Healthcare knowledge graph construction: A systematic review of the state-of-the-art, open issues, and opportunities.

The incorporation of data analytics in the healthcare industry has made significant progress, driven by the demand for efficient and effective big data analytics solutions. Knowledge graphs (KGs) have proven utility in this arena and are rooted in a number of healthcare applications to furnish better data representation and knowledge inference. However, in conjunction with a lack of a representative KG construction taxonomy, several existing approaches in this designated domain are inadequate and inferior. This paper is the first to provide a comprehensive taxonomy and a bird's eye view of healthcare KG construction. Additionally, a thorough examination of the current state-of-the-art techniques drawn from academic works relevant to various healthcare contexts is carried out. These techniques are critically evaluated in terms of methods used for knowledge extraction, types of the knowledge base and sources, and the incorporated evaluation protocols. Finally, several research findings and existing issues in the literature are reported and discussed, opening horizons for future research in this vibrant area.

Smartphone Use Among University Students During COVID-19 Quarantine: An Ethical Trigger.

To reduce the spread of COVID-19, Jordan enforced 10 weeks of home quarantine in the spring of 2020. A cross-sectional study was designed to assess this extended quarantine's effect on smartphone addiction levels among undergraduates. A random sample of 6,157 undergraduates completed an online questionnaire (mean age 19.79 ± 1.67 years; males 28.7%). The questionnaire contains different sections to collect socio-demographic, socio-economic, academic, quarantine-related information, and smartphone usage. The smartphone addiction scale-short version was used to assess the degree of addiction during the quarantine. The mean addiction score across the whole sample was 35.66 ± 12.08, while the prevalence of addiction among participants was 62.4% (63.5% in males and 61.9% in females). The majority of the participants (85%) reported that their smartphone usage during the quarantine increased or greatly increased (27.6 and 57.2%, respectively), with some 42% using their smartphones for more than 6 h a day. Nevertheless, three-quarters of the students wished to reduce their smartphone usage. Several demographic and quarantine factors have been assessed, and students' gender, the field of study, parental education, household income in addition to the location of quarantine (urban, rural) and the house specifications (apartment, independent house, with/without a garden) showed statistically significant associations with smartphone addiction during the quarantine. Female students, students studying scientific- and medical-related majors compared to those studying humanity majors, those with higher incomes, those who had been quarantined in an apartment without a garden, and those who lived in urban areas showed significantly higher addiction scores.

Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes.

BACKGROUND: Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. Such techniques are used routinely in both rodent and human species. DNA methylation is a dynamic process that plays a role in epigenetic regulation of gametogenesis and development. In mammalian oocytes, DNA methylation establishment regulates gene expression in the embryos. This regulation is particularly important for a class of genes, imprinted genes, whose expression patterns are crucial for the next generation. The aim of this work was to establish an in vitro culture system for immature mouse oocytes that will allow manipulation of specific factors for a deeper analysis of regulatory mechanisms for establishing transcription regulation-associated methylation patterns. RESULTS: An in vitro culture system was developed from immature mouse oocytes that were grown to germinal vesicles (GV) under two different conditions: normoxia (20% oxygen, 20% O2) and hypoxia (5% oxygen, 5% O2). The cultured oocytes were sorted based on their sizes. Reduced representative bisulphite sequencing (RRBS) and RNA-seq libraries were generated from cultured and compared to in vivo-grown oocytes. In the in vitro cultured oocytes, global and CpG-island (CGI) methylation increased gradually along with oocyte growth, and methylation of the imprinted genes was similar to in vivo-grown oocytes. Transcriptomes of the oocytes grown in normoxia revealed chromatin reorganisation and enriched expression of female reproductive genes, whereas in the 5% O2 condition, transcripts were biased towards cellular stress responses. To further confirm the results, we developed a functional assay based on our model for characterising oocyte methylation using drugs that reduce methylation and transcription. When histone methylation and transcription processes were reduced, DNA methylation at CGIs from gene bodies of grown oocytes presented a lower methylation profile. CONCLUSIONS: Our observations reveal changes in DNA methylation and transcripts between oocytes cultured in vitro with different oxygen concentrations and in vivo-grown murine oocytes. Oocytes grown under 20% O2 had a higher correlation with in vivo oocytes for DNA methylation and transcription demonstrating that higher oxygen concentration is beneficial for the oocyte maturation in ex vivo culture condition. Our results shed light on epigenetic mechanisms for the development of oocytes from an immature to GV oocyte in an in vitro culture model.

Whom Should Be Saved? A Proposed Ethical Framework for Allocating Scarce Medical Resources to COVID-19 Patients Using Fuzzy Logic.

COVID-19 is a global pandemic that affected the everyday life activities of billions around the world. It is an unprecedented crisis that the modern world had never experienced before. It mainly affected the economic state and the health care system. The rapid and increasing number of infected patients overwhelmed the healthcare infrastructure, which causes high demand and, thus, shortage in the required staff members and medical resources. This shortage necessitates practical and ethical suggestions to guide clinicians and medical centers when allocating and reallocating scarce resources for and between COVID-19 patients. Many studies proposed a set of ethical principles that should be applied and implemented to address this problem. In this study, five different ethical principles based on the most commonly recommended principles and aligned with WHO guidelines and state-of-the-art practices proposed in the literature were identified, and recommendations for their applications were discussed. Furthermore, a recent study highlighted physicians' propensity to apply a combination of more than one ethical principle while prioritizing the medical resource allocation. Based on that, an ethical framework that is based on Fuzzy inference systems was proposed. The proposed framework's input is the identified ethical principles, and the output is a weighted value (per patient). This value can be used as a rank or a priority factor given to the patients based on their condition and other relevant information, like the severity of their disease status. The main idea of implementing fuzzy logic in the framework is to combine more than one principle when calculating the weighted value, hence mimicking what some physicians apply in practice. Moreover, the framework's rules are aligned with the identified ethical principles. This framework can help clinicians and guide them while making critical decisions to allocate/reallocate the limited medical resources during the current COVID-19 crisis and future similar pandemics.

Effect of COVID-19 Quarantine on the Sleep Quality and the Depressive Symptom Levels of University Students in Jordan During the Spring of 2020.

Objectives: This study was designed to assess the effect of COVID-19 home quarantine and its lifestyle challenges on the sleep quality and mental health of a large sample of undergraduate University students in Jordan. It is the first study applied to the Jordanian population. The aim was to investigate how quarantine for several weeks changed the students' habits and affected their mental health. Methods: A cross-sectional study was conducted using a random representative sample of 6,157 undergraduate students (mean age 19.79 ± 1.67 years, males 28.7%) from the University of Jordan through voluntarily filling an online questionnaire. The Pittsburgh Sleep Quality Index (PSQI) and the Center for Epidemiologic Studies-Depression Scale (CES-D) were used to assess sleep quality and depressive symptoms, respectively. Results: The PSQI mean score for the study participants was 8.1 ± 3.6. The sleep quality of three-quarters of the participants was negatively affected by the extended quarantine. Nearly half of the participants reported poor sleep quality. The prevalence of poor sleep quality among participants was 76% (males: 71.5% and females: 77.8%). Similarly, the prevalence of the depressive symptoms was 71% (34% for moderate and 37% for high depressive symptoms), with females showing higher prevalence than males. The overall mean CES-D score for the group with low depressive symptoms is 9.3, for the moderate group is 19.8, while it is 34.3 for the high depressive symptoms group. More than half of the students (62.5%) reported that the quarantine had a negative effect on their mental health. Finally, females, smokers, and students with decreased income levels during the extended quarantine were the common exposures that are significantly associated with a higher risk of developing sleep disturbances and depressive symptoms. Conclusions: Mass and extended quarantine succeeded in controlling the spread of the COVID-19 virus; however, it comes with a high cost of potential psychological impacts. Most of the students reported that they suffer from sleeping disorders and had a degree of depressive symptoms. Officials should provide psychological support and clear guidance to help the general public to reduce these potential effects and overcome the quarantine period with minimum negative impacts.

Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing.

Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG islands (iCGIs) and their corresponding host genes exhibit dynamic epigenetic and gene expression patterns during development and between different tissues. We hypothesise that iCGI-associated H3K36me3, DNA methylation and transcription can influence host gene AS and/or APA. We investigate H3K36me3 and find that this histone mark is not a major regulator of AS or APA in our model system. Genomewide, we identify over 4000 host genes that harbour an iCGI in the mammalian genome, including both previously annotated and novel iCGI/host gene pairs. The transcriptional activity of these iCGIs is tissue- and developmental stage-specific and, for the first time, we demonstrate that the premature termination of host gene transcripts upstream of iCGIs is closely correlated with the level of iCGI transcription in a DNA-methylation independent manner. These studies suggest that iCGI transcription, rather than H3K36me3 or DNA methylation, interfere with host gene transcription and pre-mRNA processing genomewide and contributes to the spatiotemporal diversification of both the transcriptome and proteome.

The genetic landscape of Arab Population, Chechens and Circassians subpopulations from Jordan through HV1 and HV2 regions of mtDNA.

Mitochondrial DNA (mtDNA) is widely used in several fields including medical genetics, forensic science, genetic genealogy, and evolutionary anthropology. In this study, mtDNA haplotype diversity was determined for 293 unrelated subjects from Jordanian population (Circassians, Chechens, and the original inhabitants of Jordan). A total of 102 haplotypes were identified and analyzed among the populations to describe the maternal lineage landscape. Our results revealed that the distribution of mtDNA haplotype frequencies among the three populations showed disparity and significant differences when compared to each other. We also constructed mitochondrial haplotype classification trees for the three populations to determine the phylogenetic relationship of mtDNA haplotype variants, and we observed clear differences in the distribution of maternal genetic ancestries, especially between Arab and the minority ethnic populations. To our knowledge, this study is the first, to date, to characterize mitochondrial haplotypes and haplotype distributions in a population-based sample from the Jordanian population. It provides a powerful reference for future studies investigating the contribution of mtDNA variation to human health and disease and studying population history and evolution by comparing the mtDNA haplotypes to other populations.

Histopathologist-level quantification of Ki-67 immunoexpression in gastroenteropancreatic neuroendocrine tumors using semiautomated method.

The role of Ki-67 index in determining the prognosis and management of gastroenteropancreatic neuroendocrine tumors (GEP-NETs) has become more important yet presents a challenging assessment dilemma. Although the precise method of Ki-67 index evaluation has not been standardized, several methods have been proposed, and each has its pros and cons. Our study proposes an imaging semiautomated informatics framework [semiautomated counting (SAC)] using the popular biomedical imaging tool "ImageJ" to quantify Ki-67 index of the GEP-NETs using camera-captured images of tumor hotspots. It aims to assist pathologists in achieving an accurate and rapid interpretation of Ki-67 index and better reproducibility of the results with minimal human interaction and calibration. Twenty cases of resected GEP-NETs with Ki-67 staining that had been done for diagnostic purposes have been randomly selected from the pathology archive. All of these cases were reviewed in a multidisciplinary cancer center between 2012 and 2019. For each case, the Ki-67 immunostained slide was evaluated and five camera-captured images at 40 × magnification were taken. Prints of images were used by three pathologists to manually count the tumor cells. The digital versions of the images were used for the semiautomated cell counting using ImageJ. Statistical analysis of the Ki-67 index correlation between the proposed method and the MC revealed strong agreement on all the cases evaluates ( n = 20 ), with an intraclass correlation coefficient of 0.993, "95% CI: 0.984 to 0.997." The results obtained from the SAC are promising and demonstrate the capability of this methodology for the development of reproducible and accurate semiautomated quantitative pathological assessments. ImageJ features are investigated carefully and accurately fine-tuned to obtain the optimal sequence of steps that will accurately calculate Ki-67 index. SAC is able to accurately grade all the cases evaluated perfectly mating histopathologists' manual grading, providing reliable and efficient solution for Ki-67 index assessment.

Transcription and chromatin determinants of de novo DNA methylation timing in oocytes.

BACKGROUND: Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci. RESULTS: Given the predominant role of transcription, we sought to investigate whether transcription timing is rate limiting for de novo methylation and determines the asynchrony of methylation events. Therefore, we generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation. We find that most sequence elements, including most classes of transposable elements, acquire methylation at similar rates overall. However, methylation of CpG islands (CGIs) is delayed compared with the genome average and there are reproducible differences amongst CGIs in onset of methylation. Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. Instead, CGI methylation timing negatively correlates with enrichment for histone 3 lysine 4 (H3K4) methylation and dependence on the H3K4 demethylases KDM1A and KDM1B, implicating chromatin remodelling as a major determinant of methylation timing. We also identified differential enrichment of transcription factor binding motifs in CGIs acquiring methylation early or late in oocyte growth. By combining these parameters into multiple regression models, we were able to account for about a fifth of the variation in methylation timing of CGIs. Finally, we show that establishment of non-CpG methylation, which is prevalent in fully grown oocytes, and methylation over non-transcribed regions, are later events in oogenesis. CONCLUSIONS: These results do not support a major role for transcriptional transitions in the time of onset of DNA methylation in the oocyte, but suggest a model in which sequences least dependent on chromatin remodelling are the earliest to become permissive for methylation.

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids.

The number of children born since the origin of Assisted Reproductive Technologies (ART) exceeds 5 million. The majority seem healthy, but a higher frequency of defects has been reported among ART-conceived infants, suggesting an epigenetic cost. We report the first whole-genome DNA methylation datasets from single pig blastocysts showing differences between in vivo and in vitro produced embryos. Blastocysts were produced in vitro either without (C-IVF) or in the presence of natural reproductive fluids (Natur-IVF). Natur-IVF embryos were of higher quality than C-IVF in terms of cell number and hatching ability. RNA-Seq and DNA methylation analyses showed that Natur-IVF embryos have expression and methylation patterns closer to in vivo blastocysts. Genes involved in reprogramming, imprinting and development were affected by culture, with fewer aberrations in Natur-IVF embryos. Methylation analysis detected methylated changes in C-IVF, but not in Natur-IVF, at genes whose methylation could be critical, such as IGF2R and NNAT.

Pervasive polymorphic imprinted methylation in the human placenta.

The maternal and paternal copies of the genome are both required for mammalian development, and this is primarily due to imprinted genes, those that are monoallelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are established in the germline and maintained after fertilization. There are a large number of germline DMRs that have not yet been associated with imprinting, and their function in development is unknown. In this study, we developed a genome-wide approach to identify novel imprinted DMRs in the human placenta and investigated the dynamics of these imprinted DMRs during development in somatic and extraembryonic tissues. DNA methylation was evaluated using the Illumina HumanMethylation450 array in 134 human tissue samples, publicly available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. Forty-three known and 101 novel imprinted DMRs were identified in the human placenta by comparing methylation between diandric and digynic triploid conceptions in addition to female and male gametes. Seventy-two novel DMRs showed a pattern consistent with placental-specific imprinting, and this monoallelic methylation was entirely maternal in origin. Strikingly, these DMRs exhibited polymorphic imprinted methylation between placental samples. These data suggest that imprinting in human development is far more extensive and dynamic than previously reported and that the placenta preferentially maintains maternal germline-derived DNA methylation.

Dynamic changes in histone modifications precede de novo DNA methylation in oocytes.

Erasure and subsequent reinstatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly understood, but a number of post-translational modifications of histones are implicated in antagonizing or recruiting the de novo DNA methylation complex. In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Using a chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq) protocol optimized for low cell numbers and novel techniques for isolating primary and growing oocytes, profiles were generated for histone modifications implicated in promoting or inhibiting DNA methylation. CGIs destined for DNA methylation show reduced protective H3K4 dimethylation (H3K4me2) and trimethylation (H3K4me3) in both primary and growing oocytes, while permissive H3K36me3 increases specifically at these CGIs in growing oocytes. Methylome profiling of oocytes deficient in H3K4 demethylase KDM1A or KDM1B indicated that removal of H3K4 methylation is necessary for proper methylation establishment at CGIs. This work represents the first systematic study performing ChIP-seq in oocytes and shows that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events.

Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape.

BACKGROUND: Previously, a role was demonstrated for transcription in the acquisition of DNA methylation at imprinted control regions in oocytes. Definition of the oocyte DNA methylome by whole genome approaches revealed that the majority of methylated CpG islands are intragenic and gene bodies are hypermethylated. Yet, the mechanisms by which transcription regulates DNA methylation in oocytes remain unclear. Here, we systematically test the link between transcription and the methylome. RESULTS: We perform deep RNA-Seq and de novo transcriptome assembly at different stages of mouse oogenesis. This reveals thousands of novel non-annotated genes, as well as alternative promoters, for approximately 10 % of reference genes expressed in oocytes. In addition, a large fraction of novel promoters coincide with MaLR and ERVK transposable elements. Integration with our transcriptome assembly reveals that transcription correlates accurately with DNA methylation and accounts for approximately 85-90 % of the methylome. We generate a mouse model in which transcription across the Zac1/Plagl1 locus is abrogated in oocytes, resulting in failure of DNA methylation establishment at all CpGs of this locus. ChIP analysis in oocytes reveals H3K4me2 enrichment at the Zac1 imprinted control region when transcription is ablated, establishing a connection between transcription and chromatin remodeling at CpG islands by histone demethylases. CONCLUSIONS: By precisely defining the mouse oocyte transcriptome, this work not only highlights transcription as a cornerstone of DNA methylation establishment in female germ cells, but also provides an important resource for developmental biology research.

Protection of CpG islands against de novo DNA methylation during oogenesis is associated with the recognition site of E2f1 and E2f2.

BACKGROUND: Epigenetic reprogramming during early mammalian embryonic and germ cell development is a genome-wide process. CpG islands (CGIs), central to the regulation of mammalian gene expression, are exceptional in terms of whether, when and how they are affected by epigenetic reprogramming. RESULTS: We investigated the DNA sequences of CGIs in the context of genome-wide data on DNA methylation and transcription during oogenesis and early embryogenesis to identify signals associated with methylation establishment and protection from de novo methylation in oocytes and associated with post-fertilisation methylation maintenance. We find no evidence for a characteristic DNA sequence motif in oocyte-methylated CGIs. Neither do we find evidence for a general role of regular CpG spacing in methylation establishment at CGIs in oocytes. In contrast, the resistance of most CGIs to de novo methylation during oogenesis is associated with the motif CGCGC, the recognition site of E2f1 and E2f2, transcription factors highly expressed specifically in oocytes. This association is independent of prominent known hypomethylation-associated factors: CGI promoter activity, H3K4me3, Cfp1 binding or R-loop formation potential. CONCLUSIONS: Our results support a DNA sequence-independent and transcription-driven model of de novo CGI methylation during oogenesis. In contrast, our results for CGIs that remain unmethylated are consistent with a model of protection from methylation involving sequence recognition by DNA-binding proteins, E2f1 and E2f2 being probable candidates.

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.

We report a single-cell bisulfite sequencing (scBS-seq) method that can be used to accurately measure DNA methylation at up to 48.4% of CpG sites. Embryonic stem cells grown in serum or in 2i medium displayed epigenetic heterogeneity, with '2i-like' cells present in serum culture. Integration of 12 individual mouse oocyte datasets largely recapitulated the whole DNA methylome, which makes scBS-seq a versatile tool to explore DNA methylation in rare cells and heterogeneous populations.

Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes.

Identifying loci with parental differences in DNA methylation is key to unraveling parent-of-origin phenotypes. By conducting a MeDIP-Seq screen in maternal-methylation free postimplantation mouse embryos (Dnmt3L-/+), we demonstrate that maternal-specific methylation exists very scarcely at midgestation. We reveal two forms of oocyte-specific methylation inheritance: limited to preimplantation, or with longer duration, i.e. maternally imprinted loci. Transient and imprinted maternal germline DMRs (gDMRs) are indistinguishable in gametes and preimplantation embryos, however, de novo methylation of paternal alleles at implantation delineates their fates and acts as a major leveling factor of parent-inherited differences. We characterize two new imprinted gDMRs, at the Cdh15 and AK008011 loci, with tissue-specific imprinting loss, again by paternal methylation gain. Protection against demethylation after fertilization has been emphasized as instrumental in maintaining parent-of-origin methylation inherited from the gametes. Here we provide evidence that protection against de novo methylation acts as an equal major pivot, at implantation and throughout life.

The ß-globin locus control region in combination with the EF1α short promoter allows enhanced lentiviral vector-mediated erythroid gene expression with conserved multilineage activity.

Some gene therapy strategies are compromised by the levels of gene expression required for therapeutic benefit, and also by the breadth of cell types that require correction. We designed a lentiviral vector system in which a transgene is under the transcriptional control of the short form of constitutively acting elongation factor 1α promoter (EFS) combined with essential elements of the locus control region of the ß-globin gene (ß-LCR). We show that the ß-LCR can upregulate EFS activity specifically in erythroid cells but does not alter EFS activity in myeloid or lymphoid cells. Experiments using the green fluorescent protein (GFP) reporter or the human adenosine deaminase (ADA) gene demonstrate 3-7 times upregulation in vitro but >20 times erythroid-specific upregulation in vivo, the effects of which were sustained for 1 year. The addition of the ß-LCR did not alter the mutagenic potential of the vector in in vitro mutagenesis (IM) assays although microarray analysis showed that the ß-LCR upregulates ~9% of neighboring genes. This vector design therefore combines the benefits of multilineage gene expression with high-level erythroid expression, and has considerable potential for correction of multisystem diseases including certain lysosomal storage diseases through a hematopoietic stem cell (HSC) gene therapy approach.