bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualising uncertainty in brightfield to fluorescent image inference withBFNet
Authors: Warchal Scott , Gautier Célia , Dorval Thierry , Stephan Jean-Philippe 
Published: March 2020

AbstractPredicting fluorescently labelled cellular structures from brightfield images is a recent application of convolutional neural networks and has already proven a valuable tool in biological imaging studies. These methods reduce the need for time-consuming manual annotations for supervised datasets, potentially reduce the costs in high-throughput imaging screens, and open up a number of potentially novel analyses. However as with any prediction there can be sources of error and uncertainty. Here we present BFNet, a method to visualise the uncertainty in predicted images by applying Monte Carlo dropout during inference and calculating per-pixel variance as an uncertainty map. Our method demonstrates the ability to highlight regions of an image where prediction is difficult or impossible due to imaging artefacts such as occlusions or out-of-focus images, as well as more general uncertainty when a trained model is applied to new data from different imaging of experimental settings. We have provided a python implementation of the method which is available atgithub.com/swarchal/bfnet.
Long-read shotgun metagenome sequencing using PromethION uncovers novel bacteriophages, their abundance, and interaction with host bacterial immunity in the oral microbiota
Authors: Yahara Koji , Suzuki Masato , Hirabayashi Aki , Suzuki Yutaka , Okazaki Yusuke 
Published: March 2020

AbstractBacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including human microbiomes. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Here, we conducted a long-read metagenomic study of human saliva for the first time using PromethION that requires a smaller amount of DNA than PacBio. Our analyses, which integrated both PromethION and HiSeq data of >30 Gb per sample, revealed N50 ranging from 187-345 kb and thousands of contigs with >1 kb accounting for > 99% of all contigs on which 94-96% of HiSeq reads were mapped. We identified hundreds of viral contigs (95 phages and 333 prophages on an average per sample); 0-43.8% and 12.5-56.3% of the “most confident” phages and prophages, respectively, didn’t cluster with those reported previously and were identified as novel. Our integrated analyses identified highly abundant oral phages/prophages, including a novelStreptococcusphage cluster and nine jumbo phages/prophages. Interestingly, 86% of the phage cluster and 67% of the jumbo phages/prophages contained remote homologs of antimicrobial resistance genes, suggesting their potential role as a source of recombination to generate new resistance genes. Pan-genome analysis of the phages/prophages revealed remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. Functional annotation revealed that the highest fraction of the core genes was enriched in phage morphogenesis, followed by the fraction enriched in host cellular processes. Furthermore, our study suggested that oral phages present in human saliva are under selective pressure for escaping CRISPR immunity.ImportanceDespite the abundance and grave implications oral bacterial viruses in health and disease, little is known regarding the different groups of oral bacterial viruses, their relative abundances under various conditions, and their activities. We provided answers to these questions for the first time utilizing a recently developed sequencer that can capture and sequence long DNA fragments, including viruses, and requires only a small amount of DNA input, making it suitable for analyzing human oral samples. We identified hundreds of viral sequences, including “jumbo” viruses and a distinctive group of highly abundant oral viruses, which often contained parts of antimicrobial resistance genes; the entire repertoire of these viral genes showed remarkable diversity and supported a recently proposed hypothesis that phages modulate oral microbiota through multiple mechanisms. We also revealed genomic signs of coevolution of viruses and host bacteria that have been missed in large viromic studies in humans.
HflX controls hypoxia-induced non-replicating persistence in slow growing mycobacteria
Authors: Ngan Jie Yin Grace , Pasunooti Swathi , Tse Wilford , Meng Wei , Ngan So Fong Cam , Ng Sze Wai , Jaafar Muhammad Taufiq , Jia Huan , Cho Su Lei Sharol , Lim Jieling , Koh Hui Qi Vanessa , Abdulghani Noradibah , Pethe Kevin , Sze Siu Kwan , Lescar Julien , Alonso Sylvie 
Published: March 2020

AbstractGTPase HflX is highly conserved in prokaryotes and is a ribosome splitting factor during heat shock inE. coli.Here we report that HflX produced by slow growingM. tuberculosisandM. bovisBCG is a GTPase that plays a critical role in the pathogen’s transition to a non-replicating, drug-tolerant state in response to hypoxia. Indeed, HflX-deficientM. bovisBCG (KO) replicated markedly faster in the microaerophilic phase of a hypoxia model, that precipitated entry into dormancy. The KO displayed the hallmarks of dormant mycobacteria including phenotypic drug resistance, altered morphology, low intracellular ATP and up-regulated dormancydosregulon. KO-infected mice displayed increased bacterial burden during the chronic phase of infection, consistent with the higher replication rate observedin vitroin microaerophilic phase. Unlike fast-growing mycobacteria, BCG HlfX was not involved in antibiotic resistance under normoxia. Proteomics, pull-down and ribo-sequencing supported that mycobacterial HflX is a ribosome binding protein that controls the translational activity of the cell. Collectively, our study provides further insights into the mechanisms deployed by mycobacteria to adapt to their hypoxic microenvironment.
Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks
Authors: Elliott Kelsey H. , Chen Xiaoting , Salomone Joseph , Chaturvedi Praneet , Schultz Preston A. , Balchand Sai K. , Servetas Jeffrey D. , Zuniga Aimée , Zeller Rolf , Gebelein Brian , Weirauch Matthew T. , Peterson Kevin A. , Brugmann Samantha A. 
Published: March 2020

ABSTRACTDespite a common understanding that Gli TFs are utilized to reiterate a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. We demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the bHLH TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis further revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, ‘divergent’ Gli binding motifs (dGBMs). Functional validation revealed thesedGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.
Differential brain activity in visuo-perceptual regions during landmark-based navigation in young and healthy older adults
Authors: Ramanoël Stephen , Durteste Marion , Bécu Marcia , Habas Christophe , Arleo Angelo 
Published: March 2020

AbstractOlder adults exhibit prominent impairments in their capacity to navigate, reorient in unfamiliar environments or update their path when faced with obstacles. This decline in navigational capabilities has traditionally been ascribed to memory impairments and dysexecutive function whereas the impact of visual aging has often been overlooked. The ability to perceive visuo-spatial information such as salient landmarks is essential to navigate in space efficiently. To date, the functional and neurobiological factors underpinning landmark processing in aging remain insufficiently characterized. To address this issue, this study used functional magnetic resonance imaging (fMRI) to investigate the brain activity associated with landmark-based navigation in young and healthy older participants. Twenty-five young adults (μ=25.4 years, σ=4.7; 7F) and twenty-one older adults (μ=73.0 years, σ=3.9; 10F) performed a virtual navigation task in the scanner in which they could only orient using salient landmarks. The underlying whole-brain patterns of activity as well as the functional roles of scene-selective regions, the parahippocampal place area (PPA), the occipital place area (OPA), and the retrosplenial cortex (RSC) were analyzed. We found that older adults’ navigational abilities were diminished compared to young adults’ and that the two age groups relied on distinct navigational strategies to solve the task. Better performance during landmark-based navigation was found to be associated with increased neural activity in an extended neural network comprising several cortical and cerebellar regions. Direct comparisons between age groups further revealed that young participants had enhanced anterior temporal activity. In addition, young adults only were found to recruit occipital areas corresponding to the cortical projection of the central visual field during landmark-based navigation. The region-of-interest analysis revealed increased OPA activation in older adult participants. There were no significant between-group differences in PPA and RSC activations. These results hint at the possibility that aging diminishes fine-grained information processing in occipital and temporal regions thus hindering the capacity to use landmarks adequately for navigation. This work helps towards a better comprehension of the neural dynamics subtending landmark-based navigation and it provides new insights on the impact of age-related visuo-spatial processing changes on navigation capabilities.
In-depth characterization of Staurosporine induced proteome thermal stability changes
Authors: Chernobrovkin Alexey L. , Lengqvist Johan , Körner Cindy Caceres , Amadio Daniele , Friman Tomas , Molina Daniel Martinez 
Published: March 2020

AbstractCellular thermal shift assay (CETSA) coupled with high-resolution mass-spectrometry (MS) has proven to be indispensable tool to track thermal stability changes in cellular proteins caused by various external or internal perturbations. One of the major applications of CETSA MS is still binding profile characterization of small molecule drugs. Before applying the method for characterization of novel compound it is crucially important to understand the limitations, sensitivity and ways to improve the throughput of the different method implementations. Here we present deep comprehensive profiling of Staurosporine induced proteome thermal stability alteration utilizing different experiment layouts. By applying unbiased straightforward sample preparation and data analysis approaches we were able to compare and benchmark different experiment layouts for detecting compound-induced protein stability changes in CETSA MS experiments.
Whole transcriptome data of uninfected andNosema ceranae-infected midguts of eastern honeybee workers
Authors: Chen Huazhi , Zhou Dingding , Du Yu , Xiong Cuiling , Zheng Yanzhen , Chen Dafu , Guo Rui 
Published: March 2020

ABSTRACTApis cerana ceranais a subspecies of eastern honeybee,Apis cerana. Nosema ceranaeis a widespread fungal parasite of honeybee, causing heavy losses for beekeeping industry all over the world. In this article, total RNA of normal midguts (AcCK1, AcCK2) andN. ceranae-infected midguts ofA. c. ceranaworkers at 7 d and 10 d post inoculation (AcT1, AcT2) were respectively isolated followed by strand-specific cDNA library construction and next-generation RNA sequencing. In tolal, 56270223688, 44860946964, 78991623806, and 92712308296 raw reads were derived from AcCK1, AcCK2, AcT1 and AcT2, respectively. Following strict quality control, 54495191388, 43570608753, 76708161525, and 89467858351 clean reads were obtained, with Q30 value of 95.80%, 95.99%, 96.07% and 96.04%, and GC content of 44.20%, 43.44%, 44.83% and 43.63%, respectively. The raw data were submitted to the NCBI Sequence Read Archive database and connected to BioProject PRJNA562784. These data offers a valuable resource for deep investigation of mechanisms underlying eastern honeybee responding toN. ceranaeinfection and host-fungal parasite interaction during microsporidiosis.Value of the DataCurrent dataset offers a valuable resource for exploring mRNAs, lncRNAs and circRNAs involved in response ofA. c. ceranaworker toN. ceranaeinfection.The accessible data can be used to investigate differential expression pattern and regulatory network of non-coding RNAs inA. c. ceranaworkers’ midguts responding toN. ceranaechallenge.This data will enable a better understanding of the molecular mechanism regulating eastern honeybee-N. ceranaeinteraction.
Genetic disruption of the Blood Brain Barrier leads to protective barrier formation at the Glia Limitans
Authors: Hollier Pierre-Louis , Guimbal Sarah , Mora Pierre , Diop Aïssata , Cornuault Lauriane , Couffinhal Thierry , Gadeau Alain-Pierre , Renault Marie-Ange , Chapouly Candice 
Published: March 2020

AbstractRecent work demonstrated that Central Nervous System (CNS) inflammation induces endothelial Blood Brain Barrier (BBB) opening as well as the formation of a tight junction barrier between reactive astrocytes at the Glia Limitans. We hypothesized that these two barriers may be reciprocally regulated by each other state and further, that the CNS parenchyma may acquire protection from the reactive astrocytic Glia Limitans not only in neuro-inflammation but also when BBB integrity is compromised under resting condition, without pathology. Previous studies identified Sonic hedgehog (Shh) astrocytic secretion as implicated in stabilizing the BBB during neuropathology and we recently demonstrated that desert hedgehog (Dhh) is expressed at the BBB in adults.Here we unraveled the role of the morphogen Dhh in maintaining BBB tightness and, using endothelial Dhh knockdown as a model of permeable BBB, we demonstrated that a double barrier system comprising both the BBB and Glia Limitans, is implemented in the CNS and regulated by a crosstalk going from endothelial cell to astrocytes.First, we showed that, under neuro-inflammatory conditions, Dhh expression is severely down regulated at the BBB and that Dhh is necessary for endothelial intercellular junction integrity as Dhh knockdown leads to CNS vascular leakage. We then demonstrated that, in Dhh endothelial knockout (DhhECKO) mice which display an open BBB, astrocytes are reactive and express the tight junction Claudin 4 (Cldn4) and showed that astrocytes can respond to signals secreted by the permeable endothelial BBB by becoming reactive and expressing Cldn4. To examine the consequences of the above results on disease severity, we finally induced multiple sclerosis in DhhECKOmice versus control littermates and showed that the pathology is less severe in the knockout animals due to Glia Limitans tightening, in response to BBB leakage, which drives inflammatory infiltrate entrapment into the perivascular space. Altogether these results suggest that genetic disruption of the BBB generates endothelial signals capable of driving the implementation of a secondary barrier at the Glia Limitans to protect the parenchyma. The concept of a reciprocally regulated CNS double barrier system has implications for treatment strategies in both the acute and chronic phases of multiple sclerosis pathophysiology.
Decoding mRNA translatability and stability from 5’UTR
Authors: Jia Longfei , Mao Yuanhui , Ji Quanquan , Dersh Devin , Yewdell Jonathan W. , Qian Shu-Bing 
Published: March 2020

AbstractPrecise control of protein synthesis by engineering sequence elements in 5’ untranslated region (5’UTR) remains a fundamental challenge. To accelerate our understanding ofcis-regulatory code embedded in 5’UTR, we devised massively parallel reporter assays from a synthetic mRNA library composed of over one million 5’UTR variants. A completely randomized 10-nucleotide sequence preceding an upstream open reading frame (uORF) and downstream GFP leads to a broad range of mRNA translatability and stability in mammalian cells. While efficient translation protects mRNA from degradation, uORF translation triggers mRNA decay in a UPF1-dependent manner. We also identified translational inhibitory elements in 5’UTR with G-quadruplex as a mark for mRNA decay in the P-body. Unexpectedly, an unstructured A-rich element in 5’UTR, while enabling cap-independent translation, destabilizes mRNAs in the absence of translation. Our results not only expose diverse sequence features of 5’UTR in controlling mRNA translatability, but also reveal ribosome-dependent and -independent mRNA surveillance pathways.
Rapidly predicting vancomycin resistance ofEnterococcus faeciumthrough MALDI-TOF MS spectrum obtained in real-world clinical microbiology laboratory
Authors: Wang Hsin-Yao , Lu Ko-Pei , Chung Chia-Ru , Tseng Yi-Ju , Lee Tzong-Yi , Horng Jorng-Tzong , Chang Tzu-Hao , Wu Min-Hsien , Lin Ting-Wei , Liu Tsui-Ping , Lu Jang-Jih 
Published: March 2020

AbstractEnterococcus faeciumis one of the leading pathogens in the world. In this study, we proposed a strategy to rapidly and accurately distinguish vancomycin-resistantEnterococcus faecium(VREfm) and vancomycin-susceptibleE. faecium(VSEfm) to help doctors correctly determine the use of vancomycin by a machine learning (ML)-based algorithm. A predictive model was developed and validated to distinguish VREfmand VSEfmby analyzing MALDI-TOF MS spectra of uniqueE. faeciumisolates from different specimen types. Firstly, 5717 mass spectra, including 2795 VREfmand 2922 VSEfm, were used to develop the algorithm. And 2280 mass spectra of isolates, namely 1222 VREfmand 1058 VSEfm, were used to externally validate the algorithm. The random forest-based algorithm demonstrated good classification performances for overall specimens, whose mean AUROC in 5-fold cross validation, time-wise validation, and external validation was all greater than 0.84. For the detection of VREfmin blood, sterile body fluid, urinary tract, and wound, the AUROC in external validation was also greater than 0.84. The predictions with algorithms were significantly more accurate than empirical antibiotic use. The accuracy of antibiotics administration could be improved by 30%. And the algorithm could provide rapid antibiotic susceptibility results at least 24 hours ahead of routine laboratory tests. The turn-around-time of antibiotic susceptibility could be reduced by 50%. In conclusion, a ML algorithm using MALDI-TOF MS spectra obtained in routine workflow accurately differentiated VREfmfrom VSEfm, especially in blood and sterile body fluid, which can be applied to facilitate the clinical testing process due to its accuracy, generalizability, and rapidness.
Tape lures swell bycatch on a Mediterranean island harbouring illegal bird trapping
Authors: Sebastianelli Matteo , Savva Georgios , Moysi Michaella , Kirschel Alexander N. G. 
Published: March 2020

AbstractMediterranean islands are critical for migrating birds, providing shelter and sustenance for millions of individuals each year. Humans have long exploited bird migration through hunting and illegal trapping. On the island of Cyprus, trapping birds during their migratory peak is considered a local tradition, but has long been against the law. Illegal bird trapping is a lucrative business, however, with trappers using tape lures that broadcast species’ vocalizations because it is expected to increase numbers of target species. Yet, by how much the use of song playback increases capture rates remains underappreciated. In particular, it is not known whether song playback of target species affects bycatch rates. Here, we show with the use of playback experiments that song playback is highly effective in luring birds towards trapping sites. We found that playback increases six to eight times the number of individuals of target species captured, but also significantly increases bycatch. Our findings thus show that in contrast to popular belief that tape lures are a selective trapping method, they also lead to increased captures of non-target species, which can include species of conservation concern.
Nuclear Transport Factor 2 (NTF2) suppresses metastatic melanoma by modifying cell migration, metastasis, and gene expression
Authors: Vuković Lidija D. , White Karen H. , Gigley Jason P. , Levy Daniel L. 
Published: March 2020

SUMMARYWhile changes in nuclear structure and organization are frequently observed in cancer cells, relatively little is known about how nuclear architecture impacts cancer progression and pathology. To begin to address this question, we studied Nuclear Transport Factor 2 (NTF2) because its levels decrease during melanoma progression. We show that increasing NTF2 expression in metastatic melanoma cells reduces cell proliferation and motility while increasing apoptosis. We also demonstrate that increasing NTF2 expression in these cells significantly inhibits metastasis and increases survival of mice. Mechanistically, we show that NTF2 levels affect the expression and nuclear positioning of a number of genes associated with cell proliferation and migration. We propose that by decreasing nuclear size and/or lamin A nuclear localization, ectopic expression of NTF2 in metastatic melanoma alters chromatin organization to generate a gene expression profile with characteristics of primary melanoma, concomitantly abrogating several phenotypes associated with advanced stage cancer bothin vitroandin vivo. Thus NTF2 acts as a melanoma tumor suppressor to maintain proper nuclear structure and gene expression and could be a novel therapeutic target to improve health outcomes of melanoma patients.
ATM-deficient lung, prostate and pancreatic cancer cells are acutely sensitive to the combination of olaparib and the ATR inhibitor AZD6738
Authors: Jette Nicholas R. , Radhamani Suraj , Ye Ruiqiong , Yu Yaping , Arthur Greydon , Goutam Siddhartha , Bizmar Tarek A , Kumar Mehul , Bose Pinaki , Yip Steven , Kolinsky Michael , Lees-Miller Susan P. 
Published: March 2020

AbstractBackgroundThe ataxia telangiectasia mutated (ATM) protein kinase is mutated in several human cancers, presenting potential opportunities for targeted cancer therapy. We previously reported that the poly-ADP ribose polymerase (PARP) inhibitor olaparib induced transient G2 arrest but not cell death in ATM-deficient A549 lung cancer cells, while the combination of olaparib with the ATM-, Rad3-related (ATR) inhibitor VE-821 induced cell death. Here, we show that the clinically relevant ATR inhibitor, AZD6738, sensitizes ATM-deficient A549 lung, prostate and pancreatic cancer cells to olaparib.MethodsATM was depleted from A549 lung cancer cells, PC-3 prostate cancer cells and Panc 10.05 pancreatic cancer cells, and the effects of olaparib alone and in combination with AZD6738 were determined.ResultsThe combination of olaparib plus AZD6738 induced cell death in ATM-deficient lung, prostate and pancreatic cancer cells with little effect on their ATM-proficient counterparts.ConclusionsLung, prostate and pancreatic patients whose tumours exhibit loss or inactivation of ATM may benefit from combination of a PARP inhibitor plus an ATR inhibitor.