bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation of SARS-CoV-2 Breakthrough Infections to Time-from-vaccine; Preliminary Study
Authors: Mizrahi Barak , Lotan Roni , Kalkstein Nir , Peretz Asaf , Perez Galit , Ben-Tov Amir , Chodick Gabriel , Gazit Sivan , Patalon Tal 
Published: July 2021

AbstractThe short-term effectiveness of a two-dose regimen of the BioNTech/Pfizer mRNA BNT162b2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine was widely demonstrated. However, long term effectiveness is still unknown. A nationwide vaccination campaign was initiated early in Israel, allowing for a real-world evaluation of the interaction between protection and time-from-vaccine. The Delta (B.1.617.2) variant became the dominant strain in Israel in June 2021, as Israel is currently experiencing a new surge of cases. Leveraging the centralized computerized database of Maccabi Healthcare Services (MHS), we assessed the correlation between time-from-vaccine and incidence of breakthrough infection. We found that the risk for infection was significantly higher for early vaccinees compared to those vaccinated later. This preliminary finding should prompt further investigagions into long-term protection against different strains, and prospective clinical trials to examine the effect of a booster vaccine against breakthrough infection.
Advances in Classifying the Stages of Diabetic Retinopathy Using Convolutional Neural Networks in Low Memory Edge Devices
Authors: Paul Aditya Jyoti 
Published: July 2021

AbstractDiabetic Retinopathy (DR) is a severe complication that may lead to retinal vascular damage and is one of the leading causes of vision impairment and blindness. DR broadly is classified into two stages – non-proliferative (NPDR), where there are almost no symptoms, except a few microaneurysms, and proliferative (PDR) involving a huge number of microaneurysms and hemorrhages, soft and hard exudates, neo-vascularization, macular ischemia or a combination of these, making it easier to detect. More specifically, DR is usually classified into five levels, labeled 0-4, from 0 indicating no DR to 4 which is most severe. This paper firstly presents a discussion on the risk factors of the disease, then surveys the recent literature on the topic followed by examining certain techniques which were found to be highly effective in improving the prognosis accuracy. Finally, a convolutional neural network model is proposed to detect all the stages of DR on a low-memory edge microcontroller. The model has a size of just 5.9 MB, accuracy and F1 score both of 94% and an inference speed of about 20 frames per second.
SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1
Authors: Muterle Varela Ana Paula , Prichula Janira , Mayer Fabiana Quoos , Salvato Richard Steiner , Sant’Anna Fernando Hayashi , Gregianini Tatiana Schäffer , Martins Letícia Garay , Seixas Adriana , Veiga Ana B. G. 
Published: July 2021

ABSTRACTBackgroundGenomic surveillance of SARS-CoV-2 is paramount for understanding viral dynamics, contributing to disease control. This study analyzed SARS-CoV-2 genomic diversity in Rio Grande do Sul (RS), Brazil, including the first case of each Regional Health Coordination and cases from three epidemic peaks.MethodsNinety SARS-CoV-2 genomes from RS were sequenced and analyzed against SARS-CoV-2 datasets available in GISAID for phylogenetic inference and mutation analysis.ResultsSARS-CoV-2 lineages among the first cases in RS were B.1 (33.3%), B.1.1.28 (26.7%), B.1.1 (13.3%), B.1.1.33 (10.0%), and A (6.7%), evidencing SARS-CoV-2 introduction by both international origin and community-driven transmission. We found predominance of B.1.1.33 (50.0%) and B.1.1.28 (35.0%) during the first epidemic peak (July–August, 2020), emergence of P.2 (55.6%) in the second peak (November–December, 2020), and massive spread of P.1 and related sequences (78.4%), such as P.1-like-II, P.1.1 and P.1.2 in the third peak (February–April, 2021). Eighteen novel mutation combinations were found among P.1 genomes, and 22 different spike mutations and/or deletions among P.1 and related sequences.ConclusionsThis study shows the dispersion of SARS-CoV-2 lineages in Southern Brazil, and describes SARS-CoV-2 diversity during three epidemic peaks, highlighting the spread of P.1 and the high genetic diversity of currently circulating lineages. Genomic monitoring of SARS-CoV-2 is essential to guide health authorities’ decisions to control COVID-19 in Brazil.SummaryNinety SARS-CoV-2 genomes from Rio Grande do Sul, Brazil, were sequenced, including the first cases from 15 State Health Coordination regions and samples from three epidemic peaks. Phylogenomic inferences showed SARS-CoV-2 lineages spread, revealing its genomic diversity.
3D printed cobalt-chromium-molybdenum porous superalloy with superior antiviral activity
Authors: Arjunan Arun , Robinson John , Baroutaji Ahmad , Martí Miguel , Tuñón-Molina Alberto , Serrano-Aroca Ángel 
Published: July 2021

AbstractCOVID-19 pandemic and associated supply-chain disruptions emphasise the requirement for antimicrobial materials for on-demand manufacturing. Besides aerosol transmission, SARS-CoV-2 is also propagated through contact with virus-contaminated surfaces. As such, the development of effective biofunctional materials that can inactivate SARS-CoV-2 are critical for pandemic preparedness. Such materials will enable the rational development of antiviral devices with prolonged serviceability reducing the environmental burden of disposable alternatives. This research reveals the novel use of Laser Powder Bed Fusion (LPBF) to 3D print porous Cobalt-Chromium-Molybdenum (Co-Cr-Mo) superalloy with potent antiviral activity (100% viral inactivation in 30 mins). The porous material was rationally conceived using a multi-objective surrogate model featuring track thickness (tt) and pore diameter (ϕd) as responses. The regression analysis found the most significant parameters for Co-Cr-Mo track formation to be the interaction effects of scanning rate (Vs) and laser power (Pl) in the orderPlVs>Vs>Pl. Contrastively, the pore diameter was found to be primarily driven by the hatch spacing (Sh). The study is the first to demonstrate the superior antiviral properties of 3D printed Co-Cr-Mo superalloy against an enveloped virus used as biosafe viral model of SARS-CoV-2. The material significantly outperforms the viral inactivation time of other broadly used antiviral metals such as copper and silver from 5 hours to 30 minutes. As such the study goes beyond the current state-of-the-art in antiviral alloys to provide extra-protection to combat the SARS-COV-2 viral spread. The evolving nature of the COVID-19 pandemic brings new and unpredictable challenges where on-demand 3D printing of antiviral materials can achieve rapid solutions while reducing the environmental impact of disposable devices.Graphical abstract
Source tracking and global distribution of the mobilized tigecycline resistant gene tet(X)
Authors: Zhang Rong-min , Sun Jian , Sun Ruan-yang , Wang Min-ge , Cui Chao-yue , Fang Liang-xing , Liao Mei-na , Lu Xiao-qing , Liu Yong-xin , Liao Xiao-Ping , Liu Ya-Hong 
Published: August 2021

AbstractThe emergence of tet(X) genes has compromised the clinical use of the last-line antibiotic tigecycline. We identified 322 (1.21%) tet(X) positive samples from 12,829 human microbiome samples distributed in four continents (Asia, Europe, North America and South America) using retrospective data from worldwide. These tet(X) genes were dominated by tet(X2)-like orthologs but we also identified 12 samples carrying novel tet(X) genes, designed tet(X15) and tet(X16), that were resistant to tigecycline. The metagenomic analysis revealed these tet(X) genes distributed in anaerobes dominated by Bacteroidaceae (78.89%) of human-gut origin. The transmission of these tet(X2)-like orthologs between Bacteroidaceae and Riemerella anatipestifer was primarily promoted by the mobile elements ISBf11 and IS4351. tet(X2)-like orthologs was also developed during transmission by mutation to high-level tigecycline resistant determinants tet(X15) and tet(X16). Further tracing these tet(X) in single bacterial isolate from public repository indicated that tet(X) genes were present as early as 1960s in R. anatipestifer that was the primary tet(X) carrier at early stage (before 2000). The tet(X2) and non-tet(X2) orthologs were primarily distributed in humans and food animals respectively, and non-tet(X2) were dominated by tet(X3) and tet(X4). Genomic comparison indicated these tet(X) genes were likely to be generated during tet(X) transmission between Flavobacteriaceae and E. coli/Acinetobacter spp.., and ISCR2 played a key role in the transmission. These results suggest R. anatipestifer was the potential ancestral source of tet(X) gene. Additionally, Bacteroidaceae of human-gut origin was an important hidden reservoir and mutational incubator for the mobile tet(X) genes that enabled spread to facultative anaerobes and aerobes.
Production of human milk fat substitute by engineered strains of Yarrowia lipolytica
Authors: Bhutada Govindprasad , Menard Guillaume , Ledesma-Amaro Rodrigo , Eastmond Peter J 
Published: August 2021

ABSTRACTHuman milk fat has a distinctive stereoisomeric structure where palmitic acid is esterified to the middle (sn-2) position on the glycerol backbone of the triacylglycerol and unsaturated fatty acids to the outer (sn-1/3) positions. This configuration allows for more efficient nutrient absorption in the infant gut. However, the fat used in most infant formulas originates from plants, which tend only to esterify palmitic acid to the sn-1/3 positions. Oleaginous yeasts provide an alternative source of lipids for human nutrition. However, these yeasts also exclude palmitic acid from the sn-2 position of their triacylglycerol. Here we show that Yarrowia lipolytica can be engineered to produce triacylglycerol with more than 60% of the palmitic acid in the sn-2 position, by expression of a lysophosphatidic acid phosphatase with palmitoyl-Coenzyme A specificity, such as LPAAT2 from Chlamydomonas reinhardtii. The engineered Y. lipolytica strains can be cultured on glycerol, glucose, palm oil or a mixture of substrates, under nitrogen limited condition, to produce triacylglycerol with a fatty acid composition that resembles human milk fat, in terms of the major molecular species; palmitic, oleic and linoleic acids. Culture on palm oil or a mixture of glucose and palm oil produced the highest lipid titre in shake flask culture and a triacylglycerol composition that is most similar with human milk fat. Our data show that an oleaginous yeast can be engineered to produce a human milk fat substitute (β-palmitate), that could potentially be used as an ingredient in infant formulas.
Selective logging shows no impact on the dietary breadth of the fawn leaf-nosed bat (Hipposideros cervinus)
Authors: Hemprich-Bennett David R. , Kemp Victoria A. , Blackman Joshua , Lewis Owen T. , Struebig Matthew J. , Bernard Henry , Rossiter Stephen J. , Clare Elizabeth L. 
Published: August 2021

AbstractLogging activities degrade forest habitats across large areas of the tropics, but the impacts on trophic interactions that underpin forest ecosystems are poorly understood. DNA metabarcoding provides an invaluable tool to investigate such interactions, allowing analysis at a far greater scale and resolution than has previously been possible. We analysed the diet of the insectivorous fawn leaf-nosed batHipposideros cervinusacross a forest disturbance gradient in Borneo, using a dataset of ecological interactions from an unprecedented number of bat-derived faecal samples. Bats predominantly consumed insects from the orders Lepidoptera, Blattodea, Diptera and Coleoptera, and the taxonomic composition of their diet remained relatively consistent across sites regardless of logging disturbance. There was little difference in the richness of prey consumed in each logging treatment, indicating potential resilience of this species to habitat degradation. In fact, bats consumed a high richness of prey items, and intensive sampling is needed to reliably compare feeding ecology over multiple sites regardless of the bioinformatic procedures used.
Scaffold modelling captures the structure-function-dynamics relationship in brain microcircuits
Authors: Schepper Robin De , Geminiani Alice , Masoli Stefano , Rizza Martina Francesca , Antonietti Alberto , Casellato Claudia , D’Angelo Egidio 
Published: August 2021

1AbstractModelling brain networks with complex configuration and cellular properties requires a set of neuroinformatic tools and an organized staged workflow. We have therefore developed the Brain Scaffold Builder (BSB), a new modeling framework embedding multiple strategies for cell placement and connectivity and a flexible management of cellular and network mechanisms. With BSB, for the first time, the mouse cerebellar cortex was reconstructed and simulated at cellular resolution, using morphologically realistic multi-compartmental single-neuron models. Embedded connection rules allowed BSB to generate the cerebellar connectome, unifying a collection of scattered experimental data into a coherent construct. Naturalistic background and sensory-burst stimulation were used for functional validation against recordings in vivo, monitoring the impact of subcellular mechanisms on signal propagation and spatio-temporal processing and providing a new ground-truth about circuit organization for the prediction of neural dynamics.
Identification and functional characterization of transcriptional activators in human cells
Authors: Alerasool Nader , Lin Zhen-Yuan , Gingras Anne-Claude , Taipale Mikko 
Published: July 2021

SUMMARYTranscription is orchestrated by thousands of transcription factors and chromatin-associated proteins, but how these are causally connected to transcriptional activation or repression is poorly understood. Here, we conduct an unbiased proteome-scale screen to systematically uncover human proteins that activate transcription in a natural chromatin context. We also identify potent transactivation domains among the hits. By combining interaction proteomics and chemical inhibitors, we delineate the preference of both known and novel transcriptional activators for specific co-activators, highlighting how even closely related TFs can function via distinct co-factors. Finally, we show that many novel activators are partners in fusion events in tumors and functionally characterize a myofibroma-associated fusion between SRF and C3orf62, a potent activator. SRF-C3orf62 activates transcription in a CBP/p300-dependent manner and promotes proliferative and myogenic transcriptional programs. Our work provides a functional catalogue of potent transactivators in the human proteome and a platform for discovering transcriptional regulators at genome scale.
The Pace of Modern Life, Revisited
Authors: Sanderson Sarah , Beausoleil Marc-Olivier , O’Dea Rose E. , Wood Zachary T. , Correa Cristian , Frankel Victor , Gorné Lucas D. , Haines Grant E. , Kinnison Michael T. , Oke Krista B. , Pelletier Fanie , Pérez-Jvostov Felipe , Reyes-Corral Winer Daniel , Ritchot Yanny , Sorbara Freedom , Gotanda Kiyoko M. , Hendry Andrew P. 
Published: August 2021

ABSTRACTWild populations must continuously adapt to environmental changes or they risk extinction. Such adaptations can be measured as phenotypic rates of change and can allow us to predict patterns of contemporary evolutionary change. About two decades ago, a dataset of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this dataset to look at microevolutionary processes in relation to specific types of human disturbances. Here, we have updated the dataset adding 5675 estimates of phenotypic changes and used it to revisit established patterns of contemporary evolutionary change. Using this newer version, containing 7338 estimates of phenotypic changes, we revisit the conclusions of four published articles. We then synthesize the expanded dataset to compare rates of change across different types of human disturbance. Analyses of this expanded dataset suggests that: I. a small absolute difference in rates of change exists between human disturbed and natural populations, II. harvesting by humans results in larger rates of change than other types of disturbances, III. introduced populations have increased rates of change, and IV. body size does not increase through time. Overall, findings from earlier analyses have largely held-up in analyses of our new dataset that encompass a much larger breadth of species, traits, and human disturbances. Lastly, we found that types of human disturbances affect rates of phenotypic change, and we call for this database to serve as a steppingstone for further analyses to understand patterns of contemporary evolution.
Neural temporal context reinstatement of event structure during memory recall
Authors: Lohnas Lynn J. , Karl Healey M. , Davachi Lila 
Published: August 2021

AbstractAlthough life unfolds continuously, experiences are generally perceived and remembered as discrete events. Accumulating evidence suggests that event boundaries disrupt temporal representations and weaken memory associations. However, less is known about the consequences of event boundaries on temporal representations during retrieval, especially when temporal information is not tested explicitly. Using a neural measure of temporal context extracted from scalp electroencephalography, we found reduced temporal context similarity between studied items separated by an event boundary when compared to items from the same event. Further, while participants free recalled list items, neural activity reflected reinstatement of temporal context representations from study, including temporal disruption. A computational model of episodic memory, the Context Maintenance and Retrieval model (CMR; Polyn, Norman & Kahana, 2009), predicted these results, and made novel predictions regarding the influence of temporal disruption on recall order. These findings implicate the impact of event structure on memory organization via temporal representations.
Directional sensitivity of the cerebral pressure-flow relationship in middle and posterior cerebral arteries using the repeated squat-stand model: within-day reproducibility and impact of diurnal variation in young healthy men and women
Authors: Labrecque Lawrence , Burma Joel S , Roy Marc-Antoine , Smirl Jonathan D , Brassard Patrice 
Published: August 2021

AbstractWe recently employed repeated squat-stands (RSS) to quantify directional sensitivity of the cerebral-pressure flow relationship (i.e. hysteresis) using a novel metric. Within-day reproducibility and diurnal variation impacts of this metric are unknown. We evaluated this metric for: 1) within-day reproducibility and the extent diurnal variation has in middle (MCA; ΔMCAvT/ΔMAPT) and posterior cerebral arteries (PCA; ΔPCAvT/ΔMAPT); 2) sex differences. Absolute (ΔMCAvT/ΔMAPT ; ΔPCAvT/ΔMAPT) and relative (%MCAvT/%MAPT, %PCAvT/%MAPT) metrics were calculated at seven time-points (08:00-17:00) in 18 participants (8 women; 24 ± 3 yrs) using the minimum-to-maximum MCAv/PCAv and MAP for each RSS at 0.05 Hz and 0.10 Hz. Reproducibility was evaluated with intraclass correlation coefficient (ICC). For all metrics, reproducibility was good (0.75-0.90) to excellent (>0.90). The metric in both arteries was impacted by MAP direction at 0.10 Hz (all p < 0.024). Time-of-day influenced ΔMCAvT/ΔMAPT (0.05 Hz: p = 0.0028; 0.10 Hz: p = 0.0009), %MCAvT/%MAPT (0.05 Hz: p = 0.035; 0.10 Hz: p = 0.0087), and ΔPCAvT/ΔMAPT (0.05 Hz: p = 0.0236). Sex differences in the MCA (p = 0.0028) vanished in relative terms and was absent in the PCA. These findings demonstrate within-day reproducibility of this metric in both arteries. Moreover, hysteresis is not impacted by sex.
Mitotic Chromosome Condensation Driven by a Volume Phase Transition
Authors: Beel Andrew J. , Matteï Pierre-Jean , Kornberg Roger D. 
Published: July 2021

Procedures were devised for the reversible decondensation and recondensation of purified mitotic chromosomes. Computational methods were developed for the quantitative analysis of chromosome morphology in high throughput, enabling the recording of condensation behavior of thousands of individual chromosomes. Established physico-chemical theory for ionic hydrogels was modified for application to chromosomal material and shown to accurately predict the observed condensation behavior. The theory predicts a change of state (a “volume phase transition”) in the course of condensation, and such a transition was shown to occur. These findings, together with classical cytology showing loops of chromatin, lead to the description of mitotic chromosome structure in terms of two simple principles: contraction of length of chromatin fibers by the formation of loops, radiating from a central axis; and condensation of the chromosomal material against the central axis through a volume phase transition.One sentence summaryThe mitotic chromosome is an axially scaffolded ionic hydrogel, undergoing a volume phase transition to achieve a condensed state.
Classification of the plant-associated phenotype of Pseudomonas strains using genome properties and machine learning
Authors: Poncheewin Wasin , van Diepeningen Anne D. , van der Lee Theo AJ , Suarez-Diez Maria , Schaap Peter J. 
Published: July 2021

AbstractThe rhizosphere, the region of soil surrounding roots of plants, is colonized by a unique population of Plant Growth Promoting Rhizobacteria (PGPR). By enhancing nutrient uptake from the soil and through modulation of plant phytohormone status and metabolism, PGPR can increase the stress tolerance, growth and yield of crop plants. Many important PGPR as well as plant pathogens belong to the genus Pseudomonas. There is, however, uncertainty on the divide between phytobeneficial and phytopathogenic strains as previously thought to be signifying genomic features have limited power to separate these strains. Here the Genome properties (GP) common biological pathways annotation system was applied to establish the relationship between the genome wide GP composition and the plant-associated phenotype of 91 Pseudomonas strains representing both phenotypes. GP enrichment analysis, Random Forest model fitting and feature selection revealed 28 discriminating features. A validation dataset of 67 new strains confirmed the importance of the selected features for classification. A number of unexpected discriminating features were found, suggesting involvement of novel molecular mechanisms. The results suggest that GP annotations provide a promising computational tool to better classify the plant-associated phenotype.Author summaryWith a growing population the need to double the agricultural food production is specified. Simultaneously, there is an urgent need to implement sustainable and climate change resilient agricultural practices that preserve natural ecosystems. Cooperative microbiomes play important positive roles in plant growth development and fitness. Properly tuned, these microbiomes can significantly reduce the need for synthetic fertilizers and can replace chemicals in crop pest control. To select beneficial candidates, their traits need to be described and likewise, potential detrimental traits should be avoided. Here we applied GP-based comparative functional genomics, enrichment analysis and Random Forest model fitting to compare known phytobeneficial and phytopathogenic Pseudomonas strains. A number of unexpected discriminating features were found suggesting the involvement of novel molecular mechanisms.