bluuebunny/crossref_metadata_2025 huggingface dataset:
Translational control of polyamine metabolism by CNBP is required for Drosophila locomotor function
Authors: Coni Sonia , Falconio Federica A. , Marzullo Marta , Munafò Marzia , Zuliani Benedetta , Mosti Federica , Fatica Alessandro , Ianniello Zaira , Bordone Rosa , Macone Alberto , Agostinelli Enzo , Perna Alessia , Matkovic Tanja , Sigrist Stephan , Silvestri Gabriella , Canettieri Gianluca , Ciapponi Laura
Published: April 2021

Microsatellite expansions of CCTG repeats in the CNBP gene leads to accumulation of toxic RNA and have been associated to DM2. However, it is still unclear whether the dystrophic phenotype is also linked to CNBP decrease, a conserved CCHC-type zinc finger RNA binding protein that regulates translation and is required for mammalian development.

Here we show that depletion ofDrosophilaCNBP in muscles causes age-dependent locomotor defects that are correlated with impaired polyamine metabolism. We demonstrate that the levels of ornithine decarboxylase (ODC) and polyamines are significantly reduced upon dCNBP depletion. Of note, we show a reduction of the CNBP-polyamine axis in muscle from DM2 patients. Mechanistically, we provide evidence that dCNBP controls polyamine metabolism through binding dOdc mRNA and regulating its translation. Remarkably, the locomotor defect of dCNBP-deficient flies is rescued by either polyamine supplementation or dOdc1 overexpression. We suggest that this dCNBP function is evolutionarily conserved in vertebrates with relevant implications for CNBP-related pathophysiological conditions.

GRAPHICAL ABSTRACT

CNBP controls muscle function by regulating the polyamine metabolism

Lack of dCNBP impairs locomotor function through ODC-polyamine downregulation

dCNBP binds dOdc mRNA and regulates its translation

Polyamine supplementation or dOdc1 reconstitution rescues locomotor defects

CNBP-ODC-polyamine levels are reduced in muscle of DM2 patients
Identification that ADAM17 mediates proteolytic maturation of calcium channel auxiliary α2δ subunits, and enables calcium current enhancement
Authors: Kadurin Ivan , Dahimene Shehrazade , Page Karen M , Ellaway Joseph I. J. , Chaggar Kanchan , Troeberg Linda , Nagase Hideaki , Dolphin Annette C.
Published: April 2021

The auxiliary α2δ subunits of voltage-gated calcium (CaV) channels are key to augmenting expression and function of CaV1 and CaV2 channels, and are also important drug targets in several therapeutic areas, including neuropathic pain. The α2δ proteins are translated as pre-proteins encoding both α2and δ, and post-translationally proteolysed into α2and δ subunits, which remain associated as a complex. In this study we have identified ADAM17 as a key protease involved in proteolytic processing of pro-α2δ-1 and α2δ-3 subunits. We provide three lines of evidence: firstly, proteolytic cleavage is inhibited by chemical inhibitors of particular metalloproteases, including ADAM17. Secondly, proteolytic cleavage of both α2δ-1 and α2δ-3 is markedly reduced in cell lines by knockout ofADAM17but notADAM10. Thirdly, proteolytic cleavage is reduced by the N-terminal active domain of TIMP-3 (N-TIMP-3), which selectively inhibits ADAM17. We have found previously that proteolytic cleavage into mature α2δ is essential for the enhancement of CaVfunction, and in agreement, knockout of ADAM17 inhibited the ability of α2δ-1 to enhance both CaV2.2 and CaV1.2 calcium currents. Thus, our study identifies ADAM17 as a key protease required for proteolytic maturation of α2δ-1 and α2δ-3, and thus a potential drug target in neuropathic pain.
Genetic variants associated mRNA stability in lung
Authors: Li Jian-Rong , Tang Mabel , Li Yafang , Amos Christopher I , Cheng Chao
Published: April 2021

Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. The resultant eQTLs might affect the expression of associated genes through transcriptional or post-transcriptional regulation. In this study, we attempt to distinguish these two types of regulation by identifying genetic variants associated with mRNA stability of genes (stQTLs). Specifically, we computationally inferred mRNA stability of genes based on RNA-seq data and performed association analysis to identify stQTLs. Using the Genotype-Tissue Expression (GTEx) lung RNA-Seq data, we identified a total of 142,801 stQTLs for 3,942 genes and 186,132 eQTLs for 4,751 genes from 15,122,700 genetic variants for 13,476 genes, respectively. Interesting, our results indicated that stQTLs were enriched in the CDS and 3’UTR regions, while eQTLs are enriched in the CDS, 3’UTR, 5’UTR, and upstream regions. We also found that stQTLs are more likely than eQTLs to overlap with RNA binding protein (RBP) and microRNA (miRNA) binding sites. Our analyses demonstrate that simultaneous identification of stQTLs and eQTLs can provide more mechanistic insight on the association between genetic variants and gene expression levels.

Author Summary

In the past decade, many studies have identified genetic variants associated with gene expression level (eQTLs) in different phenotypes, including tissues and diseases. Gene expression is the result of cooperation between transcriptional regulation, such as transcriptional activity, and post-transcriptional regulation, such as mRNA stability. Here, we present a computational framework that take advantage of recently developed methods to estimate mRNA stability from RNA-Seq, which is widely used to estimate gene expression, and then to identify genetic variants associated with mRNA stability (stQTLs) in lung tissue. Compared to eQTLs, we found that genetic variants that affects mRNA stability are more significantly located in the CDS and 3’UTR regions, which are known to interact with RNA-binding proteins (RBPs) or microRNAs to regulate stability. In addition, stQTLs are significantly more likely to overlap the binding sites of RBPs. We show that the six RBPs that most significantly bind to stQTLs are all known to regulate mRNA stability. This pipeline of simultaneously identifying eQTLs and stQTLs using only RNA-Seq data can provide higher resolution than traditional eQTLs study to better understand the molecular mechanisms of genetic variants on the regulation of gene expression.
Reactive astrocytes promote proteostasis in Huntington’s disease through the JAK2-STAT3 pathway
Authors: Abjean Laurene , Haim Lucile Ben , Riquelme-Perez Miriam , Gipchtein Pauline , Derbois Céline , Palomares Marie-Ange , Petit Fanny , Hérard Anne-Sophie , Gaillard Marie-Claude , Guillermier Martine , Gaudin-Guérif Mylène , Aurégan Gwenaelle , Sagar Nisrine , Héry Cameron , Dufour Noëlle , Robil Noémie , Kabani Mehdi , Melki Ronald , De la Grange Pierre , Bemelmans Alexis P. , Bonvento Gilles , Deleuze Jean-François , Hantraye Philippe , Flament Julien , Bonnet Eric , Brohard Solène , Olaso Robert , Brouillet Emmanuel , Sauvage Maria-Angeles Carrillo-de , Escartin Carole
Published: April 2021

Huntington’s disease is a fatal neurodegenerative disease characterized by striatal neurodegeneration, aggregation of mutant Huntingtin and the presence of reactive astrocytes. Astrocytes are important partners for neurons and engage in a specific reactive response in Huntington’s disease that involves morphological, molecular and functional changes. How reactive astrocytes contribute to Huntington’s disease is still an open question, especially because their reactive state is poorly reproduced in experimental mouse models.

Here, we show that the JAK2-STAT3 pathway, a central cascade controlling astrocyte reactive response, is activated in the putamen of Huntington’s disease patients. Selective activation of this cascade in astrocytes through viral gene transfer reduces the number and size of mutant Huntingtin aggregates in neurons and improves neuronal defects in two complementary mouse models of Huntington’s disease. It also reduces striatal atrophy and increases glutamate levels, two central clinical outcomes measured by non-invasive magnetic resonance imaging. Moreover, astrocyte-specific transcriptomic analysis shows that activation of the JAK2-STAT3 pathway in astrocytes coordinates a transcriptional program that increases their intrinsic proteolytic capacity, through the lysosomal and ubiquitin-proteasome degradation systems. This pathway also enhances their production and exosomal release of the co-chaperone DNAJB1, which contributes to mutant Huntingtin clearance in neurons.

Together, our results show that the JAK2-STAT3 pathway controls a beneficial proteostasis response in reactive astrocytes in Huntington’s disease, which involves bi-directional signalling with neurons to reduce mutant Huntingtin aggregation, eventually improving disease outcomes.
Effects of BCG vaccination on donor unrestricted T cells in humans
Authors: Gela Anele , Murphy Melissa , Hadley Kate , Hanekom Willem A. , Henry Boom W. , Johnson John L. , Hoft Daniel F. , Joosten Simone A. , Ottenhoff Tom H.M. , Suliman Sara , Branch Moody D. , Lewinsohn David M. , Hatherill Mark , Seshadri Chetan , Nemes Elisa , Scriba Thomas J. ,   The Delayed BCG Study Team
Published: April 2021

Antigen classes other than proteins can be presented to T cells by near-monomorphic antigen-presenting molecules such as CD1, MR1, and butyrophilin 3A1. We sought to define the roles of donor unrestricted T (DURT) cells, including MR1-reactive MAIT cells, CD1b-reactive glucose monomycolate (GMM)-specific T cells, CD1d-reactive NKT cells, and γδ T cells, in vaccination againstMycobacterium tuberculosis. We characterized DURT cells following primary bacille Calmette-Guerin (BCG) vaccination in infants or BCG-revaccination in adults. BCG (re)vaccination did not modulate peripheral blood frequencies, T cell activation or memory profiles of MAIT cells, CD1b-restricted GMM-specific and germline-encoded mycolyl-reactive (GEM) cells or CD1d- restricted NKT cells. By contrast, BCG vaccination was associated with increased frequencies of γδ T cells as well as a novel subset of IFN-γ-expressing CD4+T cells with a CD26+CD161+TRAV1-2−phenotype in infants. More studies are required to understand the full potential of DURT cells in new TB vaccine strategies.
Enhancing and inhibitory motifs have coevolved to regulate CD4 activity
Authors: Lee Mark S. , Tuohy Peter J. , Kim Caleb , Lichauco Katrina , Parrish Heather L. , Doorslaer Koenraad Van , Kuhns Michael S.
Published: April 2021

CD4+T cells use T cell receptor (TCR)-CD3 complexes, and CD4, to respond to peptide antigens within MHCII molecules (pMHCII). We report here that, through ∼435 million years of evolution in jawed vertebrates, purifying selection has shaped motifs in the extracellular, transmembrane, and intracellular domains of eutherian CD4 that both enhance pMHCII responses and are coevolving with residues in an intracellular motif that inhibits pMHCII responses. Importantly, while CD4 interactions with the Src kinase, Lck, are classically viewed as the key determinant of CD4’s contribution to pMHCII responses, we found that without the inhibitory motif CD4-Lck interactions are not necessary for robust responses to pMHCII. In summary, motifs that mediate events on the outside and inside of CD4+T cells coevolved to finetune the relay of pMHCII-specific information across the membrane. These results have implications for the evolution and function of complex transmembrane receptors and for biomimetic engineering.
Proton pump inhibitors inhibit PHOSPHO1 activity and matrix mineralisationin vitro
Authors: Staines Katherine A. , Myers Katherine , Little Kirsty , Ralston Stuart H. , Farquharson Colin
Published: April 2021

Proton pump inhibitors (PPIs) have been associated with an increased risk of fragility fractures in pharmaco-epidemiological studies. The mechanism is unclear but it has been speculated that by neutralising gastric acid, they may reduce intestinal calcium absorption, causing secondary hyperparathyroidism and bone loss. Here we investigated that hypothesis that the skeletal effects of PPI might be mediated by inhibitory effects on the bone-specific phosphatase PHOSPHO1. We found that the all PPI tested potential inhibited the activity of PHOSPHO1 with IC50 ranging between 0.73μM for esomeprazole to 19.27μM for pantoprazole. In contrast, these PPIs did not inhibit TNAP activity. We also found that mineralisation of bone matrix in primary osteoblast cultures inhibited by several PPI in a concentration dependent manner. In contrast, the histamine-2 receptor antagonists (H2RA) nizatidine, famotidine, cimetidine and ranitidine had no inhibitory effects on PHOSPHO1 activity. Our experiments shown for the first time that PPI inhibit PHOSPHO1 activity and matrix mineralisationin vitrorevealing a potential mechanism by which these widely used drugs are associated with the risk of fractures.
Chromoanagenesis landscape in 10,000 TCGA patients
Authors: Rasnic Roni , Linial Michal
Published: April 2021

During the past decade, whole-genome sequencing of tumor biopsies and individuals with congenital disorders highlighted the phenomenon of chromoanagenesis, a single chaotic event of chromosomal rearrangement. Chromoanagenesis was shown to be frequent in many types of cancers, to occur in early stages of cancer development, and significantly impact the tumor’s nature. However, an in-depth, cancer-type dependent analysis has been somewhat incomplete due to the shortage in whole genome sequencing of cancerous samples. In this study, we extracted data from The Pan-Cancer Analysis of Whole Genome (PCAWG) and The Cancer Genome Atlas (TCGA) to construct a machine learning algorithm that can detect chromoanagenesis with high accuracy (86%). The algorithm was applied to ~10,000 TCGA cancer patients. We utilize the chromoanagenesis assignment results, to analyze cancer-type specific chromoanagenesis characteristics in 20 TCGA cancer types. Our results unveil prominent genes affected in either chromoanagenesis or non-chromoanagenesis tumorigenesis. The analysis reveals a mutual exclusivity relationship between the genes impaired in chromoanagenesis versus non-chromoanagenesis cases. We offer the discovered characteristics as possible targets for cancer diagnostic and therapeutic purposes.
Neural correlations are attenuated in the transformation from the frontal cortex to movement
Authors: Larry Noga , Joshua Mati
Published: April 2021

Correlated activity between neurons can cause variability in behavior across trials. The extent to which correlated activity affects behavior depends on the properties of its translation into movement. We developed a novel method that estimates the contribution of correlations in the frontal eye field (FEF) to pursuit eye movements. We defined a distance metric between the behavior on different trials. Based on this metric, we applied a sequence of shuffles to the neuronal responses, allowing trials to be matched with increasingly distant trials. Correlations between neurons were strongly attenuated when applying even the most constrained shuffle. Thus, only a small fraction of FEF correlations affects the behavior. We used simulations to validate our approach and demonstrate its generalizability over different models. We show that the attenuation of correlated activity through the motor pathway could stem from the interplay between the structure of the correlations and the decoder of FEF activity.
Antimicrobial activity and degradation of superhydrophobic magnesium substrates in bacterial media
Authors: Emelyanenko Alexandre M. , Kaminsky Valery V. , Pytskii Ivan S. , Emelyanenko Kirill A. , Domantovsky Alexander G. , Chulkova Elizaveta V. , Shiryaev Andrei A. , Aleshkin Andrei V. , Boinovich Ludmila B.
Published: April 2021

The interest in magnesium-based materials is promoted by their biocompatibility, bioresorbability, and by their recently found antibacterial potential. Until now the widespread use of magnesium alloys in different corrosive environments was inhibited by their weakly controllable degradation rate and poorly understood microbiologically induced corrosion behavior. To better understand the degradation and usability of magnesium-based alloys, in this study we have fabricated the superhydrophobic coatings on top of magnesium-based alloy and analyzed the behavior of this alloy in bacterial dispersions ofPseudomonas aeruginosaandKlebsiella pneumoniaecells in phosphate buffered saline. It was shown that immersion of such coatings into bacterial dispersions causes notable changes in the morphology of the samples, dependent on the bacterial dispersion composition and the type of bacterial strain. The interaction of superhydrophobic coatings with the bacterial dispersion caused the formation of biofilms and sodium polyphosphate films, which provided enhanced barrier properties for magnesium dissolution and hence for dispersion medium alkalization, eventually leading to inhibition of magnesium substrate degradation. Electrochemical data obtained for superhydrophobic samples continuously contacted with the corrosive bacterial dispersions during 48 h indicated a high level of anti-corrosion protection.
Enhancing the dark side: Asymmetric gain of cone photoreceptors underpins discrimination of visual scenes based on their skewness
Authors: Yedutenko Matthew , Howlett Marcus H.C. , Kamermans Maarten
Published: April 2021

Psychophysical data indicates humans can discriminate visual scenes based on their skewness – the ratio of dark and bright patches within a visual scene. It was also shown that on a phenomenological level this skew discrimination is described by the so-called Blackshot mechanism, which accentuates strong negative contrasts within a scene. Here we demonstrate that the underlying computation starts as early as the cone phototransduction cascade whose gain is higher for strong negative contrasts than for strong positive contrasts. We recorded from goldfish cone photoreceptors and found that the asymmetry in the phototransduction gain leads to higher amplitude of the responses to negatively than to positively skewed light stimuli. This asymmetry in the amplitude was present in the photocurrent, voltage response and cone synaptic output. These results highlight the importance of the early photoreceptor non-linearity for perception. Additionally, we found that stimulus skewness leads to a subtle change in photoreceptor kinetics. For negatively skewed stimuli, the cone’s impulse response functions peak later than for positively skewed stimulus. However, stimulus skewness does not affect the cone’s overall integration time.
Mechanical Metric for Skeletal Biomechanics Derived from Spectral Analysis of Stiffness matrix
Authors: Henyš Petr , Kuchař Michal , Hájek Petr , Hammer Niels
Published: April 2021

A new metric for the quantitative and qualitative evaluation of bone stiffness is introduced. It is based on the spectral decomposition of stiffness matrix computed with finite element method. The here proposed metric is defined as an amplitude rescaled eigenvalues of stiffness matrix. The metric contains unique information on the principal stiffness of bone and reflects both bone shape and material properties. The metric was compared with anthropometrical measures and was tested for sex sensitivity on pelvis bone. Further, the smallest stiffness of pelvis was computed under a certain loading condition and analyzed with respect to sex and direction. The metric complements anthropometrical measures and provides a unique information about the smallest bone stiffness independent from the loading configuration and can be easily computed by state-of-the-art subject specified finite element algorithms.
Interpreting Neural Networks for Biological Sequences by Learning Stochastic Masks
Authors: Linder Johannes , La Fleur Alyssa , Chen Zibo , Ljubetič Ajasja , Baker David , Kannan Sreeram , Seelig Georg
Published: April 2021

Sequence-based neural networks can learn to make accurate predictions from large biological datasets, but model interpretation remains challenging. Many existing feature attribution methods are optimized for continuous rather than discrete input patterns and assess individual feature importance in isolation, making them ill-suited for interpreting non-linear interactions in molecular sequences. Building on work in computer vision and natural language processing, we developed an approach based on deep generative modeling - Scrambler networks - wherein the most salient sequence positions are identified with learned input masks. Scramblers learn to generate Position-Specific Scoring Matrices (PSSMs) where unimportant nucleotides or residues are ‘scrambled’ by raising their entropy. We apply Scramblers to interpret the effects of genetic variants, uncover non-linear interactions between cis-regulatory elements, explain binding specificity for protein-protein interactions, and identify structural determinants ofde novodesigned proteins. We show that interpretation based on a generative model allows for efficient attribution across large datasets and results in high-quality explanations, often outperforming state-of-the-art methods.
Large-scale deployment and establishment ofWolbachiainto theAedes aegyptipopulation in Rio de Janeiro, Brazil
Authors: Moledo Gesto João Silveira , Pinto Sofia , Stehling Dias Fernando Braga , Peixoto Julia , Costa Guilherme , Kutcher Simon , Montgomery Jacqui , Green Benjamin R. , Anders Katherine L. , Ryan Peter A. , Simmons Cameron P. , O’Neill Scott L. , Moreira Luciano Andrade
Published: April 2021

Traditional methods of vector control have proven insufficient to reduce the alarming incidence of Dengue, Zika and chikungunya in endemic countries. The bacterium symbiontWolbachiahas emerged as an efficient pathogen-blocking and self-dispersing agent that reduces the vectorial potential ofAedes aegyptipopulations and potentially impairs arboviral disease transmission. In this work, we report the results of a large-scaleWolbachiaintervention in Ilha do Governador, Rio de Janeiro, Brazil.wMel-infected adults were released across residential areas between August 2017 and March 2020. Over 131 weeks, including release and post-release phases, we monitored thewMel prevalence in field specimens, and analyzed introgression profiles of two assigned intervention areas, RJ1 and RJ2. Our results revealed thatwMel successfully invaded both areas, reaching overall infection rates of 50-70% in RJ1, and 30-60% in RJ2 by the end of the monitoring period. At the neighborhood-level,wMel introgression was heterogeneous in both RJ1 and RJ2, with some profiles sustaining a consistent increase in infection rates and others failing to elicit the same. Correlation analysis revealed a weak overall association between RJ1 and RJ2 (r= 0.2849,P= 0.0236), and an association at a higher degree when comparing different deployment strategies, vehicle or backpack-assisted, within RJ1 (r= 0.4676,P< 0.0001) or RJ2 (r= 0.6263,P< 0.0001). The frequencyknockdown resistance(kdr) alleles inwMel-infected specimens from both areas was consistently high over this study. Altogether, these findings corroborate thatwMel can be successfully deployed at large-scale as part of vector control intervention strategies, and provide the basis for imminent disease impact studies in Southeastern Brazil.
Tubulin Acetylation Promotes Penetrative Capacity of Cells Undergoing Radial Intercalation
Authors: Collins Caitlin , Kim Sun K. , Ventrella Rosa , Mitchell Jen W. , Mitchell Brian
Published: April 2021

The post-translational modification of tubulin provides a wide diversity of differential functions to microtubule networks. Here we address the role of tubulin acetylation on the penetrative capacity of cells undergoing radial intercalation in the skin ofXenopusembryos. Radial intercalation is the process by which cells move apically and penetrate the epithelial barrier via inserting into the outer epithelium. As such there are two opposing forces that regulate the ability of cells to intercalate: the restrictive forces of the epithelial barrier versus the penetrative forces of the intercalating cell. By positively and negatively modulating tubulin acetylation specifically in the intercalating cells, the timing of intercalation can be altered such that cells with more acetylated microtubules penetrate the epithelium faster. Moreover, theXenopusepithelium is a complex array of variable types of vertices and we find that intercalating cells preferentially penetrate at higher order “rosette” vertices as opposed to the more prevalent tricellular vertices. We observed differential timing in the ability of cells to penetrate different types of vertices, indicating lower order vertices represent more restrictive sites of insertion. Interestingly, we are able to shift the accessibility of early intercalating cells towards the more restrictive tricellular junctions by modulating the level of tubulin acetylation and the subsequent penetrative capacity of intercalating cells. Overall our data implicate tubulin acetylation in driving tissue penetration of intercalating cells.
Embryo-to-embryo variability in RNAi knockdown efficiency of dKDM5/lid in Drosophila melanogaster
Authors: Albright Ashley , Eisen Michael
Published: April 2021

We used the maternal-Gal4 shRNA system to knock down expression of dKDM5/lid in Drosophila melanogaster embryos, and analyzed the efficacy of the knockdown by qRT-PCR. Although average relative expression of lid was significantly lower in knockdown conditions compared to the driver-only control, we observed a wide and overlapping range of relative gene expression between individual control and knockdown embryos.
Hematopoietic differentiation is characterized by a transient peak of entropy at a single cell level
Authors: Dussiau Charles , Boussaroque Agathe , Gaillard Mathilde , Bravetti Clotilde , Zaroili Laila , Knosp Camille , Friedrich Chloé , Asquier Philippe , Willems Lise , Quint Laurent , Bouscary Didier , Fontenay Michaela , Espinasse Thibault , Plesa Adriana , Sujobert Pierre , Gandrillon Olivier , Kosmider Olivier
Published: April 2021

Hematopoietic differentiation has been metaphorically represented as linear trajectories with discrete steps from hematopoietic stem cells to mature cells. While the transcriptional state of cells at the beginning or at the end of these trajectories are well described from bulk analysis, what happens in the intermediate states has remained elusive until the use of single cell approaches. Applying Shannon entropy to measure cell-to-cell variability among cells at the same stage of differentiation, we observed a transient peak of gene expression variability in all the hematopoietic differentiation pathways. Strikingly, genes with the highest entropy variation in a given differentiation pathway matched genes known as pathway-specific, whereas genes with the highest expression variation were common to all pathways. Finally, we showed that the level of cell-to-cell variation is increased in the most immature compartment of hematopoiesis in myelodysplastic syndromes. These data suggest that differentiation could be better conceptualized as a dynamical stochastic process with a transient stage of cellular indetermination.
Germline Sex Determination regulates sex-specific signaling between germline stem cells and their niche
Authors: Bhaskar Pradeep Kumar , Southard Sheryl , Baxter Kelly , Van Doren Mark
Published: April 2021

The establishment of sexual identity in germ cells is critical for the development of male and female germline stem cells (GSCs) and production of sperm vs. eggs. Thus, this process is essential for sexual reproduction and human fertility. Germ cells depend on signals from the somatic gonad to determine their sex, but in organisms such as flies, mice and humans, the sex chromosome genotype of the germ cells is also important for germline sexual development. How somatic signals and germ cell-intrinsic cues act together to regulate germline sex determination is a key question about which little is known. We have found that JAK/STAT signaling in the GSC niche promotes male identity in germ cells and GSCs, in part by activating expression of the epigenetic reader Phf7. We have also found that JAK/STAT signaling is blocked in XX (female) germ cells through the intrinsic action of the sex determination geneSex lethal, which preserves female identity. Thus, an important function of germline sexual identity is to control how GSCs respond to signals in their niche environment.
Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells
Authors: Karabağ Cefa , Jones Martin L. , Reyes-Aldasoro Constantino Carlos
Published: April 2021

In this work, the unsupervised volumetric semantic segmentation of the plasma membrane of HeLa cells as observed with Serial Block Face Scanning Electron Microscopy is described. The resin background of the images was segmented at different slices of a 3D stack of 518 slices with 8, 192 × 8, 192 pixels each. The background was used to create a distance map which helped identify and rank the cells by their size at each slice. The centroids of the cells detected at different slices were linked to identify them as a single cell that spanned a number of slices. A subset of these cells, i.e., largest ones and those not close to the edges were selected for further processing. The selected cells were then automatically cropped to smaller regions of interest of 2, 000 × 2, 000 × 300 voxels that were treated as cell instances. Then, for each of these volumes the nucleus was segmented and the cell was separated from any neighbouring cells through a series of traditional image processing steps that followed the plasma membrane. The segmentation process was repeated for all the regions selected. For one cell for which the ground truth was available, the algorithm provided excellent results in Accuracy (AC) and Jaccard Index (JI): Nucleus: JI = 0.9665, AC= 0.9975, Cell and Nucleus JI = 0.8711, AC = 0.9655, Cell only JI = 0.8094, AC = 0.9629. A limitation of the algorithm for the plasma membrane segmentation was the presence of background, as in cases of tightly packed cells. When tested for these conditions, the segmentation of the nuclear envelope was still possible. All the code and data are released openly through GitHub, Zenodo and EMPIAR.
Analytical model for rock effective elastic properties with aligned elliptical cracks embedded in transversely isotropic background
Authors: Guo Junxin , Zhao Luanxiao , Yang Zhifang , Li Hongbing
Published: April 2021

Seismic methods are often used for fracture detection and characterization, for which many analytical rock physics models have been developed to link fracture parameters to rock elastic properties. However, most of these models are limited to isotropic background and circular (penny‐shaped) fractures. In this work, we derived a more general analytical model for effective elastic properties of rocks embedded with aligned elliptical cracks in transversely isotropic background. The solutions for the case with dry cracks parallel to isotropic plane of transversely isotropic background were first derived using the corresponding Eshelby's tensor. Then, the results were extended to the case with inclined and rotated cracks under the assumption of constant crack opening displacement tensor. Finally, to obtain the results for fluid‐filled crack case, the Brown–Korringa equation was applied. To investigate the controlling factors on rock elastic properties, we studied one fractured tight sandstone sample with transversely isotropic background. The results show that rock elastic properties are insensitive to crack spin angle, but sensitive to crack inclination angle. Depending on crack inclination angle and fluid saturation, background anisotropy can either amplify or reduce the anisotropy of seismic wave velocity. Crack density and aspect ratio are found to be controlling crack parameters for rock elastic properties. The crack plane shape has negligible direct influence on rock elastic properties, whereas it has indirect influence by affecting values of crack density and aspect ratio. Compared with the numerical model and the previous analytical model for the special case with circular cracks, our model agrees well with them, which validates the accuracy of our model.
Closing the life cycle of forest trees: The difficult dynamics of seedling‐to‐sapling transitions in a subtropical rainforest
Authors: Chang‐Yang Chia‐Hao , Needham Jessica , Lu Chia‐Ling , Hsieh Chang‐Fu , Sun I‐Fang , McMahon Sean M.
Published: April 2021

Experimental and observational studies on seedling dynamics posit mechanisms that can influence forest diversity, structure and function. However, high mortality and slow growth of seedlings make it difficult to evaluate the importance of this life‐history filter to total tree life history. Quantifying the duration and transition of the seedling phase would help us understand this ‘black box’ in tree population biology.

We used a 16‐year dataset of comprehensive seedling‐to‐sapling demography from a subtropical rainforest to construct population models that capture temporal demographic fluctuations for eight major tree species. We used data‐driven demographic models and simulations to estimate the transition ratios from newly recruited seedlings to saplings of 2‐m height and the time taken to attain 2‐m height for a newly recruited seedling conditional on its survival.

Projections among species estimated that as few as 57 to more than 40,000 seedlings (with a median of 2,087) were required to make a single 2‐m high sapling. Furthermore, it would take 22–200 years (with a median of 47) for a newly recruited seedling to become a 2‐m high sapling. We found that temporal variation in demographic rates could greatly reduce the number of seedlings per established sapling, but not passage times (PTs). We also identified the importance of consistently fast growth rates for seedlings to escape the high mortality of early stages.

Synthesis. Our findings demonstrate that high mortality in the very early seedling stage severely limits the probability that a newly recruited seedling will transition to the sapling stage. Although the PTs vary, we found this to be true across species with a range of life‐history strategies. Only seedlings with consistently fast growth rates are expected to pass through this life‐history filter. Findings from seedling studies should consider how short‐term studies of seedling demography might capture the rare exceptional individuals and exceptional conditions that might define the dynamics of this seedling bottleneck.
Antifibrinolytics reduces blood loss in thoracic surgery: a systematic review and meta‐analysis
Authors: Leow Lowell , Ng Josiah , Luo Hai Dong , Choong Andrew M. T. L. , Mithiran Harish , Kofidis Theo , Tam John Kit Chung
Published: April 2021

Background

The purpose of this systematic review is to evaluate the efficacy of antifibrinolytics in non‐cardiac thoracic surgery.

Methods

We searched for all randomized controlled trials on this topic. A set of strict inclusion and exclusion criteria was developed. Six studies were meta‐analysed together then in subgroups of topical tranexamic acid and intravenous aprotinin. We compared postoperative chest drain output, transfusions requirements and duration of hospital stay where available to determine the efficacy of topical tranexamic acid or intravenous aprotinin in reducing blood loss.

Results

The use of antifibrinolytics reduces 24‐h chest drain output (−290.21 mL [−524.75, −55.66], P = 0.02, I2 = 98%), red blood cell transfusion requirements (−1.27 units [−2.24, −0.30], P = 0.01, I2 = 100%) and shortened duration of hospital stay (−1.81 days [−3.25, −0.36], P = 0.01, I2 = 96%). The subgroup analysis also supported this trend.

Conclusion

We conclude that the use of antifibrinolytics appears to reduce postoperative blood loss by reducing chest drain output, transfusion requirements and length of stay after thoracic surgery.
Evaluation of left ventricular myocardial mechanics in patients with normally functioning bicuspid aortic valves: A systematic review and meta‐analysis
Authors: Chen Huiyun , Liang Huili , Wang Tao , Zhao Hongze , Yang Jun , Chen Xin
Published: April 2021

Background

Studies have found conflicting results concerning the left ventricular (LV) myocardial deformation properties in patients with normally functioning bicuspid aortic valves (BAVs). Whether the remodeling process of LV occurs independently in patients with BAV is a matter of debate.

Method

We searched PubMed, Embase, Cochrane library, and Web of Science for cohort studies aiming to assess LV function in adults with isolated BAV compared with tricuspid aortic valve (TAV) controls. Standard mean difference (SMD) was calculated from random‐effects meta‐analyses.

Results

Eight cohort studies were included. There were significantly lower global longitudinal strain (GLS), global radial strain (GRS), global circumferential strain (GCS) in BAV than in TAV controls (GLS: SMD = 0.64, 95% CI: 0.35 to 0.92, P < .0001; GRS: SMD = −0.71, 95% CI: −1.09 to −0.32, P = .0003; GCS: SMD = 0.70, 95% CI: 0.41 to 0.98, P < .00001) and significantly higher left atrial volume index (LAVI) and E/e’ in BAV than in TAV controls (LAVI: SMD = 0.50, 95% Cl: 0.12 to 0.88, P = .01; E/e’: SMD = 0.54, 95% CI: 0.30 to 0.77, P < .00001). There was significantly higher Left ventricular mass index（LVMI） in BAV than in TAV controls (SMD = 0.51, 95% CI: 0.24 to 0.79, P = .0003). Left ventricular ejection fraction (LVEF) was not significantly different between BAV patients and TAV controls (SMD = 0.05, 95% CI: −0.16 to 0.26, P = .63).

Conclusion

The impairment of LV myocardial mechanics, including LV systolic, diastolic dysfunction and LV hypertrophy, is present in patients with normally functioning BAV. This might support the hypothesis that BAV is not only a valvular disease but also a myocardial disease.
An interpretation and modification of the SWT function
Authors: Kujawski Daniel
Published: April 2021

In this paper, a new interpretation and modification of the SWT function in terms of the total damaging energy density are proposed and discussed. The total damaging energy density is the sum of the damaging part of the strain energy density and complementary energy density corresponding to the first quadrant in damaging σD‐εD axes. For cyclic loading with a positive mean stress (σm ≥ 0), the proposed function reduces to the original SWT formulation. For cyclic loading with a negative mean stress (σm < 0), the maximum stress is augmented by 1/3 of absolute value of the mean stress. The proposed approach shows a consistent correlation of the mean stress effects for both positive and negative mean stresses.
Firm life cycle and trade credit
Authors: Hasan Mostafa Monzur , Cheung Adrian (Wai‐Kong) , Tunas Lidia , Kot Hung Wan
Published: April 2021

This study investigates the relation between firm life cycle and trade credit. We find evidence that firms in the introduction, growth, and decline stages use significantly more trade credit, whereas firms in the mature stage use significantly less trade credit. Firm life cycle works as a separate channel to affect trade credit independently from other channels proposed in the literature. These results are robust to alternative regression specifications, alternative measures of life cycle and trade credit, and the endogeneity concern. Firms in the introduction and decline stages adjust trade credit to the target level quickly compared to others.
Impacts of multi‐morbidity, hemoglobin levels, and frailty on functional disability of older adult residents of long‐term care facilities: A structural equation analysis
Authors: Liu Li‐Hsing , Kao Chia‐Chan , Wang Ruey‐Hsia , Liu Yi‐Hui
Published: April 2021

Aim

Previous studies have focused on the relationship between multi‐morbidity, frailty, and anemia or functional disability alone rather than in combination. This study aimed to explore the impacts of multi‐morbidity, hemoglobin levels, and frailty on functional disability simultaneously in older adult residents of long‐term care facilities.

Methods

This was a cross‐sectional study. Data were retrieved from the electronic health records of eight long‐term care facilities. Data from a total of 352 subjects aged at least 60 years and residing in these facilities for at least 6 months were analysed. Analytic datasets included the Barthel Index of Activities of Daily Living, the Frailty Phenotype Criteria, the number of chronic diseases, hemoglobin levels, age, and gender.

Results

The final model demonstrated acceptable goodness‐of‐fit indices, namely goodness‐of‐fit index, comparative fit index, and incremental fit index ≧0.90, root mean square error of approximation <0.08, and insignificance of χ2 (P > 0.05). Frailty, multi‐morbidity, and hemoglobin levels all had direct associations with functional disability (all P < 0.001). Hemoglobin levels had a direct association with frailty (ß = −0.11). Multi‐morbidity had an indirect association (ß = 0.04) with functional disability through hemoglobin levels. Hemoglobin levels had an indirect association (ß = 0.05) with functional disability through frailty.

Conclusions

The impacts of multi‐morbidity, hemoglobin levels, and frailty on functional disability were explored. A high‐quality disease management program, interventions for the prevention of frailty, and the provision of continued education for staff about reducing progressive frailty and functional disability for older adult residents are recommended. Geriatr Gerontol Int 2021; 21: 532–537.
Induction of stable human FOXP3+ Tregs by a parasite‐derived TGF‐β mimic
Authors: Cook Laura , Reid Kyle T , Häkkinen Elmeri , de Bie Brett , Tanaka Shigeru , Smyth Danielle J , White Madeleine PJ , Wong May Q , Huang Qing , Gillies Jana K , Ziegler Steven F. , Maizels Rick M , Levings Megan K
Published: April 2021

Immune homeostasis in the intestine is tightly controlled by FOXP3+ regulatory T cells (Tregs), defects of which are linked to the development of chronic conditions, such as inflammatory bowel disease (IBD). As a mechanism of immune evasion, several species of intestinal parasites boost Treg activity. The parasite Heligmosomoides polygyrus is known to secrete a molecule (Hp‐TGM) that mimics the ability of TGF‐β to induce FOXP3 expression in CD4+ T cells. The study aimed to investigate whether Hp‐TGM could induce human FOXP3+ Tregs as a potential therapeutic approach for inflammatory diseases. CD4+ T cells from healthy volunteers were expanded in the presence of Hp‐TGM or TGF‐β. Treg induction was measured by flow cytometric detection of FOXP3 and other Treg markers, such as CD25 and CTLA‐4. Epigenetic changes were detected using ChIP‐Seq and pyrosequencing of FOXP3. Treg phenotype stability was assessed following inflammatory cytokine challenge and Treg function was evaluated by cellular co‐culture suppression assays and cytometric bead arrays for secreted cytokines. Hp‐TGM efficiently induced FOXP3 expression (> 60%), in addition to CD25 and CTLA‐4, and caused epigenetic modification of the FOXP3 locus to a greater extent than TGF‐β. Hp‐TGM‐induced Tregs had superior suppressive function compared with TGF‐β‐induced Tregs, and retained their phenotype following exposure to inflammatory cytokines. Furthermore, Hp‐TGM induced a Treg‐like phenotype in in vivo differentiated Th1 and Th17 cells, indicating its potential to re‐program memory cells to enhance immune tolerance. These data indicate Hp‐TGM has potential to be used to generate stable human FOXP3+ Tregs to treat IBD and other inflammatory diseases.
Efficacy and safety of ethanol infusion into the vein of Marshall for mitral isthmus ablation
Authors: Lam Anna , Küffer Thomas , Hunziker Lukas , Nozica Nikolas , Asatryan Babken , Franzeck Florian , Madaffari Antonio , Haeberlin Andreas , Mühl Aline , Servatius Helge , Seiler Jens , Noti Fabian , Baldinger Samuel H. , Tanner Hildegard , Windecker Stephan , Reichlin Tobias , Roten Laurent
Published: April 2021

Introduction

Chemical ablation by retrograde infusion of ethanol into the vein of Marshall (VOM‐EI) can facilitate the achievement of mitral isthmus block. This study sought to describe the efficacy and safety of this technique.

Methods and Results

Twenty‐two consecutive patients (14 males, median age 71 years) with attempted VOM‐EI for mitral isthmus ablation were included in the study. VOM‐EI was successfully performed with a median of 4 ml of 96% ethanol in 19 patients (86%) and the mitral isthmus was successfully blocked in all (100%). Touch up endocardial and/or epicardial ablation after VOM‐EI was necessary for 12 patients (63%). Perimitral flutter was present in 12 patients (63%) during VOM‐EI and terminated or slowed by VOM‐EI in 4 and 3 patients, respectively. The low‐voltage area of the mitral isthmus region increased from 3.1 cm2 (interquartile range [IQR] 0–7.9) before to 13.2 cm2 (IQR: 8.2–15.0) after VOM‐EI and correlated significantly with the volume of ethanol injected (p = .03). Median high‐sensitive cardiac troponin‐T increased significantly from 330 ng/L (IQR: 221–516) the evening of the procedure to 598 ng/L (IQR: 382–769; p = .02) the following morning. A small pericardial effusion occurred in three patients (16%), mild pericarditis in one (5%), and uneventful VOM dissection in two (11%). After a median follow‐up of 3.5 months (IQR: 3.0–11.0), 10 of 18 patients (56%) with VOM‐EI and available follow‐up had arrhythmia recurrence. Repeat ablation was performed in five patients (50%) and peri‐mitral flutter diagnosed in three (60%).

Conclusion

VOM‐EI is feasible, safe, and effective to achieve acute mitral isthmus block.
Efficacy and prognostic factors of adjuvant radiotherapy for cutaneous squamous cell carcinoma: A systematic review and meta‐analysis
Authors: Zhang J. , Wang Y. , Wijaya W.A. , Liang Z. , Chen J.
Published: April 2021

Although adjuvant radiotherapy has been used for cutaneous squamous cell carcinoma, its outcome benefits, especially for patients with clear surgical margins, have not been statistically estimated, and the characteristics that can indicate patients who require adjuvant therapy need to be validated with more evidence. We conducted a systematic review and meta‐analysis of literature on the survival outcomes and prognostic factors in patients with cSCC treated by surgery with or without adjuvant radiotherapy. Twenty related studies involving 2605 patients met our inclusion criteria. The significant survival outcomes of adjuvant radiotherapy included lower recurrence (OR, 0.56; 95% CI, 0.36–0.85), longer disease‐free survival (OR, 2.17; 95% CI, 1.23–3.83) and longer overall survival (OR, 2.94; 95% CI, 1.75–4.91). Significant prognostic factors for poor outcomes were perineural invasion (HR, 1.61; 95% CI, 1.24–2.09), involved surgical margins (HR, 2.34; 95% CI, 1.42–3.83) and immunosuppression (HR, 3.02; 95% CI, 2.14–4.25) while adjuvant radiotherapy significantly contributed to better overall survival (HR, 0.47; 95% CI, 0.34–0.65). In conclusion, this systematic review suggests that in cutaneous squamous cell carcinoma patients with risk factors, including metastasis to the parotid gland, perineural invasion and immunosuppression, the use of adjuvant radiotherapy may be beneficial irrespective of surgical margin status.