bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstructing the Hubble diagram of gamma-ray bursts using deep learning
Authors: Tang Li , Lin Hai-Nan , Li Xin , Liu Liang 
Published: October 2021

ABSTRACT
We calibrate the distance and reconstruct the Hubble diagram of gamma-ray bursts (GRBs) using deep learning. We construct an artificial neural network, which combines the recurrent neural network and Bayesian neural network, and train the network using the Pantheon compilation of Type-Ia supernovae. The trained network is used to calibrate the distance of 174 GRBs based on the Combo-relation. We verify that there is no evident redshift evolution of Combo-relation, and obtain the slope and intercept parameters, $\gamma =0.856^{+0.083}_{-0.078}$ and $\log A=49.661^{+0.199}_{-0.217}$, with an intrinsic scatter $\sigma _{\rm int}=0.228^{+0.041}_{-0.040}$. Our calibrating method is independent of cosmological model, thus the calibrated GRBs can be directly used to constrain cosmological parameters. It is shown that GRBs alone can tightly constrain the ΛCDM model, with $\Omega _{\rm M}=0.280^{+0.049}_{-0.057}$. However, the constraint on the ωCDM model is relatively looser, with $\Omega _{\rm M}=0.345^{+0.059}_{-0.060}$ and ω &lt; −1.414. The combination of GRBs and Pantheon can tightly constrain the ωCDM model, with $\Omega _{\rm M}=0.336^{+0.055}_{-0.050}$ and $\omega =-1.141^{+0.156}_{-0.135}$.
Evolutionary Implications of the RNA N6-Methyladenosine Methylome in Plants
Authors: Miao Zhenyan , Zhang Ting , Xie Bin , Qi Yuhong , Ma Chuang 
Published: October 2021

Abstract
Epigenetic modifications play important roles in genome evolution and innovation. However, most analyses have focused on the evolutionary role of DNA modifications, and little is understood about the influence of posttranscriptional RNA modifications on genome evolution. To explore the evolutionary significance of RNA modifications, we generated transcriptome-wide profiles of N6-methyladenosine (m6A), the most prevalent internal modification of mRNA, for 13 representative plant species spanning over half a billion years of evolution. These data reveal the evolutionary conservation and divergence of m6A methylomes in plants, uncover the preference of m6A modifications on ancient orthologous genes, and demonstrate less m6A divergence between orthologous gene pairs with earlier evolutionary origins. Further investigation revealed that the evolutionary divergence of m6A modifications is related to sequence variation between homologs from whole-genome duplication and gene family expansion from local-genome duplication. Unexpectedly, a significant negative correlation was found between the retention ratio of m6A modifications and the number of family members. Moreover, the divergence of m6A modifications is accompanied by variation in the expression level and translation efficiency of duplicated genes from whole- and local-genome duplication. Our work reveals new insights into evolutionary patterns of m6A methylomes in plant species and their implications, and provides a resource of plant m6A profiles for further studies of m6A regulation and function in an evolutionary context.
RPS: a comprehensive database of RNAs involved in liquid–liquid phase separation
Authors: Liu Mengni , Li Huiqin , Luo Xiaotong , Cai Jieyi , Chen Tianjian , Xie Yubin , Ren Jian , Zuo Zhixiang 
Published: October 2021

Abstract
Liquid–liquid phase separation (LLPS) is critical for assembling membraneless organelles (MLOs) such as nucleoli, P-bodies, and stress granules, which are involved in various physiological processes and pathological conditions. While the critical role of RNA in the formation and the maintenance of MLOs is increasingly appreciated, there is still a lack of specific resources for LLPS-related RNAs. Here, we presented RPS (http://rps.renlab.org), a comprehensive database of LLPS-related RNAs in 20 distinct biomolecular condensates from eukaryotes and viruses. Currently, RPS contains 21,613 LLPS-related RNAs with three different evidence types, including ‘Reviewed’, ‘High-throughput’ and ‘Predicted’. RPS provides extensive annotations of LLPS-associated RNA properties, including sequence features, RNA structures, RNA–protein/RNA–RNA interactions, and RNA modifications. Moreover, RPS also provides comprehensive disease annotations to help users to explore the relationship between LLPS and disease. The user-friendly web interface of RPS allows users to access the data efficiently. In summary, we believe that RPS will serve as a valuable platform to study the role of RNA in LLPS and further improve our understanding of the biological functions of LLPS.
Cigarette Pack Price and Its Within-Person Association With Smoking Initiation, Smoking Progression, and Disparities among Young Adults
Authors: Parks Michael J , Patrick Megan E , Levy David T , Thrasher James F , Elliott Michael R , Fleischer Nancy L 
Published: October 2021

Abstract

Background
There is a dearth of research on within-person relationships between tobacco price and cigarette smoking initiation and progression in young adulthood. This project examines the within-person association between cigarette pack price and smoking initiation and progression between age 18 and 21/22, focusing on differences across subgroups.

Methods
Data came from the longitudinal Monitoring the Future (MTF) project. MTF examines drug use behaviors with nationally representative samples of 12th graders annually. Subsamples of 12th graders are annually selected and followed longitudinally. Among 12th graders from baseline years 2000–2014, we examined past 30-day cigarette smoking initiation among baseline never smokers (N = 15 280) and progression to daily smoking among youth who were not daily smokers at baseline (N = 26 998). We used hierarchical logistic regression and interaction terms to assess differences across sex, race/ethnicity, and parental education.

Results
The within-person relationship between pack price and smoking indicated that a one-dollar increase in pack price corresponded with a 72% decrease in the odds of initiation (AOR = 0.28, 95% CI = 0.18, 0.44) and 70% decrease in the odds of progression to daily smoking (AOR = 0.30, 95% CI = 0.21, 0.44). There was a linear age trend for both smoking initiation and progression. There were no statistically significant interactions between price and demographics, making it difficult to disentangle differences across subgroups.

Conclusions
Exposure to increased cigarette prices during young adulthood was associated with lower odds of cigarette smoking initiation and progression. Additional policies and programs beyond cigarettes prices could help reduce tobacco-related disparities in smoking initiation and progression among young adults.

Implications
There is a strong, within-person relationship between cigarette prices and smoking initiation and progression during the transition to young adulthood: higher prices are associated with decreased odds of both initiation and progression. Cigarette taxation can help to prevent smoking initiation and progression among youth, but it is less clear how taxes are associated with disparities in smoking experienced by certain subgroups. We could not draw definitive conclusions about the impact of cigarette prices on tobacco-related disparities. Tobacco taxes should be increased on a regular basis to ensure young adults experience within-person increases in prices, and complementary programs geared toward reducing tobacco-related disparities among young adults should be promoted.
Osteoarticular Infections Caused by Erysipelothrix rhusiopathiae: Case Report and Literature Review
Authors: Maillard Alexis , Wakim Yara , Itani Oula , Ousser Fateh , Bleibtreu Alexandre , Caumes Eric , Monsel Gentiane 
Published: October 2021

Abstract
We present a case of Erysipelothrix rhusiopathiae spondylodiscitis in an otherwise healthy man, occurring 1 year after exposure. The patient was cured after 6 weeks of treatment with amoxicillin followed by ciprofloxacin without surgery. Erysipelothrix rhusiopathiae can cause severe osteoarticular infections with a delayed presentation following exposure to the pathogen.
Candida Endophthalmitis Treated Successfully With Isavuconazole: A Case Report
Authors: Sng Edwin Chong Yu , Tan Ai Ling , Zhou Peijun Yvonne , Tan Tira J , Waduthantri Samanthila , Chee Soon-Phaik , Tan Ban Hock 
Published: October 2021

Abstract
Candida endophthalmitis is a serious complication of candidemia. Diagnosis requires identification of ocular lesions on dilated fundoscopy, aided by isolation of the organism from blood and/or vitreous humor. However, the initial ophthalmological examination may be negative in some cases. Experience with isavuconazole for the treatment of Candida endophthalmitis is limited. We present a case of a 65-year-old woman with metastatic breast cancer on chemotherapy who developed Candida dubliniensis endophthalmitis with initial negative ophthalmological examination. She was treated with vitrectomy and 6 weeks of oral fluconazole. Despite vitrectomy and culture-directed antifungal treatment, management was complicated by lack of response to fluconazole and intolerance to other antifungals, necessitating the use of isavuconazole, which proved efficacious.
Augmented Reality Assisted Endoscopic Transforaminal Lumbar Interbody Fusion: 2-Dimensional Operative Video
Authors: Jamshidi Aria M , Makler Vyacheslav , Wang Michael Y 
Published: October 2021

Abstract
Augmented reality (AR) is a novel technology for spine navigation. This tracking camera-integrated head-mounted display (HMD) represents a novel stereotactic computer navigation modality that has demonstrated excellent precision and accuracy with spinal instrumentation.
1
Standard computer-assisted spine navigation systems have two major shortcomings: attention shift and line-of-sight limitations. The HMD allows visualization of the surgical field and navigation data concurrently in the same field of view.
2,3
However, the use of AR in spine surgery has been limited to use for instrumentation, not for endoscopy.
Fully endoscopic transforaminal interbody fusion under conscious sedation is an effective treatment option for degenerative spondylolisthesis and spinal stenosis. Although this technique has a steep learning curve, the advantages are vast, including preservation of normal tissue, smaller incisional requirement, and reduced postoperative pain, all enabling rapid recovery after surgery. As with other endoscopic spine surgeries, this procedure has a steep learning curve and requires a robust understanding of foraminal anatomy in order to safely access the disc space.
4,5
However, with the introduction of AR, the safety and precision of this procedure could be greatly improved upon.
In this video, we present a case of a 60-yr-old female who presented with a grade 1 spondylolisthesis and severe spinal stenosis and was treated with an L4-L5 interbody fusion. All instrumentation steps and localization for the endoscopic portion of the case were performed with assistance from the AR-HMD system. Informed written consent was obtained from the patient. The participant and any identifiable individuals consented to the publication of his/her image.
Complete Removal of Bilateral Clinoidal Meningiomas Through a Pterional Approach: 3-Dimensional Operative Video
Authors: Campero Alvaro , Baldoncini Matías , Luzzi Sabino , Villalonga Juan F 
Published: October 2021

Abstract
Surgical removal of anterior clinoidal meningiomas remains a challenge because of its complicated relationship with surrounding vascular and neural structures.
1-3

This is a 39-yr-old female, with headaches, neurofibromatosis type 2, and history of 3 previous brain surgeries. The patient gave the consent to use the images and surgical video. In the imaging control, the growth of bilateral anterior clinoidal meningiomas was observed.
A right pterional approach and extradural anterior clinoidectomy was performed, and a complete resection of bilateral clinoidal meningiomas was achieved obtaining a Simpson scale resection grade 1.
The patient evolved without neurological deficits after the surgery, and the postoperative magnetic resonance imaging (MRI) evidenced a complete bilateral resection of the clinoidal meningiomas.
Clinoidal meningiomas are the unique subset of tumors because of their close proximity to neurovascular structures and can be safely excised with minimal morbidity and mortality using microsurgical techniques.
3-5
In rare cases of bilateral anterior clinoidal meningiomas such as the case presented, we recommend detailed neuroimaging analysis and consider the possibility to resect both in a single approach.
Improved thermostability of proteinase K and recognizing the synergistic effect of Rosetta and FoldX approaches
Authors: Zhao Yang , Li Daixi , Bai Xue , Luo Manjie , Feng Yan , Zhao Yilei , Ma Fuqiang , Yang Guang-Yu 
Published: October 2021

AbstractProteinase K (PRK) is a proteolytic enzyme that has been widely used in industrial applications. However, poor stability has severely limited the uses of PRK. In this work, we used two structure-guided rational design methods, Rosetta and FoldX, to modify PRK thermostability. Fifty-two single amino acid conversion mutants were constructed based on software predictions of residues that could affect protein stability. Experimental characterization revealed that 46% (21 mutants) exhibited enhanced thermostability. The top four variants, D260V, T4Y, S216Q, and S219Q, showed improved half-lives at 69°C by 12.4-, 2.6-, 2.3-, and 2.2-fold that of the parent enzyme, respectively. We also found that selecting mutations predicted by both methods could increase the predictive accuracy over that of either method alone, with 73% of the shared predicted mutations resulting in higher thermostability. In addition to providing promising new variants of PRK in industrial applications, our findings also show that combining these programs may synergistically improve their predictive accuracy.
Patient-Derived Organoids Recapitulate Intrinsic Immune Landscapes and Progenitor Populations of Glioblastoma
Authors: Watanabe Fumihiro , Hollingsworth Ethan W. , Bartley Jenna M. , Wisehart Lauren , Desai Rahil , Hartlaub Annalisa M. , Hester Mark E. , Schiapparelli Paula , Quiñones-Hinojosa Alfredo , Imitola Jaime 
Published: October 2021

SummaryGlioblastoma stem cells (GSCs) are highly self-renewing, resistant to therapy, and are able to form lethal tumors1, 2. Tumor organoids have been developed to study tumor evolution1–4, and while GSCs can form organoids for glioblastoma multiforme, our understanding of their intrinsic immune, metabolic, genetic, and molecular programs is limited. To address this, we deeply characterized GSC-derived GBM organoids using a modified protocol (GBMOsm) from several patient-derived GSCs and found they develop into complex 3D tissues with unique self-organization, cancerous metabolic states, and burdensome genetic landscapes. We discovered that GBMOsc recapitulate the presence of two important cell populations thought to drive GBM progression, SATB2+and HOPX+progenitors. Despite being devoid of immune cells, transcriptomic analysis across GBMOsc revealed an immune-like molecular program, enriched in cytokine, antigen presentation and processing, T-cell receptor inhibitors, and interferon genes. We determined that SATB2+and HOPX+populations contribute to this immune and interferon landscape in GBM in vivo and GBMOsm. Our work deepens our understanding of the intrinsic molecular and cellular architecture of GSC-derived GBMO and defines a novel GBMOsc intrinsic immune-like program.
Cell Stiffening Contributes to Complement-mediated Injury of Choroidal Endothelial Cells in Early AMD
Authors: Cabrera Andrea P. , Stoddard Jonathan , Tierno Irene Santiago , Matisioudis Nikolaos , Agarwal Mahesh , Renner Lauren , Palegar Neha , Neuringer Martha , McGill Trevor , Ghosh Kaustabh 
Published: October 2021

AbstractAge-related macular degeneration (AMD) is the leading cause of blindness in the aging population. Yet, no therapies exist for ∼85% of all AMD patients who have the dry form that is marked by degeneration of the retinal pigment epithelium (RPE) and underlying choroidal vasculature. As the choroidal vessels are crucial for RPE development and maintenance, understanding how they degenerate may lead to effective therapies for dry AMD. One likely causative factor for choroidal vascular loss is the cytolytic membrane attack complex (MAC) of the complement pathway that is abundant on choroidal vessels of humans with early dry AMD. To examine this possibility, we studied the effect of complement activation on choroidal endothelial cells (ECs) isolated from a rhesus monkey model of early AMD that, we report, exhibits MAC deposition and choriocapillaris endothelial loss similar to that seen in human early AMD. Treatment of choroidal ECs from AMD eyes with complement-competent normal human serum caused extensive actin cytoskeletal injury that was significantly less pronounced in choroidal ECs from young normal monkey eyes. We further show that ECs from AMD eyes are significantly stiffer than their younger counterparts and exhibit peripheral actin organization that is distinct from the longitudinal stress fibers in young ECs. Finally, these differences in complement susceptibility and mechanostructural properties were found to be regulated by the differential activity of small GTPases Rac and Rho because Rac inhibition in AMD cells led to simultaneous reduction in stiffness and complement susceptibility while Rho inhibition in young cells exacerbated complement injury. Thus, by identifying cell stiffness and cytoskeletal regulators Rac and Rho as important determinants of complement susceptibility, the current findings offer a new mechanistic insight into choroidal vascular loss in early AMD that warrants further investigation for assessment of translational potential.
Temporal phenomic predictions from unoccupied aerial systems can outperform genomic predictions
Authors: Adak Alper , Murray Seth C. , Anderson Steven L. 
Published: October 2021

AbstractA major challenge of genetic improvement and selection is to accurately predict individuals with the highest fitness in a population without direct measurement. Over the last decade genomic predictions (GP) based on genome-wide markers have become reliable and routine. Now phenotyping technologies, including unoccupied aerial systems (UAS also known as drones), can characterize individuals with a data depth comparable to genomics when used throughout growth. This study, for the first time, demonstrated that the prediction power of temporal UAS phenomic data can achieve or exceed that of genomic data. UAS data containing red-green-blue (RGB) bands over fifteen growth time points and multispectral (RGB, red-edge and near infrared) bands over twelve time points were compared across 280 unique maize hybrids. Through cross validation of untested genotypes in tested environments (CV2), temporal phenomic prediction (TPP) outperformed GP (0.80 vs 0.71); TPP and GP performed similarly in three other cross validation scenarios. Genome wide association mapping using area under temporal curves of vegetation indices (VIs) revealed 24.5 percent of a total of 241 discovered loci (59 loci) had associations with multiple VIs, explaining up to 51 percent of grain yield variation, less than GP and TPP predicted. This suggests TPP, like GP, integrates small effect loci well improving plant fitness predictions. More importantly, temporal phenomic prediction appeared to work successfully on unrelated individuals unlike genomic prediction.
Fecal microbiota and their association with heat stress in Bos taurus
Authors: Czech Bartosz , Szyda Joanna , Wang Kai , Luo Hanpeng , Wang Yachun 
Published: October 2021

AbstractHumans have been influencing climate changes by burning fossil fuels, farming livestock, and cutting down rainforests, which has led to global temperature rise. This problem of global warming affects animals by causing heat stress, which negatively affects their health, biological functions, and reproduction. On the molecular level, it has been proved that heat stress changes the expression level of genes and therefore causes changes in proteome and metabolome. The importance of a microbiome in many studies showed that it is considered as individuals’ “second genome”. Physiological changes caused by heat stress may impact the microbiome composition. In this study, we identified fecal microbiota associated with heat stress that was quantified by three metrics – rectal temperature, drooling, and respiratory scores and represented by their Estimated Breeding Values. For this purpose, the 16S rRNA sequencing technique was used. We analyzed the microbiota from 136 fecal samples of Chinese Holstein cows through a 16S rRNA gene sequencing approach. Sequence data were processed using a pipeline involving QIIME2 software together with SILVA database. Statistical modeling was performed using a negative binomial regression. The analysis revealed the total number of 24 genera and 12 phyla associated with heat stress metrics. Rhizobium and Pseudobutyrivibrio turned out to be the most significant genera, while Acidobacteria and Gemmatimonadetes were the most significant phyla. Phylogenetic analysis revealed that that three heat stress indicators quantify different metabolic ways of animals’ reaction to heat stress. Other studies already identified that those genera had significantly increased abundance in mice exposed to stressor-induced changes. Moreover, identified microbiota significantly associated with heat stress measures were mostly mesophilic, so their association seems to be due to heat stress-induced secondary, metabolic changes, and not directly by temperature. Moreover, high fold changes of many genera suggest that they may be used as biomarkers for monitoring the level of heat stress in cattle.
Development of a Freeze-Dried CRISPR-Cas12 Sensor for Detecting Wolbachia in the Secondary Science Classroom
Authors: Rybnicky Grant A. , Dixon Radeen A. , Kuhn Robert M. , Karim Ashty S. , Jewett Michael C. 
Published: October 2021

AbstractTraining the future synthetic biology workforce requires opportunity and exposure to biotechnology concepts and activities in secondary education. Detecting Wolbachia bacteria in arthropods using PCR has become a common way for secondary students to investigate and apply DNA technology in the science classroom. Despite this framework, cutting-edge biotechnologies like CRISPR-based diagnostics have yet to be widely implemented in the classroom. To address this gap, we present a freeze-dried CRISPR-Cas12 sensing reaction to complement traditional DNA technology education and teach synthetic biology concepts. The reactions accurately detect Wolbachia from arthropod-derived PCR samples in under 2 hours and can be stored at room temperature for over a month without appreciable degradation. The reactions are easy-to-use and cost less than $40 to implement for a classroom of 22 students including the cost of reusable equipment. We see this technology as an accessible way to incorporate synthetic biology education into existing biology curriculum, which will expand biology educational opportunities in science, technology, engineering, and mathematics (STEM) education.