bluuebunny/crossref_metadata_2025_split huggingface dataset:
Read correction for non-uniform coverages
Authors: Marchet Camille , Dufresne Yoann , Limasset Antoine 
Published: June 2019

AbstractNext generation sequencing produces large volumes of short sequences with broad applications. The noise due to sequencing errors led to the development of several correction methods. The main correction paradigm expects a high (from 30-40X) uniform coverage to correctly infer a reference set of subsequences from the reads, that are used for correction. In practice, most accurate methods use k-mer spectrum techniques to obtain a set of reference k-mers. However, when correcting NGS datasets that present an uneven coverage, such as RNA-seq data, this paradigm tends to mistake rare variants for errors. It may therefore discard or alter them using highly covered sequences, which leads to an information loss and may introduce bias. In this paper we present two new contributions in order to cope with this situation.First, we show that starting from non-uniform sequencing coverages, a De Bruijn graph can be cleaned from most errors while preserving biological variability. Second, we demonstrate that reads can be efficiently corrected via local alignment on the cleaned De Bruijn graph paths. We implemented the described method in a tool dubbed BCT and evaluated its results on RNA-seq and metagenomic data. We show that the graph cleaning strategy combined with the mapping strategy leads to save more rare k-mers, resulting in a more conservative correction than previous methods. BCT is also capable to better take advantage of the signal of high depth datasets. We suggest that BCT, being scalable to large metagenomic datasets as well as correcting shallow single cell RNA-seq data, can be a general corrector for non-uniform data. Availability: BCT is open source and available at github.com/Malfoy/BCT under the Affero GPL License.
Genomic Analyses of SLAMF7 CAR-T Cells Manufactured by Sleeping Beauty Transposon Gene Transfer for Immunotherapy of Multiple Myeloma
Authors: Miskey Csaba , Amberger Maximilian , Reiser Michael , Prommersberger Sabrina , Beckmann Julia , Machwirth Markus , Einsele Hermann , Hudecek Michael , Bonig Halvard , Ivics Zoltán ,   on behalf of the CARAMBA consortium
Published: June 2019

ABSTRACTWidespread treatment of human diseases with gene therapies necessitates the development of gene transfer vectors that integrate genetic information effectively, safely and economically. Accordingly, significant efforts have been devoted to engineer novel tools that i) achieve high-level stable gene transfer at low toxicity to the host cell; ii) induce low levels of genotoxicity and possess a ‘safe’ integration profile with a high proportion of integrations into safe genomic locations; and iii) are associated with acceptable cost per treatment and scalable/exportable vector production to serve large numbers of patients. The Sleeping Beauty (SB) transposon has been transformed into a vector system that is fulfilling these requirements.In the CARAMBA project, we use SB transposition to genetically modify T cells with a chimeric antigen receptor (CAR) specific for the SLAMF7 antigen, that is uniformly and highly expressed on malignant plasma cells in multiple myeloma. We have demonstrated that SLAMF7 CAR-T cells confer specific and very potent anti-myeloma reactivity in pre-clinical models, and are therefore preparing a Phase I/IIa clinical trial of adoptive immunotherapy with autologous, patient-derived SLAMF7-CAR T cells in multiple myeloma (EudraCT Nr. 2019-001264-30/CARAMBA-1).Here we report on the characterization of genomic safety attributes in SLAMF7 CAR-T cells that we prepared in three clinical-grade manufacturing campaigns under good manufacturing practice (GMP), using T cells that we obtained from three healthy donor volunteers. In the SLAMF7 CAR-T cell product, we determined the average transposon copy number, the genomic insertion profile, and presence of residual SB100X transposase. The data show that the SLAMF7 CAR transposon had been inserted into the T cell genome with the close-to-random distribution pattern that is typical for SB, and with an average transposon copy number ranging between 6 and 12 per T cell. No residual SB100X transposase could be detected by Western blotting in the infusion products. With these attributes, the SLAMF7 CAR-T products satisfy criteria set forth by competent regulatory authorities in order to justify administration of SLAMF7 CAR-T cells to humans in the context of a clinical trial. These data set the stage for the CARAMBA clinical trial, that will be the first in the European Union to use virus-free SB transposition for CAR-T engineering.DisclosuresThis project is receiving funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 754658 (CARAMBA).
Dissociable neural systems for unconditioned acute and sustained fear
Authors: Hudson Matthew , Seppälä Kerttu , Putkinen Vesa , Sun Lihua , Glerean Enrico , Karjalainen Tomi , Hirvonen Jussi , Nummenmaa Lauri 
Published: June 2019

AbstractFear protects organisms by increasing vigilance and preparedness, and by coordinating survival responses during life-threatening encounters. The fear circuit must thus operate on multiple timescales ranging from preparatory sustained alertness to acute fight-or-flight responses. Here we studied the brain basis of sustained (“looming”) and acute fear using naturalistic functional magnetic resonance imaging (fMRI) enabling analysis of different time-scales of fear responses. Subjects (N = 51) watched feature-length horror movies while their hemodynamic brain activity was measured with fMRI. Time-variable intersubject correlation (ISC) was used to quantify the reliability of brain activity across participants, and seed-based phase synchronization was used for characterizing dynamic connectivity. Subjective ratings of fear were obtained from a separate sample, and were used to assess how synchronization and functional connectivity varied with emotional intensity. These data suggest that acute and sustained fear are supported by distinct neural pathways, with sustained fear amplifying mainly sensory responses, and acute fear increasing activity in brainstem, thalamus, amygdala and cingulate cortices. Sustained fear increased ISC in regions associated with acute fear, and also amplified functional connectivity within this network. The results were replicated in two independent experiments with different subject samples. The functional interplay between cortical networks involved in sustained anticipation of, and acute response to, threat involves a complex and dynamic interaction that depends on the proximity of threat, and the need to employ threat appraisals and vigilance for decision making and response selection.
A resource for analyzing C. elegans’ gene expression data using transcriptional gene modules and module-weighted annotations
Authors: Cary Michael , Podshivalova Katie , Kenyon Cynthia 
Published: June 2019

AbstractIdentification of gene co-expression patterns (gene modules) is widely used for grouping functionally-related genes during transcriptomic data analysis. An organism-wide atlas of high quality fundamental gene modules would provide a powerful tool for unbiased detection of biological signals from gene expression data. Here, using a method of independent component analysis we call DEXICA, we have defined and optimized 209 modules that broadly represent transcriptional wiring of the key experimental organism C. elegans. Interrogation of these modules reveals processes that are activated in long-lived mutants in cases where traditional analyses of differentially-expressed genes fail to do so. Using this resource, users can easily identify active modules in their gene expression data and access detailed descriptions of each module. Additionally, we show that modules can inform the strength of the association between a gene and an annotation (e.g. GO term). Analysis of “module-weighted annotations” improves on several aspects of traditional annotation-enrichment tests and can aid in functional interpretation of poorly annotated genes. Interactive access to the resource is provided at http://genemodules.org/.
Reach and Grasp Altered in Pantomime String-Pulling: A Test of the Action/Perception Theory in a Bilateral Reaching Task
Authors: Singh Surjeet , Mandziak Alexei , Barr Kalob , Blackwell Ashley A , Mohajerani Majid H , Wallace Douglas G , Whishaw Ian Q 
Published: June 2019

AbstractThe action/perception theory of cortical organization is supported by the finding that pantomime hand movements of reaching and grasping are different from real movements. Frame-by-frame video analysis and MATLAB®based tracking examined real/pantomime differences in a bilaterally movement, string-pulling, pulling down a rope with hand-over-hand movements. Sensory control of string-pulling varied from visually-direct when cued, visually-indirect when non cued and somatosensory controlled in the absence of vision. Cued grasping points were visual tracked and the pupils dilated in anticipation of the grasp, but when noncued, visual tracking and pupil responses were absent. In real string-pulling, grasping and releasing the string featured an arpeggio movement in which the fingers close and open in the sequence 5 through 1 (pinki first, thumb last); in pantomime, finger order was reversed, 1 through 5. In real string-pulling, the hand is fully opened and closed to grasp and release; in pantomime, hand opening was attenuated and featured a gradual opening centered on the grasp. The temporal structure of arm movements in real string-pulling featured up-arm movements that were faster than down-arm movement. In pantomime, up/down movements had similar speed. In real string-pulling, up/down arm movements were direct and symmetric; in pantomime, they were more circular and asymmetric. That pantomime string-pulling featured less motoric and temporal complexity than real string-pulling is discussed in relation to the action/perception theory and in relation to the idea that pantomimed string-pulling may feature the substitution of gestures for real movement.Significant StatementMost laboratory studies investigating hand movements made by humans feature single hand movements, the current study presents a novel string-pulling task to study bimanual coordination of left and right hands in real and pantomime conditions. The results show that pantomime string-pulling featured less motoric and temporal complexity than real string-pulling. These findings are relevant to the contemporary theory of action and perception that the dorsal stream (parietal cortex) is related to actions and the ventral stream (temporal cortex) is related to perception.
Rescue of Tomato spotted wilt tospovirus entirely from cDNA clones, establishment of the first reverse genetics system for a segmented (-)RNA plant virus
Authors: Feng Mingfeng , Cheng Ruixiang , Chen Minglong , Guo Rong , Li Luyao , Feng Zhike , Wu Jianyan , Xie Li , Hong Jian , Zhang Zhongkai , Kormelink Richard , Tao Xiaorong 
Published: June 2019

AbstractThe group of negative strand RNA viruses (NSVs) includes not only dangerous pathogens of medical importance but also serious plant pathogens of agronomical importance. Tomato spotted wilt tospovirus (TSWV) is one of those plant NSVs that cause severe diseases on agronomic crops and pose major threats to global food security. Its negative-strand segmented RNA genome has, however, always posed a major obstacle to molecular genetic manipulation. In this study, we report the complete recovery of infectious TSWV entirely from cDNA clones, the first reverse genetics (RG) system for a segmented plant NSV. First, a replication and transcription competent mini-genome replication system was established based on 35S-driven constructs of the S(-)-genomic (g) or S(+)-antigenomic (ag) RNA template, flanked by a 5’ Hammerhead and 3’ Ribozyme sequence of Hepatitis Delta virus, a nucleocapsid (N) protein gene and codon-optimized viral RNA dependent RNA polymerase (RdRp) gene. Next, a movement competent mini-genome replication system was developed based on M(-)-gRNA, which was able to complement cell-to-cell and systemic movement of reconstituted ribonucleoprotein complexes (RNPs) of S RNA replicon. After further optimization, infectious TSWV and derivatives carrying eGFP reporters were successfully rescuedin plantavia simultaneous expression of full-length cDNA constructs coding for S(+)-agRNA, M(-)-gRNA and L(+)-agRNA. Viral rescue occurred in the additional presence of various viral suppressors of RNAi, but TSWV NSs interfered with the rescue of genomic RNA. The establishment of a RG system for TSWV now allows detailed molecular genetic analysis of all aspects of tospovirus life cycle and their pathogenicity.SignificanceFor many different animal-infecting segmented negative-strand viruses (NSVs), a reverse genetics system has been established that allows the generation of mutant viruses to study disease pathology and the role ofcis- andtrans-acting elements in the virus life cycle. In contrast to the relative ease to establish RG systems for animal-infecting NSVs, establishment of such system for the plant-infecting NSVs with a segmented RNA genome so far has not been successful. Here we report the first reverse genetics system for a segmented plant NSV, the Tomato spotted wilt tospovirus, a virus with a tripartite RNA genome. The establishment of this RG system now provides us with a new and powerful platform to study their disease pathology during a natural infection.
CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes
Authors: Efremova Mirjana , Vento-Tormo Miquel , Teichmann Sarah A. , Vento-Tormo Roser 
Published: June 2019

AbstractCell-cell communication mediated by receptor-ligand complexes is crucial for coordinating diverse biological processes, such as development, differentiation and responses to infection. In order to understand how the context-dependent crosstalk of different cell types enables physiological processes to proceed, we developed CellPhoneDB, a novel repository of ligands, receptors and their interactions1. Our repository takes into account the subunit architecture of both ligands and receptors, representing heteromeric complexes accurately. We integrated our resource with a statistical framework that predicts enriched cellular interactions between two cell types from single-cell transcriptomics data. Here, we outline the structure and content of our repository, the procedures for inferring cell-cell communication networks from scRNA-seq data and present a practical step-by-step guide to help implement the protocol. CellPhoneDB v2.0 is a novel version of our resource that incorporates additional functionalities to allow users to introduce new interacting molecules and reduce the time and resources needed to interrogate large datasets. CellPhoneDB v2.0 is publicly available at https://github.com/Teichlab/cellphonedb and as a user-friendly web interface at http://www.cellphonedb.org/. In our protocol, we demonstrate how to reveal meaningful biological discoveries from CellPhoneDB v2.0 using published data sets.
APOC2 accelerates colorectal cancer progression via modulating lipid metabolism and transcriptional activity of PHF8
Authors: Chen Jian , Xiao Chao , Wang Yupeng , Song Guohe , Wang Xiaoliang , Liu Xueni , Chen Jiayi , Lu Huijun , Kuai Jing , Qin Xuebin , Guo Weiping , Tang Huamei , Peng Zhihai 
Published: June 2019

AbstractThe apolipoproteins (APOs) are the major proteins in blood lipid transportation. Emerging evidence has demonstrated that APOs might exert important function in tumor cells, but the underlying mechanism remains inclusive. In this study, we aim to explore the relationship between APOC2 dysfunction and colorectal cancer (CRC) malignancy. By analyzing the expression of APOC2 in 507 patients with CRC, we demonstrated that the APOC2 was overexpressed and associated with poor prognosis in CRC. We then found that high levels of APOC2 resulted in proliferation, invasion and metastasis of CRC cells in vitro and in vivo. Mechanistically, we revealed that APOC2 directly interacted with FASN which resulted in decreased levels of omega-3 fatty acids and increased levels of alpha-ketoglutarate (α-KG). Both RNA-seq and ChIP-seq analysis revealed that APOC2 overexpression resulted accumulation of α-KG leads to activation on the transcriptional program of PHF8 and thereby contributed to activation on genes involved in cell proliferation, invasion and metastasis. Together, our study unveiled the oncogenic role of APOC2 in tumor cells, which sheds new light on the potential of APOC2 as a biomarker in the prognosis of CRC.
A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes
Authors: Paritosh Kumar , Yadava Satish Kumar , Singh Priyansha , Bhayana Latika , Mukhopadhyay Arundhati , Gupta Vibha , Bisht Naveen Chandra , Zhang Jianwei , Kudrna David , Copetti Dario , Wing Rod A , Lachagari Vijay Bhaskar Reddy , Pradhan Akshay Kumar , Pental Deepak 
Published: June 2019

AbstractBrassica juncea (AABB; genome size ∼920 Mb), commonly referred to as mustard, is a natural allopolyploid of two diploid species – B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ∼100x PacBio single-molecule real-time (SMRT) reads providing contigs with an N50 value of >5Mb. Assembled contigs were corrected and scaffolded with BioNano optical mapping. Three different linkage maps containing a large number of GBS markers were developed and used to anchor scaffolds/contigs to the 18 linkage groups of B. juncea. The resulting chromosome-scale assembly is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content, and gene block associations. Both A and B genomes contain highly fragmented gene block arrangements. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The genome assembly reported here will provide a fillip to the breeding work on oleiferous types of mustard that are grown extensively in the dry land areas of South Asia and elsewhere.
Robust emergence of sharply tuned place cell responses in hippocampal neurons with structural and biophysical heterogeneities
Authors: Basak Reshma , Narayanan Rishikesh 
Published: June 2019

ABSTRACTHippocampal pyramidal neurons sustain propagation of fast electrical signals and are electrotonically non-compact structures exhibiting cell-to-cell variability in their complex dendritic arborization. In this study, we demonstrate that sharp place-field tuning and several somato-dendritic functional maps concomitantly emerge despite the presence of geometrical heterogeneities in these neurons. We establish this employing an unbiased stochastic search strategy involving thousands of models that spanned several morphologies and distinct profiles of dispersed synaptic localization and channel expression. Mechanistically, employing virtual knockout models, we explored the impact of bidirectional modulation in dendritic spike prevalence on place-field tuning sharpness. Consistent with prior literature, we found that across all morphologies, virtual knockout of either dendritic fast sodium channels orN-methyl-D-aspartate receptors led to a reduction in dendritic spike prevalence, whereasA-type potassium channel knockouts resulted in a nonspecific increase in dendritic spike prevalence. However, place-field tuning sharpness was critically impaired in all three sets of virtual knockout models, demonstrating that sharpness in feature tuning is maintained by an intricate balance between mechanisms that promote and those that prevent dendritic spike initiation. From the functional standpoint of the emergence of sharp feature tuning and intrinsic functional maps, within this framework, geometric variability was compensated by a combination of synaptic democracy, the ability of randomly dispersed synapses to yield sharp tuning through dendritic spike initiation, and ion-channel degeneracy. Our results suggest electrotonically non-compact neurons to be endowed with several degrees of freedom, encompassing channel expression, synaptic localization and morphological micro-structure, in achieving sharp feature encoding and excitability homeostasis.
An integrated personal and population-based Egyptian genome reference
Authors: Wohlers Inken , Künstner Axel , Munz Matthias , Olbrich Michael , Fähnrich Anke , Calonga-Solís Verónica , Ma Caixia , Hirose Misa , El-Mosallamy Shaaban , Salama Mohamed , Busch Hauke , Ibrahim Saleh 
Published: June 2019

AbstractThe human genome is composed of chromosomal DNA sequences consisting of bases A, C, G and T – the blueprint to implement the molecular functions that are the basis of every individual’s life. Deciphering the first human genome was a consortium effort that took more than a decade and considerable cost. With the latest technological advances, determining an individual’s entire personal genome with manageable cost and effort has come within reach. Although the benefits of the all-encompassing genetic information that entire genomes provide are manifold, only a small number of de novo assembled human genomes have been reported to date 1–3, and few have been complemented with population-based genetic variation 4, which is particularly important for North Africans who are not represented in current genome-wide data sets 5–7. Here, we combine long- and short-read whole-genome next-generation sequencing data with recent assembly approaches into the first de novo assembly of the genome of an Egyptian individual. The resulting assembly demonstrates well-balanced quality metrics and is complemented with high-quality variant phasing via linked reads into haploblocks, which we can associate with gene expression changes in blood. To construct an Egyptian genome reference, we further assayed genome-wide genetic variation occurring in the Egyptian population within a representative cohort of 110 Egyptian individuals. We show that differences in allele frequencies and linkage disequilibrium between Egyptians and Europeans may compromise the transferability of European ancestry-based genetic disease risk and polygenic scores, substantiating the need for multi-ethnic genetic studies and corresponding genome references. The Egyptian genome reference represents a comprehensive population data set based on a high-quality personal genome. It is a proof of concept to be considered by the many national and international genome initiatives underway. More importantly, we anticipate that the Egyptian genome reference will be a valuable resource for precision medicine targeting the Egyptian population and beyond.