bluuebunny/crossref_metadata_2025_split huggingface dataset:
The infant pharyngeal microbiomes: origin, impact and manipulation
Authors: Theodosiou Anastasia A. , Dorey Robert B. , Read Robert C. , Jones Christine E. 
Published: October 2020

Purpose of review
There has been an exponential increase in research into infant microbiome evolution, and it appears that pharyngeal microbiota are associated with clinical phenotypes (e.g. infection and asthma). Although broad consensus views are emerging, significant challenges and uncertainties remain.

Recent findings
Infant pharyngeal microbiome research is limited by low biomass, high temporal diversity and lack of agreed standards for sampling, DNA sequencing and taxonomic reporting. Analysis of amplicon sequence variants and improved cost and availability of whole-genome sequencing are promising options for improving taxonomic resolution of such studies. Infant respiratory microbiomes arise, at least in part, from maternal flora (e.g. the respiratory tract and breastmilk), and are associated with environmental and clinical factors (e.g. mode of feeding and delivery, siblings, daycare attendance, birth season and antibiotic usage). Interventional research to modify the infant pharyngeal microbiota has recently been reported, using dietary supplements.

Summary
Further work is needed to improve characterization of the infant pharyngeal microbiomes, including routes of bacterial acquisition, role of environmental factors and associations with disease phenotypes. Methodological standards are desirable to facilitate more reproducible, comparable research. Improved understanding may enable manipulation of infant pharyngeal microbiota to improve clinical outcomes.
Automated Analysis of Medial Gastrocnemius Muscle-Tendon Junction Displacements During Isolated Contractions and Walking Using Deep Neural Networks
Authors: Krupenevich Rebecca L. , Funk Callum J. , Franz Jason R. 
Published: October 2020

AbstractDirect measurement of muscle-tendon junction (MTJ) position is important for understanding dynamic tendon behavior and muscle-tendon interaction in healthy and pathological populations. Traditionally, obtaining MTJ position during functional activities is accomplished by manually tracking the position of the MTJ in cine B-mode ultrasound images – a laborious and time-consuming process. Recent advances in deep learning have facilitated the availability of user-friendly open-source software packages for automated tracking. However, these software packages were originally intended for animal pose estimation and have not been widely tested on ultrasound images. Therefore, the purpose of this paper was to evaluate the efficacy of deep neural networks to accurately track medial gastrocnemius MTJ positions in cine B-mode ultrasound images across tasks spanning controlled loading during isolated contractions to physiological loading during treadmill walking. Cine B-mode ultrasound images of the medial gastrocnemius MTJ were collected from 15 subjects (6M/9F, 23 yr, 71.9 kg, 1.8 m) during treadmill walking at 1.25 m/s and during maximal voluntary isometric plantarflexor contractions (MVICs). Five deep neural networks were trained using 480 labeled images collected during walking, and were then used to predict MTJ position in images from novel subjects 1) during walking (novel-subject), and 2) during MVICs (novel-condition). We found an average mean absolute error of 1.26±1.30 mm and 2.61±3.31 mm in the novel-subject and novel-condition evaluations, respectively. We believe this approach to MTJ position tracking is an accessible and time-saving solution, with broad applications for many fields, such as rehabilitation or clinical diagnostics.
Engineering supramolecular organizing centers for optogenetic control of innate immune responses
Authors: Tan Peng , He Lian , Zhou Yubin 
Published: October 2020

AbstractThe spatiotemporal organization of oligomeric protein complexes and translocons, such as the supramolecular organizing centers (SMOC) made of MyDDosome and MAVSome, are essential for transcriptional activation of host inflammatory responses and immune metabolisms. Light-inducible assembly of MyDDosome and MAVSome are presented herein to induce activation of nuclear factor-kB (NF-κB) and type-I interferons (IFNs). Engineering of SMOCs and the downstream transcription factor permits programmable and customized innate immune operations in a light-dependent manner. These synthetic molecular tools will likely enable optical and user-defined modulation of innate immunity at a high spatiotemporal resolution to facilitate mechanistic studies of distinct modes of innate immune activations and potential intervention of immune disorders and cancer.
Mitochondrial LonP1 protease is implicated in the degradation of unstable Parkinson disease-associated DJ-1/PARK 7 missense mutants
Authors: Sánchez-Lanzas Raúl , Castaño José G. 
Published: October 2020

AbstractDJ-1/PARK7mutations are linked with familial forms of early onset Parkinson disease (PD). We have studied the degradation of untagged DJ-1 WT and missense mutants in mouse embryomic fibroblasts obtained from DJ-1 null mice, an approach closer to the situation in patients carrying homozygous mutations. The results showed that the mutants: L10P, M26I, A107P, P158DEL, L166P, E163K and L172Q are unstable proteins, while A39S, E64D, R98Q, A104T, D149A, A171S, K175E and A179T are as stable as the DJ-1 WT. Inhibition of proteasomal and autophagic-lysosomal pathways had little effect on their degradation. Immunofluorescence and biochemical fractionation studies indicated that M26I, A107P, P158DEL, L166P, E163K and L172Q mutants associate with mitochondria. Silencing of mitochondrial matrix protease LonP1 produced a strong reduction of the degradation of those mitochondrialy associated DJ-1 mutants, but not of mutant L10P. These results demonstrated a mitochondrial pathway of degradation of those DJ-1 missense mutants implicated in PD pathogenesis.
Inhibition of Sphingosine-1-Phosphate signaling in pancreatic ductal adenocarcinoma leads to downregulation of growth and invasion
Authors: Rheinheimer Brenna A. , Cardenas Alex , Camacho Luis , Ong Evan S. , Jie Tun , Heimark Ronald L. 
Published: October 2020

AbstractBackgroundDeregulated phosphorylation of sphingosine by the sphingosine kinases and signaling through the EDG family of receptors enhances growth and survival in many cell types. Therefore, we sought to elucidate the effect of alterations in the ceramide/sphingosine/S1P rheostat on driving human pancreatic ductal adenocarcinoma towards a malignant phenotype.MethodsPancreatic cancer cell lines were treated with exogenous S1P, FTY720, and siRNA to Sphk1. Migration was evaluated by wound healing assays, cell growth by MTT assays, and invasion by tumorsphere assays. Expression of S1PR1, S1PR3, Sphk1, and Sphk2 were measured by quantitative PCR, western blot, and immunohistochemistry.ResultsS1PR1, S1PR3, and Sphk2 were overexpressed in all pancreatic cancer cell lines. Sphk1 translocated from the cytoplasm to the nucleus in cells located at the leading edge of cell clusters. Exogenous S1P increased cell migration while treatment with FTY720 and Sphk1 siRNA decreased cell growth and invasion.ConclusionsOur results suggest that increased S1PR1 expression may be an early event in pancreatic cancer pathogenesis. Additionally, altered Sphk1 localization may provide a mechanism through which pancreatic ductal adenocarcinoma cells at the leading edge invade into the surrounding matrix. Finally, inhibition of sphingosine-1-phosphate signaling may provide a novel therapeutic target for patients with metastatic disease.
The interplay of HSP90s with YDA regulates main body axis formation during early embryogenesis in Arabidopsis
Authors: Samakovli Despina , Tichá Tereza , Vavrdová Tereza , Závorková Natálie , Pecinka Ales , Ovečka Miroslav , Šamaj Jozef 
Published: October 2020

AbstractThe YODA kinase (YDA) pathway is intimately associated with the control ofArabidopsis thalianaembryo development but little is known regarding its regulators. Using genetic analysis, HEAT SHOCK PROTEINS 90 (HSP90s) emerge as potent regulators of YDA in the process of embryo development and patterning. This study is focused on the characterization and quantification of early embryonal traits of single and doublehsp90andydamutants. The mutant analysis was supported by expression analyses of cell-specificWUSCHEL-RELATED HOMEOBOX2 (WOX2) andWOX8genes during early embryonic development. Chromatin immunoprecipitation assays corroborated the involvement of YDA and HSP90s in the epigenetic control of chromatin remodeling during early embryogenesis. Genetic interactions among HSP90s and members of the YDA signaling pathway affected the development of both embryo proper and suspensor. Impaired function of HSP90s or YDA had an impact on the spatiotemporal expression ofWOX8andWOX2suggesting their essential role in cell fate determination and interference with auxin distribution. Hence, the interplay between HSP90s and YDA signaling cascade mediates the epigenetic control regulating the transcriptional networks shaping early embryo development.
Enhanced Anticoagulation Activity of Functional RNA Origami
Authors: Krissanaprasit Abhichart , Key Carson M. , Froehlich Kristen , Pontula Sahil , Mihalko Emily , Dupont Daniel M. , Andersen Ebbe S. , Kjems Jørgen , Brown Ashley C. , LaBean Thomas H. 
Published: October 2020

AbstractAnticoagulants are commonly utilized during surgeries and to treat thrombotic diseases like stroke and deep vein thrombosis. However, conventional anticoagulants have serious side-effects, narrow therapeutic windows, and lack safe reversal agents (antidotes). Here, an alternative RNA origami displaying RNA aptamers as target-specific anticoagulant, is described. Improved design and construction techniques for self-folding, single-molecule RNA origami as a platform for displaying pre-selected RNA aptamers with precise orientational and spatial control, are reported. Nuclease resistance is added using 2’-fluoro-modified pyrimidines duringin vitrotranscription. When four aptamers are displayed on the RNA origami platform, the measured thrombin inhibition and anticoagulation activity is higher than observed for free aptamers, ssRNA-linked RNA aptamers, and RNA origami displaying fewer aptamers. Importantly, thrombin inhibition is immediately switched off by addition of specific reversal agents. Results for ssDNA and ssPNA (peptide nucleic acid) antidotes show restoration of 75% and 95% coagulation activity, respectively. To demonstrate potential for practical, long-term storage for clinical use, RNA origami was freeze-dried, and stored at room temperature. Freshly produced and freeze-dried RNA show identical levels of activity in coagulation assays. Compared to current commercial intravenous anticoagulants, RNA origami-based molecules show promise as safer alternatives with rapid activity switching for future therapeutic applications.
The genetic architecture of medication-use
Authors: Rohde Palle Duun , Sørensen Peter , Nyegaard Mette 
Published: October 2020

AbstractGenomics has been forecasted to revolutionise human health by improving medical treatment through a better understanding of the molecular mechanisms of human diseases. Despite great successes of the last decade’s genome-wide association studies (GWAS), the results have to a limited extent been translated to genomic medicine. We propose, that one route to get closer to improved medical treatment is by understanding the genetics of medication-use. Here we obtained entire medication profiles from 335,744 individuals from the UK Biobank and performed a GWAS to identify which common genetic variants are major drivers of medication-use. We analysed 9 million imputed genetic variants, estimated SNP heritability, partitioned the genomic variance across functional categories, and constructed genetic scores for medication-use. In total, 59 independent loci were identified for medication-use and approximately 18% of the total variation was attributable to common genetic (minor allele frequency >0.01) variants. The largest fraction of variance was captured by variants with low to medium minor allele frequency. In particular coding and conserved regions, as well as transcription start sites, displayed significantly enrichment of heritability. The average correlation between medication-use and predicted genetic scores was 0.14. These results demonstrate that medication-useper seis a highly polygenic complex trait and that individuals with higher genetic liability are on average more diseased and have a higher risk for adverse drug reactions. These results provide an insight into the genetic architecture of medication use and pave the way for developments of multicomponent genetic risk models that includes the genetically informed medication-use.
Virtual brain grafting: Enabling whole brain parcellation in the presence of large lesions
Authors: Radwan Ahmed M. , Emsell Louise , Blommaert Jeroen , Zhylka Andrey , Kovacs Silvia , Theys Tom , Sollmann Nico , Dupont Patrick , Sunaert Stefan 
Published: October 2020

AbstractBrain atlases and templates are at the heart of neuroimaging analyses, for which they facilitate multimodal registration, enable group comparisons and provide anatomical reference. However, as atlas-based approaches rely on correspondence mapping between images they perform poorly in the presence of structural pathology. Whilst several strategies exist to overcome this problem, their performance is often dependent on the type, size and homogeneity of any lesions present. We therefore propose a new solution, referred to as Virtual Brain Grafting (VBG), which is a fully-automated, open-source workflow to reliably parcellate MR images in the presence of a broad spectrum of focal brain pathologies, including large, bilateral, intra- and extra-axial, heterogeneous lesions with and without mass effect.The core of the VBG approach is the generation of a lesion-free T1-weighted input image which enables further image processing operations that would otherwise fail. Here we validated our solution based on Freesurfer recon-all parcellation in a group of 10 patients with heterogeneous gliomatous lesions, and a realistic synthetic cohort of glioma patients (n=100) derived from healthy control data and patient data.We demonstrate that VBG outperforms a non-VBG approach assessed qualitatively by expert neuroradiologists and Mann-Whitney U tests to compare corresponding parcellations (real patients U(6,6) = 33, z = 2.738, P < .010, synthetic patients U(48,48) = 2076, z = 7.336, P < .001). Results were also quantitatively evaluated by comparing mean dice scores from the synthetic patients using one-way ANOVA (unilateral VBG = 0.894, bilateral VBG = 0.903, and non-VBG = 0.617, P < .001). Additionally, we used linear regression to show the influence of lesion volume, lesion overlap with, and distance from the Freesurfer volumes of interest, on labelling accuracy.VBG may benefit the neuroimaging community by enabling automated state-of-the-art MRI analyses in clinical populations, for example by providing input data for automated solutions for fiber tractography or resting-state fMRI analyses that could also be used in the clinic. To fully maximize its availability, VBG is provided as open software under a Mozilla 2.0 license (https://github.com/KUL-Radneuron/KUL_VBG).Graphical abstract:(A) shows T1 images from two patients with gliomatous lesions. VBG is a lesion replacement/filling workflow with one approach for unilateral lesions (uVBG) and another for bilateral lesions (bVBG). (B) shows the recon-all approach selected, (C) & (D) show the output, tissue segmentations (C) and whole brain parcellations (D). If VBG is not used (non-VBG) recon-all may finish with some errors in the parcellations (left) or fail to generate a parcellation entirely (right). However, using either VBG method allows recon-all to complete where it had previously failed and also improves parcellation quality.
Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment
Authors: Pauken Kristen E. , Shahid Osmaan , Lagattuta Kaitlyn A. , Mahuron Kelly M. , Luber Jacob M. , Lowe Margaret M. , Huang Linglin , Delaney Conor , Long Jaclyn M. , Fung Megan E. , Newcomer Kathleen , Tsai Katy K. , Chow Melissa , Guinn Samantha , Kuchroo Juhi R. , Burke Kelly P. , Schenkel Jason M. , Rosenblum Michael D. , Daud Adil I. , Sharpe Arlene H. , Singer Meromit 
Published: October 2020

AbstractThe ability to monitor anti-tumor CD8+T cell responses in the blood has tremendous therapeutic potential. Here, we used paired single-cell RNA sequencing and T cell receptor (TCR) sequencing to detect and characterize “tumor matching” (TM) CD8+T cells in the blood of mice with MC38 tumors and melanoma patients using the TCR as a molecular barcode. TM cells showed increased activation compared to non-matching T cells in blood, and appeared less exhausted than matching counterparts in tumor. Importantly, PD-1, which has been used to identify putative circulating anti-tumor CD8+T cells, showed poor sensitivity for identifying TM cells. By leveraging the transcriptome we identified candidate cell surface marker panels for TM cells in mice and melanoma patients, and validated NKG2D, CD39, and CX3CR1 in mice. These data demonstrate that the TCR can be used to identify tumor-relevant populations for comprehensive characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells.SummaryUsing single-cell RNA-sequencing coupled with TCR sequencing, we detected CD8+T cell clones shared between blood and tumor in mice and melanoma patients, characterized these matching clones in blood and tumor, and identified potential biomarkers for their isolation in blood.
Cryo-electron tomography of the herpesvirus procapsid reveals interactions of the portal with the scaffold and a shift on maturation
Authors: Buch Michael H. C. , Newcomb William W. , Winkler Dennis C. , Steven Alasdair C. , Heymann J. Bernard 
Published: October 2020

AbstractHerpes simplex virus type 1 (HSV-1) requires seven proteins to package its genome through a vertex in its capsid, one of which is the portal protein, pUL6. The portal protein is also thought to facilitate assembly of the procapsid. While the portal has been visualized in mature capsids, we aimed to elucidate its role in the assembly and maturation of procapsids using cryo-electron tomography. We identified the portal vertex in individual procapsids, calculated a subtomogram average, and compared that with the portal vertex in empty mature capsids (A-capsids). The resulting maps show the portal on the interior surface with its narrower end facing outwards, while maintaining close contact with the capsid shell. In the procapsid, the portal is embedded in the underlying scaffold, suggesting that assembly involves a portal – scaffold complex. During maturation, the capsid shell angularizes with a corresponding outward movement of the vertices. We found that in A-capsids, the portal translocates further than the adjacent capsomers and strengthens its contacts with the capsid shell. Our methodology also allowed us to determine the number of portal vertices in each capsid, with most having one per capsid, but some none or two, and rarely three. The predominance of a single portal per capsid supports facilitation of the assembly of the procapsid.ImportanceHerpes simplex virus type 1 (HSV-1) infects a majority of humans, causing mostly mild disease but in some cases progressing towards life-threatening encephalitis. Understanding the life cycle of the virus is important to devise countermeasures. Production of the virion starts with the assembly of an icosahedral procapsid including DNA packaging proteins at a vertex, one of which is the dodecameric portal protein. The procapsid then undergoes maturation and DNA packaging through the portal, driven by a terminase complex. We used cryo-electron tomography to visualize the portal in procapsids and compare them to mature empty capsids. We found the portal located inside one vertex interacting with the scaffold protein in the procapsid. On maturation, the scaffold dissociates, the capsid angularizes, and the portal moves outward, associating closely with the capsid shell. These transformations may provide a basis for the development of drugs to prevent HSV-1 infections.
Detection of stress functional responses in bacterial populations under dry soil conditions show potential microbial mechanisms to resist drought conditions
Authors: Sarkar Soumyadev , Ward Kaitlyn , Jansson Janet K. , Lee Sonny T.M. 
Published: October 2020

AbstractClimate change is predicted to have a negative effect on the grasslands of the United States and will be detrimental to the economy and environment. The changing precipitation levels would also have an effect on the structural and functional potential of associated soil microbiome communities, which in turn will regulate the health of the plants during stressful conditions. In this study, we applied metagenomics analyses to capture the responses of the bacterial populations under drier soil conditions. We collected soil from two sites (dry and wet) at the Konza Long-Term Ecological Research field station in Kansas, which had characteristic features of the native prairies. Soil drying resulted in a significant shift in the bacterial population at the community level. Following that, fifteen bacterial genomes were short-listed based on the availability in the public database, higher relative abundance in dry soils than in wet, and also according to their contributions in drier soil. The potential microbial mechanisms were elucidated when an in-depth analysis of the functional genes was performed. Translation elongation factor EF-Tu, thiamine biosynthesis protein, and catalase were identified as a part of the overall stress functional responses in the bacterial population in this study. We speculate that these identified bacterial populations are important for maintaining the health of the soil under dry conditions. Genes and/or pathways found in this study provide insights into microbial mechanisms that these bacterial populations might employ to resist challenging drought conditions.
SARS-CoV-2 viral budding and entry can be modeled using virus-like particles
Authors: Plescia Caroline B. , David Emily A. , Patra Dhabaleswar , Sengupta Ranjan , Amiar Souad , Su Yuan , Stahelin Robert V. 
Published: October 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first discovered in December 2019 in Wuhan, China and expeditiously spread across the globe causing a global pandemic. While a select agent designation has not been made for SARS-CoV-2, closely related SARS-CoV-1 and MERS coronaviruses are classified as Risk Group 3 select agents, which restricts use of the live viruses to BSL-3 facilities. Such BSL-3 classification make SARS-CoV-2 research inaccessible to the majority of functioning research laboratories in the US; this becomes problematic when the collective scientific effort needs to be focused on such in the face of a pandemic. In this work, we assessed the four structural proteins from SARS-CoV-2 for their ability to form viruslike particles (VLPs) from human cells to form a competent system for BSL-2 studies of SARS-CoV-2. Herein, we provide methods and resources of producing, purifying, fluorescently and APEX2-labeling of SARS-CoV-2 VLPs for the evaluation of mechanisms of viral budding and entry as well as assessment of drug inhibitors under BSL-2 conditions.