bluuebunny/crossref_metadata_2025_split huggingface dataset:
Current trends and future perspective of probiotic yeasts research in Indonesia
Authors: Astuti Rika Indri , Prastya Muhammad Eka , Wulan Rahayu , Anam Khairul , Meryandini Anja 
Published: March 2023

AbstractIndonesia is a mega biodiversity country with various local wisdom, including the enormous variety of fermented foods and beverages. Indonesian researchers have conducted an intensive study to understand the diversity of microbes on those fermented products, one of which shows probiotic properties. Compared to that lactic acid bacteria, the study on probiotic yeasts is less explored. Probiotic yeast isolates are commonly isolated from traditional Indonesian fermented products. Saccharomyces, Pichia, and Candida are among Indonesia’s most popular genera of probiotic yeasts, primarily applied in poultry and human health. The exploration of functional probiotic characteristics, such as antimicrobial, antifungal, antioxidant, and immunomodulator, has been widely reported from these local probiotic yeast strains. In vivo studies in a model organism such as mice conclude the prospective functional probiotic characteristics of the yeast isolates. Employment of current technology, such as omics, is essential in elucidating those functional properties. Advanced research and development of probiotic yeasts in Indonesia are gaining significant attention currently. For instance, probiotic yeasts-mediated fermentation in the production of kefir and kombucha are among the trend with promising economic value. The future trends of probiotic yeasts research in Indonesia are discussed in this review to give valuable sight into the application of indigenous probiotic yeasts in various fields.
From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes
Authors: Bradford Yvonne M , Van Slyke Ceri E , Howe Douglas G , Fashena David , Frazer Ken , Martin Ryan , Paddock Holly , Pich Christian , Ramachandran Sridhar , Ruzicka Leyla , Singer Amy , Taylor Ryan , Tseng Wei-Chia , Westerfield Monte 
Published: March 2023

Abstract
Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for genetic, genomic, and phenotypic data that result from research using D. rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity.
Relationship between normalized permeability and resistivity index in hydrate-bearing sediments: fractal model and numerical simulation
Authors: Tian Haitao , Liu Lele , Zhu Linqi , Ge Xinmin , Ding Pinbo , Cai Jianchao 
Published: March 2023

SUMMARYPermeability is a critical factor in evaluating the fluid flow capacity and production performance of natural gas hydrate reservoirs. The similarity of electrical conduction and hydraulic flow makes it possible to predict reservoir permeability using electrical data. Clarifying the relationship between the permeability and resistivity of sediments with different hydrate growth habits contributes to the efficient exploration and development of natural gas hydrate resources. In this work, normalized permeability and the resistivity index models for grain-coating (GC) and pore-filling (PF) hydrates are developed based on the fractal geometry theory, forming a new relationship between normalized permeability and resistivity index. The empirical exponent is determined by fractal dimension. Meanwhile, we selected five sets of 3-D computed tomography (CT) images of quartz sand with different particle sizes, GC and PF hydrate digital rocks are constructed using random simulation methods. The numerical simulation of permeability and resistivity index is carried out, based on the pore microstructure images, the box counting method was used to calculate the fractal dimension and analyse the relationship between pore space and transport paths. Furthermore, the pore radius, throat radius and pore connection number are extracted through the pore network method to study the evolution of pore space. The results show that the tortuosity fractal dimension is a critical parameter in the relationship between normalized permeability and resistivity index. The proposed analytical expressions are validated by laboratory and well log data, and the exponent ranges cover existing hydrate permeability–resistivity index data. The models provide the possibility to predict the normalized permeability of hydrate reservoirs based on electrical data alone.
Exploring food environment interventions for diet-related outcomes using a food sovereignty framework: a systematic review
Authors: Lofton Saria , Simonovich Shannon D , Buscemi Joanna , Grant Alexis , O’Donnell Alexander , Nwafor Gilliane , Reid Madeline 
Published: March 2023

SummaryBuilding local food systems through a food sovereignty lens, harnessing the right of people to control their own food systems, may enhance healthy food access and increase the consumption of fruits and vegetables in local communities. While research to date has described the outcomes of various multilevel, multicomponent food systems interventions, no known literature reviews to date have systematically examined food system interventions and dietary and health outcomes through the context of a food sovereignty lens. Utilization of a food sovereignty framework allows for the incorporation of key food systems and community-based concepts in the food environment literature. The purpose of this systematic review was to describe and summarize the efficacy of community-based local food system interventions, using the food sovereignty framework, for both pediatric and adult populations and their impact on health behaviors and physiological outcomes. We searched for peer-reviewed articles using Scopus, PubMed, PsychInfo and CINAHL databases and identified 11 articles that met the inclusion criteria for this study. Seven studies found that food systems interventions had a significant positive effect on improving health outcomes, three had null findings and one had null or negative results. Two studies utilized a community-based participatory approach. The most successful interventions involved community-based engagement involving multiple aspects of the food system and involving both children and adults for maximum impact. Our results inform how community-based food systems interventions can be guided by food sovereignty principles to improve health outcomes, such as body weight and fruit and vegetable intake, for both pediatric and adult populations.
The Quran and the Sword
Authors: Auriol Emmanuelle , Platteau Jean-Philippe , Verdier Thierry 
Published: March 2023

AbstractThis paper elucidates the willingness of an autocrat to push through institutional reforms in a context where traditional authorities represented by religious clerics are averse to them and where the military control the means of repression and can potentially stage a coup. We show that although the autocrat always wants to co-opt the military, this is not necessarily true of the clerics. Exclusive co-option of the military obtains where the loyalty of the autocrat’s army is strong while the organizational strength of religious movements is rather low. Radical institutional reforms can then be implemented. Empirically, the dominant regime in contemporary Muslim countries is the regime of double co-option where the autocrat resorts to a double-edged tactic: pleasing the official clerics by slowing the pace of reforms and ensuring the loyalty of the military so as to put down clerics-led rebellions.
A high-quality reference genome for the critically endangered Aeolian wall lizard, Podarcis raffonei
Authors: Gabrielli Maëva , Benazzo Andrea , Biello Roberto , Ancona Lorena , Fuselli Silvia , Iannucci Alessio , Balacco Jennifer , Mountcastle Jacqueline , Tracey Alan , Ficetola Gentile Francesco , Salvi Daniele , Sollitto Marco , Fedrigo Olivier , Formenti Giulio , Jarvis Erich D , Gerdol Marco , Ciofi Claudio , Trucchi Emiliano , Bertorelle Giorgio 
Published: March 2023

Abstract
The Aeolian wall lizard, Podarcis raffonei, is an endangered species endemic to the Aeolian archipelago, Italy, where it is present only in 3 tiny islets and a narrow promontory of a larger island. Because of the extremely limited area of occupancy, severe population fragmentation and observed decline, it has been classified as Critically Endangered by the International Union for the Conservation of Nature (IUCN). Using Pacific Biosciences (PacBio) High Fidelity (HiFi) long-read sequencing, Bionano optical mapping and Arima chromatin conformation capture sequencing (Hi-C), we produced a high-quality, chromosome-scale reference genome for the Aeolian wall lizard, including Z and W sexual chromosomes. The final assembly spans 1.51 Gb across 28 scaffolds with a contig N50 of 61.4 Mb, a scaffold N50 of 93.6 Mb, and a BUSCO completeness score of 97.3%. This genome constitutes a valuable resource for the species to guide potential conservation efforts and more generally for the squamate reptiles that are underrepresented in terms of available high-quality genomic resources.
Detection and estimation of the cosmic dipole with the einstein telescope and cosmic explorer
Authors: Mastrogiovanni S , Bonvin C , Cusin G , Foffa S 
Published: March 2023

ABSTRACTOne of the open issues of the standard cosmological model is the value of the cosmic dipole measured from the Cosmic Microwave Background (CMB), as well as from the number count of quasars and radio sources. These measurements are currently in tension, with the number count dipole being 2–5 times larger than expected from CMB measurements. This discrepancy has been pointed out as a possible indication that the cosmological principle is not valid. In this paper, we explore the possibility of detecting and estimating the cosmic dipole with gravitational waves (GWs) from compact binary mergers detected by the future next-generation detectors Einstein Telescope and Cosmic Explorer. We model the expected signal and show that for binary black holes, the dipole amplitude in the number count of detections is independent of the characteristics of the population and provides a systematic-free tool to estimate the observer velocity. We introduce techniques to detect the cosmic dipole from number counting of GW detections and estimate its significance. We show that a GW dipole consistent with the amplitude of the dipole in radio galaxies would be detectable with &gt;3σ significance with a few years of observation (106 GW detections) and estimated with a 16 per cent precision, while a GW dipole consistent with the CMB one would require at least 107 GW events for a confident detection. We also demonstrate that a total number Ntot of GW detections would be able to detect a dipole with amplitude $v_o/c \simeq 1/\sqrt{N_{\rm tot}}$.
Sarecycline inhibits protein translation inCutibacterium acnes70S ribosome using a two-site mechanism
Authors: Lomakin Ivan B , Devarkar Swapnil C , Patel Shivali , Grada Ayman , Bunick Christopher G 
Published: March 2023

AbstractAcne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.
SpliceTools, a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing
Authors: Flemington Erik K , Flemington Samuel A , O’Grady Tina M , Baddoo Melody , Nguyen Trang , Dong Yan , Ungerleider Nathan A 
Published: March 2023

Abstract
As a fundamental aspect of normal cell signaling and disease states, there is great interest in determining alternative splicing (AS) changes in physiologic, pathologic, and pharmacologic settings. High throughput RNA sequencing and specialized software to detect AS has greatly enhanced our ability to determine transcriptome-wide splicing changes. Despite the richness of this data, deriving meaning from sometimes thousands of AS events is a substantial bottleneck for most investigators. We present SpliceTools, a suite of data processing modules that arms investigators with the ability to quickly produce summary statistics, mechanistic insights, and functional significance of AS changes through command line or through an online user interface. Utilizing RNA-seq datasets for 186 RNA binding protein knockdowns, nonsense mediated RNA decay inhibition, and pharmacologic splicing inhibition, we illustrate the utility of SpliceTools to distinguish splicing disruption from regulated transcript isoform changes, we show the broad transcriptome footprint of the pharmacologic splicing inhibitor, indisulam, we illustrate the utility in uncovering mechanistic underpinnings of splicing inhibition, we identify predicted neo-epitopes in pharmacologic splicing inhibition, and we show the impact of splicing alterations induced by indisulam on cell cycle progression. Together, SpliceTools puts rapid and easy downstream analysis at the fingertips of any investigator studying AS.
Proximal binding of dCas9 at a DNA double strand break stimulates homology-directed repair as a local inhibitor of classical non-homologous end joining
Authors: Feng Yi-Li , Liu Si-Cheng , Chen Ruo-Dan , Sun Xiu-Na , Xiao Jing-Jing , Xiang Ji-Feng , Xie An-Yong 
Published: March 2023

AbstractIn CRISPR/Cas9 genome editing, the tight and persistent target binding of Cas9 provides an opportunity for efficient genetic and epigenetic modification on genome. In particular, technologies based on catalytically dead Cas9 (dCas9) have been developed to enable genomic regulation and live imaging in a site-specific manner. While post-cleavage target residence of CRISPR/Cas9 could alter the pathway choice in repair of Cas9-induced DNA double strand breaks (DSBs), it is possible that dCas9 residing adjacent to a break may also determine the repair pathway for this DSB, providing an opportunity to control genome editing. Here, we found that loading dCas9 onto a DSB-adjacent site stimulated homology-directed repair (HDR) of this DSB by locally blocking recruitment of classical non-homologous end-joining (c-NHEJ) factors and suppressing c-NHEJ in mammalian cells. We further repurposed dCas9 proximal binding to increase HDR-mediated CRISPR genome editing by up to 4-fold while avoiding exacerbation of off-target effects. This dCas9-based local inhibitor provided a novel strategy of c-NHEJ inhibition in CRISPR genome editing in place of small molecule c-NHEJ inhibitors, which are often used to increase HDR-mediated genome editing but undesirably exacerbate off-target effects.
Variable Landscape of PD-L1 Expression in Breast Carcinoma as Detected by the DAKO 22C3 Immunohistochemistry Assay
Authors: Danziger Natalie , Sokol Ethan S , Graf Ryon P , Hiemenz Matthew C , Maule Jake , Parimi Vamsi , Palmieri Carlo , Pusztai Lajos , Ross Jeffrey S , Huang Richard S P 
Published: March 2023

AbstractBackgroundIn 2020, pembrolizumab was approved as a therapy for triple-negative breast cancer (TNBC) with the companion diagnostic DAKO 22C3 programmed death ligand-1 (PD-L1) immunohistochemistry assay. The study aimed to determine the landscape of PD-L1 expression as detected by the DAKO 22C3 PD-L1 assay in breast cancer subtypes and compare the clinicopathologic and genomic characteristics of PD-L1 positive and negative TNBC.MethodsPD-L1 expression using the DAKO 22C3 antibody was scored using a combined positive score (CPS) and positive status was defined as CPS ≥10. Comprehensive genomic profiling was performed using the FoundationOne CDx assay.ResultsOf the 396 BC patients stained with DAKO 22C3, the majority were HR+/HER2− and TNBC (42% and 36%, respectively). Median PD-L1 expression and frequency of CPS ≥10 was highest in TNBC cases (median: 7.5, 50% CPS ≥10) and lowest in the HR+/HER2− group (median: 1.0, 15.5% CPS ≥10) (P &lt; .0001). A comparison of PD-L1 positive and PD-L1 negative TNBC demonstrated no significant differences in clinicopathologic or genomic characteristics. TNBC tissue samples from the breast did have an observed enrichment for PD-L1 positivity compared to TNBC tissue samples from a metastatic site (57% vs. 44%), but this was not statistically significant (P = .1766). In the HR+/HER2− group, genomic alterations in TP53, CREBBP, and CCNE1 were more prevalent and genomic loss of heterozygosity was higher in the PD-L1(+) group compared to the PD-L1(−) group.ConclusionsThe subtypes of breast cancer have distinct patterns of PD-L1 expression, supporting that further research of immunotherapies may include specific evaluation of optimum cutoffs for non-TNBC patients. In TNBC, PD-L1 positivity is not associated with other clinicopathologic or genomic features and should be integrated into future studies of immunotherapy efficacy.
Pion–nucleon sigma term σπNand deeply bound pionic atoms
Authors: Ikeno Natsumi , Nishi Takahiro , Itahashi Kenta , Nose-Togawa Naoko , Tani Akari , Hirenzaki Satoru 
Published: March 2023

AbstractWe investigate the possibility of determining the value of the pion–nucleon sigma term σπN precisely by the experimental observables of deeply bound pionic atoms. We discuss the sensitivity of the observables to σπN and take into account the typical errors of up-to-date experiments on deeply bound pionic atoms. We find that the gap in the binding energies and the width of the deeply bound pionic states are good observables for σπN value determination with experimental data. We also discuss the expected difficulties for the accurate determination of the value of σπN due to the correlation between the σ term and the potential parameter in the pion–nucleus optical potential.
A randomized, double-blind, placebo-controlled, parallel group study on the effects of a cathepsin S inhibitor in primary Sjögren’s syndrome
Authors: Bentley Darren , Fisher Benjamin A , Barone Francesca , Kolb Fabrice A , Attley Gemma 
Published: March 2023

Abstract

Objectives
Primary SS (pSS) is a chronic autoimmune disorder characterized by mucosal dryness and systemic symptoms. We tested the effects of inhibition of cathepsin S using the potent and selective inhibitor RO5459072 on disease activity and symptoms of pSS.

Methods
This was a randomized, double-blind, placebo-controlled, parallel-group, Phase IIA study to investigate the effects of RO5459072 (100 mg twice daily; 200 mg per day). Seventy-five patients with pSS were randomized 1:1 to receive either RO5459072 or placebo for 12 weeks. The primary outcome was the proportion of patients with a ≥3 point reduction from baseline in EULAR SS Disease Activity Index (ESSDAI) score. We also investigated the effects of RO5459072 on quality of life, exocrine gland function, biomarkers related to SS, and safety and tolerability.

Results
The proportion of patients showing an improvement in ESSDAI score was not significantly different between the RO5459072 and placebo arms. No clinically meaningful treatment effects were observed in favour of RO5459072 for all secondary outcomes. Analysis of soluble biomarkers indicated target engagement between RO5459072 and cathepsin S. There were modest decreases in the number of circulating B cells and T cells in the RO5459072 group, although these did not reach significance. RO5459072 was safe and well-tolerated.

Conclusions
There was no clinically relevant improvement in ESSDAI score (primary endpoint), and no apparent benefit in favour of RO5459072 in any of the secondary clinical endpoints. Further work is needed in order to understand the mechanisms of MHC-II-mediated immune stimulation in pSS.

Trial registration
ClinicalTrials.gov; NCT02701985.
“Spin” among abstracts of randomized controlled trials in sleep medicine: a research-on-research study
Authors: Guo Feiyang , Zhao Tingting , Zhai Qianglan , Fang Xiaolin , Yue Haoze , Hua Fang , He Hong 
Published: March 2023

Abstract

Study Objectives
“Spin,” using reporting strategies to distort study results, can mislead readers of medical research. This study aimed to evaluate the prevalence and characteristics of “spin” among randomized controlled trial (RCT) abstracts published in sleep medicine journals, and to identify factors associated with its presence and severity.

Methods
The search for RCTs published between 2010 and 2020 were conducted in seven reputable journals of sleep medicine. Abstracts of RCTs with statistically nonsignificant primary outcomes were included and analyzed for “spin,” according to predetermined “spin” strategies. Chi-square tests or logistic regression analyses were performed to detect the association between characteristics of included abstracts and the presence and severity of “spin.”

Results
A total of 114 RCT abstracts were included in this study, of which 89 (78.1%) were identified as having at least one type of “spin” strategy. Sixty-six abstracts (57.9%) had “spin” in the Results section, 82 (71.9%) abstracts presented with “spin” in the Conclusions section. The presence of “spin” varied significantly among RCTs based on the different categories of research area (p = 0.047) and the statistician involvement (p = 0.045). Furthermore, research area (p = 0.019) and funding status (p = 0.033) were significant factors associated with the severity of “spin.”

Conclusions
The prevalence of “spin” is high among RCT abstracts in sleep medicine. This raises the need for researchers, editors, and other stakeholders to be aware of the issue of “spin” and make joint efforts to eliminate it in future publications.