Miracle-dz/UniFAR-FTUs huggingface dataset:
Duplicated Myosin V Genes in Teleosts Show Evolutionary Rate Variations among the Motor and Cargo-Binding Domains

Abstract We analyzed evolutionary rates of conserved, duplicated myosin V (myo5) genes in nine teleost species to examine the outcomes of duplication events. Syntenic analysis and ancestral chromosome mapping suggest one tandem gene duplication event leading to the appearance of myo5a and myo5c, two rounds of whole genome duplication for vertebrates, and an additional round of whole genome duplication for teleosts account for the presence and location of the myo5 genes and their duplicates in teleosts and other vertebrates and the timing of the duplication events. Phylogenetic analyses reveal a previously unidentified myo5 clade that we refer to now as myo5bb. Analysis using dN/dS rate comparisons revealed large regions within duplicated myo5 genes that are highly conserved. Codons identified in other studies as encoding functionally important portions of the Myo5a and Myo5b proteins are shown to be highly conserved within the newly identified myo5bb clade and in other myo5 duplicates. As much as 30% of 319 codons encoding the cargo-binding domain in the myo5aa genes are conserved in all three codon positions in nine teleost species. For the myo5bb cargo-binding domain, 6.6% of 336 codons have zero substitutions in all nine teleost species. Using molecular evolution assays, we identify the myo5bb branch as being subject to evolutionary rate variation with the cargo-binding domain, having 20% of the sites under positive selection and the motor domain having 8% of its sites under positive selection. The high number of invariant codons coupled with relatively high dN/dS values in the region of the myo5 genes encoding the ATP-binding domain suggests the encoded proteins retain function and may have acquired novel functions associated with changes to the cargo-binding domain.
Is neutrophil gelatinase-associated lipocalin a good diagnostic marker for renal injury in asphyxiated preterm infants?

Background: The objective of this study is to evaluate the value of neutrophil gelatinase-associated lipocalin (NGAL) for becoming a good endogenous marker of renal function in asphyxial preterm babies. Materials and Methods: This is a two-center retrospective study. Between October 2016 and October 2017, 71 asphyxial preterm infants were included in asphyxia group. Seventy babies were randomly included in control group. Samples were tested at 24, 48, and 96 h after birth. Quantitative data were compared by independent sample t-test or repeated measures ANOVA. For qualitative data, Pearson's Chi-squared test was performed. Draw ROC and compare the area under the curve (AUC), 95% confidence interval for AUC, specificity (Spe), sensitivity (Sen), and Youden index (Sen+Spe-1) at 24-h, 48-h, and 96-h time points. Results: (1) There are no significant differences concerning on baseline data. However, blood gas, Apgar score, and resuscitation showed a significant difference (P < 0.05). (2) In 24-h samples, only uNGAL and estimated glomerular filtration rate (eGFR) showed differences between the two groups (P < 0.05). In 48-h samples, significant differences could be found in uKIM-1, uNGAL, blood urea nitrogen, and eGFR (P < 0.05). In 96-h samples, almost all indicators have significant differences except urine output and eGFR (P < 0.05). (3) All biomarkers showed statistical difference in the three time points (P < 0.05), but only uNGAL showed a downward trend after the increase of expression. (4) uNGAL has better Sen and Spe than other indicators (24-h AUC 0.870, Youden index 0.606; 48-h AUC 0.879, Youden index 0.692; and 96-h AUC 0.806, Youden index 0.606). Conclusion: uNGAL has a better distinguishability in asphyxial neonates compared with other indicators. Certainly, a larger sample, prospective study is still needed.
The Value of Prognostic Nutritional Index in Follicular Lymphoma

Objectives: Previous studies reported that prognostic nutritional index (PNI), a marker of host inflammatory and nutritional status, is associated with prognoses in a number of cancer types. Thus, we investigated PNI at diagnosis as a prognostic factor in FL. Methods: We reviewed FL patients in Tuen Mun Hospital, Hong Kong from 2000 to 2014 (n=88). PNI was calculated by serum albumin (g/L)+5×absolute lymphocyte count (109/L). We determined the best PNI cut-off value using receiver-operating characteristic curves. The extent to which progression-free survival (PFS) and overall survival differed by PNI cut-off was assessed using Kaplan-Meier and log-rank tests. Cox proportional hazards model was utilized to adjust for covariates. Results: The best cut-off value for PNI was determined to be 45. Patients with high PNI (>45) had a higher complete response (CR) rate after primary treatment, 46 of 61 (75.4%) patients with high PNI had CR, compared with 10 of 23 (43.5%) for low PNI (2-sample test of proportions P-value=0.006). Further, higher PNI at relapse as a continuous variable was associated with superior postprogression survival with a hazard ratio (HR) 0.88 (95% confidence interval [CI], 0.81-0.96). In multivariate analysis, high PNI at diagnosis had superior PFS (adjusted HR of 0.37; 95% CI, 0.15-0.93). Conclusions: PNI was shown to be independent prognostic factor of PFS in FL. It is a cheap and widely available biomarker. Future study is needed to validate its prognostic value and clinical utility in a prospective cohort.
Content guidance for mobile phones short message service (SMS)-based antiretroviral therapy adherence and appointment reminders: a review of the literature

ABSTRACT Mobile phones are increasingly being used to support health activities, including the care and management of people living with HIV/AIDS. Short message service (SMS) has been explored as a means to optimize and support behaviour change. However, there is minimal guidance on messaging content development. The purpose of this review was to inform the content of SMS messages for mobile health (mHealth) initiatives designed to support anti-retroviral therapy adherence and clinic appointment keeping in resource-limited settings. PubMed, OvidMedline, Google Scholar, K4Health’s mHealth Evidence database, the mHealth Working Group project resource, and Health COMpass were searched. A request to online communities for recommendations on message content was also made. 1010 unique sources were identified, of which 51 were included. The information was organized into three categories: pre-message development, message development, and security and privacy. Fifteen of the publications explicitly provided their message content. Important lessons when developing the content of SMS were: (1) conducting formative research; (2) grounding content in behaviour change theory; and (3) reviewing proposed content with experts. Best practices exist for developing message content for behaviour change. Efforts should be continued to apply lessons learned from the existing literature to inform mHealth initiatives supporting HIV/AIDS care and treatment.
Genome and Transcriptome Sequencing of the Astaxanthin-Producing Green Microalga, Haematococcus pluvialis

Abstract Haematococcus pluvialis is a freshwater species of Chlorophyta, family Haematococcaceae. It is well known for its capacity to synthesize high amounts of astaxanthin, which is a strong antioxidant that has been utilized in aquaculture and cosmetics. To improve astaxanthin yield and to establish genetic resources for H. pluvialis, we performed whole-genome sequencing, assembly, and annotation of this green microalga. A total of 83.1 Gb of raw reads were sequenced. After filtering the raw reads, we subsequently generated a draft assembly with a genome size of 669.0 Mb, a scaffold N50 of 288.6 kb, and predicted 18,545 genes. We also established a robust phylogenetic tree from 14 representative algae species. With additional transcriptome data, we revealed some novel potential genes that are involved in the synthesis, accumulation, and regulation of astaxanthin production. In addition, we generated an isoform-level reference transcriptome set of 18,483 transcripts with high confidence. Alternative splicing analysis demonstrated that intron retention is the most frequent mode. In summary, we report the first draft genome of H. pluvialis. These genomic resources along with transcriptomic data provide a solid foundation for the discovery of the genetic basis for theoretical and commercial astaxanthin enrichment.
Decode-and-Forward Two-Way Relaying with Network Coding and Opportunistic Relay Selection

In this paper, we study a decode-and-forward two-way relaying network. We propose an opportunistic two-way relaying (O-TR) scheme based on joint network coding and opportunistic relaying. In the proposed scheme, one single "best relay" is selected by MaxMin criterion to perform network coding on two decoded symbols sent from two sources, and then to broadcast the network-coded symbols back to the two sources. The performance of the proposed scheme is analyzed, and verified through Monte Carlo simulations. Results show that the proposed scheme achieves a better performance compared to the fully-distributed space-time two-way relaying (FDST-TR), which has been identified as the best decode-and-forward two-way relaying method so far.
Representation and Manipulation of Genomic Tuples in R

GenomicTuples is an R/Bioconductor package (R Core Team 2016; Wolfgang Huber et al 2015) that defines general purpose containers for storing and manipulating genomic tuples. A genomic tuple of size m is of the form chromosome:strand:{pos_1, pos_2, . , pos_m} where pos_1 < pos_2 < . < pos_m are positions along the chromosome. The difference between a genomic tuple and a genomic range/interval is like that of a difference between an ordered set and an interval. For example, the genomic 2-tuple chr3:+:{65, 77} differs from the genomic range chr3:+:[65, 77] by not including any of the intervening loci, chr3:+:66 to chr3:+:76.
Genomic kinship construction to enhance genetic analyses in the human connectome project data

Imaging genetic analyses quantify genetic control over quantitative measurements of brain structure and function using coefficients of relationship (CR) that code the degree of shared genetics between subjects. CR can be inferred through self‐reported relatedness or calculated empirically using genome‐wide SNP scans. We hypothesized that empirical CR provides a more accurate assessment of shared genetics than self‐reported relatedness. We tested this in 1,046 participants of the Human Connectome Project (HCP) (480 M/566 F) recruited from the Missouri twin registry. We calculated the heritability for 17 quantitative traits drawn from four categories (brain diffusion and structure, cognition, and body physiology) documented by the HCP. We compared the heritability and genetic correlation estimates calculated using self‐reported and empirical CR methods Kinship‐based INference for GWAS (KING) and weighted allelic correlation (WAC). The polygenetic nature of traits was assessed by calculating the empirical CR from chromosomal SNP sets. The heritability estimates based on whole‐genome empirical CR were higher but remained significantly correlated (r ∼0.9) with those obtained using self‐reported values. Population stratification in the HCP sample has likely influenced the empirical CR calculations and biased heritability estimates. Heritability values calculated using empirical CR for chromosomal SNP sets were significantly correlated with the chromosomal length (r 0.7) suggesting a polygenic nature for these traits. The chromosomal heritability patterns were correlated among traits from the same knowledge domains; among traits with significant genetic correlations; and among traits sharing biological processes, without being genetically related. The pedigree structures generated in our analyses are available online as a web‐based calculator (www.solar-eclipse-genetics.org/HCP).
Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1

Abstract As the second most common malignant bone tumor in children and adolescents, Ewing sarcoma is initiated and exacerbated by a chimeric oncoprotein, most commonly, EWS-FLI1. In this study, we apply epigenomic analysis to characterize the transcription dysregulation in this cancer, focusing on the investigation of super-enhancer and its associated transcriptional regulatory mechanisms. We demonstrate that super-enhancer-associated transcripts are significantly enriched in EWS-FLI1 target genes, contribute to the aberrant transcriptional network of the disease, and mediate the exceptional sensitivity of Ewing sarcoma to transcriptional inhibition. Through integrative analysis, we identify MEIS1 as a super-enhancer-driven oncogene, which co-operates with EWS-FLI1 in transcriptional regulation, and plays a key pro-survival role in Ewing sarcoma. Moreover, APCDD1, another super-enhancer-associated gene, acting as a downstream target of both MEIS1 and EWS-FLI1, is also characterized as a novel tumor-promoting factor in this malignancy. These data delineate super-enhancer-mediated transcriptional deregulation in Ewing sarcoma, and uncover numerous candidate oncogenes which can be exploited for further understanding of the molecular pathogenesis for this disease.
"That's What Everyone Else Is Saying...": Collaborative Reflection-in-Action during Creative Activities

: With the progression of more user-friendly music production software packages (i.e., Apple’s GarageBand) and the importance of social media, learners are engaging with music without having any formal education on important musical concepts. It has been suggested that novice music learners should start with what they know how to intuitively do already, which will allow them to move to more sophisticated musical concepts (e.g., notation, intervals). However, music production is becoming more a group project than a solitary one in which everyone in a group has a voice. A fourth grade classroom (N = 36) engaged in a music curriculum using the learning software Impromptu. Findings suggest that when students are able to reflect-in-action, their reflections become building blocks for others in the group to use and add to their knowledge base.
Impact of resilience on health in older adults: a cross-sectional analysis from the International Mobility in Aging Study (IMIAS)

Objectives Self-rated health (SRH) is a predictor of objective health measures, including mortality and morbidity. The link between resilience and SRH among the elderly is unclear. We aim to examine whether resilience aligns with SRH and, secondarily, whether resilience can override the negative health consequences of adverse childhood experiences (ACE). Design and setting We use 2012, 2014 and 2016 data from the International Mobility in Aging Study, a longitudinal cohort study that collects survey and biophysical data from Albania, Brazil, Colombia and Canada. The main independent variables were resilience and ACE (social and economic). Participants Community-dwelling 65–74 year olds (in 2012) were recruited through primary care registers. The sample size of the study was 1506. Primary outcome The outcome measure was SRH. Results We found that sex, site, economic ACE, current income sufficiency, current depressive symptoms, current physical function and current resilience were associated with current SRH. In regression analyses, we showed that the association between ACE and SRH disappeared once factors such as sex, site, income, depression, physical health and resilience were considered. Conclusions The association between resilience and health poses a compelling argument for building resilience throughout life.
Comprehensive review of the identification of essential genes using computational methods: focusing on feature implementation and assessment

Essential genes have attracted increasing attention in recent years due to the important functions of these genes in organisms. Among the methods used to identify the essential genes, accurate and efficient computational methods can make up for the deficiencies of expensive and time-consuming experimental technologies. In this review, we have collected researches on essential gene predictions in prokaryotes and eukaryotes and summarized the five predominant types of features used in these studies. The five types of features include evolutionary conservation, domain information, network topology, sequence component and expression level. We have described how to implement the useful forms of these features and evaluated their performance based on the data of Escherichia coli MG1655, Bacillus subtilis 168 and human. The prerequisite and applicable range of these features is described. In addition, we have investigated the techniques used to weight features in various models. To facilitate researchers in the field, two available online tools, which are accessible for free and can be directly used to predict gene essentiality in prokaryotes and humans, were referred. This article provides a simple guide for the identification of essential genes in prokaryotes and eukaryotes.
Dynamics of intracellular stress-induced tRNA trafficking

Abstract Stress is known to induce retrograde tRNA translocation from the cytoplasm to the nucleus but translocation kinetics and tRNA-spatial distribution have not been characterized previously. We microinject fluorescently-labeled tRNA into living cells and use confocal microscopy to image tRNA spatial distribution in single cells at various levels of starvation and to determine translocation rate constants. Retrograde tRNA translocation occurs reversibly, within minutes after nutrition depletion of the extracellular medium. Such nutritional starvation leads to down-regulation of tRNA nuclear import and nearly complete curtailment of its nuclear export. Nuclear tRNA accumulation is suppressed in cells treated with the translation inhibitor puromycin, but is enhanced in cells treated with the microtubule inhibitor nocodazole. tRNA in the cytoplasm exhibits distinct spatial distribution inconsistent with diffusion, implying that such distribution is actively maintained. We propose that tRNA biological complexes and/or cytoplasmic electric fields are the likely regulators of cytoplasmic tRNA spatial distribution.
New Fluvirucinins C1 and C2 Produced by a Marine Derived Actinomycete

Two new fluvirucin aglycones, named fluvirucinins C1 and C2 (1-2), have been isolated from the ethyl acetate mycelial cake extract of the fermentation broth of a marine sponge-associated actinomycete. Fluvirucinins C1 (1) and C2 (2) represent a new type of 14-membered macrolactam aglycon, structurally related with the common aglycon of the known fluvirucins. Their structures were elucidated on the basis of 1D and 2D NMR analyses, as well as HRESIMS experiments. The antimicrobial and cytotoxic activities of compounds 1 and 2 have been evaluated, but no significant activities found for fluvirucinins C1 and C2.
High dosage of zinc modulates T-cells in a time-dependent manner within porcine gut-associated lymphatic tissue

Abstract Zn serves as a powerful feed additive to reduce post-weaning diarrhoea in pigs. However, the mechanisms responsible for Zn-associated effects on the adaptive immune responses following feeding of a very high dosage of Zn remain elusive. In this study, we examined the T-cell response in gut-associated lymphatic tissues of seventy-two weaned piglets. Piglets received diets with 57 mg Zn/kg (low Zn concentration, LZn), 164 mg Zn/kg (medium Zn concentration, MZn) or 2425 mg Zn/kg (high Zn concentration, HZn) mg Zn/kg feed for 1, 2 or 4 weeks. We observed that feeding the HZn diet for 1 week increased the level of activated T-helper cells (CD4+ and CD8α dim) compared with feeding MZn and LZn (P<0·05). In addition, we observed higher transcript amounts of interferon γ and T-box 21 (TBET) in the HZn group compared with the MZn and LZn groups (P<0·05). A gene set enrichment analysis revealed an over-representation of genes associated with ‘cytokine signalling in immune system’. Remarkably, feeding of a very high Zn dosage led to a switch in the immune response after 2 weeks. We detected higher relative cell counts of CD4+CD25high regulatory T-helper cells (P<0·05) and a higher expression of forkhead box P3 (FOXP3) transcripts (P<0·05). After 4 weeks of feeding a high-dosage Zn diet, the relative CD4+ T-cell count (P<0·05) and the relative CD8β + T-cell count (P<0·1) were reduced compared with the MZn group. We hypothesise that after 1 week the cellular T-helper 1 response is switched on and after 2 weeks it is switched off, leading to decreased numbers of T-cells.
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

Motivation: Logic modeling is a useful tool to study signal transduction across multiple pathways. Logic models can be generated by training a network containing the prior knowledge to phospho-proteomics data. The training can be performed using stochastic optimization procedures, but these are unable to guarantee a global optima nor to report the complete family of feasible models. This, however, is essential to provide precise insight in the mechanisms underlaying signal transduction and generate reliable predictions. Results: We propose the use of Answer Set Programming (ASP) to explore exhaustively the space of feasible logic models. Towards this end, we have developed caspo, an open-source Python package which provides a powerful platform to learn and characterize logic models by leveraging the rich modeling language and solving technologies of ASP. We illustrate the usefulness of caspo by revisiting a model of pro-growth and inflammatory pathways in liver cells. We show that, if experimental error is taken into account, there are thousands (11,700) of models compatible with the data. Despite the large number, we can extract structural features from the models, such as links that are always (or never) present or modules that appear in a mutual exclusive fashion. To further characterize this family of models, we investigate the input-output behavior of the models. We find 91 behaviors across the 11,700 models and we suggest new experiments to discriminate among them. Our results underscore the importance of characterizing in a global and exhaustive manner the family of feasible models, with important implications for experimental design. Availability: caspo is freely available for download (license GPLv3) and as a web service at http://caspo.genouest. org/.
1.7  μm wavelength tunable gain-switched fiber laser and its application to spectroscopic photoacoustic imaging.

Recently demonstrated bond-selective photoacoustic (PA) imaging has revealed the importance of 1.7 μm laser sources. In this Letter, we demonstrate a gain-switched thulium-doped fiber laser with continuous tuning from 1690 to 1765 nm by using an electrically driven acousto-optical tunable filter. Micro-joule laser pulses with a shot-to-shot intensity variation of 1.6% and a pulse duration of 150 ns are obtained. The laser source is then harnessed to implement a PA microscopy system, of which the lateral resolution is estimated to be 15.6 μm by scanning the edge of a black tape. The PA spectra of butter, rapeseed oil, and adipose tissue are measured, and they show a consistent absorption peak of around 1720 nm. Photoacoustic microscopy imaging of the adipose tissue demonstrates a high optical absorption contrast of lipids and the superiority of the laser for spectroscopic PA detection.