bluuebunny/crossref_metadata_2025 huggingface dataset:
Perceived Discrimination Trajectories and Depressive Symptoms Among Middle-Aged and Older Black Adults
Authors: White Kellee , Bell Bethany A , Huang Shuo J , Williams David R
Published: September 2020

Background and Objectives

Perceived discrimination is a risk factor for poor mental health. However, most studies measure discrimination at one time point, which does not account for heterogeneity in the cumulative patterning of exposure to discrimination. To address this gap, we examine the association between discrimination trajectories and depressive symptoms among black middle-aged and older adults.

Research Design and Methods

Data were analyzed from a subsample of black Health and Retirement Study respondents (2006–2018, N = 2926, older than 50 years). General discrimination and racial discrimination trajectories were constructed based on the Everyday Discrimination Scale using repeated measures latent profile analyses. We examined the extent to which the association between discrimination trajectories are differentially associated with depressive symptoms (8-item Center for Epidemiological Studies-Depression scale) using negative binomial regression models adjusted for potential confounders. Effect modification by age and gender was tested.

Results

Individuals in the persistently high (incident rate ratio [IRR]: 1.70; 95% confidence interval [CI]: 1.49–1.95) and moderate general discrimination trajectories (IRR: 1.19; 95% CI: 1.06–1.33) were more likely to have elevated depressive symptoms in comparison to those in the persistently low trajectory. This relationship was strongest among older adults aged older than 65 years. Respondents in the persistently high racial discrimination trajectory (IRR: 1.50; 95% CI: 1.29–1.73) had a higher risk of elevated depressive symptoms in comparison to respondents in the persistently low trajectory. Sensitivity analyses indicated that there was an independent association between persistently high racial discrimination trajectory class and elevated depressive symptoms, after adjusting for racial discrimination measured at a single time point.

Discussion and Implications

Characterizing longitudinal patterns of perceived discrimination may facilitate the stratification of mental health risk and vulnerability among black middle-aged and older adults. Trajectories of racial discrimination may inform risk of worse depressive symptoms more accurately than a single assessment of discrimination.
Piezoelectricity as a mechanism on generation of electromagnetic precursors before earthquakes
Authors: Wang Jeen-Hwa
Published: September 2020

To produce the electromagnetic (E&M) precursors of an earthquake, the existence of electric field due to stress-induced charges on the ground surface or in shallow depths of upper crust inside the fault zone is a basic condition. Here, we consider the piezoelectric effect or the elastic–electric coupling as a major mechanism on generating such an electric field. A 1-D model based on the elastic mechanics and electromagnetic Maxwell equations is built up to formulate the relationship between electric field and slip as well as stress on a fault before an earthquake. From the model, we may estimate the low-bound values of stress and slip to yield the critical electric field, Ec, for generation of electromagnetic signals. The normal and shear stresses on the fault planes for three faulting types are constructed. The normal stress is stronger than the shear stress to result in piezoelectricity. The depth ranges for yielding an average normal stress being able to generate Ec are similar for thrust and strike-slip faults and deep for normal faults. The possibility of generating Ec is almost the same for thrust and strike-slip faults and low for normal faults. The pre-earthquake slip could be related to nucleation phases or microfractures. The possible occurrence time of E&M signals may be several 10 min to few hours before impending earthquakes. The major factor in yielding a piezoelectric field to generate the TEC anomalies before an earthquake is the existence of fault gouges composed mainly of clays. A thick gouge layer with low electric resistivity and a piezoelectric coupling coefficient ≥0.67 × 10−12 coul  nt–1 is an important condition for yielding piezoelectricity.
The Psychological Impact of Military Operations on Civilians and the UN Human Rights Committee Japalali Decision: Exploring Mental Anguish under a Vida Digna, Right to Life Prism
Authors: Solomon Solon
Published: September 2020

Among international scholars, much emphasis has been given on how in situations of warfare, international humanitarian law can impact upon international human rights law (IHRL). The opposite scenario has been little explored. On this account, the article will explore how under the influence of IHRL in instances of wounded civilians feeling mental anguish as a result of their uncertainty whether or not they will remain alive, a state can be found as violating these civilians’ right to life vida digna facet. At the same time, the article will proceed to analyze how such vida digna mental anguish parameter must be seen not just as general carte blanche for expanding the notion of psychological injury beyond cases of mental harm in all military operations, but as relevant only in instances, like ‘kill or capture’ operations where the state is seen in a position to consider in advance the conditions under which a military engagement takes place.
On the possibility of baryon acoustic oscillation measurements at redshift z > 7.6 with the Roman space telescope
Authors: Satpathy Siddharth , An Zhaozhou , Croft Rupert A C , Di Matteo Tiziana , Tenneti Ananth , Feng Yu , Heitmann Katrin , Rossi Graziano
Published: September 2020

The Nancy Grace Roman Space Telescope (RST), with its field of view and high sensitivity will make surveys of cosmological large-scale structure possible at high redshifts. We investigate the possibility of detecting baryon acoustic oscillations (BAO) at redshifts z > 7.6 for use as a standard ruler. We use data from the hydrodynamic simulation bluetides in conjunction with the gigaparsec-scale Outer Rim simulation and a model for patchy reionization to create mock RST High Latitude Survey grism data for Lyman α emission line selected galaxies at redshifts z = 7.4 to z = 10, covering 2280 deg2. We measure the monopoles of galaxies in the mock catalogues and fit the BAO features. We find that for a line flux of $L = 7\times 10^{-17} \ {\rm erg\, s^{-1}\, cm}^{-2}$, the 5σ detection limit for the current design, the BAO feature is partially detectable (measured in three out of four survey quadrants analysed independently). The resulting root mean square error on the angular diameter distance to z = 7.7 is 7.9 ${{\ \rm per\ cent}}$. If we improve the detection sensitivity by a factor of two (i.e. $L = 3.5\times 10^{-17} \ {\rm erg\, s^{-1}\, cm}^{-2}$), the distance error reduces to $1.4{{\ \rm per\ cent}}$. We caution that many more factors are yet to be modelled, including dust obscuration, the damping wing due to the intergalactic medium, and low redshift interlopers. If these issues do not strongly affect the results, or different observational techniques (such as use of multiple lines) can mitigate them, RST, or similar instruments may be able to constrain the angular diameter distance to the high redshift universe.
Windowing artefacts likely account for recent claimed detection of oscillating cosmic scale factor
Authors: Brownsberger Sasha R , Stubbs Christopher W , Scolnic Daniel M
Published: September 2020

Using the Pantheon data set of Type Ia supernovae, a recent publication (R20 in this work) reports a  2σ detection of oscillations in the expansion history of the Universe. The study conducted by R20 is wholly worthwhile. However, we demonstrate that there is a $\gt 10{{\ \rm per\ cent}}$ chance of statistical fluctuations in the Pantheon data producing a false oscillatory signal larger than the oscillatory signal that R20 report. Their results are a less than 2σ detection. Applying the R20 methodology to simulated Pantheon data, we determine that these oscillations could arise due to analysis artefacts. The uneven spacing of Type Ia supernovae in redshift space and the complicated analysis method of R20 impose a structured throughput function. When analysed with the R20 prescription, about $11{{\ \rm per\ cent}}$ of artificial ΛCDM data sets produce a stronger oscillatory signal than the actual Pantheon data. Our results underscore the importance of understanding the false ‘signals’ that can be introduced by complicated data analyses.
Jovian electrons at the Earth orbit and stationary structures in the solar wind
Authors: Logachev Yu I , Daibog E I , Kecskeméty K
Published: September 2020

This work studies the influence of the structure of inner heliospheric magnetic field on the propagation of Jovian electrons from Jupiter to the Earth orbit. Beginning from 1974, 13-month variations of relativistic Jovian electron fluxes were recorded by spacecraft near the Earth. 22 synodic cycles are analysed. The best connection in each cycle was found within a narrow longitudinal interval with an angular divergence of the planets 230 ± 20°, when the Parker field line connecting the two planets is formed at solar wind speed 450 ± 50 km s−1. Such invariability for more than 45 yr could not be accidental. We attribute the observed phenomenon to the long-term presence of recurrent stationary structures in the solar wind generated near the Sun. This assumption is confirmed by comparing the time profiles of the solar wind speed measured over all solar rotations in the solar activity minima in 1975 and 2007–2008.
Observing imprints of black hole event horizon on X-ray spectra
Authors: Banerjee Srimanta , Gilfanov Marat , Bhattacharyya Sudip , Sunyaev Rashid
Published: September 2020

A fundamental difference between a neutron star (NS) and a black hole (BH) is the absence of a physical surface in the latter. For this reason, any remaining kinetic energy of the matter accreting on to a BH is advected inside its event horizon. In the case of an NS, on the contrary, accreting material is decelerated on the NS surface, and its kinetic energy is eventually radiated away. Copious soft photons produced by the NS surface will affect the properties of the Comptonized component dominating spectra of X-ray binaries in the hard state. Thus, parameters of the Comptonized spectra – the electron temperature kTe and the Compton y-parameter, could serve as an important tool for distinguishing BHs from NSs. In this paper, we systematically analyse heretofore the largest sample of spectra from the BH and NS X-ray binaries in the hard state for this purpose, using archival RXTE/PCA and RXTE/HEXTE observations. We find that the BHs and NSs occupy distinctly different regions in the y − kTe plane with NSs being characterized by systematically lower values of y-parameter and electron temperature. Due to the shape of the boundary between BHs and NSs on the y − kTe plane, their 1D y and kTe distributions have some overlap. A cleaner one parameter diagnostic of the nature of the compact object in X-ray binaries is provided by the Compton amplification factor A, with the boundary between BHs and NSs lying at A ≈ 3.5–4. This is by far the most significant detection of the imprint of the event horizon on the X-ray spectra for stable stellar-mass BHs.
The Dekel-Zhao profile: a mass-dependent dark-matter density profile with flexible inner slope and analytic potential, velocity dispersion, and lensing properties
Authors: Freundlich Jonathan , Jiang Fangzhou , Dekel Avishai , Cornuault Nicolas , Ginzburg Omry , Koskas Rémy , Lapiner Sharon , Dutton Aaron , Macciò Andrea V
Published: September 2020

We explore a function with two shape parameters for the dark-matter halo density profile subject to baryonic effects, which is a special case of the general Zhao family of models applied to simulated dark-matter haloes by Dekel et al. This profile has variable inner slope and concentration parameter, and analytic expressions for the gravitational potential, velocity dispersion, and lensing properties. Using the Numerical Investigation of a Hundred Astrophysical Objects cosmological simulations, we find that it provides better fits than the Einasto profile and the generalized NFW profile with variable inner slope, in particular towards the halo centres. We show that the profile parameters are correlated with the stellar-to-halo mass ratio Mstar/Mvir. This defines a mass-dependent density profile describing the average dark-matter profiles in all galaxies, which can be directly applied to observed rotation curves of galaxies, gravitational lenses, and semi-analytic models of galaxy formation or satellite–galaxy evolution. The effect of baryons manifests itself by a significant flattening of the inner density slope and a 20 per cent decrease of the concentration parameter for Mstar/Mvir = 10−3.5–10−2, corresponding to $M_{\rm star} \!\sim \! 10^{7-10}\, \mathrm{ M}_\odot$. The accuracy by which this profile fits simulated galaxies is similar to certain multiparameter mass-dependent profiles, but its fewer parameters and analytic nature make it most desirable for many purposes.
Inclination damping on Callisto
Authors: Downey Brynna G , Nimmo Francis , Matsuyama Isamu
Published: September 2020

Callisto is thought to possess a subsurface ocean, which will dissipate energy due to obliquity tides. This dissipation should have damped any primordial inclination within 1 Gyr – and yet Callisto retains a present-day inclination. We argue that Callisto’s inclination and eccentricity were both excited in the relatively recent past (∼0.3 Gyr). This excitation occurred as Callisto migrated outwards according to the ‘resonance-locking’ model and passed through a 2:1 mean-motion resonance with Ganymede. Ganymede’s orbital elements were likewise excited by the same event. To explain the present-day orbital elements, we deduce a solid-body tidal k2/Q ≈ 0.05 for Callisto and a significantly lower value for Ganymede.
Collisional excitation of the formyl radical (HCO) by molecular hydrogen
Authors: Dagdigian Paul J
Published: September 2020

This paper addresses the need for accurate rate coefficients for transitions between fine- and hyperfine-structure resolved rotational transitions in the formyl (HCO) radical induced by collisions with the two nuclear spin modifications of H2, the dominant molecule in the interstellar medium (ISM). These rate coefficients, as well as radiative transition rate coefficients, are required for accurate determination of the abundance of HCO in the ISM. Time-independent close-coupling quantum scattering calculations have been used to compute rate coefficients for (de-)excitation of HCO in collisions with para- and ortho-H2. These calculations utilized a potential energy surface for the interaction of HCO with H2 recently computed by the explicitly correlated RCCSD(T)-F12a coupled-cluster method. Rate coefficients for temperatures ranging from 5 to 400 K were calculated for all transitions among the fine and hyperfine levels associated with the first 22 rotational levels of HCO, whose energies are less than or equal to 144 K.
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue
Authors: Gyllborg Daniel , Langseth Christoffer Mattsson , Qian Xiaoyan , Choi Eunkyoung , Salas Sergio Marco , Hilscher Markus M , Lein Ed S , Nilsson Mats
Published: September 2020

Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-cell RNA-sequencing data, providing an additional spatial dimension to investigate multiplexed gene expression, cell types, disease architecture or even data driven discoveries. In situ sequencing (ISS) method based on padlock probes and rolling circle amplification has been used to spatially resolve gene transcripts in tissue sections of various origins. Here, we describe the next iteration of ISS, HybISS, hybridization-based in situ sequencing. Modifications in probe design allows for a new barcoding system via sequence-by-hybridization chemistry for improved spatial detection of RNA transcripts. Due to the amplification of probes, amplicons can be visualized with standard epifluorescence microscopes for high-throughput efficiency and the new sequencing chemistry removes limitations bound by sequence-by-ligation chemistry of ISS. HybISS design allows for increased flexibility and multiplexing, increased signal-to-noise, all without compromising throughput efficiency of imaging large fields of view. Moreover, the current protocol is demonstrated to work on human brain tissue samples, a source that has proven to be difficult to work with image-based spatial analysis techniques. Overall, HybISS technology works as a targeted amplification detection method for improved spatial transcriptomic visualization, and importantly, with an ease of implementation.
TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function
Authors: Chen Si-Yi , Yue Tao , Lei Qian , Guo An-Yuan
Published: September 2020

T cells and the T-cell receptor (TCR) repertoire play pivotal roles in immune response and immunotherapy. TCR sequencing (TCR-Seq) technology has enabled accurate profiling TCR repertoire and currently a large number of TCR-Seq data are available in public. Based on the urgent need to effectively re-use these data, we developed TCRdb, a comprehensive human TCR sequences database, by a uniform pipeline to characterize TCR sequences on TCR-Seq data. TCRdb contains more than 277 million highly reliable TCR sequences from over 8265 TCR-Seq samples across hundreds of tissues/clinical conditions/cell types. The unique features of TCRdb include: (i) comprehensive and reliable sequences for TCR repertoire in different samples generated by a strict and uniform pipeline of TCRdb; (ii) powerful search function, allowing users to identify their interested TCR sequences in different conditions; (iii) categorized sample metadata, enabling comparison of TCRs in different sample types; (iv) interactive data visualization charts, describing the TCR repertoire in TCR diversity, length distribution and V-J gene utilization. The TCRdb database is freely available at http://bioinfo.life.hust.edu.cn/TCRdb/ and will be a useful resource in the research and application community of T cell immunology.
Implementation of CSR Legislation in India through the Lens of Its Beneficiaries: A Case Study of Malwa Region, Punjab, India
Authors: Kumar Nishant , Kumar Chauhan Deepak
Published: September 2020

This study examines how the Indian CSR law has been implemented and enforced by companies and industries situated in the Malwa region of Punjab state in India. Malwa region, one of the most industrialized clusters of the state, is also simultaneously one of its most polluted areas. Given the severe health effects that these polluting industries cause, implementing the law on CSR in its true spirit is of grave importance. This study uses in-depth interviews of the intended project beneficiaries to determine the state of implementation of the Indian CSR regulatory framework for the selected geographical region. Using the above methodology, this article suggests that businesses should strive at mitigation of the risks of their production and manufacturing activities to the community and the environment. Rather, CSR is viewed by companies as donating part of the companies’ profits to CSR activities, and undertaking social-welfare activities to meet statutory obligations. Hence, this article further determines that there is a need to implement the CSR law in its true spirit by developing an understanding among the companies on the concept and importance of CSR, which goes beyond profit donations. This article concludes with several policy recommendations that can be utilized by the government to strengthen the state of implementation of the law in not only the Malwa region, but also the entire country.
Effects of prolonged elevated temperature on leaf gas exchange and other leaf traits in young olive trees
Authors: Miserere Andrea , Rousseaux M Cecilia , Ploschuk Edmundo L , Brizuela M Magdalena , Curcio Matías H , Zabaleta Romina , Searles Peter S
Published: September 2020

Despite the economic importance of long-lived crop species in the Mediterranean Basin and their expansion to new warmer regions, their potential responses to prolonged temperature increases have not been adequately addressed. The objectives of this study were to: (i) assess leaf gas exchange responses to prolonged elevated temperature in young olive trees; (ii) evaluate some additional leaf traits such as stomatal density and size under these same conditions; and (iii) determine whether photosynthetic acclimation to temperature was apparent. A field experiment with two temperature levels was conducted using well-irrigated, potted olive trees (cvs. Arbequina, Coratina) grown in open-top chambers during the summer and early fall in two growing seasons. The temperature levels were a near-ambient control (T0) and a heated (T+) treatment (+4 °C). Maximum photosynthetic rate (Amax), stomatal conductance (gs), transpiration (E) and chlorophyll fluorescence were measured. Stomatal size and density and trichome density were also determined. The Amax, gs and chlorophyll fluorescence were little affected by heating. However, leaf E was higher at T+ than T0 in the summer in both seasons due in large part to the moderate increase in vapor pressure deficit that accompanied heating, and consequently water-use efficiency was reduced in heated leaves. When reciprocal temperature measurements were conducted in mid-summer of the second season, Amax values of T0 and T+ leaves were higher under the temperature level at which they grew than when measured at the other temperature level, which suggests some thermal acclimation. Stomatal size and density were greater in T+ than in T0 grown leaves in some cases, which was consistent with a greater E in T+ leaves when measured at both temperature levels. These results suggest that acclimation to long-term changes in temperature must be carefully considered to help determine how olive trees will be influenced by global warming.
Healing Our Own: A Randomized Trial to Assess Benefits of Peer Support
Authors: Rivera-Chiauzzi Enid Y. , Smith Heather A. , Moore-Murray Tanya , Lee Colleen , Goffman Dena , Bernstein Peter S. , Chazotte Cynthia
Published: September 2020

Objectives

This study aimed to develop and evaluate a structured peer support program to address the needs of providers involved in obstetric adverse outcomes.

Methods

In this pilot randomized controlled trial, participants were providers who experienced an obstetric-related adverse outcome. Providers were randomly assigned to routine support (no further follow-up) or enhanced support (follow-up with a trained peer supporter). Participants completed surveys at baseline, 3 months, and 6 months. The primary outcome was the use of resources and the perception of their helpfulness. Secondary outcomes were the effect on the recovery stages and the duration of use of peer support.

Results

Fifty participants were enrolled and randomly assigned 1:1 to each group; 42 completed the program (enhanced, 23; routine, 19). The 2 groups were not significantly different with respect to event type, demographics, or baseline stage; in both groups, most participants started at the stage 6 thriving path. Most participants required less than 3 months of support: 65.2% did not need follow-up after the first contact, and 91.3% did not need follow-up after the second contact. Participants who transitioned from an early stage of recovery (stages 1–3) to the stage 6 thriving path reported that they most often sought support from peers (P = 0.02) and departmental leadership (P = 0.07). Those in the enhanced support group were significantly more likely to consider departmental leadership as one of the most helpful resources (P = 0.02).

Conclusions

For supporting health care providers involved in adverse outcomes, structured peer support is a practicable intervention that can be initiated with limited resources.
Application of the modified Nutrition Risk in Critically Ill score to nutritional risk stratification of trauma victims: A multicenter observational study
Authors: Iwuchukwu Chinenye , O’Keefe Grant E. , Day Andrew G. , Jiang Xuran , Heyland Daren K.
Published: September 2020

BACKGROUND

The modified Nutrition Risk in Critically Ill (mNUTRIC) score was developed to identify patients most likely to benefit from nutritional therapies and to stratify or select study subjects for clinical trials. The score is not validated in trauma victims in whom adequate nutritional support is important and difficult to achieve. We sought to determine whether a higher mNUTRIC score was associated with worse outcomes and whether caloric and protein intake improved outcome more in patients classified as high risk relative to those classified as low risk.

METHODS

We analyzed a prospectively collected database of patients from intensive care units globally. The primary outcome was 60-day hospital mortality, and the secondary outcome was time to discharge alive. We compared outcomes between high and low mNUTRIC score groups and also tested whether the association between outcome and nutrition intake was modified by the mNUTRIC score.

RESULTS

A total of 771 trauma patients were included. Most (585; 76%) had a low-risk mNUTRIC (0–4) score, and 186 (24%) had a high-risk (5–9) mNUTRIC score. The overall 60-day mortality was 13%. Patients in the high mNUTRIC group had a higher risk of death than those in the low mNUTRIC group (adjusted odds ratio, 2.6; 95% confidence interval, 1.7–4.2). Overall, there was no relationship between caloric or protein intake and clinical outcomes. However, patients in the high mNUTRIC group fared better with increasing caloric and protein intake, whereas subjects in the low mNUTRIC score group did not (pvalues for interaction with the mNUTRIC score for time to discharge alive wasp= 0.014 for calories and wasp= 0.004 for protein).

CONCLUSION

A high mNUTRIC score identifies trauma patients at higher risk for poor outcomes and those who may benefit from higher caloric and protein intake.

LEVEL OF EVIDENCE

Epidemiological/Prognostic, level III.
Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia
Authors: Shen Ya , Chen Sheng-Chung , Lai Mei-Chin , Huang Hsing-Hua , Chiu Hsiu-Hui , Tang Sen-Lin , Rogozin Denis Yu , Degermendzhy Andrey G.
Published: September 2020

A halotolerant, psychrotolerant and methylotrophic methanogen, strain SY-01T, was isolated from the saline Lake Tus in Siberia. Cells of strain SY-01Twere non-motile, cocci and 0.8–1.0 µm in diameter. The only methanogenic substrate utilized by strain SY-01Twas methanol. The temperature range of growth for strain SY-01Twas from 4 to 40 °C and the optimal temperature for growth was 30 °C. The pH range of growth was from pH 7.2 to 9.0, with optimal growth at pH 8.0. The NaCl range of growth was 0–1.55 M with optimal growth at 0.51 M NaCl. The G+C content of the genome of strain SY-01Twas 43.6 mol % as determined by genome sequencing. Phylogenetic analysis revealed that strain SY-01Twas most closely related toMethanolobus zinderiSD1T(97.3 % 16S rRNA gene sequence similarity), and had 95.5–97.2 % similarities to otherMethanolobusspecies with valid names. Genome relatedness between strain SY-01Tand DSM 21339Twas computed using average nucleotide identity and digital DNA–DNAhybridization, which yielded values of 79.7 and 21.7 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01Trepresents a novel species of the genusMethanolobus, and the nameMethanolobus halotoleranssp. nov. is proposed. The type strain is SY-01T(=BCRC AR10051T=NBRC 113166T=DSM 107642T).
Specific induction of double negative B cells during protective and pathogenic immune responses
Authors: Ruschil Christoph , Gabernet Gisela , Lepennetier Gildas , Heumos Simon , Kaminski Miriam , Hrasko Zsuzsanna , Irmler Martin , Beckers Johannes , Ziemann Ulf , Nahnsen Sven , Owens Greg P. , Bennett Jeffrey L. , Hemmer Bernhard , Kowarik Markus C.
Published: September 2020

1

Double negative (DN) (CD19+CD20lowCD27−IgD−) B cells are expanded in patients with autoimmune and infectious diseases; however their role in the humoral immune response remains unclear. Using systematic flow cytometric analyses of peripheral blood B cell subsets, we observed an inflated DN B cell population in patients with variety of active inflammatory conditions: myasthenia gravis, Guillain-Barré syndrome, neuromyelitis optica spectrum disorder, meningitis/encephalitis, and rheumatic disorders. Furthermore, we were able to induce DN B cells in healthy subjects following vaccination against influenza and tick borne encephalitis virus. Transcriptome analysis revealed a gene expression profile in DN B cells that clustered with naïve B cells, memory B cells, and plasmablasts. Immunoglobulin VH transcriptome sequencing and analysis of recombinant antibodies revealed clonal expansion of DN B cells, that were targeted against the vaccine antigen. Our study suggests that DN B cells are expanded in multiple inflammatory neurologic diseases and represent an inducible B cell population that responds to antigenic stimulation, possibly through an extra-follicular maturation pathway.
Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block
Authors: Wang Zhenxing , Butel Nicolas , Santos-González Juan , Simon Lauriane , Wärdig Cecilia , Köhler Claudia
Published: September 2020

Hybridization of plants that differ in number of chromosome sets (ploidy) frequently causes endosperm failure and seed arrest, a phenomenon referred to as triploid block. Mutation inNRPD1, encoding the largest subunit of the plant-specific RNA Polymerase IV (Pol IV), can suppress the triploid block. Pol IV generates short RNAs required to guidede novomethylation in the RNA-directed DNA methylation (RdDM) pathway. In this study, we found that the ability of mutants in the RdDM pathway to suppress the triploid block depends on their degree of inbreeding. Whilenrpd1is able to suppress in the first homozygous generation, mutants inRDR2,NRPE1, andDRM2require at least one additional round of inbreeding to exert a suppressive effect. Inbreeding ofnrpd1was connected with a transgenerational loss of non-CG DNA methylation on sites jointly regulated by CHROMOMETHYLASES 2 and 3. Our data thus reveal that loss of RdDM function differs in its effect in early and late generations and that Pol IV acts at an early stage of triploid block establishment.

One-sentence summary

Inbreeding of mutants impaired in RdDM components transgenerationally enhanced their ability to suppress the triploid block.
COVID-19 Biomarkers in research: Extension of the OncoMX cancer biomarker data model to capture biomarker data from other diseases
Authors: Gogate N , Lyman D , Crandall K.A , Kahsay R , Natale D.A , Sen S , Mazumder R
Published: September 2020

Scientists, medical researchers, and health care workers have mobilized worldwide in response to the outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; SCoV2). Preliminary data have captured a wide range of host responses, symptoms, and lingering problems post-recovery within the human population. These variable clinical manifestations suggest differences in influential factors, such as innate and adaptive host immunity, existing or underlying health conditions, co-morbidities, genetics, and other factors. As COVID-19-related data continue to accumulate from disparate groups, the heterogeneous nature of these datasets poses challenges for efficient extrapolation of meaningful observations, hindering translation of information into clinical applications. Attempts to utilize, analyze, or combine biomarker datasets from multiple sources have shown to be inefficient and complicated, without a unifying resource. As such, there is an urgent need within the research community for the rapid development of an integrated and harmonized COVID-19 Biomarker Knowledgebase. By leveraging data collection and integration methods, backed by a robust data model developed to capture cancer biomarker data we have rapidly crowdsourced the collection and harmonization of COVID-19 biomarkers. Our resource currently has 138 unique biomarkers. We found multiple instances of the same biomarker substance being suggested as multiple biomarker types during our extensive cross-validation and manual curation. As a result, our Knowledgebase currently has 265 biomarker type combinations. Every biomarker entry is made comprehensive by bringing in together ancillary data from multiple sources such as biomarker accessions (canonical UniProtKB accession, PubChem Compound ID, Cell Ontology ID, Protein Ontology ID, NCI Thesaurus Code, and Disease Ontology ID), BEST biomarker category, and specimen type (Uberon Anatomy Ontology) unified with ontology standards. Our preliminary observations show distinct trends in the collated biomarkers. Most biomarkers are related to the immune system (SAA,TNF-∝, and IP-10) or coagulopathies (D-dimer, antithrombin, and VWF) and a few have already been established as cancer biomarkers (ACE2, IL-6, IL-4 and IL-2). These trends align with proposed hypotheses of clinical manifestations compounding the complexity of COVID-19 pathobiology. We explore these trends as we put forth a COVID-19 biomarker resource that will help researchers and diagnosticians alike. All biomarker data are freely available fromhttps://data.oncomx.org/covid19.
Epigenetic Evolution of ACE2 and IL-6 Genes as Non-Canonical Interferon-Stimulated Genes Correlate to COVID-19 Susceptibility in Vertebrates
Authors: Sang Eric R. , Tian Yun , Miller Laura C. , Sang Yongming
Published: September 2020

Current novel coronavirus disease (COVID-19) has spread globally within a matter of months. The virus establishes a success in balancing its deadliness and contagiousness, and causes substantial differences in susceptibility and disease progression in people of different ages, genders and pre-existing comorbidities. Since these host factors are subjected to epigenetic regulation, relevant analyses on some key genes underlying COVID-19 pathogenesis were performed to longitudinally decipher their epigenetic correlation to COVID-19 susceptibility. The genes of host angiotensin-converting enzyme 2 (ACE2, as the major virus receptor) and interleukin (IL)-6 (a key immune-pathological factor triggering cytokine storm) were shown to evince active epigenetic evolution via histone modification and cis/trans-factors interaction across different vertebrate species. Extensive analyses revealed that ACE2 ad IL-6 genes are among a subset of non-canonical interferon-stimulated genes (non-ISGs), which have been designated recently for their unconventional responses to interferons (IFNs) and inflammatory stimuli through an epigenetic cascade. Furthermore, significantly higher positive histone modification markers and position weight matrix (PWM) scores of keycis-elements corresponding to inflammatory and IFN signaling, were discovered in both ACE2 and IL6 gene promoters across representative COVID-19-susceptible species compared to unsusceptible ones. Findings characterize ACE2 and IL-6 genes as non-ISGs that respond differently to inflammatory and IFN signaling from the canonical ISGs and their epigenetic properties may serve as biomarkers to longitudinally predict COVID-19 susceptibility in vertebrates and partially explain COVID-19 inequality in people of different subgroups.
Does the Inertia of a Cell Depend Upon its Information-Content?
Authors: Elewa Ahmed
Published: September 2020

A time dilation factor is derived from information entropy via the holographic principle. By imagining the embryonic cell as a hologram, time dilation during embryogenesis is predicted from the entropy of active genetic information and shown to be consistent with observed lengths of cell duration. The connection between entropy and cell duration as well as the corollary of increase in cellular mass with the reduction in information entropy are discussed. This preprint is the second in a series exploring the value ofDevelopmental Spacetimeas a framework for falsifiable predictions about the universe.
Generation of nonlinear and spatially-organized 3D cultures on a microfluidic chip using photoreactive thiol-ene and methacryloyl hydrogels
Authors: Ortiz-Cárdenas Jennifer E. , Zatorski Jonathan M. , Arneja Abhinav , Montalbine Alyssa N. , Munson Jennifer M. , Luckey Chance John , Pompano Rebecca R.
Published: September 2020

Micropatterning techniques for 3D cell cultures enable the recreation of tissue-level structures, but their combination with well-defined, microscale fluidic systems for perfusion remains challenging. To address this technological gap, we developed a user-friendly in-situ micropatterning protocol that integrates photolithography of crosslinkable, cell-laden hydrogels with a simple microfluidic housing, and tested the impact of crosslinking chemistry on stability and spatial resolution. Working with gelatin functionalized with photo-crosslinkable moieties, we found that inclusion of cells at high densities (≥ 107/mL) during crosslinking did not impede thiol-norbornene gelation, but decreased the storage moduli of methacryloyl hydrogels. Hydrogel composition and light dose were selected to match the storage moduli of soft tissues. The cell-laden precursor solution was flowed into a microfluidic chamber and exposed to 405 nm light through a photomask to generate the desired pattern. The on-chip 3D cultures were self-standing, and the designs were interchangeable by simply swapping out the photomask. Thiol-ene hydrogels yielded highly accurate feature sizes from 100 – 900 μm in diameter, whereas methacryloyl hydrogels yielded slightly enlarged features. Furthermore, only thiol-ene hydrogels were mechanically stable under perfusion overnight. Repeated patterning readily generated multi-region cultures, either separately or adjacent, including non-linear boundaries that are challenging to obtain on-chip. As a proof-of-principle, primary human T cells, were patterned on-chip with high regional specificity. Viability remained high (> 85%) after overnight culture with constant perfusion. We envision that this technology will enable researchers to pattern 3D cultures under fluidic control in biomimetic geometries that were previously difficult to obtain.
Human-Brain Artificial-Intelligence Matrix
Authors: Ibrahim John
Published: September 2020

Human-Brain Artificial-Intelligence Matrix is a new technology aims to connect the human brain with the machine for the purpose of enabling the human brain to perform defined functions even if it becomes unable to perform them such as performing the function of vision in case of blindness, the function of hearing in case of deafness, Performing the function of motion in case of paralysis and many other functions. This technology will be based on the Cognition Theory which I argue about that the whole process of cognition can be treated quantum-mechanically. The cognition starts when a neuron sends data to be processed in the brain and ends in an effector to respond. The data “action potential” is a current of particles which can be described quantum-mechanically as a wave-impulse based on the dual nature of the particles. The neurons are a net of entangled cells classically and quantum-mechanically. When the action potential changes the potential of the neurons, it creates quantum mechanical potential wells and barriers. The action potential perfectly transmits in and out the neurons through quantum mechanical tunnels. The form of energy before processing is not the same after, but the amount of energy is always conserved. Since the neurons are entangled during the action potential transmission, the brain and effector will be entangled during the action potential processing. The effector’s cognition of data must be a discrete cognition of single-valued data from its self-adjoint matrix which entangled with brain matrix.
Back to the future: a refined single user photostation for massively scaling herbarium digitization
Authors: Davis Charles C. , Kennedy Jonathan A. , Grassa Christopher J.
Published: September 2020

The digitization and online mobilization of herbarium specimens has greatly facilitated their access and helped ignite a revolution in the biodiversity sciences (Drew et al., 2017; Hedrick et al., 2020; Nelson et al., 2015; Soltis, 2017; Sweeney et al., 2018; Thiers et al., 2016). These efforts have mobilized millions of specimens with significant economies of scale and accelerated advances in scientific investigations, including phenological studies of climate change, species range assessments, and biotic interactions (Hedrick et al., 2020; Meineke et al., 2019; Meineke et al., 2018; Pearson et al., 2020; Willis et al., 2017). In addition, the use of natural history collections to answer scientific questions using only their digitized representation, rather than the physical specimen itself–i.e., Digitization 2.0sensuHedrick et al. (2020)–has sparked the integration and development of new scholarly disciplines and lines of inquiry not previously possible. Despite these exciting new directions, however, Digitization 1.0sensuHedrick et al. (2020)–i.e., the generation of digitized products from the physical specimen–remains an active area of innovation and development. This relates to both hardware and workflow innovations as well as their integration with advancements in software. Along these lines, innovations in these areas have greatly increased the cost-effectiveness of digitizing herbarium specimens and enabled the successful mobilization of entire collections and whole floristic regions (Heerlien et al., 2015; Pignal and Michiels, 2012; Schorn et al., 2016; Slijkhuis, 2014; Sweeney et al., 2018; van Oever and Gofferjé, 2012). Here, we present a novel photostation and workstation design for imaging herbarium specimen that represents a dramatic improvement upon existing approaches and is scalable for large and small institutions alike.
Myogenic Vasoconstriction Requires Canonical Gq/11Signaling of the Angiotensin II Type 1a Receptor in the Murine Vasculature
Authors: Cui Yingqiu , Kassmann Mario , Nickel Sophie , Zhang Chenglin , Alenina Natalia , Anistan Yoland Marie , Schleifenbaum Johanna , Bader Michael , Welsh Donald G. , Huang Yu , Gollasch Maik
Published: September 2020

Background

The myogenic response is an inherent vasoconstrictive property of resistance arteries to keep blood flow constant in response to increases in intravascular pressure. Angiotensin II (Ang II) type 1 receptors (AT1R) are broadly distributed, mechanoactivated receptors, which have been proposed to transduce myogenic vasoconstriction. However, the AT1R subtype(s) involved and their downstream G protein- and β-arrestin-mediated signaling pathways are still elusive.

Objective

To characterize the function of AT1aR and AT1bR in the regulation of the myogenic response of resistance size arteries and possible downstream signaling cascades mediated by Gq/11and/or β-arrestins.

Methods

We usedAgtr1a-/-,Agtr1b-/-and tamoxifen-inducible smooth muscle-specific AT1aR knockout mice (SM-Agtr1amice). FR900359, [Sar1, Ile4, Ile8] Ang II (SII) and TRV120055 were used as selective Gq/11protein inhibitor and biased agonists to activate non-canonical β-arrestin and canonical Gq/11signaling of the AT1R, respectively.

Results

Myogenic and Ang II-induced vasoconstrictions were diminished in the perfused renal vasculature ofAgtr1a-/-andSM-Agtr1amice. Similar results were observed in isolated pressurized mesenteric and cerebral arteries. Myogenic tone and Ang II-induced vasoconstrictions were normal in arteries fromAgtr1b-/-mice. The Gq/11blocker FR900359 decreased myogenic tone and Ang II vasoconstrictions while selective biased targeting of AT1R β-arrestin signaling pathways had no effects.

Conclusion

The present study demonstrates that myogenic arterial constriction requires Gq/11-dependent signaling pathways of mechanoactivated AT1aR but not G protein-independent, noncanonical alternative signaling pathways in the murine mesenteric, cerebral and renal circulation.
Hybrid Chemomechanical Promotion of PEDOT Adhesion onto Flexible Microelectrode Arrays for Chronic Neural Stimulation
Authors: Kouhani Mohammad Hossein Mazaheri , Istomin Alexander , Datta Proyag , Talbot Neil H.
Published: September 2020

Advances in neural prosthetic technologies demand ever increasing novelty in material composition to enhance the mechanical and electrochemical properties of existing microelectrode arrays. Conductive polymers present advantages such as mechanical flexibility, outstanding biocompatibility, remarkable electrical properties and, most of all, cellular agreement. However, for long-term chronic applications, they fall short in their electrochemical endurance and mechanical adhesion to their substrate materials. Multiple electrochemical approaches have been investigated to improve the adherence of Poly(3,4-ethylenedioxythiophene) (PEDOT) to underlying metallic thin films. In this work, an electrochemical treatment of diazonium salt on platinum microelectrodes is incorporated as an electrochemical adhesion promoter for PEDOT and it is further combined with using the highly microporous geometry of Platinum Grey (Pt-Grey); a technology developed by Second Sight Medical Products Inc (SSMP). The intertwined mechanical integration of Pt-Grey and PEDOT molecules together with the covalent binding agency of diazonium salt demostrate a composite coating technology with long-term stability of more than 452 days while providing >70× enhancement to the interfacial capacitive impedance.
New insights into homoeologous copy number variations in the hexaploid wheat genome
Authors: Juery Caroline , Concia Lorenzo , De Oliveira Romain , Papon Nathan , Ramírez-González Ricardo , Benhamed Moussa , Uauy Cristobal , Choulet Frédéric , Paux Etienne
Published: September 2020

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to theTriticeaedispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.

Core ideas

Only one half of hexaploid wheat genes are in triads,i.e. in a 1:1:1 ratio across subgenomes

Triads are likely part of the core genome; dyads and tetrads belong to the dispensable genome

Subgenome dominance and biased fractionation are absent in hexaploid wheat

Subgenome differences are related to two successive waves of post-polyploid diploidization