bluuebunny/crossref_metadata_2025 huggingface dataset:
Intrinsic color diversity of nearby Type Ia supernovae
Authors: Arima Noriaki , Doi Mamoru , Morokuma Tomoki , Takanashi Naohiro
Published: January 2021

It has been reported that the extinction law for Type Ia supernovae (SNe Ia) may be different from the one in the Milky Way, but the intrinsic color of SNe Ia and the dust extinction are observationally mixed. In this study, we examine photometric properties of SNe Ia in the nearby universe (z ≲ 0.04) to investigate the SN Ia intrinsic color and the dust extinction. We focus on the Branch spectroscopic classification of 34 SNe Ia and morphological types of host galaxies. We carefully study the distribution of their peak colors on the B − V, V − R color–color diagram, as well as the color excess and absolute magnitude deviation from the stretch-color relation of the bluest SNe Ia. We find that SNe Ia which show the reddest color occur in early-type spirals and the trend holds when divided into Branch sub-types. The dust extinction becomes close to the Milky Way like extinction if we exclude some peculiar red Broad Line (BL) sub-type SNe Ia. Furthermore, two of these red BLs occur in elliptical galaxies, a less-dusty environment, suggesting intrinsic color diversity in BL sub-type SNe Ia.
Mutations in a Golden2-Like Gene Cause Reduced Seed Weight in Barley albino lemma 1 Mutants
Authors: Taketa Shin , Hattori Momoko , Takami Tsuneaki , Himi Eiko , Sakamoto Wataru
Published: January 2021

The albino lemma 1 (alm1) mutants of barley (Hordeum vulgare L.) exhibit obvious chlorophyll-deficient hulls. Hulls are seed-enclosing tissues on the spike, consisting of the lemma and palea. The alm1 phenotype is also expressed in the pericarp, culm nodes and basal leaf sheaths, but leaf blades and awns are normal green. A single recessive nuclear gene controls tissue-specific alm1 phenotypic expression. Positional cloning revealed that the ALM1 gene encodes a Golden 2-like (GLK) transcription factor, HvGLK2, belonging to the GARP subfamily of Myb transcription factors. This finding was validated by genetic evidence indicating that all 10 alm1 mutants studied had a lesion in functionally important regions of HvGLK2, including the three alpha-helix domains, an AREAEAA motif and the GCT box. Transmission electron microscopy revealed that, in lemmas of the alm1.g mutant, the chloroplasts lacked thylakoid membranes, instead of stacked thylakoid grana in wild-type chloroplasts. Compared with wild type, alm1.g plants showed similar levels of leaf photosynthesis but reduced spike photosynthesis by 34%. The alm1.g mutant and the alm1.a mutant showed a reduction in 100-grain weight by 15.8% and 23.1%, respectively. As in other plants, barley has HvGLK2 and a paralog, HvGLK1. In flag leaves and awns, HvGLK2 and HvGLK1 are expressed at moderate levels, but in hulls, HvGLK1 expression was barely detectable compared with HvGLK2. Barley alm1/Hvglk2 mutants exhibit more severe phenotypes than glk2 mutants of other plant species reported to date. The severe alm1 phenotypic expression in multiple tissues indicates that HvGLK2 plays some roles that are nonredundant with HvGLK1.
Influence of Plant Host and Organ, Management Strategy, and Spore Traits on Microbiome Composition
Authors: Gdanetz Kristi , Noel Zachary , Trail Frances
Published: January 2021

Microbiomes from maize and soybean were characterized in a long-term three-crop rotation research site, under four different land management strategies, to begin unraveling the effects of common farming practices on microbial communities. The fungal and bacterial communities of leaves, stems, and roots in host species were characterized across the growing season using amplicon sequencing and compared with the results of a similar study on wheat. Communities differed across hosts and among plant growth stages and organs, and these effects were most pronounced in the bacterial communities of the wheat and maize phyllosphere. Roots consistently showed the highest number of bacterial operational taxonomic units compared with aboveground organs, whereas the α-diversity of fungi was similar between above- and belowground organs. Network analyses identified putatively influential members of the microbial communities of the three host plant species. The fungal taxa specific to roots, stems, or leaves were examined to determine whether the specificity reflected their life histories based on previous studies. The analysis suggests that fungal spore traits are drivers of organ specificity in the fungal community. Identification of influential taxa in the microbial community and understanding how community structure of specific crop organs is formed will provide a critical resource for manipulations of microbial communities. The ability to predict how organ-specific communities are influenced by spore traits will enhance our ability to introduce them sustainably.
Randomized Controlled Trial Comparing Silver-Impregnated Fibrous Hydrocolloid Dressings With Silver Sulfadiazine Cream Dressings for the Treatment of Fracture Blisters to Determine Time to Surgical Readiness
Authors: Wiese Karin R. , van Heukelum Marcus , Lombard Carl J. , Ferreira Nando , Burger Marilize C.
Published: January 2021

Objectives:

To investigate, in patients with fracture blisters, the time to surgical readiness in those treated with silver-impregnated fibrous hydrocolloid (SFH) dressings compared with those treated with topical silver sulfadiazine (SS) cream and to determine the direct costs associated with both treatments.

Design:

A single-blind, randomized controlled trial.

Setting:

The study was conducted at Tygerberg Hospital, a tertiary care facility, and Worcester Provincial Hospital, a secondary care facility, Western Cape, South Africa.

Patients:

Patients >18 years of age with one or more fracture blisters overlying fractures requiring surgical fixation were considered for inclusion.

Main Outcome Measurements:

The main outcome was the time to surgical readiness, after complete re-epithelialization of the affected site, in both groups. The direct cost associated with each treatment and the daily cost associated with hospital stay per day were recorded.

Results:

At an interim analysis, 70 patients had been enrolled and completed the study protocol with 35 patients per group. Groups were balanced across patient and clinical demographic characteristics. A significant difference of 4 days (95% confidence interval: 2.9–5.1 days,P< 0.001) in the mean time to surgical readiness (SFH group, 5.3 days vs. SS group, 9.3 days) was observed. No difference between the time to surgical procedure as well as the total length of hospital stay between the 2 groups was observed.

Conclusion:

This study reports that SFH dressings are a cost-effective treatment option for the management of fracture blisters evidenced by a significant accelerated time to blister re-epithelialization compared with a commonly described method of SS cream dressings.

Level of evidence:

Therapeutic Level 1. See Instructions for Authors for a complete description of levels of evidence.

Level of Evidence:

Therapeutic Level I. See Instructions for Authors for a complete description of levels of evidence.
An Improvised Pulmonary Telerehabilitation Program for Postacute COVID-19 Patients Would Be Feasible and Acceptable in a Low-Resource Setting
Authors: Bickton Fanuel Meckson , Chisati Enock , Rylance Jamie , Morton Ben
Published: January 2021

Postacute COVID-19 patients are at risk of long-term functional impairment, and the rehabilitation community is calling for action preparing for a “tsunami of rehabilitation needs” in this patient population. In the absence of standard guidelines and local evidence, a 3-wk pulmonary telerehabilitation program was successfully delivered to a postacute severe COVID-19 patient in Malawi. The patient experienced persistent dyspnea and fatigue, with a remarkable impact on his health status. On the final assessment, all his respiratory severity scores had fallen by more than their thresholds for clinical significance. He reported no continued or new complaints, was walking longer distances, had returned to work, and was discharged from follow-up. Our case shows that an improvised pulmonary telerehabilitation program for postacute COVID-19 patients could be feasible and acceptable in a low-resource setting. Benefits include reducing risk of transmission and use of personal protective equipment.
Mechanical Stretch Inhibition Sensitizes Proprioceptors to Compressive Stresses
Authors: Das Ravi , Lin Li-Chun , Català-Castro Frederic , Malaiwong Nawaphat , Sanfeliu Neus , Porta-de-la-Riva Montserrat , Pidde Aleksandra , Krieg Michael
Published: January 2021

A repetitive gait cycle is an archetypical component within the behavioural repertoire of many if not all animals including humans. It originates from mechanical feedback within proprioceptors to adjust the motorprogram during locomotion and thus leads to a periodic orbit in a low dimensional space. Here, we investigate the mechanics, molecules and neurons responsible for proprioception inCaenorhabditis (C.) elegansto gain insight into how mechanosensation shapes the orbital trajectory to a well-defined limit cycle. We used genome editing, force spectroscopy and multiscale modeling and found that alternating tension and compression with the spectrin network of a single proprioceptor encodes body posture and informs TRP-4/NOMPC and TWK-16/TREK2 homologs of mechanosensitive ion channels during locomotion. In contrast to a widely accepted model of proprioceptive ‘stretch’ reception, we found that proprioceptors activated under compressive stressesin vivoandin vitro, and speculate that this property is conserved across function and species.
A low-cost mouse cage warming system provides improved intra-ischemic and post-ischemic body temperature control – application for reducing variability in experimental stroke studies
Authors: Hong Sung-Ha , Hong Jeong-Ho , Lahey Matthew T. , Zhu Liang , Stephenson Jessica M. , Marrelli Sean P.
Published: January 2021

Experimental guidelines have been proposed to improve the rigor and reproducibility of experimental stroke studies in rodents. As brain temperature is a strong determinant of ischemic injury, tight management of brain or body temperature (Tcore) during the experimental protocol is highly recommended. However, little guidance is provided regarding how or for how long temperature support should be provided. We compared a commonly used heat support method (cage on heating pad) with a low-cost custom built warm ambient air cage (WAAC) system. Both heat support systems were evaluated for the middle cerebral artery occlusion (MCAo) model in mice. The WAAC system provided improved temperature control (more normothermic Tcore and less Tcore variation) during the intra-ischemic period (60 min) and post-ischemic period (3 hrs). Neurologic deficit score showed significantly less variance at post-stroke day 1 (PSD1) in WAAC system mice. Mean infarct volume was not statistically different by heat support system, however, standard deviation was 54% lower in the WAAC system group. In summary, we provide a simple low-cost heat support system that provides superior Tcore management in mice during the intra-ischemic and post-ischemic periods, which results in reduced variability of experimental outcomes.

Highlights

We describe the fabrication of a low-cost mouse cage warming system (warmed ambient air cage; WAAC system) that can be assembled and applied in any stroke laboratory.

The WAAC system provides more precise control of post-stroke mouse body temperature compared with traditional heating pad warming system.

The more precise control of post-stroke core temperature reduces variability in some experimental measures in more severely injured mice.
Methylsulfonylmethane and sesame seed oil improve hyperlipidemia and polyunsaturated fatty acid metabolism in thedb/dbmouse
Authors: Fili Cameron V. , Lin Ling , Chapman Jonathan , Hamilton David , Yates Charles R.
Published: January 2021

Background

An estimated 463 million people worldwide suffer from diabetes, and that number is projected to rise significantly to 700 million by 2045. One of the hallmarks of type 2 diabetes and metabolic syndrome is alterations in the lipid profile and polyunsaturated fatty acid metabolism.

Objective

The objective of this study was to identify lipid alterations in leptin receptor deficientdb/dbmice, a type 2 diabetes model, to establish a baseline biological signature for the evaluation of natural products with purported lipid-altering activity.

Methods

Six-week old maledb/dbmice (n = 10/group) were randomized to the following groups: 1) diabetic control with no treatment, 2) methylsulfonylmethane (MSM) treatment (3.81 ± 0.33 g/kg), 3) sesame seed oil (SSO) treatment (23.54 ± 2.91 mg/kg), and 4) MSM and SSO combination treatment, receiving the same dosages of MSM and SSO as the single treatment groups. Eight-week old male C57BL6/J mice (n=10) were used as a non-diabetic control group.

Results

Serum triglycerides and total cholesterol were significantly increased in thedb/db model compared to nondiabetic control, mimicking diabetes in people. High-density lipoprotein (HDL) was significantly increased in alldb/dbtreatment groups, with the most significant effect in the MSM and SSO combination group, with a corresponding decrease in non-HDL cholesterol. Serum total polyunsaturated fatty acid (PUFA) levels were significantly reduced in diabetic mice compared with control mice. In contrast, treatment with SSO alone reversed this effect such that fed mice exhibited serum PUFA levels comparable to control mice.

Conclusions

Treatment ofdb/dbmice with MSM and SSO improved commonly measured clinical parameters in serum lipid panels. The combination of MSM and SSO treatment’s effects on HDL and non-HDL cholesterol and fatty acid metabolism could lead to improved clinical outcomes in diabetics, such as reduced incidence of atherosclerosis and hepatic steatosis.
Bovine neutrophils release extracellular traps and cooperate with macrophages inMycobacterium aviumsubsp.paratuberculosisclearancein vitro
Authors: Ladero-Auñon I , Molina E , Holder A , Kolakowski J , Harris H , Urkitza A , Anguita J , Werling D , Elguezabal N
Published: January 2021

Mycobacterium aviumsubsp.paratuberculosis(Map) is the underlying pathogen causing bovine paratuberculosis (PTB), an enteric granulomatous disease that mainly affects ruminants and for which an effective treatment is needed. Macrophages are the primary target cells for Map, which survives and replicates intracellularly by inhibiting phagosome maturation. Neutrophils are present at disease sites during the early stages of the infection, but seem to be absent in the late stage, in contrast to healthy tissue. Although neutrophil activity has been reported to be impaired following Map infection, their role in PTB pathogenesis has not been fully defined. Neutrophils are capable of releasing extracellular traps consisting of extruded DNA and proteins that immobilize and kill microorganisms, but this mechanism has not been evaluated against Map. Our main objective was to study the interaction of neutrophils with macrophages during anin vitromycobacterial infection. For this purpose, neutrophils and macrophages from the same animal were cultured alone or together in the presence of Map orMycobacterium bovisBacillus-Calmette-Guérin (BCG). Extracellular trap release, mycobacteria killing as well as IL-1β and IL-8 release were assessed. Neutrophils released extracellular traps against mycobacteria when cultured alone and in the presence of macrophages without direct cell contact, but resulted inhibited in direct contact. Macrophages were extremely efficient at killing BCG, but ineffective at killing Map. In contrast, neutrophils showed similar killing rates for both mycobacteria. Co-cultures infected with Map showed the expected killing effect of combining both cell types, whereas co-cultures infected with BCG showed a potentiated killing effect beyond the expected one, indicating a potential synergistic cooperation. In both cases, IL-1β and IL-8 levels were lower in co-cultures, suggestive of a reduced inflammatory reaction. These data indicate that cooperation of both cell types can be beneficial in terms of decreasing the inflammatory reaction while the effective elimination of Map can be compromised. These results suggest that neutrophils are effective at Map killing and can exert protective mechanisms against Map that seem to fail during PTB disease after the arrival of macrophages at the infection site.
Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback betweende novoDNA methylation and chromatin condensates
Authors: Olmeda Fabrizio , Lohoff Tim , Clark Stephen J , Benson Laura , Krüger Felix , Reik Wolf , Rulands Steffen
Published: January 2021

Recent breakthroughs in single-cell genomics allow probing molecular states of cells with unprecedented detail along the sequence of the DNA. Biological function relies, however, on emergent processes in the three-dimensional space of the nucleus, such as droplet formation through phase separation. Here, we use single-cell multi-omics sequencing to develop a theoretical framework to rigorously map epigenome profiling along the DNA sequence onto a description of the emergent spatial dynamics in the nucleus. Drawing on scNMT-seq multi-omics sequencingin vitroandin vivowe exemplify our approach in the context of exit from pluripotency and globalde novomethylation of the genome. We show how DNA methylation patterns of the embryonic genome are established through the interplay between spatially correlated DNA methylation and topological changes to the DNA. This feedback leads to the predicted formation of 30-40nm sized condensates of methylated DNA and determines genome-scale DNA methylation rates. We verify these findings with orthogonal single cell multi-omics data that combine the methylome with HiC measurements. Notably, this scale of chromatin organization has recently been described by super-resolution microscopy. Using this framework, we identify local methylation correlations in gene bodies that precede transcriptional changes at the exit from pluripotency. Our work provides a general framework of how mechanistic insights into emergent processes underlying cell fate decisions can be gained by the combination of single-cell multi-omics and methods from theoretical physics that have not been applied in the context of genomics before.

Highlights

We develop methodology to infer collective spatio-temporal processes in the physical space of the nucleus from single-cell methylome sequencing experiments.

We show that DNA methylation relies on a feedback betweende novomethylation and nanoscale changes in DNA topology, leading to the formation of methylation condensates.

Chromatin condensates at this scale have recently been described by high-resolution microscopy but have remained without mechanistic explanation.

Using this framework, we identify changes in the distribution of DNA methylation marks in gene bodies that precede gene silencing at the exit from pluripotency.
Fabrication of silver doped nano hydroxyapatite-carrageenan hydrogels for articular cartilage applications
Authors: Swain Subhasmita , Kwon Tae Yub , Rautray Tapash R.
Published: January 2021

It can be found from the results that nano hydroxyapatite- silver -3.0 wt% carageenan (nHA-Ag-CG3.0) improved the mechanical properties of the as-formed hydrogel scaffold after incorporation of higher CG concentration. The Young’s modulus of hydroxyapatite- silver - 1.5wt% carageenan (nHA-Ag-CG1.5) was found to be 0.36 ± 0.07 MPa that increased in case of nHA-Ag-CG3.0 demonstrating better interfacial compatibility of their matrix with respect to the reinforcement. This increase in reinforcement concentration resulted in higher stiffness that dissipated energy. The higher swelling ratio is envisaged to induce better cell adhesion and proliferation. The biodegradability test was performed in phosphate buffered saline at body temperature for 3 weeks. The biodegradability rate of nHA-Ag-CG1.5 was found to be equivalent to nHA-Ag-CG3.0 hydrogels at day 7 while it increased faster in nHA-Ag-CG3.0 on days 14 and 21 that may be ascribed to the possible interaction of nHA and Ag with their CG matrix. The bacterial cell viability ofStaphylococcus aureus(S. aureus)was performed after 10 h, 20 h and 30 h of culture. The nHA-Ag-CG1.5 exhibited restrained growth ofS. aureusas compared to nHA-Ag-CG3.0 and these results were validated by CLSM analysis. Hence, nHA-Ag-CG3.0 may be considered to have more cytocompatibility than nHA-Ag-CG 1.5.
Zebrafish Polycomb repressive complex-2 critical roles are largely Ezh2- over Ezh1-driven and concentrate during early embryogenesis
Authors: Yette Gabriel A. , Stewart Scott , Stankunas Kryn
Published: January 2021

Polycomb repressive complex-2 (PRC2) methylation of histone H3 lysine-27 (H3K27me) is associated with stable transcriptional repression. PRC2 famously silencesHoxgenes to maintain anterior-posterior segment identities but also enables early cell fate specification, restrains progenitor cell differentiation, and canalizes cell identities. Zebrafish PRC2 genetic studies have focused onezh2,which, with its paralogezh1, encodes the H3K27 methyltransferase component.ezh2loss-of-function mutants reinforce essential vertebrate PRC2 functions during early embryogenesis albeit with limited contributions to body plan establishment. However, redundancy withezh1and the lethality of maternal-zygotic homozygousezh2nulls could obscure additional early developmental and organogenesis roles of PRC2. Here, we combine new and existing zebrafishezh1andezh2alleles to show collective maternal/zygoticezh2exclusively provides earliest embryonic PRC2 H3K27me3 activity. Zygoticezh1, which becomes progressively expressed asezh2levels dissipate, has minor redundant and noncompensatory larval roles but itself is not required for viability or fertility. Zygotic Ezh2/PRC2 promotes correct craniofacial bone shape and size by maintaining proliferative pre-osteoblast pools. Anezh2allelic series including disrupted maternalezh2uncovers axial skeleton homeotic transformations and pleiotropic organogenesis defects. Further, once past a critical early window, we show zebrafish can develop near normally with minimal bulk H3K27me3. Our results suggest Ezh2-containing PRC2 stabilizes rather than instructs early developmental decisions while broadly contributing to organ size and embellishment.
The DAXX-SREBP axis promotes oncogenic lipogenesis and tumorigenesis
Authors: Mahmud Iqbal , Tian Guimei , Wang Jia , Lewis Jessica , Waddell Aaron , Lydon McKenzie L. , Zhao Lisa Y. , Li Jian-Liang , Purayil Hamsa Thayele , Huo Zhiguang , Daaka Yehia , Garrett Timothy J. , Liao Daiqing
Published: January 2021

De novo lipogenesis produces lipids for membrane biosynthesis and cell signaling. Elevated lipogenesis is a major metabolic feature in cancer cells. In breast and other cancer types, genes involved in lipogenesis are highly upregulated, but the mechanisms that control their expression remain poorly understood. DAXX modulates gene expression through binding to diverse transcription factors although the functional impact of these diverse interactions remains to be defined. Our recent analysis indicates that DAXX is overexpressed in diverse cancer types. However, mechanisms underlying DAXX’s oncogenic function remains elusive. Using global integrated transcriptomic and lipidomic analyses, we show that DAXX plays a key role in lipid metabolism. DAXX depletion attenuates, while its overexpression enhances, lipogenic gene expression, lipid synthesis and tumor growth. Mechanistically, DAXX interacts with SREBP1 and SREBP2 and activates SREBP-mediated transcription. DAXX associates with lipogenic gene promoters through SREBPs. Underscoring the critical roles for the DAXX-SREBP interaction for lipogenesis, SREBP2 knockdown attenuates tumor growth in cells with DAXX overexpression, and a DAXX mutant unable to bind SREBPs are incapable of promoting lipogenesis and tumor growth. Our results identify the DAXX-SREBP axis as an important pathway for tumorigenesis.
A new method for improving extraction efficiency and purity of urine and plasma cell-free DNA
Authors: Lin Selena Y. , Luo Yue , Marshall Matthew M. , Johnson Barbara J. , Park Sung R. , Wang Zhili , Su Ying-Hsiu
Published: January 2021

This study assessed three commercially available cell-free DNA (cfDNA) extraction kits and the impact of a PEG-based DNA cleanup procedure (DNApure) on cfDNA quality and yield. Six normal donor urine and plasma samples, and specimens from four pregnant (PG) women carrying male fetuses underwent extractions with the JBS cfDNA extraction kit (kit J), MagMAX Cell-Free DNA Extraction kit (kit M), and QIAamp Circulating Nucleic Acid Kit (kit Q). Recovery of a PCR product spike-in, endogenousTP53,and Y-chromosome DNA was used to assess kit performance. Nucleosomal-sized DNA profiles varied among the kits, with prominent multi-nucleosomal-sized peaks present in urine and plasma DNA isolated by kits J and M only. Kit J recovered significantly more spike-in DNA compared with kit M or Q (p<0.001) from urine, and similar amounts from plasma (p=0.12). Applying DNApure to kit M- and Q-isolated DNA significantly improved the amplification efficiency of spike-in DNA from urine (p<0.001) and plasma (p≤0.013). Furthermore, kit J isolated significantly more Y-chromosome DNA from PG urine compared to kit Q (p=0.05). We conclude that DNApure provides an efficient means of improving the yield and purity of cfDNA and minimizing effects of pre-analytical biospecimen variability on liquid biopsy assay performance.
PEDF and Derived Peptides Prevent Apoptosis and Promote Differentiation of Retinal Photoreceptors
Authors: Michelis Germán , German Olga Lorena , Villasmil Rafael , Rotstein Nora P. , Politi Luis , Becerra S Patricia
Published: January 2021

Pigment epithelium-derived factor (PEDF) is a cytoprotective protein for the retina. We hypothesize that this protein acts on neuronal survival and differentiation of photoreceptor cells in culture. The purpose of the present study was to evaluate the neurotrophic effects of PEDF and its fragments in anin vitromodel of cultured primary retinal neurons that die spontaneously in the absence of trophic factors. Results show that PEDF protected photoreceptor precursors from apoptosis, preserved mitochondrial function and promoted polarization of opsin enhancing their developmental process, as well as induced neurite outgrowth in amacrine neurons. These effects were abolished by an inhibitor of the PEDF receptor or receptor-derived peptides that block ligand/receptor interactions. While all the activities were specifically conferred by short peptide fragments (17 amino acid residues) derived from the PEDF neurotrophic domain, no effects were triggered by peptides from the PEDF antiangiogenic region. The observed effects on retinal neurons imply a specific activation of the PEDF receptor by a small neurotrophic region of PEDF. Our findings support the neurotrophic PEDF peptides as neuronal guardians for the retina, highlighting their potential as promoters of retinal differentiation, and inhibitors of retina cell death and its blinding consequences.
Analysis of next- and third-generation RNA-Seq data reveals the structures of alternative transcription units in bacterial genomes
Authors: Wang Qi , Liu Zhaoqian , Yan Bo , Chou Wen-Chi , Ettwiller Laurence , Ma Qin , Liu Bingqiang
Published: January 2021

Alternative transcription units (ATUs) are dynamically encoded under different conditions or environmental stimuli in bacterial genomes, and genome-scale identification of ATUs is essential for studying the emergence of human diseases caused by bacterial organisms. However, it is unrealistic to identify all ATUs using experimental techniques, due to the complexity and dynamic nature of ATUs. Here we present the first-of-its-kind computational framework, named SeqATU, for genome-scale ATU prediction based on next-generation RNA-Seq data. The framework utilizes a convex quadratic programming model to seek an optimum expression combination of all of the to-be-identified ATUs. The predicted ATUs inE. colireached a precision of 0.77/0.74 and a recall of 0.75/0.76 in the two RNA-Sequencing datasets compared with the benchmarked ATUs from third-generation RNA-Seq data. We believe that the ATUs identified by SeqATU can provide fundamental knowledge to guide the reconstruction of transcriptional regulatory networks in bacterial genomes.
A systematic CRISPR screen reveals an IL-20/IL20RA-mediated peritoneal immune crosstalk to prevent the ovarian cancer metastasis
Authors: Li Jia , Qin Xuan , Shi Jie , Wang Xiaoshuang , Li Tong , Xu Mengyao , Chen Xiaosu , Zhao Yujia , Han Jiahao , Piao Yongjun , Zhang Wenwen , Qu Pengpeng , Wang Longlong , Xiang Rong , Shi Yi
Published: January 2021

Transcoelomic spread of cancer cells across the peritoneal cavity occurs in most initially diagnosed ovarian cancer (OC) patients and accounts for most cancer-related death. However, how OC cells interact with peritoneal stromal cells to evade the immune surveillance remains largely unexplored. Here, through anin vivogenome-wide CRISPR/Cas9 screen, we identified IL20RA, which decreased dramatically in OC patients during peritoneal metastasis, as a key factor preventing the transcoelomic metastasis of OC. Reconstitution of IL20RA in highly metastatic OC cells greatly suppresses the transcoelomic metastasis. OC cells, when disseminate into the peritoneal cavity, greatly induce peritoneum mesothelial cells to express IL-20 and IL-24, which in turn activate the IL20RA downstream signaling in OC cells to produce mature IL-18, eventually resulting in the polarization of macrophages into the M1-like subtype to clear the cancer cells. Thus, we show an IL-20/IL20RA-mediated crosstalk between OC and mesothelial cells that supports a metastasis-repressing immune microenvironment.
B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells
Authors: Yu Bingfei , Qi Yanyan , Li Rui , Shi Quanming , Satpathy Ansuman , Chang Howard Y.
Published: January 2021

The long noncoding RNA (lncRNA) XIST establishes X chromosome inactivation (XCI) in female cells in early development and thereafter is thought to be largely dispensable. Here we show XIST is continually required in adult human B cells to silence a subset of X-linked immune genes such asTLR7. XIST-dependent genes lack promoter DNA methylation and require continual XIST-dependent histone deacetylation. XIST RNA-directed proteomics and CRISPRi screen reveal distinctive somatic cell-specific XIST complexes, and identify TRIM28 that mediates Pol II pausing at promoters of X-linked genes in B cells. XIST dysregylation, reflected by escape of XIST-dependent genes, occurs in CD11c+ atypical memory B cells across single-cell transcriptome data in patients with female-biased autoimmunity and COVID-19 infection. XIST inactivation with TLR7 agonism suffices to promote isotype-switched atypical B cells. These results suggest cell-type-specific diversification of lncRNA-protein complexes increase lncRNA functionalities, and expand roles for XIST in sex-differences in biology and medicine.

HIGHLIGHTS

XIST prevents escape of genes with DNA hypomethylated promoters in B cells.

XIST maintains X-inactivation through continuous deacetylation of H3K27ac.

XIST ChIRP-MS and allelic CRISPRi screen reveal a B cell-specific XIST cofactor TRIM28.

XIST loss and TLR7 stimulation promotes CD11c+ atypical B cell formation.
Transfer and Fixation of Denatured RNA in Polyacrylamide Gels to Membranes by Electrophoretic Transfer
Authors: Green Michael R. , Sambrook Joseph
Published: January 2021

Polyacrylamide gels, unlike agarose gels, have a highly cross-linked matrix that does not permit efficient, quantitative, or reproducible transfer by passive diffusion. Polyacrylamide gels should therefore be transferred by electroblotting (also known as “electrophoretic transfer”). Because this approach requires the use of a transfer buffer of low ionic strength, nylon membranes are generally used. The membrane is placed directly on the gel, and the gel together with its membrane is then sandwiched between layers of filter paper and placed in a special cassette that, in turn, is placed in a tank of buffer; the cassette is oriented such that the membrane side of the gel faces the positively charged anode. A voltage gradient is applied perpendicular to the direction of the initial electrophoresis of the gel, forcing the sample to migrate out of the gel and onto the membrane.
Comparative study on Life Cycle Assessment of buildings in developed countries and Sri Lanka
Authors: Amarasinghe Isuri Anuradha , Soorige Dumindu , Geekiyanage Devindi
Published: January 2021

Purpose

Life cycle assessment (LCA) has considerably contributed to increasing the environmental friendliness of buildings in developed countries. However, it is hard to find evidence on the application of LCA for buildings in developing countries; particularly, Sri Lanka. There is a lack of research to compare the status of LCA of buildings in developed countries vs developing countries. In this context, the purpose of this study aims to examine the status of LCA implementation for buildings between developed countries and Sri Lanka, a developing country.

Design/methodology/approach

The exploratory research was adapted, and in-depth interviews were held with LCA professionals from Sri Lanka and developed countries, respectively.

Findings

Relatively less attention has been paid to the implementation of LCA for buildings in Sri Lanka compared to the developed countries due to the time and effort required to collect life cycle inventory data and limited stakeholder understanding of the LCA. Hence, this study proposed improvements, including the development of LCA databases containing region-specific data and conducting programmes to raise stakeholders' awareness to address the gaps in Sri Lanka.

Research limitations/implications

The identified LCA implementation process for buildings could be used as a guide for first-time LCA users, and it equally makes a valued reference for experienced practitioners.

Originality/value

A limited number of the studies formulate a comparison between the LCA for building in developed countries and developing countries. This research attempts to address this knowledge gap.
Adaptive finite element–discrete element analysis for stratal movement and microseismic behaviours induced by multistage propagation of three-dimensional multiple hydraulic fractures
Authors: Wang Yongliang
Published: January 2021

Purpose

Optimized three-dimensional (3D) fracture networks are crucial for multistage hydrofracturing. To better understand the mechanisms controlling potential disasters as well as to predict them in 3D multistage hydrofracturing, some governing factors, such as fluid injection-induced stratal movement, compression between multiple hydraulic fractures, fracturing fluid flow, fracturing-induced microseismic damaged and contact slip events, must be properly simulated via numerical models. This study aims to analyze the stratal movement and microseismic behaviours induced by multistage propagation of 3D multiple hydraulic fractures.

Design/methodology/approach

Adaptive finite element–discrete element method was used to overcome the limitations of conventional finite element methods in simulating 3D fracture propagation. This new approach uses a local remeshing and coarsening strategy to ensure the accuracy of solutions, reliability of fracture propagation path and computational efficiency. Engineering-scale numerical models were proposed that account for the hydro-mechanical coupling and fracturing fluid leak-off, to simulate multistage propagation of 3D multiple hydraulic fractures, by which the evolution of the displacement, porosity and fracture fields, as well as the fracturing-induced microseismic events were computed.

Findings

Stratal movement and compression between 3D multiple hydraulic fractures intensify with increasing proximity to the propagating fractures. When the perforation cluster spaces are very narrow, alternate fracturing can improve fracturing effects over those achieved via sequential or simultaneous fracturing. Furthermore, the number and magnitude of microseismic events are directly proportional to the stratal movement and compression induced by multistage propagation of fracturing fracture networks.

Originality/value

Microseismic events induced by multistage propagation of 3D multiple hydraulic fractures and perforation cluster spaces and fracturing scenarios that impact the deformation and compression among fractures in porous rock matrices are well predicted and analyzed.
An evolutionary algorithm for controlling numerical convergence of the radiative transfer equation with participating media using TVD interpolation schemes
Authors: Torres-Aguilar Carlos Enrique , Moreno-Bernal Pedro , Xamán Jesús , Zavala Guillen Ivett , Hernández-López Irving Osiris
Published: January 2021

Purpose

This paper aims to present an evolutionary algorithm (EA) to accelerate the convergence for the radiative transfer equation (RTE) numerical solution using high-order and high-resolution schemes by the relaxation coefficients optimization.

Design methodology/approach

The objective function minimizes the residual value difference between iterations in each control volume until its difference is lower than the convergence criterion. The EA approach is evaluated in two configurations, a two-dimensional cavity with scattering media and absorbing media.

Findings

Experimental results show the capacity to obtain the numerical solution for both cases on all interpolation schemes tested by the EA approach. The EA approach reduces CPU time for the RTE numerical solution using SUPERBEE, SWEBY and MUSCL schemes until 97% and 135% in scattering and absorbing media cases, respectively. The relaxation coefficients optimized every two numerical solution iterations achieve a significant reduction of the CPU time compared to the deferred correction procedure with fixed relaxation coefficients.

Originality/value

The proposed EA approach for the RTE numerical solution effectively reduces the CPU time compared to the DC procedure with fixed relaxation coefficients.
A mixed method for measuring incompatibilities between manufacturing approaches and off-site construction
Authors: Luo Jianing , Zhang Hong , Sher William
Published: January 2021

Purpose

The purpose of this research is to measure incompatibilities between the manufacturing approaches (MA) used by the manufacturing industries, and those used for the off-site construction (OSC) of buildings. The aim is to explore which of these approaches could be integrated into OSC in a precise manner as viewed by architects as well as how this might occur.

Design/methodology/approach

An empirical research and empirical cycle (EC) was adopted as a methodological framework to measure incompatibilities. A combination of quantitative and qualitative mixed methods was explored through a literature-based case study of prefabricated houses and cars, nine real-life projects built by the second author's research team and the first-named author's practical experiences of leading these projects, based on a logic framework derived from the authors’ reflections of their architectural practices.

Findings

The findings quantitatively present the incompatibilities between cars (automobile bodies) and prefabricated houses. Design-related aspects have the most potential for integration (42.3% increment). The key lessons were identified as specific design philosophies and related guidelines for architects.

Research limitations/implications

The findings are limited to single types of products (cars) and buildings (prefabricated houses) in particular regions. The key lessons just present a preliminary evaluation of the application of the design philosophies and related guidelines in nine real-life projects to comply with word limit constraints.

Practical implications

This study could help architects and other practitioners to locate and target and alleviated incompatibilities between MA and OSC. It could also precisely identify integration shortcomings to optimize decision-making as well as technical pathways for possible and effective breakthroughs.

Social implications

This study provides fundamental research as a starting point for further discussion and development. A series of additional in-depth investigations combined with case studies are planned for the future. These could provide alternative study approaches to develop more appropriate architectural design methodologies and more streamlined processes.

Originality/value

The research contributes an alternative architectural perspective when measuring incompatibilities between MA and OSC. The results highlight the implications of precise measurement and provide guidance for architects. These facilitate the effective and successful integration of MA into OSC of buildings and promote the uptake of lean construction (LC) in OSC.
A visual and rhetorical perspective on management control systems
Authors: Söderlund Carina , Hansson Magnus
Published: January 2021

Purpose

The purpose of this paper is to explore the role and function of visuals, visual communication and information design as they relate to management control systems and visual management (VM) in lean-inspired organisations. This paper helps expand knowledge on how visual and design studies can contribute to research on VM as part of a management control system.

Design/methodology/approach

A study is outlined, which was conducted at a multinational manufacturing company to investigate employees’ perceptions and use of visual devices on the shop floor, including their related reactions and behaviour. The study is delimited to operation management, lean manufacturing and lean boards (i.e. daily management boards and performance measurement boards).

Findings

The findings point out the persuasive purpose of lean boards, as well as the metaphoric and persuasive functions of the visuals and information design in management control systems.

Originality/value

Visual research and design research are rare within studies of management control systems. There is a need to perform research that takes into account the role and function of visual communication and information design in VM. The proposed areas for future research can provide design principles, as well as insights into the complexity of visual communication and information design in VM and management control studies.
The driving mindsets of innovation: curiosity, creativity and clarity
Authors: Walsh Christian , Knott Paul , Collins Jamie
Published: January 2021

Purpose

Innovation is an essential process for growth and well-being of organisations and society in general but is difficult to manage successfully. Through a better understanding of the innovation mindsets as established strategists use them in practice, this paper aims to improve firms’ success rates of innovation.

Design/methodology/approach

To examine how innovation processes play out in dynamic environments, the authors undertook a longitudinal two-year multi-case study in the high-tech sector.

Findings

Strategists in this study showed distinct phases in their successful innovation journey with three dominant mindsets of curiosity, creativity and clarity. The curiosity phase includes actions focused on discovering and understanding the implications and significance of an opportunity. The creativity phase includes actions focused on creating and testing a wide range of options. The clarity phase consists of actions focused on resourcing and implementing change.

Practical implications

In adopting this framework for use in the field, the authors recommend strategists take time for discovering and getting to core understanding in the curiosity phase. They should then take action by creating and actively testing a broad range of solution ideas in the creativity phase. Finally, organisations need to take care with clear direction and communication when resourcing and implementing in the clarity phase.

Originality/value

This novel framework which emerged from the longitudinal field research describes the mindsets of innovation and how these are used at different phases in the innovation process.
Effectiveness of performance measurement framework on manufacturers supply chain – case of Saudi Arabia
Authors: El-Garaihy Wael Hassan
Published: January 2021

Purpose

This study aims to provide a collaborative supply chain system using a combination of two already existed methods, i.e. levels of decision-making and supply chain operation reference (SCOR).

Design/methodology/approach

A two-phase methodology was conducted based on field analysis and survey analysis. Field analysis included a critical analysis of literature related to supply chain performance measurement and identified related indicators.

Findings

In a survey analysis, a questionnaire was developed to test the established indicators from managers and employees of manufacturing companies. It formulated a novel model for the performance measurement of the supply chain (SC) which included 4 factors (customer, efficiency, flexibility and product), with a total of 31 sub-components.

Originality/value

The structure provides a tied horizontal (SCOR) and vertical (progressive decision) in relation to the features that characterize the SC performance. This system enables the decision-makers to make decisions at the strategic, tactical and operational levels. It reflects the performance measures reliability, authenticity and its application in various SC. It also improves communication with the regional party while ensuring a preventive schedule for maintenance.
Examining the moderating role of perceived risk and web atmospherics in online luxury purchase intention
Authors: Jain Sheetal
Published: January 2021

Purpose

Recently, internet has turned out to be the fastest growing channel for luxury sales. Surprisingly, very few studies have focused on understanding the major drivers behind online luxury goods consumption, particularly in the emerging market context. Therefore, the key objectives of this study are to, first, develop a framework to understand factors affecting consumers' intention to purchase luxury fashion goods online. Second, measure the moderating effect of perceived risk and web atmospherics on the relationship between attitude toward buying luxury fashion goods online and online luxury purchase intention.

Design/methodology/approach

Data were collected through structured questionnaires from a sample of 250 luxury fashion consumers in India. Collected data were analyzed through confirmatory factor analysis (CFA) and Hayes Process macro in SPSS.

Findings

Study findings indicate that perceived usefulness, perceived ease of use, perceived enjoyment and price consciousness have a direct as well as an indirect relationship via attitude on online luxury purchase intention. The results also revealed that web atmospherics moderate the relationship between attitude toward buying luxury fashion goods online and online luxury purchase intention.

Originality/value

This is one of the first studies that explores the moderating role of perceived risk and web atmospherics in the context of luxury market. It will help luxury marketers to develop appropriate strategies for selling luxury goods online in emerging markets like India.