bluuebunny/crossref_metadata_2025_split huggingface dataset:
GenGraph: a python module for the simple generation and manipulation of genome graphs
Authors: Ambler Jon Mitchell , Mulaudzi Shandukani , Mulder Nicola 
Published: October 2019

Abstract

Background
As sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of Mycobacterium tuberculosis, one must often choose between using a genome that is closely related to the isolate, or one that is annotated in detail. One promising solution to this problem is through the graph based representation of collections of genomes as a single genome graph. Though there are currently a handful of tools that can create genome graphs and have demonstrated the advantages of this new paradigm, there still exists a need for flexible tools that can be used by researchers to overcome challenges in genomics studies.

Results
We present GenGraph, a Python toolkit and accompanying modules that use existing multiple sequence alignment tools to create genome graphs. Python is one of the most popular coding languages for the biological sciences, and by providing these tools, GenGraph makes it easier to experiment and develop new tools that utilise genome graphs. The conceptual model used is highly intuitive, and as much as possible the graph structure represents the biological relationship between the genomes. This design means that users will quickly be able to start creating genome graphs and using them in their own projects. We outline the methods used in the generation of the graphs, and give some examples of how the created graphs may be used. GenGraph utilises existing file formats and methods in the generation of these graphs, allowing graphs to be visualised and imported with widely used applications, including Cytoscape, R, and Java Script.

Conclusions
GenGraph provides a set of tools for generating graph based representations of sets of sequences with a simple conceptual model, written in the widely used coding language Python, and publicly available on Github.
Convergent evolution in toothed whale cochleae
Authors: Park Travis , Mennecart Bastien , Costeur Loïc , Grohé Camille , Cooper Natalie 
Published: October 2019

AbstractBackgroundOdontocetes (toothed whales) are the most species-rich marine mammal lineage. The catalyst for their evolutionary success is echolocation - a form of biological sonar that uses high-frequency sound, produced in the forehead and ultimately detected by the cochlea. The ubiquity of echolocation in odontocetes across a wide range of physical and acoustic environments suggests that convergent evolution of cochlear shape is likely to have occurred. To test this, we used SURFACE; a method that fits Ornstein-Uhlenbeck (OU) models with stepwise AIC (Akaike Information Criterion) to identify convergent regimes on the odontocete phylogeny, and then tested whether convergence in these regimes was significantly greater than expected by chance.ResultsWe identified three convergent regimes: (1) True’s (Mesoplodon mirus) and Cuvier’s (Ziphius cavirostris) beaked whales; (2) sperm whales (Physeter macrocephalus) and all other beaked whales sampled; and (3) pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales and Dall’s porpoise (Phocoenoides dalli). Interestingly the ‘river dolphins’, a group notorious for their convergent morphologies and riverine ecologies, do not have convergent cochlear shapes. The first two regimes were significantly convergent, with habitat type and dive type significantly correlated with membership of the sperm whale + beaked whale regime.ConclusionsThe extreme acoustic environment of the deep ocean likely constrains cochlear shape, causing the cochlear morphology of sperm and beaked whales to converge. This study adds support for cochlear morphology being used to predict the ecology of extinct cetaceans.
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Authors: Ibn-Salem Jonas , Andrade-Navarro Miguel A. 
Published: October 2019

Abstract

Background
Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues.

Results
While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are co-immunoprecipitated and sequenced. This produces minor ChIP-seq signals at loop anchor regions close to the directly bound site. We use the position and shape of ChIP-seq signals around CTCF motif pairs to predict whether they interact or not. We implemented this approach in a prediction method, termed Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C). We applied 7C to all CTCF motif pairs within 1 Mb in the human genome and validated predicted interactions with high-resolution Hi-C and ChIA-PET. A single ChIP-seq experiment from known architectural proteins (CTCF, Rad21, Znf143) but also from other TFs (like TRIM22 or RUNX3) predicts loops accurately. Importantly, 7C predicts loops in cell types and for TF ChIP-seq datasets not used in training.

Conclusion
7C predicts chromatin loops which can help to associate TF binding sites to regulated genes. Furthermore, profiling of hundreds of ChIP-seq datasets results in novel candidate factors functionally involved in chromatin looping. Our method is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC.
RNA-Seq based transcriptome analysis during bovine viral diarrhoea virus (BVDV) infection
Authors: Liu Cun , Liu Yanhan , Liang Lin , Cui Shangjin , Zhang Yanming 
Published: October 2019

Abstract

Background
Bovine viral diarrhoea virus (BVDV) is the member of the genus Pestivirus within the Flaviviridae family and responsible for severe economic losses in the cattle industry. BVDV can employ ‘infect-and-persist’ strategy and ‘hit-and-run’ strategy to remain associated with hosts and thus contributes to BVDV circulation in cattle herds. BVDV have also evolved various strategies to evade the innate immunity of host. To further understand the mechanisms by which BVDV overcomes the host cell innate immune response and provide more clues for further understanding the BVDV-host interaction, in this descriptive study, we conducted a investigation of differentially expressed genes (DEGs) of the host during BVDV infection by RNA-Seq analysis.

Results
Our analysis identified 1297, 1732, 3072, and 1877 DEGs in the comparison groups mock vs. MDBK cells infected with BVDV post 2 h (MBV2h), mock vs. MBV6h, mock vs. MBV12h, and mock vs. MBV24h, respectively. The reproducibility and repeatability of the results were validated by RT-qPCR. Enrichment analyses of GO annotations and KEGG pathways revealed the host DEGs that are potentially induced by BVDV infection and may participate in BVDV-host interactions. Protein-protein interaction (PPI) network analyses identified the potential interactions among the DEGs. Our findings suggested that BVDV infection induced the upregulation of genes involved in lipid metabolism. The expression of genes that have antiviral roles, including ISG15, Mx1, OSA1Y, were found to be downregulated and are thus potentially associated with the inhibition of host innate immune system during BVDV infection. The expression levels of F3, C1R, KNG1, CLU, C3, FB, SERPINA5, SERPINE1, C1S, F2RL2, and C2, which belong to the complement and coagulation signalling cascades, were downregulated during BVDV infection, which suggested that the complement system might play a crucial role during BVDV infection.

Conclusion
In this descriptive study, our findings revealed the changes in the host transcriptome expression profile during BVDV infection and suggested that BVDV-infection induced altering the host’s metabolic network, the inhibition of the expression of antiviral proteins and genes within the complement system might be contributed to BVDV proliferation. The above findings provided unique insights for further studies on the mechanisms underlying BVDV-host interactions.
Water-deficit responsive microRNAs in the primary root growth zone of maize
Authors: Seeve Candace M. , Sunkar Ramanjulu , Zheng Yun , Liu Li , Liu Zhijie , McMullen Michael , Nelson Sven , Sharp Robert E. , Oliver Melvin J. 
Published: October 2019

Abstract

Background
MicroRNA-mediated gene regulatory networks play a significant role in plant growth and development and environmental stress responses.

Results
We identified 79 microRNAs (miRNAs) and multiple miRNA variants (isomiRs) belonging to 26 miRNA families in the primary root growth zone of maize seedlings grown at one of three water potentials: well-watered (− 0.02 MPa), mild water deficit stress (− 0.3 MPa), and severe water deficit stress (− 1.6 MPa). The abundances of 3 miRNAs (mild stress) and 34 miRNAs representing 17 families (severe stress) were significantly different in water-deficit stressed relative to well-watered controls (FDR < 0.05 and validated by stem loop RT-qPCR). Degradome sequencing revealed 213 miRNA-regulated transcripts and trancriptome profiling revealed that the abundance of 77 (miRNA-regulated) were regulated by water-defecit stress. miR399e,i,j-3p was strongly regulated by water-defcit stress implicating the possibility of nutrient deficiency during stress.

Conclusions
We have identified a number of maize miRNAs that respond to specific water deficits applied to the primary root growth zone. We have also identified transcripts that are targets for miRNA regulation in the root growth zone under water-deficit stress. The miR399e,i,j-3p that is known to regulate phosphate uptake in response to nutrient deficiencies responds to water-deficit stress, however, at the seedling stage the seed provides adequate nutrients for root growth thus miR399e,i,j-3p may play a separate role in water-deficit responses. A water-deficit regulated maize transcript, similar to known miR399 target mimics, was identified and we hypothesized that it is another regulatory player, moderating the role of miR399e,i,j-3p, in primary root growth zone water deficit responses.
Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent
Authors: Choi In-Su , Schwarz Erika N. , Ruhlman Tracey A. , Khiyami Mohammad A. , Sabir Jamal S. M. , Hajarah Nahid H. , Sabir Mernan J. , Rabah Samar O. , Jansen Robert K. 
Published: October 2019

AbstractBackgroundOrganelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae).ResultsPhylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus,Libidibia,Haematoxylum, andLeucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2,7,11and13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2,rpl2,rpl10,rps1,rps19,sdh3,sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2,ccmFcandrps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasiticLophophytum(Balanophoraceae).ConclusionThis study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.
Potential use of a diluted high-relaxivity gadolinium-based intra-articular contrast agent for magnetic resonance arthrography: an in-vitro study
Authors: Messina Carmelo , Albano Domenico , Orlandi Davide , Chianca Vito , Corazza Angelo , Ferrari Federica , Gitto Salvatore , Sconfienza Luca Maria 
Published: October 2019

Abstract

Background
Magnetic resonance arthrography (MRA) requires intra-articular injection of gadolinium-based diluted paramagnetic contrast material. To our knowledge, gadobenate dimeglumine (Gd-BOPTA) has never been used for intra-articular applications. Our aim was to test in vitro different concentrations of Gd-BOPTA to be potentially used to perform MRA.

Methods
Gd-BOPTA was diluted in saline (NaCl 0.9%) to achieve different concentrations (4 mmol/l; 2 mmol/l; 1 mmol/l; 0.67 mmol/l; 0.5 mmol/l). Six sets of five sterile pipes were prepared with 5 ml of each solution, five sets added with 0.5 ml of fresh synovial fluid. Two separate pipes were prepared with 5 ml of gadopentetate dimeglumine (Gd-DTPA) at 2 mmol/l, one pipe added with 0.5 ml of synovial fluid. Pipes were imaged using a T1-weighted sequence at 1.5 T. For each pipe, signal intensity (SI) in arbitrary units (au) was measured.

Results
SI reproducibility range was 86–99%. Mean Gd-BOPTA SI in pipes containing synovial fluid increased from 1236 ± 8au (0.5 mmol/l) up to 1610 ± 44au (1 mmol/l) and down to 1405 ± 33au (4 mmol/l). Mean Gd-BOPTA SI in pipes without synovial fluid increased from 1184 ± 29au (0.5 mmol/l) up to 1530 ± 38au (1 mmol/l), and down to 1347 ± 39au (4 mmol/l). SI of pipes without synovial fluid was lower than that of pipes with synovial fluid for both Gd-BOPTA and Gd-DTPA (P ≤ 0.002). Regarding pipes with synovial fluid, mean Gd-DTPA SI at 2 mmol/l was 1246 ± 27au. Compared with Gd-BOPTA, SI was not different at 0.5 mmol/l (− 0.2%, P = 0.587) while it was higher (P < 0.001) at all other concentrations (range + 13.3%[4 mmol/l] − + 28.3%[1 mmol/l]). Regarding pipes without synovial fluid, mean Gd-DTPA SI at 2 mmol/l was 1275 ± 56au. Compared with Gd-BOPTA, SI was lower at 0.5 mmol/l (− 6.8%,P < 0.001), while it was higher (P < 0.001) at all other concentrations (range + 6.1%[4 mmol/l] − + 19.6% [1 mmol/l]).

Conclusions
In vitro, Gd-BOPTA at 1 mmol/ had a + 28% SI increase in comparison to Gd-DTPA 2 mmol/l. SI similar to Gd-DTPA can be obtained using one fourth concentration of Gd-BOPTA.
The diffuse involvement of anti-N-methyl-D-aspartate receptor encephalitis in brain: a case report
Authors: Jiang Yun , Ma Jianpeng , Gong Tao , Hao Hongjun , Chen Haibo 
Published: October 2019

Abstract

Background
Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is a severe and most common autoimmune encephalitis in patients under 40 years old. Anti-NMDAR encephalitis has various clinical and neuroimaging findings. Here we report a special case of an anti-NMDAR encephalitis who had diffuse lesions in bilateral hemispheres with mild mass effects in left basal ganglia area.

Case presentations
A 28-year-old female anti-NMDAR encephalitis patient mainly presented with headache and fever. Brain magnetic resonance image (MRI) showed slightly contrasted diffuse lesions, involving the left temporal and frontal lobes, left basal ganglia area and splenium of corpus callosum, as well as the right frontal lobe, with mild edema surrounded in the left basal ganglia area. Cerebrospinal fluid (CSF) revealed a moderate pleocytosis with normal protein and glucose levels. Anti-NMDAR antibodies were identified in CSF. Transvaginal ovarian ultrasound did not reveal an ovarian teratoma. The patient was treated with immunoglobulin and steroid, and had a good recovery.

Conclusions
Anti-NMDAR encephalitis has no special clinical manifestations and brain MRI is highly variable, which could be unremarkable or abnormal involving white and grey matters. The extensive lesions in frontal and temporal lobes, and basal ganglia area, with mild mass effects, have not been described previously. Recognition of various changes in brain MRI will enable the early detection of anti-NMDAR antibody and then effective treatments.
Revisiting: “A pre-post study of a multi-country scale up of resuscitation training of facility birth attendants: does helping babies breathe training save lives?”
Authors: Berkelhamer Sara , Singhal Nalini 
Published: October 2019

Abstract

Background
Helping Babies Breathe (HBB) is a low cost, skills-based neonatal resuscitation education program designed specifically for use in low resource settings. Studies from Tanzania, India and Nepal have demonstrated that HBB training results in decreased rates of fresh still birth and/or neonatal mortality. However, less is known regarding the impact of training on neonatal mortality at a population level. Bellad et al. utilized (BMC Pregnancy Childbirth. 2016;16 (1):222) utilized population based registries to evaluate outcomes before and after training of facility birth attendants. Their study entitled “A pre-post study of a multi-country scale up of resuscitation training of facility birth attendants: Does Helping Babies Breathe training save lives?” suggested facility based training was not associated with consistent improvements in neonatal mortality on a population level.

Discussion
Combining outcomes from three diverse settings may have under-estimated the impact of HBB training. We remain concerned that the modest benefits observed in the Kenyan site were lost with compiling of data.

Summary
The statement that HBB “was not associated with consistent improvements in mortality” may lead to the mistaken conclusion that improvements in neonatal mortality were not seen, when in fact, they were in selected cohorts. With numerous studies demonstrating potential for reduced neonatal mortality as a result of HBB training, we encourage interpretation of these findings in the context of local care.
Effects of sanitation practices on adverse pregnancy outcomes in India: a conducive finding from recent Indian demographic health survey
Authors: Patel Ratna , Gupta Ajay , Chauhan Shekhar , Bansod Dhananjay W. 
Published: October 2019

Abstract

Background
Several risk factors predisposing women and their live-borns to adverse outcomes during pregnancy have been documented. Little is known about sanitation being a factor contributing to adverse pregnancy outcomes in India. The role of sanitation in adverse pregnancy outcomes remains largely unexplored in the Indian context. This study is an attempt to bring the focus on sanitation as a factor in adverse pregnancy outcome. Along with the sanitation factors, few confounder variables have also been studied in order to understand the adverse pregnancy outcomes.

Methods
The study is based on the fourth round of National Family Health Survey (NFHS-IV) covering 26,972 married women in the age-group 15–49. The study variables include the mother’s age, Body Mass Index (BMI), education, anemia, and Antenatal care (ANC) visits during their last pregnancy. The household level variable includes place of residence, religion, caste, wealth index, access to toilet, type of toilet, availability of water within toilet premises, and facility of hand wash near the toilet. Children study variables include Low Birth Weight (LBW), the order of birth (Parity), and the death of the children of the women in the last 5 years. The target variable Adverse Pregnancy Outcome (APO) was constructed using children born with low birth weight or died during the last pregnancy.

Results
We calculated both adjusted as well as unadjusted odds ratios for a better understanding of the association between sanitation and adverse pregnancy outcomes. Findings from the study showed that women who did not have access to a toilet within the house had a higher risk of adverse pregnancy outcome. In the multivariable model, no association was observed for adverse pregnancy outcome among women who did not have access to toilet and women who used shared toilet. Teenage (15–19 years), uneducated, underweight and anemic mothers were more likely to face APO as compare to other mothers in similar characteristics group.

Conclusions
Our findings contribute to the decidedly less available literature on maternal sanitation behaviour and adverse pregnancy outcomes. Our results support that sanitation is a very significant aspect for women who are about to deliver a baby as there was an association between sanitation and adverse pregnancy outcome. Education on sanitation practices is the need of the hour as much as it needs to follow.