bluuebunny/crossref_metadata_2025 huggingface dataset:
Postoperative chylothorax following lung cancer surgery with an aberrant course of thoracic duct: a case report
Authors: Nakamura Daisuke , Toishi Masayuki , Sakaizawa Takao , Koike Sachie , Nishimura Hideki
Published: October 2021

Postoperative chylothorax occurs relatively rarely after pulmonary resections, often caused intraoperatively by injury to the thoracic duct. We describe a case of postoperative chylothorax after lung cancer surgery with an aberrant thoracic duct course. A 66-year-old man showed abnormal findings on chest computed tomography (CT) during health screening and was suspected with primary lung cancer. Then, he underwent a right upper lobectomy with mediastinal lymph-node dissection. The histopathological findings confirmed lung adenocarcinoma. However, the patient developed a postoperative chylothorax and underwent revision surgery. An abnormally running thoracic duct, which was expected to flow into the right venous angle, was found at the cranial side of the right superior mediastinal dissection area and was clipped. Considering the many variations in the route of the thoracic duct, thoracic surgeons should remain alert for postoperative chylothorax when performing lung cancer surgery with mediastinal lymph-node dissection and prepare treatment strategies accordingly.
Development and Validation of a Clinical Risk Score to Predict Hospitalization Within 30 Days of Coronavirus Disease 2019 Diagnosis
Authors: Aboumrad Maya , Zwain Gabrielle , Smith Jeremy , Neupane Nabin , Powell Ethan , Dempsey Brendan , Reyes Carolina , Satram Sacha , Young-Xu Yinong
Published: October 2021

Introduction

Early identification of patients with coronavirus disease 2019 (COVID-19) who are at risk for hospitalization may help to mitigate disease burden by allowing healthcare systems to conduct sufficient resource and logistical planning in the event of case surges. We sought to develop and validate a clinical risk score that uses readily accessible information at testing to predict individualized 30-day hospitalization risk following COVID-19 diagnosis.

Methods

We assembled a retrospective cohort of U.S. Veterans Health Administration patients (age ≥ 18 years) diagnosed with COVID-19 between March 1, 2020, and December 31, 2020. We screened patient characteristics using Least Absolute Shrinkage and Selection Operator logistic regression and constructed the risk score using characteristics identified as most predictive for hospitalization. Patients diagnosed before November 1, 2020, comprised the development cohort, while those diagnosed on or after November 1, 2020, comprised the validation cohort. We assessed risk score discrimination by calculating the area under the receiver operating characteristic (AUROC) curve and calibration using the Hosmer–Lemeshow (HL) goodness-of-fit test. This study was approved by the Veteran’s Institutional Review Board of Northern New England at the White River Junction Veterans Affairs Medical Center (Reference no.:1473972-1).

Results

The development and validation cohorts comprised 11,473 and 12,970 patients, of whom 4,465 (38.9%) and 3,669 (28.3%) were hospitalized, respectively. The independent predictors for hospitalization included in the risk score were increasing age, male sex, non-white race, Hispanic ethnicity, homelessness, nursing home/long-term care residence, unemployed or retired status, fever, fatigue, diarrhea, nausea, cough, diabetes, chronic kidney disease, hypertension, and chronic obstructive pulmonary disease. Model discrimination and calibration was good for the development (AUROC = 0.80; HL P-value = .05) and validation (AUROC = 0.80; HL P-value = .31) cohorts.

Conclusions

The prediction tool developed in this study demonstrated that it could identify patients with COVID-19 who are at risk for hospitalization. This could potentially inform clinicians and policymakers of patients who may benefit most from early treatment interventions and help healthcare systems anticipate capacity surges.
Military Pain Medicine: Sustaining the Fighting Force
Authors: Hughey Scott , Spevak Christopher , Stedje-Larsen Eric
Published: October 2021

Active duty military service members (ADSMs) suffer disproportionately from chronic pain. In the USA, military pain physicians serve an important role in the treatment of pain conditions in addition to the maintenance of the fighting force. Expanding roles for pain physicians, including novel therapies, consulting roles for opioid policy, and usefulness in a deployed setting create enormous value for military pain physicians. Ongoing force structure changes, including proposed reduction in the U.S. Military’s healthcare workforce may significantly impact pain care and the health of the fighting forces. Military pain physicians support a variety of different roles in the military healthcare system. Ultimately, maintaining a robust faculty of pain physicians allows for both preservation of the fighting forces and a ready medical force.
Reconstructing the Hubble diagram of gamma-ray bursts using deep learning
Authors: Tang Li , Lin Hai-Nan , Li Xin , Liu Liang
Published: October 2021

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 < −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

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

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

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

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

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

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

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

Proteinase 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

Glioblastoma 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

Age-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

A 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

Humans 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

Training 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.
Diversity-induced plant history and soil history effects modulate plant responses to global change
Authors: Dietrich Peter , Schumacher Jens , Eisenhauer Nico , Roscher Christiane
Published: October 2021

Global change has dramatic impacts on grassland diversity. However, little is known about how fast species can adapt to these changes and how this affects their responses to global change. To close this gap, we performed a common garden experiment testing whether plant responses to global change are influenced by the selection history of the plants and the conditioning history of soil at different levels of plant diversity. Therefore, we collected seeds and took soil samples from 14-year old plant communities of a biodiversity experiment. Offspring of plants from low- and high-diversity communities were either grown in their own soil or in soil of a different community, and were either exposed to drought, increased nitrogen input, or a combination of both. Results show that, under nitrogen addition, offspring of plants selected at high diversity produced more biomass than those selected at low diversity, while drought neutralized differences in biomass production. Moreover, under the influence of global change drivers, mainly soil, and to a lesser extent plant history, influenced the expression of plant traits. Our results show that plant diversity modulates plant-soil interactions and growth strategies of plants, which feedback on the eco-evolutionary pathways of the plants and thus their responses to global change.
Quantitative live-imaging of Aquilegia floral meristems reveals distinct patterns of floral organ initiation and cell-level dynamics of floral meristem termination
Authors: Min Ya , Conway Stephanie J. , Kramer Elena M.
Published: October 2021

In-depth investigation of any developmental process in plants requires knowledge of both the underpinning molecular networks and how they directly determine patterns of cell division and expansion over time. Floral meristems (FM) produce floral organs, after which they undergo floral meristem termination (FMT), and precise control of organ initiation and FMT is crucial to reproductive success of any flowering plant. Using a live confocal imaging, we characterized developmental dynamics during floral organ primordia initiation and FMT in Aquilegia coerulea (Ranunculaceae). Our results have uncovered distinct patterns of primordium initiation between stamens and staminodes compared to carpels, and provided insight into the process of FMT, which is discernable based on cell division dynamics preceding carpel initiation. To our knowledge, this is the first quantitative live imaging of meristem development in a system with numerous whorls of floral organs as well as an apocarpous gynoecium. This study provides crucial information for our understanding of how the spatial-temporal regulation of floral meristem behavior is achieved in both an evolutionary and developmental context.
In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm
Authors: Novakovsky Gherman , Sasaki Shugo , Fornes Oriol , Omur Meltem E. , Huang Helen , Lim Nathaniel , Cherkasov Artem , Pavlidis Paul , Mostafavi Sara , Lynn Francis C. , Wasserman Wyeth W.
Published: October 2021

Improving methods for human embryonic stem cell differentiation represents a challenge in modern regenerative medicine research. Using drug repurposing approaches, we discover small molecules that regulate the formation of definitive endoderm. Among them are inhibitors of known processes involved in endoderm differentiation (mTOR, PI3K, and JNK pathways) and a new compound, with an unknown mechanism of action, capable of inducing endoderm formation in the absence of growth factors in the media. Optimization of the classical protocol by including this compound achieves the same differentiation efficiency with a 90% cost reduction. The gene expression profile induced by the compound suggests that it is an inhibitor of the MYC pathway. The proposed in silico procedure for candidate molecule selection has broad potential for improving stem cell differentiation protocols.
StarBeast3: Adaptive Parallelised Bayesian Inference of the Multispecies Coalescent
Authors: Douglas Jordan , Jiménez-Silva Cinthy L. , Bouckaert Remco
Published: October 2021

As genomic sequence data becomes increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent methods address these issues. This is achieved by embedding a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3 – a software package for efficient Bayesian inference of the multispecies coalescent model via Markov chain Monte Carlo. We gain efficiency by introducing cutting-edge proposal kernels and adaptive operators, and StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore, gene tree inference is parallelised, allowing the software to scale with the size of the problem. We validated our software and benchmarked its performance using three real and two synthetic datasets. Our results indicate that StarBeast3 is up to one-and-a-half orders of magnitude faster than StarBeast2, and therefore more than two orders faster than *BEAST, depending on the dataset and on the parameter, and is suitable for multispecies coalescent inference on large datasets (100+ genes). StarBeast3 is open-source and is easy to set up with a friendly graphical user interface.
Higher education responses to COVID-19 in the United States: Evidence for the impacts of university policy
Authors: Klein Brennan , Generous Nicholas , Chinazzi Matteo , Bhadricha Zarana , Gunashekar Rishab , Kori Preeti , Li Bodian , McCabe Stefan , Green Jon , Lazer David , Marsicano Christopher R. , Scarpino Samuel V. , Vespignani Alessandro
Published: October 2021

With a dataset of testing and case counts from over 1,400 institutions of higher education (IHEs) in the United States, we analyze the number of infections and deaths from SARS-CoV-2 in the counties surrounding these IHEs during the Fall 2020 semester (August to December, 2020). We used a matching procedure designed to create groups of counties that are aligned along age, race, income, population, and urban/rural categories—socio-demographic variables that have been shown to be correlated with COVID-19 outcomes. We find that counties with IHEs that remained primarily online experienced fewer cases and deaths during the Fall 2020 semester; whereas before and after the semester, these two groups had almost identical COVID-19 incidence. Additionally, we see fewer deaths in counties with IHEs that reported conducting any on-campus testing compared to those that reported none. We complement the statistical analysis with a case study of IHEs in Massachusetts—a rich data state in our dataset—which further highlights the importance of IHE-affiliated testing for the broader community. The results in this work suggest that campus testing can itself be thought of as a mitigation policy and that allocating additional resources to IHEs to support efforts to regularly test students and staff would be beneficial to mitigating the spread of COVID-19 in the general population.
3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa
Authors: Mondragón-Palomino Octavio , Poceviciute Roberta , Lignell Antti , Griffiths Jessica A. , Takko Heli , Ismagilov Rustem F.
Published: October 2021

Improving our understanding of host-microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the 3D spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 days after recovery when overall bacterial loads returned to pre-antibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern was resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that bacterial taxa are distributed differently within crypts, with Lactobacilli laying closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.

Significance Statement

Many human diseases are causally linked to the gut microbiota, yet the field still lacks mechanistic understanding of the underlying complex interactions because existing tools cannot simultaneously quantify microbial communities and their intact native context. In this work, we provide a new approach to tissue clearing and preservation that enables visualization, in 3D and at scales ranging from centimeters to micrometers, of the complete biogeography of the host-microbiota interface. We combine this new tool with sequencing and multiplexed labelling of the microbiota to provide the field with a platform on which to discover patterns in the spatial distribution of microbes. We validated this platform by quantifying the distribution of bacteria in the cecal mucosa at different stages of antibiotic exposure. This approach will enable researchers to formulate and test new hypotheses about host-microbe and microbe-microbe interactions.
A Systematic Interrogation of MHC Class I Peptide Presentation Identifies Constitutive and Compensatory Protein Degradation Pathways
Authors: Mamrosh Jennifer L. , Sherman David J. , Cohen Joseph R. , Johnston James A. , Joubert Marisa K. , Li Jing , Lipford J. Russell , Lomenick Brett , Moradian Annie , Prabhu Siddharth , Sweredoski Michael J. , Lugt Bryan Vander , Verma Rati , Deshaies Raymond J.
Published: October 2021

The adaptive immune system distinguishes self from non-self by surveying peptides generated from degradation of intracellular proteins that are loaded onto MHC Class I molecules for display on the cell surface. While early studies reported that the bulk of cell surface MHC Class I complexes require the ubiquitin-proteasome system (UPS) for their generation, this conclusion has been challenged. To better understand MHC Class I peptide origins, we sought to carry out a comprehensive, quantitative census of the MHC Class I peptide repertoire in the presence and absence of UPS activity. We introduce optimized methodology to enrich for authentic Class I-bound peptides in silico and then quantify by mass spectrometry their relative amounts upon perturbation of the ubiquitin-proteasome system. Whereas most peptides are dependent on the proteasome and ubiquitination for their generation, a surprising 30% of the MHC Class I repertoire, enriched in peptides of mitochondrial origin, appears independent of these pathways. A further ∼10% of Class I-bound peptides were found to be dependent on the proteasome but independent of ubiquitination for their generation. Notably, clinically achievable partial inhibition of the proteasome resulted in display of novel peptides antigens, at least one of which promotes immune system activation. Our results suggest that generation of MHC Class I•peptide complexes is more complex than previously recognized and also provide evidence for compensatory peptide-generating pathways when canonical pathways are impaired.
A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use
Authors: Hegarty Bridget , Dai Zihan , Raskin Lutgarde , Pinto Ameet , Wigginton Krista , Duhaime Melissa
Published: October 2021

Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.
A sensitive and specific genetically encodable biosensor for potassium ions
Authors: Wu Sheng-Yi , Wen Yurong , Serre Nelson Bernard Calixte , Laursen Cathrine Charlotte Heiede , Dietz Andrea Grostøl , Taylor Brian R. , Aggarwal Abhi , Rancic Vladimir , Becker Michael , Ballanyi Klaus , Podgorski Kaspar , Hirase Hajime , Nedergaard Maiken , Fendrych Matyáš , Lemieux M. Joanne , Eberl Daniel F. , Kay Alan R. , Campbell Robert E. , Shen Yi
Published: October 2021

Potassium ions (K+) play a critical role as an essential electrolyte in all biological systems. Here we report the crystal structure-guided optimization and directed evolution of an improved genetically encoded fluorescent K+ biosensor, GINKO2. GINKO2 is highly sensitive and specific for K+ and enables in vivo detection of K+ dynamics in multiple species.
Vernalization-triggered expression of the antisense transcriptCOOLAIRis mediated byCBFgenes
Authors: Jeon Myeongjune , Jeong Goowon , Yang Yupeng , Luo Xiao , Jeong Daesong , Kyung Jinseul , Hyun Youbong , He Yuehui , Lee Ilha
Published: October 2021

To synchronize flowering time with spring, many plants undergo vernalization, a floral-promotion process triggered by exposure to long-term winter cold. InArabidopsis thaliana, this is achieved through cold-mediated epigenetic silencing of the floral repressor,FLOWERING LOCUS C(FLC).COOLAIR, a cold-induced antisense RNA transcribed from theFLClocus, has been proposed to facilitateFLCsilencing. Here, we show that C-repeat (CRT)/dehydration-responsive elements (DREs) at the 3′-end ofFLCand CRT/DRE-binding factors (CBFs) are required for cold-mediated expression ofCOOLAIR. CBFs bind to CRT/DREs at the 3′-end ofFLC, bothin vitroandin vivo, and CBF levels increase gradually during vernalization. Cold-inducedCOOLAIRexpression is severely impaired incbfsmutants in which allCBFgenes are knocked-out. Conversely,CBF-overexpressing plants show increasedCOOLAIRlevels even at warm temperatures. We show thatCOOLAIRis induced by CBFs during early stages of vernalization but COOLAIR levels decrease in later phases asFLCchromatin transitions to an inactive state to which CBFs can no longer bind. We also demonstrate thatcbfsandFLCΔCOOLAIRmutants exhibit a normal vernalization response despite their inability to activateCOOLAIRexpression during cold, revealing thatCOOLAIRis not required for the vernalization process.
Can DNA help trace the local trade of pangolins? A genetic assessment of white-bellied pangolins from the Dahomey Gap (West Africa)
Authors: Zanvo Stanislas , Djagoun Sylvestre C.A.M. , Azihou Akomian F. , Djossa Bruno , Afiademanyo Komlan , Olayemi Ayodedji , Agbangla Clément , Sinsin Brice , Gaubert Philippe
Published: October 2021

We conducted in the Dahomey Gap (DG) a pioneer study on the genetic tracing of the African pangolin trade. We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellites loci. Tree-based assignment procedure showed the ‘endemicity’ of the pangolin trade, as strictly fed by the lineage endemic to the DG (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, inbreeding depression and lack of geographic structure. We identified a 92-98% decline in DGL effective population size 200-500 ya –concomitant with major political transformations along the ‘Slave Coast’– leading to contemporaneous estimates inferior to minimum viable population size. Genetic tracing suggested that wildlife markets from the DG sourced through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of same individuals on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies and cross-validation with observed data that could trace five traded pangolins to their forest origin, c. 200-300 km away from the markets. Although the genetic toolkit that we designed from traditional markers can prove helpful to trace the pangolin trade, our tracing ability was limited by the lack of population structure within DGL. Given the deleterious combination of genetic, demographic and trade-related factors affecting DGL populations, the conservation status of white-bellied pangolins in the DG should be urgently re-evaluated.