bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening of anti-Acinetobacter baumannii phytochemicals, based on the potential inhibitory effect on OmpA and OmpW functions
Authors: Shahryari Shahab , Mohammadnejad Parvin , Noghabi Kambiz Akbari 
Published: July 2021

SummaryTherapeutic options, including last-line or combined antibiotic therapies for multi-drug resistant (MDR) strains of Acinetobacter baumannii are ineffective. The outer membrane protein A (OmpA) and outer membrane protein W (OmpW) are two porins known for their different cellular functions. Identification of natural compounds with the potentials to block these putative porins can attenuate the growth of the bacteria and control the relating diseases. The current work aimed to screen a library of 384 phytochemicals according to their potentials to be used as a drug, and potentials to inhibit the function of OmpA and OmpW in A. baumannii. The phytocompounds were initially screened based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET) drug-like properties. Afterward, the selected ligands were subjected to standard docking calculations against the predicted three-dimensional structure of OmpA and OmpW in A. baumannii. We identified three phytochemicals (isosakuranetin, aloe-emodin and pinocembrin) possessing appreciable binding affinity towards the selected binding pocket of OmpA and OmpW. Molecular dynamics (MD) simulation analysis confirmed the stability of the complexes. Amongst them, isosakuranetin was suggested as the best phytocompound for further in vitro and in vivo study.
Wall-associated Receptor Kinase and The Expression Profiles in Wheat Responding to Fungal Stress
Authors: Zhang Hong , Li Hanping , Zhang Xiangyu , Yan Wenqian , Deng Pingchuan , Zhang Yining , Peng Shanlin , Wang Yajuan , Wang Changyou , Ji Wanquan 
Published: July 2021

AbstractCell wall-associated kinases (WAKs), which are encoded by conserved gene families in plants, are crucial for development and responses to diverse stresses. However, the wheat (Triticum aestivum L.) WAKs have not been systematically classified, especially those involved in protecting plants from disease. Here, we classified 129 WAK proteins (encoded by 232 genes) and 75 WAK-Like proteins (WAKLs; encoded by 109 genes) into four groups, via a phylogenetic analysis. An examination of protein sequence alignment revealed diversity in the GUB-domain of WAKs structural organization, but it was usually characterized by a PYPFG motif followed by CxGxGCC motifs, while the EGF-domain was usually initiated with a YAC motif, and eight cysteine residues were spliced by GNPY motif. The expression profiles of WAK-encoding homologous genes varied in response to Blumeria graminis f. sp. tritici (Bgt), Puccinia striiformis f. sp. tritici (Pst) and Puccinia triticina (Pt) stress. A quantitative real-time polymerase chain reaction (qRT-PCR) analysis proved that TaWAK75 and TaWAK76b were involved in wheat resistance to Bgt. This study revealed the structure of the WAK-encoding genes in wheat, which may be useful for future functional elucidation of wheat WAKs responses to fungal infections.
Pooled screening of CAR T cells identifies non-native signaling domains for next-generation immunotherapies
Authors: Goodman Daniel B. , Azimi Camillia S. , Kearns Kendall , Garakani Kiavash , Garcia Julie , Patel Nisarg , Hwang Byungjin , Lee David , Park Emily , Ye Chun Jimmie , Marson Alex , Bluestone Jeff A. , Roybal Kole T. 
Published: July 2021

SUMMARYChimeric antigen receptors (CARs) repurpose natural signaling components to retarget T cells to refractory cancers, but have shown limited efficacy against solid tumors. Here, we introduce ‘CAR Pooling’, a multiplexed approach to rapidly identify CAR designs with clinical potential. Forty CARs with diverse immune costimulatory domains were assessed in pooled assays for their ability to stimulate critical T cell effector functions during repetitive stimulation that mimics long-term tumor antigen exposure. Several non-native domains from the TNF receptor family exhibited enhanced proliferation (CD40) or cytotoxicity (BAFF-R and TACI) relative to clinical benchmarks, and fell into distinct states of memory, cytotoxicity, and metabolism. BAFF-R CAR T cells were enriched for a highly cytotoxic and NK-cell-like innate phenotype previously associated with positive clinical outcomes. ‘CAR Pooling’ enables efficient exploration of how CAR design affects cell activity and can be applied to optimize receptors across a range of applications and cell types.
Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing
Authors: Sparta Breanne , Hamilton Timothy , Aragones Samuel D. , Deeds Eric J. 
Published: July 2021

AbstractSingle-cell RNA sequencing (scRNA-seq) aims to characterize how variation in gene expression is distributed across cells in tissues and organisms. Yet, effective comprehension of these extremely high-dimensional datasets remains a critical barrier to progress in biological research. In standard analyses of scRNA-seq data, feature selection steps aim to reduce the dimensionality of the data by focusing on a subset of genes that are the most biologically variable across a set of cells. Ideally, these features provide the genes that are the most informative for partitioning groups of transcriptionally distinct cells, each representing a different cell type or identity. In this work, we propose a simple feature selection model where a binomial sampling process for each mRNA species produces a null model of technical variation. To compare our model to existing methods, we use scRNA-seq data where cell identities have been establisheda priorifor each cell, and characterize whether different feature sets retain biologically varying genes, distort neighborhood structures, and allow popular clustering algorithms to partition groups of cells into their established classes. We find that our model of biological variation, which we term “Differentially Distributed Genes” or DDGs, outperforms existing methods, and enables dimensionality reduction without loss of critical structure within the data set.
A corollary discharge mediates saccade related inhibition of single units in mnemonic structures of the human brain
Authors: Katz Chaim N. , Schjetnan Andrea G.P. , Patel Kramay , Barkley Victoria , Hoffman Kari , Kalia Suneil K. , Duncan Katherine , Valiante Taufik A. 
Published: July 2021

AbstractDespite the critical link between visual exploration and memory, little is known about how single-unit activity (SUA) in the human mesial temporal lobe (MTL) is modulated by saccadic eye movements (SEMs). Here we characterize SEM associated SUA modulations, unit-by-unit, and contrast them to image onset, and to occipital lobe SUA. We reveal evidence for a corollary discharge (CD)-like modulatory signal that accompanies SEMs, inhibiting/exciting a unique population of broad/narrow spiking units, respectively, before and during SEMs, and with directional selectivity. These findings comport well with the timing, directional nature, and inhibitory circuit implementation of a CD. Additionally, by linking SUA to event-related potentials (ERPs), which are directionally modulated following SEMs, we recontextualize the ERP associated with SEM as a proxy for both the strength of inhibition and saccade direction, providing a mechanistic underpinning for the more commonly recorded SEM-related ERP in the human brain.
The retrotransposonR2maintainsDrosophilaribosomal DNA repeats
Authors: Nelson Jonathan O. , Slicko Alyssa , Yamashita Yukiko M. 
Published: July 2021

AbstractRibosomal DNA (rDNA) loci contain the hundreds of tandemly repeated copies of ribosomal RNA genes needed to support cellular viability. This repetitiveness makes it highly susceptible to copy number (CN) loss, threatening multi-generational maintenance of rDNA. How this threat is counteracted to avoid extinction of the lineage has remained unclear. Here, we show that the rDNA-specific retrotransposonR2is essential for rDNA CN maintenance in theDrosophilamale germline, despite the perceived disruptive nature of transposable elements. Depletion ofR2led to defective rDNA CN maintenance, causing a decline in fecundity over generations and eventual extinction. This study reveals that active retrotransposons can provide a benefit to their hosts, contrary to their reputation as genomic parasites, which may contribute to their widespread success throughout taxa.One Sentence SummaryThe retrotransposonR2initiates restoration of ribosomal DNA copies to trans-generationally maintain essential locus.
Age-related differences in encoding-retrieval similarity and their relationship to false memory
Authors: Chamberlain Jordan D. , Bowman Caitlin R. , Dennis Nancy A. 
Published: July 2021

AbstractTypical aging is associated with increases in false memory rates among older adults. Such errors are frequently associated with differential neural activity during encoding and retrieval in older compared to younger adults within visual cortices, hippocampus, and front-parietal regions. It remains unknown how pattern similarity reductions relate to false memories in healthy aging. Using encoding-retrieval similarity (ERS) analyses in a sample of younger and older adults, we examined how the similarity of neural patterns between memory phases associated with target and lure objects was impacted by age and contributed to false memory rates. Single-item ERS for targets and lures was reduced by age throughout much of the ventral visual stream and the posterior hippocampus. Furthermore, ERS associated with perceptual lures within the visual stream maintained differential relationships with false memory. Finally, a global ERS metric accounted for age deficits in single-item ERS, but did not contribute to false memory rates. These findings highlight the contribution of age-related reductions in ERS across multiple representational levels to false memories in healthy aging.
Paleoecological implications of Lower-Middle Triassic stromatolites and microbe-metazoan build-ups in the Germanic Basin: Insights into the aftermath of the Permian – Triassic crisis
Authors: Pei Yu , Hagdorn Hans , Voigt Thomas , Duda Jan-Peter , Reitner Joachim 
Published: July 2021

AbstractThe aftermath of the Permian – Triassic crisis is characterized by ubiquitous occurrences of microbial sediments around the world. For instance, Triassic deposits of the Germanic Basin have shown to provide a rich record of stromatolites as well as of microbe-metazoan build-ups with non-spicular demosponges. Despite their paleoecological significance, however, all of these microbialites have only rarely been studied. This study aims to fill this gap by examining and comparing microbialites from the Upper Buntsandstein (Olenekian, Early Triassic) and the lower Middle Muschelkalk (Anisian, Middle Triassic). By combining analytical petrography (optical microscopy, micro X-ray fluorescence, Raman spectroscopy) and geochemistry (δ13Ccarb, δ18Ocarb), we show that all studied microbialites formed in hypersaline lagoons to sabkha environments. Olenekian deposits in Jena and surroundings and Anisian strata at Werbach contain stromatolites. Anisian successions at Hardheim, in contrast, host microbe-metazoan build-ups. Thus, the key-difference is the absence or presence of non-spicular demosponges in microbialites. After the Permian – Triassic crisis, the widespread microbialites (e.g., stromatolites/microbe-metazoan build-ups) possibly resulted from suppressed ecological competition and occupied the vacant ecological niche. It seems plausible that microbes and non-spicular demosponges had a mutualistic relationship and it is tempting to speculate that the investigated microbial-metazoan build-ups reflect an ancient evolutionary and ecologic association. Furthermore, both microbes and non-spicular demosponges may benefit from elevated salinities. Perhaps it was minor differences in salinities that controlled whether or not non-spicular demosponges could develop.
TNF-α levels in respiratory samples are associated with SARS-CoV-2 infection
Authors: Pereson Matias J. , Badano Maria Noel , Aloisi Natalia , Chuit Roberto , de Bracco MME , Bare Patricia 
Published: July 2021

ABSTRACTPurposeThe aim of this study was to measure levels of IL-6 and TNF-α in respiratory samples from individuals with symptoms compatible with COVID-19 and analyze their association with SARS-CoV-2 presence.MethodsSARS-CoV-2 detection was performed using the CDC (USA) real-time RT-PCR primers, probes and protocols. Cytokine concentrations were measured using commercial reagents based on enzyme linked immunosorbent assay (ELISA).ResultsTNF-α median levels were greater in COVID19 (+) symptomatic group (5.88 (1.36 - 172.1) pg/ml) compared to COVID19 (−) symptomatic individuals (2.87 (1.45 – 69.9) pg/ml) (p=0.0003). No significant differences were shown in IL-6 median values between COVID-19 (+) and (−) symptomatic patients (5.40 (1.7 - 467) pg/ml and 6.07 (1.57 – 466.6) pg/ml respectively). In addition, increased TNF-α levels (greater than 10 pg/ml), but not IL-6, were associated with SARS-CoV-2 presence (OR= 5.7; p=0.006; 95% CI= 1,551 to 19,11).ConclusionsWe found a statistically significant association between the production of local TNF-α and the presence of the virus in early stages of infection. IL-6 showed high levels in swabs from some symptomatic patients but independent from SARS-CoV-2 presence and viral load, individual’s age and gender. On the contrary, TNF-α evaluation confirmed the presence of inflammatory response but mostly related to COVID-19. More studies are required in order to characterize the cytokine profile expressed at the site of infection of SARS-CoV-2 and its implications in disease outcomes.
Diversification models conflate likelihood and prior, and cannot be compared using conventional model-comparison tools
Authors: May Michael R. , Rothfels Carl J. 
Published: July 2021

AbstractTime-calibrated phylogenetic trees are a tremendously powerful tool for studying evolutionary, ecological, and epidemiological phenomena. Such trees are predominantly inferred in a Bayesian framework, with the phylogeny itself treated as a parameter with a prior distribution (a “tree prior”). However, we show that the tree “parameter” consists, in part, of data, in the form of taxon samples. Treating the tree as a parameter fails to account for these data and compromises our ability to compare among models. Since accuracy of the inferred phylogeny strongly depends on how well the tree prior approximates the true diversification process that gave rise to the tree, the inability to accurately compare competing tree priors has broad implications for applications based on time-calibrated trees. We outline potential remedies to this problem, and provide guidance for researchers interested in assessing the fit of tree models.
WDR82-binding long non-coding RNA lncEry controls mouse erythroid differentiation and maturation
Authors: Yang Shangda , Sun Guohuan , Wu Peng , Chen Cong , Kuang Yijin , Zheng Zhaofeng , He Yicheng , Gu Quan , Lu Ting , Zhu Caiying , Wang Fengjiao , Gou Fanglin , Yang Zining , Zhao Xiangnan , Yuan Shiru , Yang Liu , Lu Shihong , Li Yapu , Lv Xue , Dong Fang , Ma Yanni , Yu Jia , Ng Lai Guan , Shi Lihong , Liu Jing , Cheng Hui , Cheng Tao 
Published: July 2021

ABSTRACTHematopoietic differentiation is controlled by both genetic and epigenetic regulators. Long non-coding RNAs (lncRNAs) have been demonstrated to be important for normal hematopoiesis, but their function in erythropoiesis needs to be further explored. We profiled the transcriptomes of 16 murine hematopoietic cell populations by deep RNA-sequencing and identified a novel lncRNA, Gm15915, that was highly expressed in erythroid-related progenitors and erythrocytes. For this reason, we named it lncEry. We also identified a novel lncEry isoform, which was also the principal transcript that has not been reported before. LncEry depletion impaired erythropoiesis, indicating the important role of the lncRNA in regulating erythroid differentiation and maturation. Mechanistically, we found that lncEry interacted with WD repeat-containing protein 82 (WDR82) to promote the transcription of Klf1 and globin genes and thus control the early and late stages of erythropoiesis, respectively. These findings identified lncEry as an important player in the transcriptional regulation of erythropoiesis.
International opportunity development of born global firms: the role of institutions
Authors: Romanello Rubina , Karami Masoud , Gerschewski Stephan , Evers Natasha , He Cici Xiao 
Published: July 2021

PurposeThe purpose of the study is to investigate the international opportunity development process of born global firms embedded in two different institutional contexts: China, an emerging economy and Italy, a developed country. Drawing on the entrepreneurial opportunity literature and institutional theory, this study explores and draws insights into how home country institutions of born globals can influence the international opportunity development process of the firms.Design/methodology/approachThis paper adopts a qualitative case study approach with in-depth, semi-structured interviews of six born global companies from China and Italy. In doing so, this study uses a flexible pattern matching design, which is consistent with the qualitative research design of the paper.FindingsThe findings of the study indicate that home institutions play an influential, yet differential role in the international opportunity development processes of Chinese and Italian born global firms. While the Italian firms shape their opportunities mainly through product innovation, their Chinese counterparts develop opportunities primarily through networks embedded in their home institutional context.Originality/valueThe key contributions of the paper relate to an integrated analysis of the international opportunity development process of born globals in China and Italy based on institutional theory, which has received limited attention in the international entrepreneurship literature. In addition, the study advances the similarities and differences in the international opportunity development process in two different countries, thus providing valuable insights for policymakers and practitioners to enter international markets successfully.
Intellectual capital, bank stability and risk-taking: evidence from Asian emerging markets
Authors: Dalwai Tamanna , Singh Dharmendra , S. Ananda 
Published: July 2021

Purpose
The purpose of this paper is to investigate the impact of intellectual capital (IC) efficiency on the banks’ risk-taking and stability of Asian emerging markets.

Design/methodology/approach
This study uses a sample of 204 listed banks from 12 Asian emerging countries for the period 2010 to 2019. Data were analyzed using Ordinary Least Squares regression and checked for robustness using system generalized methods moment (GMM) estimation. The dependent variable of bank stability is measured using Z-score-based return on assets (ROA) and return on equity (ROE). The second dependent variable of bank risk is proxied by the standard deviation of ROA, ROE, non-performing loans and loan loss provision.

Findings
The results suggest the IC efficiency has no association with bank risk-taking and stability. The findings lend no support to the resource-based theory. The robustness of this result is confirmed by the system GMM estimation. However, support is found for the competition fragility view as high market power is associated with low risk-taking. The IC subcomponents, human capital efficiency (HCE) report a negative coefficient for bank risk-taking thereby having no support for the hypothesized relationships. Diversified banks with a higher deposit to total asset ratio resort to high risk-taking.

Research limitations/implications
IC efficiency does not have an impact on the bank’s risk-taking behavior and stability for Asian banks. Managers can use these findings to improve their IC and boost investor confidence. Regulatory authorities should increase its monitoring function of banks when the GDP decreases as risk-taking behavior are galvanized during this period.

Originality/value
This research is one of the first to provide empirical evidence of IC efficiency’s relationship with bank stability and bank risk-taking. The implications are useful for policymakers, managers and governing bodies to enhance the banks’ IC efficiency.
A framework of urban entrepreneurship for women breadwinners
Authors: Ziyae Babak , Sadeghi Hossein , Shahamat Nejad Mina , Tajpour Mehdi 
Published: July 2021

Purpose
Today, urban entrepreneurship is considered one of the vital strategies that directed cities toward self-control by reducing the unemployment rate and its arising problems, creating sustainable revenue and preparing the ground for citizens’ independence. This paper aims to present an integrated foresight framework and establish the boundary conditions for urban entrepreneurship of women breadwinners. The study explains how particular women solve workplace-specific poverty and foster urban wealth by developing startups, new businesses or ventures.

Design/methodology/approach
The current research uses a qualitative method and uses the grounded theory approach. Data were collected by selecting 24 outstanding women entrepreneurs using snowball sampling and semi-structured interviews in Tehran Metropolitan.

Findings
The results of the study reveal that the main aspects of the model of urban entrepreneurship consist of causal factors, intervening factors and contextual conditions. By shaping the policies and organizing educational plans, training courses and empowering of women, as well as the establishment of supportive units for the development, identification of the opportunities, developing protective rules, the factors as mentioned above lead to cultural, social and economic development, tendency toward entrepreneurship and development of entrepreneurship among women.

Originality/value
This study undertakes a first of its kind cross-disciplinary conceptual analysis at the level of how women breadwinners foster urban wealth using developing new businesses, startups or ventures. Despite the importance of urban entrepreneurship, theories for understanding the nexus of urban contexts remain underdeveloped. Therefore, there is still a theoretical gap and lack of research; hence, the current study tries to shed light on the topic and fill this gap in the body of knowledge.