bluuebunny/crossref_metadata_2025_split huggingface dataset:
Matrix Extension of the CompactDry™ “Nissui” YMR for Enumeration of Yeasts and Molds in Dried Cannabis Flower: AOAC Performance Tested MethodSM 092002
Authors: Hamilton Lauren , Klavins Anna , Malherbe Rianna , Youngblood Jessa , Ito Yusuke , Hsiung Andre 
Published: May 2022

Abstract

Background
CompactDry™ Yeast/Mold Rapid (YMR) is a ready-to-use dry media sheet using a chromogenic medium with selective agents for the enumeration of yeasts and molds in a variety of food products after incubation at 25 ± 1°C for 3 days. The method is certified as AOAC Performance Tested MethodSM 092002.

Objective
The CompactDry YMR method was validated for a matrix extension to cannabis flower through the AOAC Emergency Response Validation process.

Methods
The performance of the CompactDry YMR was compared to Dichloran Rose Bengal Chloramphenicol (DRBC) agar for the enumeration of yeasts and molds in cannabis flower. Matrix data were normalized by log10 transformation, and performance indicators included repeatability, difference of means (DOM), and inclusivity/exclusivity.

Results
The results demonstrated that the CompactDry YMR method is equivalent to the DRBC agar method at 72 h of incubation. In the independent laboratory validation study, there was no significant difference in detection, enumeration, or repeatability between the CompactDry YMR method and DRBC agar at 72 h. Eighteen inclusivity and 16 exclusivity strains specific to cannabis plant materials that were not evaluated in the original CompactDry YMR method validation were tested in this study. All inclusivity organisms produced typical colonies on the CompactDry YMR. The two exclusivity bacterial strains that showed growth on CompactDry YMR at 72 h were inoculated at a high concentration.

Conclusions
CompactDry YMR is equivalent in performance to traditional culture media detection methods of yeasts and molds.

Highlights
CompactDry YMR will streamline dried cannabis flower testing.
A Rationale for Safe Ventilation With Inhalation Injury: An Editorial Review
Authors: Dries David J , Tawfik Pierre N 
Published: May 2022

Abstract
Lung injury from smoke inhalation manifests as airway and parenchymal damage, at times leading to the acute respiratory distress syndrome. From the beginning of this millennium, the approach to mechanical ventilation in the patient with acute respiratory distress syndrome was based on reduction of tidal volume to 6 ml/kg of ideal body weight, maintaining a ceiling of plateau pressure, and titration of driving pressure (plateau pressure minus PEEP). Beyond these broad constraints, there is little specification for the mechanics of ventilator settings, consideration of the metabolic impact of the disease process on the patient, or interaction of patient disease and ventilator settings. Various studies suggest that inhomogeneity of lung injury, which increases the risk of regional lung trauma from mechanical ventilation, may be found in the patient with smoke inhalation. We now appreciate that energy transfer principles may affect optimal ventilator management and come into play in damaged heterogenous lungs. Mechanical ventilation in the patient with inhalation injury should consider various factors. Self-injurious respiratory demand by the patient can be reduced using analgesia and sedation. Dynamic factors beginning with rate management can reduce the incidence of potentially damaging ventilation. Moreover, preclinical study is underway to examine the flow of gas based on the ventilator mode selected, which may also be a factor triggering regional lung injury.
Myofibroblastoma of the Breast: Diagnosis, Pathology, and Management
Authors: Zamora Kathryn W , Talley Rachel , Hermecz Brittany N , Wei Shi 
Published: May 2022

Abstract
Myofibroblastomas are rare benign spindle cell tumors that occur within both male and female breasts. They are composed of fibroblasts and myofibroblasts and are not associated with malignant potential. On mammographic and sonographic imaging, these tumors may present as oval circumscribed masses that overlap with the appearance of many benign entities, including fibroadenomas. Occasionally, the tumors may demonstrate interval growth or mimic imaging features of malignancy and require biopsy. Correct pathologic diagnosis is important because many morphologic variants exist, which complicates pathologic interpretation. The purpose of this article is to review the range of imaging manifestations and histopathological findings and to discuss current management.
Development and validation of a nomogram for prognosis of sinonasal adenocarcinoma (a nomogram for sinonasal adenocarcinoma)
Authors: Huang Hesen , Chen Kaiqin , Deng Lifeng , Chen Yaling , Zhao Dean , Lin Wei 
Published: May 2022

Abstract

Background
The incidence of sinonasal adenocarcinoma is low, and there are few studies on survival and prognosis. Therefore, we aim to develop and validate a prognostic model for predicting the overall survival of sinonasal adenocarcinoma and provide guidance for clinical management.

Methods
Patients who were diagnosed as sinonasal adenocarcinoma through Surveillance, Epidemiology, and End Results database between 1975 and 2015 were randomly divided into a training group and validation group. Univariate, multivariate survival analysis was performed to screen independent survival factors. A nomogram was established to predict the overall survival rate of sinonasal adenocarcinoma. Receiver operating characteristic curve and calibration plot were performed to verify the discrimination and accuracy of the model. A decision curve analysis was performed to verify the clinical applicability of the model.

Results
A total of 423 patients with sinonasal adenocarcinoma were randomly divided into training group (n = 299) and verification group (n = 124). We established and verified the Nomo map including age, marriage, grade, surgery and tumour size. The c-index of Surveillance, Epidemiology, and End Results stage, T stage and this model are 0.635, 0.626 and 0.803, respectively. The survival rate of the high-risk group scored by this model was lower than that of the low-risk group (P &lt; 0.001). Decision curve analysis shows that the model has advantages in predicting survival rates.

Conclusion
Our model is considered to be a useful tool for predicting the overall survival of sinonasal adenocarcinoma, with good discrimination and clinical applicability. We hope that this model will help rhinologists to make clinical decisions and manage patients diagnosed with sinonasal adenocarcinoma.
Big Fish in Small (and Big) Ponds: A Study of Careers
Authors: DeVaro Jed , Gürtler Oliver , Gürtler Marc , Deutscher Christian 
Published: May 2022

Abstract
Talented, ambitious workers (big fish) often join highly competitive organizations (big ponds), though they sometimes instead choose less competitive organizations (small ponds) offering brighter promotion prospects. Big fish exist in both types of organizations, though average worker ability is higher in big ponds. Top executives enjoy higher wages in big ponds. Choosing a big pond allows workers to signal high ability. Workers sometimes overestimate or underestimate their abilities, choosing the wrong pond. Big ponds tend to be larger in total employment. All of the preceding phenomena are shown to be consistent with equilibrium in a new theoretical model of careers. (JEL J24, M53)
How to set up and run a multi-centre trainee-led collaborative project
Authors: Nasser Ahmed A H , Archer James E , Chauhan Govind Singh , Thompson Calum , Osman Khabab , Nandra Rajpal , Dewan Varun 
Published: May 2022

Abstract
The multi-centre trainee-led collaborative research model improves the generalizability of results, efficiency of data collection, quality of data and sample size. Although an enormous amount of effort and resources are sometimes required, the final results lead to a standard that is unachievable by conventional studies. In this article, we summarize a step-by-step guide on how to set up and run a multi-centre trainee-led collaborative project.
Arabidopsis ETHYLENE INSENSITIVE 3 directly regulates the expression of PG1β-like family genes in response to aluminum stress
Authors: Jin Jing , Essemine Jemaa , Xu Zhan , Duan Jianli , Shan Chi , Mei Zhiling , Zhu Jian , Cai Weiming 
Published: May 2022

Abstract
The genes in the subfamily PG1β (beta subunit of poly-galacturonase isoenzyme 1) have a clear effect on the biosynthesis pathway of pectin, a main component of the cell wall. However, the detailed functions of the PG1β-like gene members in Arabidopsis (AtPG1–3) have not yet been determined. In this study, we investigated their functional roles in response to aluminum (Al) stress. Our results indicate that the PG1β-like gene members are indeed involved in the Al-stress response and they can modulate its accumulation in roots to achieve optimum root elongation and hence better seedling growth. We found that transcription factor EIN3 (ETHYLENE INSENSITIVE 3) alters pectin metabolism and the EIN3 gene responds to Al stress to affect the pectin content in the root cell walls, leading to exacerbation of the inhibition of root growth, as reflected by the phenotypes of overexpressing lines. We determined that EIN3 can directly bind to the promoter regions of PG1–3, which act downstream of EIN3. Thus, our results show that EIN3 responds to Al stress in Arabidopsis directly through regulating the expression of PG1–3. Hence, EIN3 mediates their functions by acting as a biomarker in their molecular biosynthesis pathways, and consequently orchestrates their biological network in response to Al stress.
A scoping review of bryophyte microbiota: diverse microbial communities in small plant packages
Authors: Chen Ko-Hsuan , Nelson Jessica 
Published: May 2022

AbstractPlant health depends not only on the condition of the plant itself but also on its diverse community of microbes, or microbiota. Just like the better-studied angiosperms, bryophytes (mosses, liverworts, and hornworts) harbor diverse communities of bacteria, archaea, fungi, and other microbial eukaryotes. Bryophytes are increasingly recognized as important model systems for understanding plant evolution, development, physiology, and symbiotic interactions. Much of the work on bryophyte microbiota in the past focused on specific symbiont types for each bryophyte group, but more recent studies are taking a broader view acknowledging the coexistence of diverse microbial communities in bryophytes. Therefore, this review integrates studies of bryophyte microbes from both perspectives to provide a holistic view of the existing research for each bryophyte group and on key themes. The systematic search also reveals the taxonomic and geographic biases in this field, including a severe under-representation of the tropics, very few studies on viruses or eukaryotic microbes beyond fungi, and a focus on mycorrhizal fungi studies in liverworts. Such gaps may have led to errors in conclusions about evolutionary patterns in symbiosis. This analysis points to a wealth of future research directions that promise to reveal how the distinct life cycles and physiology of bryophytes interact with their microbiota.
Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea reproductive phenology
Authors: Li Yongle , Lake Lachlan , Chauhan Yashvir S , Taylor Julian , Sadras Victor O 
Published: May 2022

AbstractWater deficit often hastens flowering of pulses partially because droughted plants are hotter. Separating temperature-independent and temperature-dependent effects of drought is important to understand, model, and manipulate phenology. We define a new trait, drought effect on phenology (DEP), as the difference in flowering time between irrigated and rainfed crops, and use FST genome scanning to probe for genomic regions under selection for this trait in chickpea (Cicer arietinum). Owing to the negligible variation in daylength in our dataset, variation in phenology with sowing date was attributed to temperature and water; hence, genomic regions overlapping for early- and late-sown crops would associate with temperature-independent effects and non-overlapping genomic regions would associate with temperature-dependent effects. Thermal-time to flowering was shortened with increasing water stress, as quantified with carbon isotope composition. Genomic regions on chromosomes 4–8 were under selection for DEP. An overlapping region for early and late sowing on chromosome 8 revealed a temperature-independent effect with four candidate genes: BAM1, BAM2, HSL2, and ANT. The non-overlapping regions included six candidate genes: EMF1, EMF2, BRC1/TCP18, BZR1, NPGR1, and ERF1. Modelling showed that DEP reduces the likelihood of drought and heat stress at the expense of increased likelihood of cold stress. Accounting for DEP would improve genetic and phenotypic models of phenology.
Melatonin biosynthesis and signal transduction in plants in response to environmental conditions
Authors: Liu Gaofeng , Hu Qian , Zhang Xin , Jiang Jiafu , Zhang Yang , Zhang Zixin 
Published: May 2022

Abstract
Melatonin, the most widely distributed hormone in nature, plays important roles in plants. Many physiological processes in plants are linked to melatonin, including seed germination, anisotropic cell growth, and senescence. Compared with animals, different plants possess diverse melatonin biosynthetic pathways and regulatory networks. Whereas melatonin biosynthesis in animals is known to be regulated by ambient signals, little is known about how melatonin biosynthesis in plants responds to environmental signals. Plants are affected by numerous environmental factors, such as light, temperature, moisture, carbon dioxide, soil conditions, and nutrient availability at all stages of development and in different tissues. Melatonin content exhibits dynamic changes that affect plant growth and development. Melatonin plays various species-specific roles in plant responses to different environmental conditions. However, much remains to be learned, as not all environmental factors have been studied, and little is known about the mechanisms by which these factors influence melatonin biosynthesis. In this review, we provide a detailed, systematic description of melatonin biosynthesis and signaling and of the roles of melatonin in plant responses to different environmental factors, providing a reference for in-depth research on this important issue.
ABSCISIC ACID INSENSITIVE 5 mediates light–ABA/gibberellin crosstalk networks during seed germination
Authors: Li Zenglin , Luo Xiaofeng , Wang Lei , Shu Kai 
Published: May 2022

AbstractAppropriate timing of seed germination is crucial for plant survival and has important implications for agricultural production. Timely germination relies on harmonious interactions between endogenous developmental signals, especially abscisic acid (ABA) and gibberellins (GAs), and environmental cues such as light. Recently, a series of investigations of a three-way crosstalk between phytochromes, ABA, and GAs in the regulation of seed germination demonstrated that the transcription factor ABSCISIC ACID INSENSITIVE 5 (ABI5) is a central mediator in the light–ABA/GA cascades. Here, we review current knowledge of ABI5 as a key player in light-, ABA-, and GA-signaling pathways that precisely control seed germination. We highlight recent advances in ABI5-related studies, focusing on the regulation of seed germination, which is strictly controlled at both the transcriptional and the protein levels by numerous light-regulated factors. We further discuss the components of ABA and GA signaling pathways that could regulate ABI5 during seed germination, including transcription factors, E3 ligases, protein kinases, and phosphatases. The precise molecular mechanisms by which ABI5 mediates ABA–GA antagonistic crosstalk during seed germination are also discussed. Finally, some potential research hotspots underlying ABI5-mediated seed germination regulatory networks are proposed.
A mechanistic target of rapamycin inhibitor, everolimus safely ameliorated lupus nephritis in a patient complicated with tuberous sclerosis
Authors: Okita Yasutaka , Yoshimura Maiko , Katada Yoshinori , Saeki Yukihiko , Ohshima Shiro 
Published: May 2022

ABSTRACT
A 26-year-old woman with tuberous sclerosis complex (TSC) received outpatient treatment for the complication of systemic lupus erythematosus (SLE) at our hospital. She visited our hospital with a chief complaint of pitting oedema in bilateral lower legs for 3 days. The urinalysis showed massive proteinuria with a lot of white blood cell casts. The blood tests revealed hypoalbuminaemia, hypercholesterolaemia, hypocomplementaemia, and elevated anti-double-stranded DNA antibody titre. Renal biopsy was not performed because of multiple renal angiomyolipomas, which was one of the features of TSC. She was diagnosed with a nephrotic state due to lupus nephritis. Although she had a standard therapy with high-dose corticosteroid and mycophenolate mofetil and tacrolimus, complete remission had not been achieved leading to a steroid-dependent nephrotic syndrome. During the follow-up, the angiomyolipomas became larger and had a risk of rupture at the age of 29 years. Everolimus, a mechanistic target of rapamycin (mTOR) inhibitor, was started for the treatment of angiomyolipomas, and mycophenolate mofetil and tacrolimus were terminated instead. The activity of lupus nephritis was surprisingly ameliorated, and the amount of corticosteroid successfully tapered. Everolimus has been continued for 6 years without severe side effects. Accumulating evidence suggests that the activated mTOR pathway plays a key role in the pathogenesis of SLE. We reported the long-term efficacy and safety of everolimus for refractory SLE in a patient with TSC for the first time. This case suggests that everolimus can be a promising option for the treatment of lupus nephritis.
BioTransformer 3.0—a web server for accurately predicting metabolic transformation products
Authors: Wishart David S , Tian Siyang , Allen Dana , Oler Eponine , Peters Harrison , Lui Vicki W , Gautam Vasuk , Djoumbou-Feunang Yannick , Greiner Russell , Metz Thomas O 
Published: May 2022

Abstract
BioTransformer 3.0 (https://biotransformer.ca) is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. It combines machine learning approaches with a rule-based system to predict small-molecule metabolism in human tissues, the human gut as well as the external environment (soil and water microbiota). Simply stated, BioTransformer takes a molecular structure as input (SMILES or SDF) and outputs an interactively sortable table of the predicted metabolites or transformation products (SMILES, PNG images) along with the enzymes that are predicted to be responsible for those reactions and richly annotated downloadable files (CSV and JSON). The entire process typically takes less than a minute. Previous versions of BioTransformer focused exclusively on predicting the metabolism of xenobiotics (such as plant natural products, drugs, cosmetics and other synthetic compounds) using a limited number of pre-defined steps and somewhat limited rule-based methods. BioTransformer 3.0 uses much more sophisticated methods and incorporates new databases, new constraints and new prediction modules to not only more accurately predict the metabolic transformation products of exogenous xenobiotics but also the transformation products of endogenous metabolites, such as amino acids, peptides, carbohydrates, organic acids, and lipids. BioTransformer 3.0 can also support customized sequential combinations of these transformations along with multiple iterations to simulate multi-step human biotransformation events. Performance tests indicate that BioTransformer 3.0 is 40–50% more accurate, far less prone to combinatorial ‘explosions’ and much more comprehensive in terms of metabolite coverage/capabilities than previous versions of BioTransformer.
GNAT toxins evolve toward narrow tRNA target specificities
Authors: Bikmetov Dmitry , Hall Alexander M J , Livenskyi Alexei , Gollan Bridget , Ovchinnikov Stepan , Gilep Konstantin , Kim Jenny Y , Larrouy-Maumus Gerald , Zgoda Viktor , Borukhov Sergei , Severinov Konstantin , Helaine Sophie , Dubiley Svetlana 
Published: May 2022

Abstract
Type II toxin–antitoxin (TA) systems are two-gene modules widely distributed among prokaryotes. GNAT toxins associated with the DUF1778 antitoxins represent a large family of type II TAs. GNAT toxins inhibit cell growth by disrupting translation via acetylation of aminoacyl-tRNAs. In this work, we explored the evolutionary trajectory of GNAT toxins. Using LC/MS detection of acetylated aminoacyl-tRNAs combined with ribosome profiling, we systematically investigated the in vivo substrate specificity of an array of diverse GNAT toxins. Our functional data show that the majority of GNAT toxins are specific to Gly-tRNA isoacceptors. However, the phylogenetic analysis shows that the ancestor of GNAT toxins was likely a relaxed specificity enzyme capable of acetylating multiple elongator tRNAs. Together, our data provide a remarkable snapshot of the evolution of substrate specificity.
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective
Authors: Botas Jorge , Rodríguez del Río Álvaro , Giner-Lamia Joaquín , Huerta-Cepas Jaime 
Published: May 2022

Abstract
Synteny conservation analysis is a well-established methodology to investigate the potential functional role of unknown prokaryotic genes. However, bioinformatic tools to reconstruct and visualise genomic contexts usually depend on slow computations, are restricted to narrow taxonomic ranges, and/or do not allow for the functional and interactive exploration of neighbouring genes across different species. Here, we present GeCoViz, an online resource built upon 12 221 reference prokaryotic genomes that provides fast and interactive visualisation of custom genomic regions anchored by any target gene, which can be sought by either name, orthologous group (KEGGs, eggNOGs), protein domain (PFAM) or sequence. To facilitate functional and evolutionary interpretation, GeCoViz allows to customise the taxonomic scope of each analysis and provides comprehensive annotations of the neighbouring genes. Interactive visualisation options include, among others, the scaled representations of gene lengths and genomic distances, and on the fly calculation of synteny conservation of neighbouring genes, which can be highlighted based on custom thresholds. The resulting plots can be downloaded as high-quality images for publishing purposes. Overall, GeCoViz offers an easy-to-use, comprehensive, fast and interactive web-based tool for investigating the genomic context of prokaryotic genes, and is freely available at https://gecoviz.cgmlab.org