bluuebunny/crossref_metadata_2025_split huggingface dataset:
Considering light–matter interactions in the Friedmann equations
Authors: Vavryčuk V. 
Published: May 2022

Recent observations indicate that the Universe is not transparent but partially opaque due to absorption of light by ambient cosmic dust. This implies that the Friedmann equations valid for the transparent universe must be modified for the opaque universe. This paper studies a scenario in which the opacity rises with redshift. In this case, the light–matter interactions become important, because cosmic opacity produces radiation pressure that counterbalances gravitational forces. The presented theoretical model assumes the Universe is expanding according to the standard FLRW metric but with the scale factor

a
(
t
)

depending on both types of forces: gravity as well as radiation pressure. The modified Friedmann equations predict a cyclic expansion/contraction evolution of the Universe within a limited range of scale factors with no initial singularity. The model avoids dark energy and removes some other tensions of the standard cosmological model. The paper demonstrates that considering light–matter interactions in cosmic dynamics is crucial and can lead to new cosmological models essentially different from the standard

Λ

CDM model. This emphasizes the necessity of new observations and studies of cosmic opacity and cosmic dust at high redshifts for more realistic modelling of the evolution of the Universe.
Identification of key molecules and biological processes in TCF21 treated tumor pericytes
Authors: Zhao Guofang , Zhang Donghong , Wang Mengshan 
Published: May 2022

AbstractColorectal cancer has become a major public health problem in the US. Transcription factor 21 (TCF21) is reported to be silenced in colorectal cancer tissues. However, the mechanism of TCF21 in tumor pericytes is still unclear. In our study, we aim to identify the key biological processes and signaling pathways by analyzing the RNA-seq data. The GSE200064 was produced by the Illumina NovaSeq 6000 (Homo sapiens). The KEGG and GO analyses showed that MAPK signaling pathway and complement/coagulation cascades are the major changed signaling pathways in the progression of tumor pericytes with overexpression of TCF21. Moreover, we identified several interactive molecules including VEGFA, MMP2, CCL2, COL3A1, COL1A2, CXCL12, ELN, PDGFRB, VWF, and APOE. These findings may benefit the study of colorectal cancer treatment.
Immunogenicity of BNT162b2 Vaccine Booster Dose in Patients with Inflammatory Bowel Disease Receiving Infliximab Combination Therapy: A Prospective Observational Study
Authors: Shehab Mohammad , Alrashed Fatema , Alfadhli Ahmad , Alsayegh Abdulwahab , Aldallal Usama , Cherian Preethi , Alkhair Irina , Thanaraj Thangavel Alphonse , Channanath Arshad , Dashti Ali A. , Albanaw Anwar , Ali Hamad , Abu-Farha Mohamed , Abubaker Jehad , Al-Mulla Fahd 
Published: May 2022

AbstractIntroductionFew data exist regarding the immunogenicity of third dose of BNT162b2 relative to second dose in patients with inflammatory bowel disease (IBD) on different immunosuppressive therapies. We investigated the immunogenicity of BNT162b2 vaccine booster dose in patients with IBD on infliximab combination therapy.MethodsThis is prospective single center observational study conducted between January 1st, 2022 until February 28th, 2022. Patients were recruited at the time of attendance at the infusion center. Eligibility criteria included patients with confirmed diagnosis of IBD who are receiving infliximab with azathioprine or 6-mercaptopurine and have received two or three-dose of BNT162b2 vaccine. Patients were excluded if they were infected or had symptoms of SARS-CoV-2 previously since the start of the pandemic or received other vaccines than the BNT162b2. Our primary outcome was the concentrations of SARS-CoV-2 antibodies Immunoglobulin G (IgG) and neutralizing antibodies 40-45 weeks from the first dose of BNT162b2 in patients with IBD receiving infliximab combination therapy. Medians with interquartile range (IQR) were calculated.Results162 patients with IBD and receiving infliximab combination therapy were recruited and the number of patients in each group was 81. Median (IQR) SARS-CoV-2 IgG levels were significantly lower after the second dose [125 BAU/mL (43, 192)] compared to patients who received the third booster dose [207 BAU/mL (181, 234)] (p = 0.003). Neutralizing antibody levels were also lower after the second dose [80 BAU/mL (21, 95)] compared to patients who received the third booster dose [96 BAU/mL (93, 99)] (p = <0.001). The percentage of patients who achieved positive SARS-CoV-2 IgG levels in the third (booster) dose group was higher (96.3%) than those in second dose group (90%)(p = 0.026). Percentage of patients who received third (booster) dose and achieved positive SARS-CoV-2-neutralizing antibody level was 100%, whereas it was lower (88.9%) in patients who received second dose only (p=0.009).ConclusionMost patients with IBD on infliximab combination therapy had positive SARS-CoV-2 IgG and neutralizing antibody concentrations 40-45 weeks post BNT162b2 vaccination. However, SARS-CoV-2 IgG and neutralizing antibody concentrations were lower in patients who received 2 doses only compared to patients who received a third dose.
Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation
Authors: Meshcheryakov Vladimir A. , Pan Wenfei , Li Tianjie , Wang Yi , Ghosh Gourisankar , Wang Vivien Ya-Fan 
Published: May 2022

AbstractThe mammalian NF-κB p52:p52 homodimer together with its cofactor Bcl3 activates transcription of κB sites with a central G/C base pair (bp), while it is inactive toward κB sites with a central A/T bp. To understand the molecular basis for this unique property of p52, we have determined its structure in complex with a P-selectin(PSel)-κB DNA (5’-GGGGTGACCCC-3’) (central bp is underlined) and variants changing the central bp to A/T or swapping the flanking bp. The structures reveal a nearly two-fold widened minor groove in the central region of the DNA as compared to all other currently available NF-κB-DNA complex structures, which have a central A/T bp. Molecular dynamics (MD) simulations show free DNAs exist in distinct preferred conformations, and p52:p52 homodimer induces the least amount of conformational changes on the more transcriptionally active natural PSel-κB DNA in the bound form. Our binding assays further demonstrate that the fast kinetics driven by entropy is correlated with higher transcriptional activity. Overall, our studies have revealed a novel conformation for κB DNA in complex with NF-κB and suggest the importance of binding kinetics, dictated by free DNA conformational and dynamic states, in controlling transcriptional activation for NF-κB.
Patterning of the female reproductive tract along antero-posterior and dorso-ventral axes is dependent on Amhr2+ mesenchyme in mice
Authors: Jia Shuai , Wilbourne Jillian , Crossen McKenna J , Zhao Fei 
Published: May 2022

AbstractMorphogenesis of the female reproductive tract is regulated by the mesenchyme. However, the identity of the mesenchymal lineage that directs the patterning of the female reproductive tract has not been determined. Using in vivo genetic cell ablation, we identified Amhr2+ mesenchyme as an essential mesenchymal population in patterning the female reproductive tract. After partial ablation of Amhr2+ mesenchymal cells, the oviduct failed to develop its characteristic coiling due to decreased epithelial proliferation and tubule elongation during development. The uterus displayed a reduction in size and showed decreased cellular proliferation in both epithelial and mesenchymal compartments. More importantly, in the uterus, partial ablation of Amhr2+ mesenchyme caused abnormal lumen shape and altered the direction of its long axis from the dorsal-ventral axis to the left-right axis (i.e. perpendicular to the dorsal-ventral axis). Despite these morphological defects, epithelia underwent normal differentiation into secretory and ciliated cells in the oviduct and glandular epithelial cells in the uterus. These results demonstrated that Amhr2+ mesenchyme can direct female reproductive tract morphogenesis by regulating epithelial proliferation and lumen shape without affecting the differentiation of epithelial cell types.
A unique epigenomic landscape defines CD8+ tissue-resident memory T cells
Authors: Buquicchio Frank A. , Fonseca Raissa , Belk Julia A. , Evrard Maximilien , Obers Andreas , Qi Yanyan , Daniel Bence , Yost Kathryn E. , Satpathy Ansuman T. , Mackay Laura K. 
Published: May 2022

SummaryMemory T cells provide rapid and long-term protection against infection and tumors. The memory CD8+ T cell repertoire contains phenotypically and transcriptionally heterogeneous subsets with specialized functions and recirculation patterns. While these T cell populations have been well characterized in terms of differentiation potential and function, the epigenetic changes underlying memory T cell fate determination and tissue-residency remain largely unexplored. Here, we examined the single-cell chromatin landscape of CD8+ T cells over the course of acute viral infection. We reveal an early bifurcation of memory precursors displaying distinct chromatin accessibility and define epigenetic trajectories that lead to a circulating (TCIRC) or tissue-resident memory T (TRM) cell fate. While TRM cells displayed a conserved epigenetic signature across organs, we demonstrate that these cells exhibit tissue-specific signatures and identify transcription factors that regulate TRM cell populations in a site-specific manner. Moreover, we demonstrate that TRM cells and exhausted T (TEX) cells are distinct epigenetic lineages that are distinguishable early in their differentiation. Together, these findings show that TRM cell development is accompanied by dynamic alterations in chromatin accessibility that direct a unique transcriptional program resulting in a tissue-adapted and functionally distinct T cell state.Graphical AbstractHighlightsscATAC atlas reveals the epigenetic variance of memory CD8+ T cell subsets over the course of acute infectionEarly bifurcation of memory precursors leads to circulating versus tissue-resident cell fatesIntegrating transcriptional and epigenetic analyses identified organ-specific TRM cell regulators including HIC1 and BACH2Epigenetic distinction of TRM cells and TEX cell subsets
Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating
Authors: Cotter Daniel J. , Severson Alissa L. , Carmi Shai , Rosenberg Noah A. 
Published: May 2022

AbstractBy providing additional opportunities for coalescence within families, the presence of consanguineous unions in a population reduces coalescence times relative to non-consanguineous populations. First-cousin consanguinity can take one of six forms differing in the configuration of sexes in the pedigree of the male and female cousins who join in a consanguineous union: patrilateral parallel, patrilateral cross, matrilateral parallel, matrilateral cross, bilateral parallel, and bilateral cross. Considering populations with each of the six types of first-cousin consanguinity individually and a population with a mixture of the four unilateral types, we examine coalescent models of consanguinity. We previously computed, for first-cousin consanguinity models, the mean coalescence time for X-chromosomal loci and the limiting distribution of coalescence times for autosomal loci. Here, we use the separation-of-time-scales approach to obtain the limiting distribution of coalescence times for X-chromosomal loci. This limiting distribution has an instantaneous coalescence probability that depends on the probability that a union is consanguineous; lineages that do not coalesce instantaneously coalesce according to an exponential distribution. We study the effects on the coalescence time distribution of the type of first-cousin consanguinity, showing that patrilateral-parallel and patrilateral-cross consanguinity have no effect on X-chromosomal coalescence time distributions and that matrilateral-parallel consanguinity decreases coalescence times to a greater extent than does matrilateral-cross consanguinity.
Commonality of Odorant Receptor Choice Mechanism Revealed by Analysis of a Highly Represented Odorant Receptor Transgene
Authors: Makhlouf Melanie , D’Hulst Charlotte , Omura Masayo , Rosa Alessandro , Mina Raena , Bernal-Garcia Sergio , Lempert Eugene , Saraiva Luis R. , Feinstein Paul 
Published: May 2022

AbstractIn the mouse, more than 1,100 odorant receptors (ORs) are expressed in a monogenic and monoallelic fashion, referred to as singular gene expression. Using a 21bp singular-choice enhancer (x21), we radically increase representation of olfactory sensory neurons (OSNs) choosing a 5×21 enhanced OR transgene, but not overexpression of its mRNA on a per cell basis. RNA-sequencing and differential expression analysis identified 425 differentially expressed genes (DEGs). ORs make up 86% of all DEGs, of which 325 have decreased representation and 40 have increased representation. Underrepresented ORs include Class I, Class II and TAAR genes and within each of their respective olfactory bulb domains: DI, DII, and DIII (TAAR) we committedly observe multiple homogeneous glomeruli with an OR1A1-identity. The underrepresentation of endogenous, class-specific ORs across evolutionarily distinct cell types in favor of the expression of the 5×21-OR1A1 transgene argues that a common mechanism of singular gene choice is present for all OR-expressing OSNs.
Gaining insight into the allometric scaling of trees by utilizing 3d reconstructed tree models - a SimpleForest study
Authors: Hackenberg Jan , Disney Mathias , Bontemps Jean-Daniel 
Published: May 2022

Forestry utilizes volume predictor functions utilizing as input the diameter at breast height. Some of those functions take the power formY=a∗Xb. In fact this function is fundamental for the biology field of allometric scaling theories founded round about a century ago. The theory describes the relationships between organs/body parts and the complete body of organisms.With digital methods we can generate 3d forest point clouds non destructively in short time frames. SimpleForest is one free available tool which generates fully automated ground and tree models from high resoluted forest plots. Generated topological ordered cylinder models are called commonly QSMs.We use SimpleForest QSMs an build a function which estimates the total supported wood volume at any given point of the tree. As input we use the supported soft wood volume for those query points. Instead of measuring directly the soft wood volume we use as a proxy the number of supported twigs. We argue with the pipe model theory for the correctness of the proxy.We can use the named relationship to also filter our QSMs made of an open data set of tree clouds. The filter corrects overestimated radii. And we compare the corrected QSM volume against the harvested reference data for 66 felled trees. We also found QSM data of TreeQSM, a competitive and broadly accepted QSM modeling tool. Our RMSE was less than 40% of the tree QSM RMSE. And for other error measures, the r2adj. and the CCC, the relative improvement looked even better with 27% and 21% respectively.We consider this manuscript as highly impactful because of the magnitude of quality improvement we do. The relation between soft volume and total volume distributions seems to be really strong and tree data can easily also be used as example data for the generic field of allometric scaling.
Interacting cortical gradients of neural timescales and functional connectivity and their relationship to perceptual behavior
Authors: Boring Matthew J. , Richardson R. Mark , Ghuman Avniel Singh 
Published: May 2022

AbstractCognitive acts take place over a large range of temporal scales. Numerous corresponding gradients in neurodynamic timescales and long-range cortical interactions are believed to provide organizational constraints to the brain and influence neural populations’ roles in cognition. However, it is unclear if gradients in various types of neural timescales and functional connectivity arise from related or distinct neurophysiological processes and if they influence behavior. Here, intracranial recordings from 4,090 electrode contacts in 35 individuals were used to systematically map gradients of multiple aspects of neurodynamics, neural timescales, and functional connectivity, and assess their interactions along category-selective ventral temporal cortex. Opposing functional connectivity gradients, with decreasing connectivity to visually responsive regions and increasing connectivity to regions that were not visually responsive, were observed along the ventral visual hierarchy. Endogenous neural timescales were correlated with functional connectivity to visually responsive regions after removing the effects of shared anatomical gradients, suggesting that these properties influence one another. Different stimulus evoked and endogenous timescales exhibited gradients with longer dynamics along the ventral visual hierarchy, but none of these timescales were significantly correlated with one another. This suggests that local neural timescales depend on neural and cognitive context and different timescales may arise through distinct neurophysiological processes. Furthermore, activity from neural populations with faster endogenous timescales and stronger functional connectivity to visually responsive regions was more predictive of perceptual behavior during a visual repeat detection task. These results reveal interrelationships and key distinctions among neural timescale and functional connectivity gradients that together can influence behavior.
The characteristics of high-dark-diversity habitats derived from lidar
Authors: Moeslund Jesper Erenskjold , Clausen Kevin Kuhlmann , Dalby Lars , Fløjgaard Camilla , Pärtel Meelis , Pfeifer Norbert , Hollaus Markus , Brunbjerg Ane Kirstine 
Published: May 2022

AbstractA key aspect of nature conservation is knowledge of which aspects of nature to conserve or restore to favor the characteristic diversity of plants in a given area. Here, we used a large plant dataset with > 40.000 plots combined with airborne laser scanning (lidar) data to reveal the local characteristics of habitats having a high plant dark diversity – i.e., absence of suitable species – at national extent (> 43.000 km2). Such habitats have potential for reaching high realized diversity levels and hence are important in a conservation context. We calculated 10 different lidar based metrics (both terrain and vegetation structure) and combined these with 7 different field-based measures (soil chemistry and species indicators). We then used Integrated Nested Laplace Approximation for modelling plant dark diversity across 33 North European habitat types (open landscapes and forests) selected by the European communities to be important. In open habitat types high-dark-diversity habitats had relatively low pH, high nitrogen content, tall homogenous vegetation and overall relatively homogenous terrains (high terrain openness) although with a rather high degree of local microtopographical variations. High-dark-diversity habitats in forests had relatively tall vegetation, few natural-forest indicators, low potential solar radiation input and a low cover of small woody plants. Our results highlight important vegetation, terrain and soil related factors that managers and policymakers should be aware of in conservation and restoration projects to ensure a natural plant diversity, for example low nutrient loads, natural microtopography and open forests with old-growth elements such as dead wood and rot attacks.
Resetting of H3K4me2 during mammalian parental-to-zygote transition
Authors: Wang Chong , Shi Yong , Guo Jia , Hu Kaiyue , Wang Yaqian , Li Yang , Xu Jiawei 
Published: May 2022

ABSTRACTUpon sperm and oocyte fertilization, drastic histone modification reprograming occurs during preimplantation development. However, the global H3K4me2 landscape and its dynamics reprogramming in this period remains largely unknown. Herein we investigate the erasure and re-establishment of H3K4me2 in mouse GV, MII and embryos using an improved approach called Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for histone modification with high-throughput sequencing. We find H3K4me2 extensively exists as a non-canonical pattern in mouse GV oocytes and early embryos. Interestingly, H3K4me2 is erased in MII oocyte and re-established in late 2-cell stage. Importantly, mouse embryos acquire widespread H3K4me2 in CpG-rich and hypomethylated regulatory regions in 4-cell stage, as well as 8-cell stage, but drastic changes happen upon ICM, these CpG-rich H3K4me2 regulatory regions then resolve to either active or repressed states. In summary, our study not only unveil that H3K4me2 transition from parental to zygote, but also provide a H3K4me2 profile during early embryo development, and this will enhance our comprehension to epigenetic reprogramming during mouse early development and in vitro fertilization.HighlightH3K4me2 present differential patterns in sperm and oocytes, as no-canonical pattern in GV oocytes but canonical of sperm in mouse.GV H3K4me2 peaks were almost erased in MII oocytes, and reconstructed accompanying ZGA occurred, the first landscape of H3K4me2 during early mammalian development was provided.Non-canonical H3K4me2 in mammalian embryos and pervasive H3K4me2 in CpG-rich regulatory regions in 4 and 8-cell embryos.CpG-rich H3K4me2 regulatory regions resolve to either active or repressed states in ICM.
Nucleus accumbens D1- and D2-expressing neurons control the balance between feeding and activity-mediated energy expenditure
Authors: Walle Roman , Petitbon Anna , Fois Giulia R. , Varin Christophe , Montalban Enrica , Hardt Lola , Contini Andrea , Angelo Maria Florencia , Potier Mylène , Ortole Rodrigue , Oummadi Asma , De Smedt-Peyrusse Véronique , Adan Roger A , Giros Bruno , Chaouloff Francis , Ferreira Guillaume , de Kerchove d’Exaerde Alban , Ducrocq Fabien , Georges François , Trifilieff Pierre 
Published: May 2022

ABSTRACTAccumulating evidence points to dysregulations of common brain systems in eating disorders (ED), the Nucleus Accumbens (NAc) in particular. However, to which extent alterations in NAc activity contribute to ED-like dimensions remains unclear. Using chemogenetic manipulations of dopamine D1 receptor-expressing and D2-expressing neuronal subpopulations of the NAc in male mice, we assessed their respective roles in incentive processes, food intake and the balance between feeding and exercise-mediated energy expenditure. We found that D1-neurons facilitate effort for a food reward but decreased food intake, while D2-neurons have opposite effects. The anorexigenic influence of D1-neurons was accompanied by increased voluntary exercise while the orexigenic effect of D2-neurons was concomitant with decreased running, congruent with D2-neurons being more active than D1-neurons during feeding while it is the opposite during running. Chronic manipulations of each subpopulations had limited effects on energy balance. However, repeated activation of D1-neurons combined with inhibition of D2-neurons biased behavior toward activity-related energy expenditure leading to weight/fat loss, whilst the opposite manipulations favored energy intake and hence weight/fat gain. Strikingly, concomitant activation of D1-neurons and inhibition of D2-neurons precipitated weight loss in anorexia models. These results suggest that dysregulations of NAc dopaminoceptive neurons might be at the core of EDs.