge were more predictive of 7-day readmissions, while baseline characteristics were less predictive. Improvements in predicting early 7-day readmissions will likely require new risk factors proximal to the day of discharge.
Individual differences in the course of youth depression: The importance of renitence and reversion
Authors: Hawrilenko Matthew J. , Masyn Katherine E. , Cerutti Janine , Dunn Erin C.
Published: November 2019

Studies of developmental trajectories of depression are important for understanding its etiology. Existing studies have been limited by short time frames and no studies have explored a key factor: differential patterns of responding to life events. This paper introduces a novel analytic technique, growth mixture modeling with structured residuals, to examine the course of youth depression symptoms in a large, prospective cohort (N=11,641, ages 4-16.5). Age-specific critical points were identified at ages 10 and 13 where depression symptoms spiked for a minority of children. However, most depression risk was due to dynamic responses to environmental events, drawn not from a small pool of persistently depressed children, but a larger pool of children who varied across higher and lower symptom levels.
Statistical considerations for drawing conclusions about recovery
Authors: Lohse Keith R. , Hawe Rachel L. , Dukelow Sean P. , Scott Stephen H.
Published: November 2019

Background

Numerous studies have found associations when change scores are regressed onto initial impairments in people with stroke (slopes ≈ 0.7). However, there are important statistical considerations that limit the conclusions we can draw about recovery from these studies.

Objective

To provide an accessible “check-list” of conceptual and analytical issues on longitudinal measures of stroke recovery. Proportional recovery is an illustrative example, but these considerations apply broadly to studies of change over time.

Methods

Using a pooled dataset of N = 373 Fugl-Meyer Assessment (FMA) upper extremity scores, we ran simulations to illustrate three considerations: (1) how change scores can be problematic in this context; (2) how “nil” and non-zero null-hypothesis significance tests can be used; and (3) how scale boundaries can create the illusion of proportionality, while other analytical procedures (e.g., post-hoc classifications) can augment this problem.

Results

Our simulations highlight several limitations of common methods for analyzing recovery over time. Critically, we find that uniform recovery (in the population) leads to similar group-level statistics (regression slopes) and individual-level classifications (into fitters and non-fitters) that have been claimed as evidence for the proportional recovery rule.

Conclusions

Our results highlight that one cannot identify whether proportional recovery is true or not based on commonly used methods. We illustrate how these techniques (regressing change scores onto baseline values), measurement tools (bounded scales), and post-hoc classifications (e.g., “non-fitters”) can create spurious results. Going forward the field needs to carefully consider the influence of these factors on how we measure, analyze, and conceptualize recovery.
Sort-purification of human CD34+CD90+cells reduces target cell population and improves lentiviral transduction for gene therapy
Authors: Radtke Stefan , Pande Dnyanada , Cui Margaret , Perez Anai M. , Chan Yan-Yi , Enstrom Mark , Schmuck Stefanie , Berger Andrew , Eunson Tom , Adair Jennifer E. , Kiem Hans-Peter
Published: November 2019

ABSTRACT

Hematopoietic stem cell (HSC) gene therapy has the potential to cure many genetic, malignant and infectious diseases. We have shown in a nonhuman primate (NHP) HSC gene therapy and transplantation model that the CD34+CD90+cell fraction was exclusively responsible for multilineage engraftment and hematopoietic reconstitution. Here we show the translational potential of this HSC-enriched CD34 subset for lentivirus-mediated gene therapy. Alternative HSC-enrichment strategies include the purification of CD133+cells or CD38low/-subsets of CD34+cells from human blood products. We directly compared these strategies to the isolation of CD90+cells using a GMP-grade flow-sorting protocol with clinical applicability. We show that CD90+cell selection results in 40-fold fewer target cells in comparison to CD133+or CD38low/-CD34 subsets without compromising the engraftment potentialin vivo. Single cell RNA sequencing confirmed nearly complete depletion of lineage committed progenitor cells in CD90+fractions compared to alternative selections. Importantly, lentiviral transduction efficiency in purified CD90+cells resulted in up to 3-fold higher levels of engrafted gene-modified blood cells. These studies should have important implications for the manufacturing of patient-specific HSC gene therapy and genome editing products.
Electrode pooling: boosting the yield of extracellular recordings with switchable silicon probes
Authors: Lee Kyu Hyun , Ni Yu-Li , Colonell Jennifer , Karsh Bill , Putzeys Jan , Pachitariu Marius , Harris Timothy D. , Meister Markus
Published: November 2019

State-of-the-art silicon probes for electrical recording from neurons have thousands of recording sites. However, due to volume limitations there are typically many fewer wires carrying signals off the probe, which restricts the number of channels that can be recorded simultaneously. To overcome this fundamental constraint, we propose a novel method called electrode pooling that uses a single wire to serve many recording sites through a set of controllable switches. Here we present the framework behind this method and an experimental strategy to support it. We then demonstrate its feasibility by implementing electrode pooling on the Neuropixels 1.0 electrode array and characterizing its effect on signal and noise. Finally we use simulations to explore the conditions under which electrode pooling saves wires without compromising the content of the recordings. We make recommendations on the design of future devices to take advantage of this strategy.
All talk? Left temporal alpha oscillations are not specific to verbal-analytical processing during conscious motor control
Authors: Parr Johnny V. V. , Gallicchio Germano , Harrison Neil R. , Johnen Ann-Kathrin , Wood Greg
Published: November 2019

The present study tested the validity of inferring verbal-analytic motor processing from EEG left-temporal alpha activity. Participants (n = 20) reached for and transport a jar under three conditions: one control condition and two self-talk conditions aimed at eliciting either task-unrelated verbal processing or task-related conscious control, while 32-channel EEG and kinematics were recorded. Compared to the control condition, both self-talk conditions elicited greater self-reported levels of verbal processing, but only the task-related self-talk condition was accompanied by greater left temporal activity (i.e., EEG alpha power decreased) during movement production. However, this increase was not localised to the left temporal region but was rather evident over all scalp regions examined, suggesting an interpretation more consistent with diminished neural efficiency. No effects for left temporal-frontal (T7-Fz) connectivity were detected across conditions. Our results failed to endorse left-temporal EEG alpha activity as valid index of verbal-analytic processing during motor tasks.
Successful mating and hybridisation in two closely related flatworm species despite significant differences in reproductive morphology and behaviour
Authors: Singh Pragya , Ballmer Daniel , Laubscher Max , Schärer Lukas
Published: November 2019

Speciation is usually a gradual process, in which reproductive barriers between two species accumulate over time. Reproductive traits, like genital morphology and mating behaviour, are some of the fastest diverging characters and can serve as reproductive barriers. The free-living flatworm Macrostomum lignano, an established model for studying sex in hermaphrodites, and its congener M. janickei are closely related, but differ substantially in their male intromittent organ (stylet) morphology. Here, we examine whether these morphological differences are accompanied by differences in behavioural traits, and whether these could represent barriers to successful mating and hybridization between the two species. Our data shows that the two species differ in many aspects of their mating behaviour, with M. janickei having a five-fold longer copulation duration, copulating less frequently, and having a longer and more delayed suck behaviour (a postcopulatory behaviour likely involved in sexual conflict). Interestingly, and despite these significant morphological and behavioural differences, the two species mate readily with each other in heterospecific pairings, often showing behaviours of intermediate duration. Although both species have similar fecundity in conspecific pairings, the heterospecific pairings revealed clear postmating barriers, as only few heterospecific pairings produced F1 hybrids. These hybrids had a stylet morphology that was intermediate between that of the parental species, and they could successfully backcross to both parental species. Finally, in a mate choice experiment we tested if the worms preferentially mated with conspecifics over heterospecifics, since such a preference could represent a premating barrier. Interestingly, the experiment showed that the nearly two-fold higher mating rate of M. lignano caused it to mate more with conspecifics, leading to assortative mating, while M. janickei ended up mating more with heterospecifics. Thus, while the two species can hybridize, the mating rate differences could possibly lead to higher fitness costs for M. janickei compared to M. lignano.
Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes
Authors: Marin-Gonzalez Alberto , Pastrana Cesar L. , Bocanegra Rebeca , Martín-González Alejandro , Vilhena J.G. , Pérez Rubén , Ibarra Borja , Aicart-Ramos Clara , Moreno-Herrero Fernando
Published: November 2019

A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions in vivo. The crystallographic structure of A-tracts has been well characterized. However, their response to forces remains unknown and the variability of their flexibility reported for different length scales has precluded a comprehensive description of the mechanical properties of these molecules. Here, we rationalize the mechanical properties of A-tracts across multiple length scales using a combination of single-molecule experiments and theoretical polymer models applied to DNA sequences present in the C. elegans genome. Atomic Force Microscopy imaging shows that phased A-tracts induce long-range (∼200 nm) bending. Moreover, the enhanced bending originates from an intrinsically bent structure rather than as a consequence of larger flexibility. In support of this, our data were well described with a theoretical model based on the worm-like chain model that includes intrinsic bending. Magnetic tweezers experiments confirm that the observed bent is intrinsic to the sequence and does not rely on particular ionic conditions. Using optical tweezers, we assess the local rigidity of A-tracts at high forces and unravel an unusually stiff character of these sequences, as quantified by their large stretch modulus. Our work rationalizes the complex multiscale flexibility of A-tracts, shedding light on the cryptic character of these sequences.
Description ofCorynebacterium rouxiisp. nov., a novel member of thediphtheriaespecies complex
Authors: Badell Edgar , Hennart Mélanie , Rodrigues Carla , Passet Virginie , Dazas Melody , Panunzi Leonardo , Bouchez Valérie , Carmi-Leroy Annick , Toubiana Julie , Brisse Sylvain
Published: November 2019

A group of six clinical isolates previously identified asCorynebacterium diphtheriaebiovar Belfanti, isolated from human cutaneous or peritoneum infections and from one dog, were characterized by genomic sequencing, biochemical analysis and mass spectrometry (MALDI-TOF MS). The six isolates were negative for the diphtheria toxin gene. Phylogenetic analyses showed that the six isolates (including FRC0190T) are clearly demarcated fromC. diphtheriae, C. belfantii, C. ulceransandC. pseudotuberculosis. The average nucleotide identity of FRC0190TwithC. diphtheriaeNCTC 11397Twas 92.6%, and was 91.8% withC. belfantiiFRC0043T.C. diphtheriaesubsp.lausannensestrain CHUV2995Tappeared to be a later heterotypic synonym ofC. belfantii(ANI, 99.3%). Phenotyping data revealed an atypical negative or heterogeneous intermediate maltose fermentation reaction for the six isolates. MALDI-TOF MS differentiated the new group from the otherCorynebacteriumtaxa by the presence of specific spectral peaks.rpoBsequences showed identity to atypical, maltose-negativeC. diphtheriaebiovar Belfanti isolates previously described from two cats in the USA. We propose the nameCorynebacterium rouxiisp. nov. for the novel group, with FRC0190T(= CIP 111752T= DSM 110354T) as type strain.
Neuro-functional correlates of protective effects of wheel-running exercise against cocaine locomotor sensitization in mice: a [18F]fallypride microPET study
Authors: Becker Guillaume , Lespine Louis-Ferdinand , Bahri Mohamed Ali , Serrano Maria Elisa , Lemaire Christian , Luxen André , Tirelli Ezio , Plenevaux Alain
Published: November 2019

Wheel-running exercise in laboratory rodents (animal model useful to study the neurobiology of aerobic exercise) decreases behavioral markers of vulnerability to addictive properties of various drugs of abuse including cocaine. However, neurobiological mechanisms underpinning this protective effect are far from being fully characterized and understood. Here, 28-day-old female C57BL/6J mice were housed with (n=48) or without (n=48) a running wheel for 6 weeks before being tested for acute locomotor responsiveness and initiation of locomotor sensitization to intraperitoneal injections of 8 mg/kg cocaine. The long-term expression of sensitization took place 3 weeks after the last session. On the day after, all mice underwent a microPET imaging session with [18F]fallypride radiotracer (dopamine 2/3 receptor (D2/3R) antagonist). Exercised mice were less sensitive to acute and sensitized cocaine hyperlocomotor effects, such attenuation being particularly well-marked for long-term expression of sensitization (η2p = 0.262). Additionally, we found that chronic administrations of cocaine was associated with a clear-cut increase of [18F]fallypride binding potential in mouse striatum (η2p = 0.170), presumably reflecting an increase in postsynaptic D2/3R density in this region. Finally, we found evidence that wheel-running exercise was associated with a moderate decrease in D2/3R density in striatum (η2p = 0.075), a mechanism that might contribute to protective properties of such form of exercise against drugs of abuse vulnerability.
Out of the Mediterranean Region: worldwide biogeography of snapdragons and relatives (tribe Antirrhineae, Plantaginaceae)
Authors: Gorospe Juan Manuel , Monjas David , Fernández-Mazuecos Mario
Published: November 2019

Aim

The tribe Antirrhineae, including snapdragons, toadflaxes and relatives, is a model group for plant evolutionary research. It is widely distributed across the Northern Hemisphere and the Neotropics, but displays an uneven distribution of diversity, with more than 50% of species and subspecies in the Mediterranean Region. Here we conducted the first detailed, worldwide biogeographic analysis of the Antirrhineae and tested two alternative hypotheses (time-for-speciation vs. diversification rate differences) to explain the uneven distribution of diversity.

Location

Worldwide, with a focus on the Mediterranean Region.

Taxon

tribe Antirrhineae (Plantaginaceae).

Methods

A phylogenetic biogeographic approach was taken, accounting for area connections through time. Ancestral ranges, dispersal events, speciation and lineage accumulation within areas were estimated. Diversification rates for taxa present and absent in the Mediterranean Region were compared, accounting for the effect of a floral key innovation (nectar spur).

Results

A proto-Mediterranean origin in the Late Eocene was estimated, and the Mediterranean Region stood out as the main centre for speciation and dispersal. Congruent patterns of long-distance dispersal from the Mediterranean Region to North America were recovered for at least two amphiatlantic clades. A significant floristic exchange between the Mediterranean and south-western Asia was detected. We found no evidence of different diversification rates between lineages inside and outside the Mediterranean Region.

Main conclusions

The Mediterranean Region played a key role in the origin of the current distribution of the Antirrhineae. However, the higher species richness found in this region appears to be the result of a time-for-speciation effect rather than of increased diversification rates. The establishment of current mediterranean climates in the Northern Hemisphere appears to have contributed to the recent diversification of the group, in combination with colonisation of adjacent regions with arid and semi-arid climates.
Sox2 and Sox3 are essential for development and regeneration of the zebrafish lateral line
Authors: Undurraga Cristian A. , Gou Yunzi , Sandoval Pablo C. , Nuñez Viviana A. , Allende Miguel L. , Riley Bruce B. , Hernández Pedro P. , Sarrazin Andres F.
Published: November 2019

The recovery of injured or lost sensory neurons after trauma, disease or aging is a major scientific challenge. Upon hearing loss or balance disorder, regeneration of mechanosensory hair cells has been observed in fish, some amphibians and under special circumstances in birds, but is absent in adult mammals. In aquatic vertebrates, hair cells are not only present in the inner ear but also in neuromasts of the lateral line system. The zebrafish lateral line neuromast has an almost unlimited capacity to regenerate hair cells. This remarkable ability is possible due to the presence of neural stem/progenitor cells within neuromasts. In order to further characterize these stem cells, we use the expression of the neural progenitor markers Sox2 and Sox3, transgenic reporter lines, and morphological and topological analysis of the different cell types within the neuromast. We reveal new sub-populations of supporting cells, the sustentacular supporting cells and the neuromast stem cells. In addition, using loss-of-function and mutants ofsox2andsox3, we find that the combined activity of both genes is essential for lateral line development and regeneration. The capability of sox2/sox3 expressing stem cells to produce new hair cells, hair cell-precursors, and supporting cells after damage was analyzed in detail by time-lapse microscopy and immunofluorescence. We are able to provide evidence that sox2/3 expressing cells are the main contributors to the regenerated neuromast, and that their daughter cells are able to differentiate into most cell types of the neuromast.
Modeling time-varying brain networks with a self-tuning optimized Kalman filter
Authors: Pascucci D. , Rubega M. , Plomp G.
Published: November 2019

Brain networks are complex dynamical systems in which directed interactions between different areas evolve at the sub-second scale of sensory, cognitive and motor processes. Due to the highly non-stationary nature of neural signals and their unknown noise components, however, modeling dynamic brain networks has remained one of the major challenges in contemporary neuroscience. Here, we present a new algorithm based on an innovative formulation of the Kalman filter that is optimized for tracking rapidly evolving patterns of directed functional connectivity under unknown noise conditions. The Self-Tuning Optimized Kalman filter (STOK) is a novel adaptive filter that embeds a self-tuning memory decay and a recursive regularization to guarantee high network tracking accuracy, temporal precision and robustness to noise. To validate the proposed algorithm, we performed an extensive comparison against the classical Kalman filter, in both realistic surrogate networks and real electroencephalography (EEG) data. In both simulations and real data, we show that the STOK filter estimates time-frequency patterns of directed connectivity with significantly superior performance. The advantages of the STOK filter were even clearer in real EEG data, where the algorithm recovered latent structures of dynamic connectivity from epicranial EEG recordings in rats and human visual evoked potentials, in excellent agreement with known physiology. These results establish the STOK filter as a powerful tool for modeling dynamic network structures in biological systems, with the potential to yield new insights into the rapid evolution of network states from which brain functions emerge.

Author summary

During normal behavior, brains transition between functional network states several times per second. This allows humans to quickly read a sentence, and a frog to catch a fly. Understanding these fast network dynamics is fundamental to understanding how brains work, but up to now it has proven very difficult to model fast brain dynamics for various methodological reasons. To overcome these difficulties, we designed a new Kalman filter (STOK) by innovating on previous solutions from control theory and state-space modelling. We show that STOK accurately models fast network changes in simulations and real neural data, making it an essential new tool for modelling fast brain networks in the time and frequency domain.
Chronic loss of STAG2 leads to altered chromatin structure contributing to de-regulated transcription in AML
Authors: Smith James S , Craig Stephanie G , Liberante Fabio G , Lappin Katrina M , Crean Clare M , McDade Simon S , Thompson Alexander , Mills Ken I , Savage Kienan I
Published: November 2019

The cohesin complex plays a major role in folding the human genome into 3D structural domains. Mutations in members of the cohesin complex are known early drivers of myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML), with STAG2 the most frequently mutated complex member. Here we use functional genomics to investigate the impact of chronic STAG2 loss on three-dimensional genome structure and transcriptional programming in a clinically relevant model of chronic STAG2 loss. The chronic loss of STAG2 led to loss of smaller loop domains and the maintenance/formation of large domains which in turn led to altered genome compartmentalisation. These changes in genome structure were linked with altered gene expression, including deregulation of the HOXA locus and the MAPK signalling pathway, which may contribute to disease development and response to therapy.

AUTHOR SUMMARY

Acute myeloid leukaemia (AML) and myelodysplastic syndromes (MDS) are clonal malignant diseases that affect the myeloid blood cell lineage. Around 40 different mutations have been identified as being associated with MDS and AML; several mutations effect genes in the cohesin complex particularly STAG2. STAG2 is an X-linked gene that is pivotal to the cohesin complex and the mutations result in a truncated gene and loss of function. We have introduced a clinically relevant truncating mutation into an isogeneic AML model. This has shown that changes in the sizes of loop and domains formed in the genome resulting in appropriate gene compartmentalisations. The associated changes in gene transcription has resulted in deregulation of HOX genes, essential for development and differentiation, and in the MAPK signalling pathway that could a therapeutic target.