Transcriptomic analysis delineates preterm prelabor rupture of membranes from preterm labor in preterm fetal membranes

BACKGROUND

Globally, preterm birth remains the leading cause of death in children younger than 5 years old. Spontaneous preterm birth is comprised of two events that may or may not occur simultaneously: preterm labor and preterm prelabor rupture of membranes (PPROM). To further explore the concept that spontaneous preterm birth can result from the initializing of two separate but overlapping pathological events, we compared fetal membrane tissue from preterm labor deliveries to fetal tissue from preterm labor with PPROM deliveries. We hypothesized that the fetal membrane tissue from preterm labor with PPROM cases will have an RNA-seq profile divergent from the fetal membrane tissue from preterm labor controls.

METHODS

Chorioamnion, separated into amnion and chorion, was collected from eight gestationally age-matched cases and controls within 15 min of birth, and analyzed using RNA sequencing. Pathway enrichment analyses and functional annotations of differentially expressed genes were performed using KEGG and Gene Ontogeny Pathway enrichment analyses.

RESULTS

A total of 1466 genes were differentially expressed in the amnion, and 484 genes were differentially expressed in the chorion (log2 fold change > 1, FDR < 0.05) in cases (preterm labor with PPROM), versus controls (preterm labor only). In the amnion, the most significantly enriched (FDR < 0.01) KEGG pathway among down-regulated genes was the extracellular matrix receptor interaction pathway. Seven of the most significantly enriched pathways were comprised of multiple genes from the COL family, including COL1A, COL3A1, COL4A4, and COL4A6. In the chorion, the most significantly enriched KEGG pathways in up-regulated genes were chemokine, NOD receptor, Toll-like receptor, and cytokine-cytokine receptor signaling pathways. Similarly, KEGG pathway enrichment analysis for up-regulated genes in the amnion included three inflammatory pathways: cytokine-cytokine interaction, TNF signaling and the CXCL family. Six genes were significantly up regulated in chorionic tissue discriminated between cases (preterm labor with PPROM) and controls (preterm labor only) including GBP5, CXCL9, ALPL, S100A8, CASP5 and MMP25.

CONCLUSIONS

In our study, transcriptome analysis of preterm fetal membranes revealed distinct differentially expressed genes for PPROM, separate from preterm labor. This study is the first to report transcriptome data that reflects the individual pathophysiology of amnion and chorion tissue from PPROM deliveries.

Active Sites and Their Individual Turnover Frequencies for Ethylene Hydrogenation on Reduced Graphene Aerogel

Graphene aerogel (GA) was reduced at various temperatures to prepare a series of reduced graphene aerogels (rGAs) with different surface characteristics. Detailed characterization demonstrated that an increase in the thermal reduction temperature leads to an increase in surface area accompanied by an increase in surface density of defect sites formed by the removal of the oxygen-containing functional groups. rGA samples were then tested for ethylene hydrogenation under identical conditions. A comparison of catalytic performances of each catalyst demonstrated that the rGA sample prepared by reduction in Ar at 900 °C (rGA-900) provides the highest performance compared with others prepared at lower temperatures. Next, we analyzed the per-gram activity of each catalyst as a sum of individual contributions from different defect sites quantified by Raman spectroscopy and CHNS-O analysis to determine the individual turnover frequencies (TOFs) of each active site. This analysis identified polyene-like structures and interstitial defects associated with amorphous sp2 bonded carbon atoms as the dominant active sites responsible for hydrogenation. A comparison of their TOFs further indicated that the polyene-like structures provide approximately ten times higher TOF compared to those associated with the amorphous carbon defects. These results, identifying the dominant active centers and quantifying their corresponding TOFs, provide opportunities toward the rational design of GA-based carbocatalysts.

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup

OBJECTIVE

Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space.

PROCESS

A list of relevant factors was developed through GenTBI workgroup discussions in multiple in-person and online meetings, along with review of pertinent publications. This list was then summarized and reviewed to achieve consensus among the group members.

CONCLUSIONS

Substantial informatics research and development are needed to fully realize the clinical potential of such technologies. The development of larger datasets is crucial to emulating the success AI is achieving in other domains. It is important that AI methods do not exacerbate existing socio-economic, racial, and ethnic disparities. Genomic data standards are critical to effectively scale such technologies across institutions. With so much uncertainty, complexity and novelty in genomics and medicine, and with an evolving regulatory environment, the current focus should be on using these technologies in an interface with clinicians that emphasizes the value each brings to clinical decision-making.

Composite of MIL-101(Cr) with a Pyrrolidinium-Based Ionic Liquid Providing High CO2 Selectivity

Capturing CO₂ selectively from flue gas and natural gas addresses the criteria of a sustainable society. In this work, we incorporated an ionic liquid (IL) (1-methyl-1-propyl pyrrolidinium dicyanamide, [MPPyr][DCA]) into a metal organic framework (MOF), MIL-101(Cr), by wet impregnation and characterized the resulting [MPPyr][DCA]/MIL-101(Cr) composite in deep detail to identify the interactions between [MPPyr][DCA] molecules and MIL-101(Cr). Consequences of these interactions on the CO₂/N₂, CO₂/CH₄, and CH₄/N₂ separation performance of the composite were examined by volumetric gas adsorption measurements complemented by the density functional theory (DFT) calculations. Results showed that the composite offers remarkably high CO₂/N₂ and CH₄/N₂ selectivities of 19,180 and 1915 at 0.1 bar and 15 °C corresponding to 1144- and 510-times improvements, respectively, as compared to the corresponding selectivities of pristine MIL-101(Cr). At low pressures, these selectivities reached practically infinity, making the composite completely CO₂-selective over CH₄ and N₂. The CO₂/CH₄ selectivity was improved from 4.6 to 11.7 at 15 °C and 0.001 bar, yielding a 2.5-times improvement, attributed to the high affinity of [MPPyr][DCA] toward CO₂, validated by the DFT calculations. These results offer broad opportunities for the design of composites where ILs are incorporated into the pores of MOFs for high performance gas separation applications to address the environmental challenges.

Integrating Molecular Simulations with Machine Learning Guides in the Design and Synthesis of [BMIM][BF4]/MOF Composites for CO2/N2 Separation

Considering the existence of a large number and variety of metal-organic frameworks (MOFs) and ionic liquids (ILs), assessing the gas separation potential of all possible IL/MOF composites by purely experimental methods is not practical. In this work, we combined molecular simulations and machine learning (ML) algorithms to computationally design an IL/MOF composite. Molecular simulations were first performed to screen approximately 1000 different composites of 1-n-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF₄]) with a large variety of MOFs for CO₂ and N₂ adsorption. The results of simulations were used to develop ML models that can accurately predict the adsorption and separation performances of [BMIM][BF₄]/MOF composites. The most important features that affect the CO₂/N₂ selectivity of composites were extracted from ML and utilized to computationally generate an IL/MOF composite, [BMIM][BF₄]/UiO-66, which was not present in the original material data set. This composite was finally synthesized, characterized, and tested for CO₂/N₂ separation. Experimentally measured CO₂/N₂ selectivity of the [BMIM][BF₄]/UiO-66 composite matched well with the selectivity predicted by the ML model, and it was found to be comparable, if not higher than that of all previously synthesized [BMIM][BF₄]/MOF composites reported in the literature. Our proposed approach of combining molecular simulations with ML models will be highly useful to accurately predict the CO₂/N₂ separation performances of any [BMIM][BF₄]/MOF composite within seconds compared to the extensive time and effort requirements of purely experimental methods.

Clinical features of patients with MTAP-deleted bladder cancer

Advanced urothelial carcinoma continues to have a dismal prognosis despite several new therapies in the last 5 years. FGFR2 and FGFR3 mutations and fusions, PD-L1 expression, tumor mutational burden, and microsatellite instability are established predictive biomarkers in advanced urothelial carcinoma. Novel biomarkers can optimize the sequencing of available treatments and improve outcomes. We describe herein the clinical and pathologic features of patients with an emerging subtype of bladder cancer characterized by deletion of the gene MTAP encoding the enzyme S-Methyl-5'-thioadenosine phosphatase, a potential biomarker of response to pemetrexed. We performed a retrospective analysis of 61 patients with advanced urothelial carcinoma for whom demographics, pathologic specimens, next generation sequencing, and clinical outcomes were available. We compared the frequency of histology variants, upper tract location, pathogenic gene variants, tumor response, progression free survival (PFS) and overall survival (OS) between patients with tumors harboring MTAP deletion (MTAP-del) and wild type tumors (MTAP-WT). A propensity score matching of 5 covariates (age, gender, presence of variant histology, prior surgery, and prior non-muscle invasive bladder cancer) was calculated to compensate for disparity when comparing survival in these subgroups. Non-supervised clustering analysis of differentially expressed genes between MTAP-del and MTAP-WT urothelial carcinomas was performed. MTAP-del occurred in 19 patients (31%). Tumors with MTAP-del were characterized by higher prevalence of squamous differentiation (47.4 vs 11.9%), bone metastases (52.6 vs 23.5%) and lower frequency of upper urinary tract location (5.2% vs 26.1%). Pathway gene set enrichment analysis showed that among the genes upregulated in the MTAP-del cohort, at least 5 were linked to keratinization (FOXN1, KRT33A/B, KRT84, RPTN) possibly contributing to the higher prevalence of squamous differentiation. Alterations in the PIK3 and MAPK pathways were more frequent when MTAP was deleted. There was a trend to inferior response to chemotherapy among MTAP-del tumors, but no difference in the response to immune checkpoint inhibitors or enfortumab. Median progression free survival after first line therapy (PFS1) was 5.5 months for patients with MTAP-WT and 4.5 months for patients with MTAP-del (HR = 1.30; 95% CI, 0.64-2.63; P = 0.471). There was no difference in the time from metastatic diagnosis to death (P = 0.6346). Median OS from diagnosis of localized or de novo metastatic disease was 16 months (range 1.5-60, IQR 8-26) for patients with MTAP-del and 24.5 months (range 3-156, IQR 16-48) for patients with MTAP-WT (P = 0.0218), suggesting that time to progression to metastatic disease is shorter in MTAP-del patients. Covariates did not impact significantly overall survival on propensity score matching. In conclusion, MTAP -del occurs in approximately 30% of patients with advanced urothelial carcinoma and defines a subgroup of patients with aggressive features, such as squamous differentiation, frequent bone metastases, poor response to chemotherapy, and shorter time to progression to metastatic disease.

Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein

Heme oxygenase-1 (HO-1) is a rate-limiting enzyme in degrading heme into biliverdin and iron. HO-1 can also enter the nucleus and regulate gene transcription independent of its enzymatic activity. Whether HO-1 can alter gene expression through direct binding to target DNA remains unclear. Here, we performed HO-1 CHIP-seq and then employed 3D structural modeling to reveal putative HO-1 DNA binding domains. We identified three probable DNA binding domains on HO-1. Using the Proteinarium, we identified several genes as the most highly connected nodes in the interactome among the HO-1 gene binding targets. We further demonstrated that HO-1 modulates the expression of these key genes using Hmox1 deficient cells. Finally, mutation of four conserved amino acids (E215, I211, E201, and Q27) within HO-1 DNA binding domain 1 significantly increased expression of Gtpbp3 and Eif1 genes that were identified within the top 10 binding hits normalized by gene length predicted to bind this domain. Based on these data, we conclude that HO-1 protein is a putative DNA binding protein, and regulates targeted gene expression. This provides the foundation for developing specific inhibitors or activators targeting HO-1 DNA binding domains to modulate targeted gene expression and corresponding cellular function.

Protein Network Analysis of Whole Exome Sequencing of Severe Preeclampsia

Preeclampsia is a hypertensive disorder of pregnancy, which complicates up to 15% of US deliveries. It is an idiopathic disorder associated with several different phenotypes. We sought to determine if the genetic architecture of preeclampsia can be described by clusters of patients with variants in genes in shared protein interaction networks. We performed a case-control study using whole exome sequencing on early onset preeclamptic mothers with severe clinical features and control mothers with uncomplicated pregnancies between 2016 and 2020. A total of 143 patients were enrolled, 61 women with early onset preeclampsia with severe features based on ACOG criteria, and 82 control women at term, matched for race and ethnicity. A network analysis and visualization tool, Proteinarium, was used to confirm there are clusters of patients with shared gene networks associated with severe preeclampsia. The majority of the sequenced patients appear in two significant clusters. We identified one case dominant and one control dominant cluster. Thirteen genes were unique to the case dominated cluster. Among these genes, LAMB2, PTK2, RAC1, QSOX1, FN1, and VCAM1 have known associations with the pathogenic mechanisms of preeclampsia. Using bioinformatic analysis, we were able to identify subsets of patients with shared protein interaction networks, thus confirming our hypothesis about the genetic architecture of preeclampsia.

Investigation on chemical composition, antioxidant activity and SARS-CoV-2 nucleocapsid protein of endemic Ferula longipedunculata Peşmen

The essential and fatty oils were investigated and a quantitative analysis of the root, green and stem parts of F. Longipedunculata was performed by GC-MS and HPLC-TOF/MS and their antioxidant (DPPH method) activities and potential binding of phytochemicals against SARS-CoV-2 nucleocapsid were determined using Molegro Virtual Docker software. In the root part of the plant, the prominent components of oil were β-phellandrene (53.46%), ocimene (6.79%), 4-terpineol (5.94%) and santalol (5.03%). According to the quantitative results, vanillic acid (141.35 mg/kg), ferulic acid (126.19 mg/kg) and 4-hydroxybenzoic acid (119.92 mg/kg) were found in the roots; quercetin-3-β-O-glycoside (1737.70 mg/kg), quercetin (531.35 mg/kg) and ferulic acid (246.22 mg/kg) were found in the in the green part; and fumaric acid (2100.21 mg/kg), quercetin-3-β-O-glycoside (163.24 mg/kg), vanillic acid (57.59 mg/kg) were detected in the stem part. The antioxidant activity of all parts of the plant was higher than the control with BHT. Silibinin, rutin, and neohesperidin exhibited a stronger affinity than nucleotides. In the silico analysis, many of the phytochemicals were attached with strong hydrogen-bonds and electrostatic effects to the amino acids to which nucleotides are bound. The results indicated that the plant showed antioxidant effects and can be effective against SARS-CoV-2 thanks to the different phytochemical compounds it contains.

A novel alkali activated magnesium silicate as an effective and mechanically strong adsorbent for methylene blue removal

A novel, cheap, and easy-to-synthesize sepiolite-based alkali-activated material (Sep-AAM), synthesized by the reaction of a magnesium silicate source, sepiolite, with sodium silicate solution, demonstrating high mechanical strength and methylene blue (MB) removal performance is introduced. Kinetics data indicated that MB adsorption occurs through pseudo-second-order adsorption kinetics model, while the Langmuir isotherm model provided a better fit to adsorption isotherms. The Sep-AAM provided a removal capacity of 99.92 mg g^-1 at 50 °C, setting a new benchmark value among the materials used for this purpose. Thermodynamical parameters indicated that the adsorption of MB onto Sep-AAM was endothermic and the interaction between Sep-AAM and MB included weak chemical bonding. Regenerability of the Sep-AAM in powder and monolith forms was confirmed up to four-cycles. Structural parameters determined by several characterization tools demonstrated that the surface hydroxyl groups are responsible for the superior MB adsorption performance. The mechanical strength measurements showed that Sep-AAM in monolith form displayed a remarkable compressive strength value of 40 MPa. To establish a new approach forward on the development of AAMs for wastewater treatment, this study shows that sepiolite can effectively be utilized and Sep-AAM provides a sustainable solution for dye removal with advanced mechanical properties.

Influence of ionic liquids on the electronic environment of atomically dispersed Ir on (MgO) (100)

Recently, ionic liquids (ILs) have been used as ligands for single-site Ir(CO)2 complexes bound to metal-oxide supports because of their electron-donor/acceptor capacities. The combined effects of supports and ILs as...

Proteomic analysis of a murine model of lung hypoplasia induced by oligohydramnios

Severe oligohydramnios (OH) due to prolonged loss of amniotic fluid can cause pulmonary hypoplasia. Animal model of pulmonary hypoplasia induced by amniotic fluid drainage is partly attributed to changes in mechanical compression of the lung. Although numerous studies on OH-model have demonstrated changes in several individual proteins, however, the underlying mechanisms for interrupting normal lung development in response to a decrease of amniotic fluid volume are not fully understood. In this study, we used a proteomic approach to explore differences in the expression of a wide range of proteins after induction of OH in a mouse model of pulmonary hypoplasia to find out the signaling/molecular pathways involved in fetal lung development. Liquid chromatography-massspectromery/mass spectrometry analysis found 474 proteins that were differentially expressed in OH-induced hypoplastic lungs in comparison to untouched (UnT) control. Among these proteins, we confirmed the downregulation of AKT1, SP-D, and CD200, and provided proof-of-concept for the first time about the potential role that these proteins could play in fetal lung development.

A golden ratio for foramen magnum: an anatomical pilot study

BACKGROUND

The foramen magnum (FM) is an important landmark because of its close relationship to key structures such as the brainstem and spinal cord, an extension of the medulla oblongata. Because of the similarity in their shape, the existence of a relationship between cranial length and anteroposterior diameter of the FM, and between cranial width and transverse diameter of the FM may reveal the magnificent harmony of the skull and FM. Based on this idea, we investigated the existence of this harmony in skulls that we used in our study.

MATERIALS AND METHODS

In this study, 60 adult dry skulls belonging to the Turkish population were examined. The anteroposterior and transverse diameters of the foramen magnum and the length and width of the skull were measured. Measurements were made directly on the skull using a digital sliding caliper. New indices and ratios were applied with those measurements.

RESULTS

Our study suggests that FM width and FM length could be estimated by using the cranial length and cranial width measurements in the skull by accepting the mean of these coefficients (4.62) as the golden ratio. The average of the coefficients of cranial width to FM width ratio [4.62 ± 0.35 (95% CI: 4.52-4.70)] and the average of the coefficients of cranial length to the FM length ratio [4.62 ± 0.50 (95% CI): 4.49-4.76)] were found to be equal to each other. In order to check the accuracy of this hypothesis, FM width and FM lengths were estimated with the help of new equations.

CONCLUSIONS

In the present study, the ratio between the anteroposterior and transverse diameters of both FM and the cranium was estimated at 4.62, indicating a magnificent harmony between cranial and subcranial structures. With this ratio, it is easy to estimate FM's size based on simple cranial measurements.

Enhanced Water Purification Performance of Ionic Liquid Impregnated Metal-Organic Framework: Dye Removal by [BMIM][PF6]/MIL-53(Al) Composite

We incorporated a water-stable ionic liquid (IL), 1-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF₆], into a water-stable metal-organic framework (MOF), MIL-53(Al), to generate the [BMIM][PF₆]/MIL-53(Al) composite. This composite was examined for water purification by studying its capacity for methylene blue (MB) and methyl orange (MO) removal from aqueous solutions having either single dye or a mixture of both. Data illustrated that the removal efficiency and the maximum adsorption capacity of MIL-53(Al) were increased several times upon [BMIM][PF₆] incorporation. For instance, within 1 min, 10 mg of pristine MIL-53(Al) adsorbed 23.3% MB from 10 mg/L of MB solution, while [BMIM][PF₆]/MIL-53(Al) composite was adsorbed 82.3% MB in an identical solution. In the case of MO, 10 mg of pristine MIL-53(Al) achieved 27.8 and 53.6% MO removal from 10 mg/L of MO solution, while [BMIM][PF₆]/MIL-53(Al) composite removed 61.4 and 99.2% within 5 min and 3 h, respectively. Moreover, upon [BMIM][PF₆] incorporation, the maximum MB and MO adsorption capacities of the pristine MOF were increased from 84.5 to 44 mg/g to 204.9 to 60 mg/g, respectively. The adsorption of dyes in pristine MIL-53(Al) and [BMIM][PF₆]/MIL-53(Al) followed a pseudo-second-order kinetic model and a Langmuir isotherm model. In a mixture of both dyes, the IL/MOF composite showed a doubled MB selectivity after the IL incorporation. The composite was successfully regenerated at least two times after its use in water purification to remove MB, MO, and their mixtures. Infrared (IR) spectra indicated that the MB/MO adsorption occurs on [BMIM][PF₆]/MIL-53(Al) by electrostatic interactions, hydrogen bonding, and π-π interactions. These results showed that [BMIM][PF₆]/MIL-53(Al) composite is a highly promising material for efficient water purification.

Successful long-term limb salvage using cephalic and small saphenous vein grafts: A case report

In this case report, we present a patient scheduled for operation due to critical leg ischemia in whom a bilateral great saphenous vein (GSV) had already been used during previous cardiac and peripheral vascular surgeries. The patient underwent femorofemoral crossover bypass from left to right with a small saphenous vein and right femoropopliteal bypass with cephalic vein (CV) during the same session. Distal pulses became palpable, and symptoms regressed dramatically following the operation. A control computed tomographic angiography scan revealed no signs of graft stenosis 32 months after the surgery. Despite the recent advances in synthetic graft materials, small saphenous and CVs should be remembered as alternative long-standing conduits in the absence of the GSV.

Towards complete elucidation of structural factors controlling thermal stability of IL/MOF composites: effects of ligand functionalization on MOFs

In this work, we incorporated an ionic liquid (IL), 1-n-butyl-3-methylimidazolium methyl sulfate ([BMIM][MeSO4]) into two different metal organic frameworks (MOFs), UiO-66, and its amino-functionalized counterpart, NH2-UiO-66, to investigate the effects of ligand-functionalization on the thermal stability limits of IL/MOF composites. The as-synthesized IL/MOF composites were characterized in detail by combining x-ray diffraction, scanning electron microscopy, Brunauer-Emmett-Teller analysis, x-ray fluorescence, infrared spectroscopies (FTIR), and their thermal stability limits were determined by thermogravimetric analysis (TGA). Characterization data confirmed the successful incorporation of the IL into each MOF and indicated the presence of direct interactions between them. A comparison of the interactions in [BMIM][MeSO4]-incorporated UiO-66 and NH2-UiO-66 with those in their 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6])-incorporated counterparts showed that the hydrophilic IL, [BMIM][MeSO4], interacts with the 1,4-benzenedicarboxylate (BDC) ligand of the UiO-66, while the hydrophobic IL, [BMIM][PF6], is interacting with the joints where zirconium metal cluster coordinates with BDC ligand. The TGA data demonstrated that the composite with the ligand-functionalized MOF, NH2-UiO-66, exhibited a lower percentage decrease in the maximum tolerable temperature compared to those of IL/UiO-66 composites. Moreover, it is discovered that when the IL is hydrophilic, its hydrogen bonding ability can be utilized to designate an interaction site on MOF's ligand structure, leads to a lower reduction in thermal stability limits. These results provide insights for the rational design of IL/MOF composites and contribute towards the complete elucidation of structural factors controlling the thermal stability.

Mechanical stretch regulates the expression of specific miRNA in extracellular vesicles released from lung epithelial cells

The underlying mechanism of normal lung organogenesis is not well understood. An increasing number of studies are demonstrating that extracellular vesicles (EVs) play critical roles in organ development by delivering microRNAs (miRNA) to neighboring and distant cells. miRNAs are important for fetal lung growth; however, the role of miRNA-EVs (miRNAs packaged inside the EVs) during fetal lung development is unexplored. The aim of this study was to examine the expression of miRNA-EVs in MLE-12, a murine lung epithelial cell line subjected to mechanical stretch in vitro with the long-term goal to investigate their potential role in the fetal lung development. Both cyclic and continuous mechanical stretch regulate miRNA differentially in EVs released from MLE-12 and intracellularly, demonstrating that mechanical signals regulate the expression of miRNA-EVs in lung epithelial cells. These results provide a proof-of-concept for the potential role that miRNA-EVs could play in the development of fetal lung.

MIL-53(Al) as a Versatile Platform for Ionic-Liquid/MOF Composites to Enhance CO2 Selectivity over CH4 and N2

Five different imidazolium-based ionic liquids (ILs) were incorporated into a metal-organic framework (MOF), MIL-53(Al), to investigate the effect of IL incorporation on the CO2 separation performance of MIL-53(Al). CO2 , CH4 , and N2 adsorption isotherms of the IL/MIL-53(Al) composites and pristine MIL-53(Al) were measured to evaluate the effect of the ILs on the CO2 /CH4 and CO2 /N2 selectivities of the MOF. Of the composite materials that were tested, [BMIM][PF6 ]/MIL-53(Al) exhibited the largest increase in CO2 /CH4 selectivity, 2.8-times higher than that of pristine MIL-53(Al), whilst [BMIM][MeSO4 ]/MIL-53(Al) exhibited the largest increase in CO2 /N2 selectivity, 3.3-times higher than that of pristine MIL-53(Al). A comparison of the CO2 separation potentials of the IL/MOF composites showed that the [BMIM][BF4 ]- and [BMIM][PF6 ]-incorporated MIL-53(Al) composites both showed enhanced CO2 /N2 and CO2 /CH4 selectivities at pressures of 1-5 bar compared to composites of CuBTC and ZIF-8 with the same ILs. These results demonstrate that MIL-53(Al) is a versatile platform for IL/MOF composites and could help to guide the rational design of new composites for target gas-separation applications.

VIVA (VIsualization of VAriants): A VCF File Visualization Tool

High-throughput sequencing produces an extraordinary amount of genomic data that is organized into a number of high-dimension datasets. Accordingly, visualization of genomic data has become essential for quality control, exploration, and data interpretation. The Variant Call Format (VCF) is a text file format generated during the variant calling process that contains genomic information and locations of variants in a group of sequenced samples. The current workflow for visualization of genomic variant data from VCF files requires use of a combination of existing tools. Here, we describe VIVA (VIsualization of VAriants), a command line utility and Jupyter Notebook based tool for evaluating and sharing genomic data for variant analysis and quality control of sequencing experiments from VCF files. VIVA combines the functionality of existing tools into a single command to interactively evaluate and share genomic data, as well as create publication quality graphics.

Retained Acetylated Histone Four in Bull Sperm Associated With Fertility

Bull fertility, ability of the sperm to fertilize and activate the egg and support embryo development, is vital for cattle reproduction and production. Even though majority of histones are replaced by protamines, some histones are retained in sperm. It is known that chromatin remodeling during spermatogenesis results in dynamic changes in sperm chromatin structure through post-translational modifications (PTM) of sperm histones, which are important for regulation of gene expression. However, amounts of sperm Histone 4 (H4), its acetylated form (H4 acetyl), and to what extent these molecular attributes influence sperm chromatin structure and bull fertility are unknown. These gaps in the knowledge base are important because they are preventing advances in the fundamental science of bovine male gamete and improvement of bull fertility. The objective of this study was to test the hypothesis that expression dynamics as well as PTM of sperm H4 are associated with bull fertility. Flow cytometry was utilized to quantify H4 and H4 acetylated form in sperm from seven high and seven low fertility Holstein bulls. The results indicated that the average number of cells with H4 or H4 acetyl expression in high and low fertility bull sperm were 34.6 ± 20.4, 1.88 ± 1.8, 15.2 ± 20.8, and 1.4 ± 1.2, respectively. However, the sperm enriched in both H4 and H4 acetyl were different between high and low fertility groups (3.5 ± 0.6; 1.8 ± 0.8; P = 0.043). The localization and detection of H4 and H4 acetylation were measured by immunocytochemistry which revealed that H4 and H4 acetylation were equally distributed in the sperm head of high and low fertility sires. Western blotting results confirmed the presence of the H4 and its acetylated form in the sperm. Bioinformatics studies demonstrated that H4 is highly conserved among mammalians, and have significant gene ontology on spermatogenesis, early embryo implantation, and sperm capacitation. The results are significant because it demonstrates the replacement of canonical histone H4 into modified H4 acetylation in sperm and regulate its dynamics which is crucial for bull fertility and reproductive biotechnology. These findings advance fundamental science of mammalian early development and reproductive biotechnology.

Improving CO2 Separation Performance of MIL-53(Al) by Incorporating 1-n-Butyl-3-Methylimidazolium Methyl Sulfate

1-n-Butyl-3-methylimidazolium methyl sulfate is incorporated into MIL-53(Al). Detailed characterization is done by X-ray fluorescence, Brunauer-Emmett-Teller surface area, scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, and thermogravimetric analysis. Results show that ionic liquid (IL) interacts directly with the framework, significantly modifying the electronic environment of MIL-53(Al). Based on the volumetric gas adsorption measurements, CO2, CH4, and N2 adsorption capacities decreased from 112.0, 46.4, and 19.6 cc (STP) gMIL-53(Al) -1 to 42.2, 13.0, and 4.3 cc (STP) gMIL-53(Al) -1 at 5 bar, respectively, upon IL incorporation. Data show that this postsynthesis modification leads to more than two and threefold increase in the ideal selectivity for CO2 over CH4 and N2 separations, respectively, as compared with pristine MIL-53(Al). The isosteric heat of adsorption (Qst) values show that IL incorporation increases CO2 affinity and decreases CH4 and N2 affinities. Cycling adsorption-desorption measurements show that the composite could be regenerated with almost no decrease in the CO2 adsorption capacity for six cycles and confirm the lack of any significant IL leaching. The results offer MIL-53(Al) as an excellent platform for the development of a new class of IL/MOF composites with exceptional performance for CO2 separation.

Effect of prematurity on genome wide methylation in the placenta

Background

Preterm birth is a significant clinical problem and an enormous burden on society, affecting one in eight pregnant women and their newborns. Despite decades of research, the molecular mechanism underlying its pathogenesis remains unclear. Many studies have shown that preterm birth is associated with health risks across the later life course. The “fetal origins” hypothesis postulates that adverse intrauterine exposures are associated with later disease susceptibility. Our recent studies have focused on the placental epigenome at term. We extended these studies to genome-wide placental DNA methylation across a wide range of gestational ages. We applied methylation dependent immunoprecipitation/DNA sequencing (MeDIP-seq) to 9 placentas with gestational age from 25 weeks to term to identify differentially methylated regions (DMRs).

Results

Enrichment analysis revealed 427 DMRs with nominally significant differences in methylation between preterm and term placentas (p < 0.01) and 21 statistically significant DMRs after multiple comparison correction (FDR p < 0.05), of which 62% were hypo-methylated in preterm placentas vs term placentas. The majority of DMRs were in distal intergenic regions and introns. Significantly enriched pathways identified by Ingenuity Pathway Analysis (IPA) included Citrulline-Nitric Oxide Cycle and Fcy Receptor Mediated Phagocytosis in macrophages. The DMR gene set overlapped placental gene expression data, genes and pathways associated evolutionarily with preterm birth.

Conclusion

These studies form the basis for future studies on the epigenetics of preterm birth, “fetal programming” and the impact of environment exposures on this important clinical challenge.

Electronic supplementary material

The online version of this article (10.1186/s12881-019-0835-6) contains supplementary material, which is available to authorized users.

Analysis of CH4 Uptake over Metal-Organic Frameworks Using Data-Mining Tools

A database containing 2224 data points for CH₄ storage or delivery in metal-organic frameworks (MOFs) was analyzed using machine-learning tools to extract knowledge for generalization. The database was first reviewed to observe the basic trends and patterns. It was then analyzed using decision trees and artificial neural networks (ANN) to extract hidden information and develop rules and heuristics for future studies. Five-fold cross validations were used in each analysis to test the validity of the models with data not seen before. Decision-tree analyses were carried out using six user-defined descriptors and two structural properties, separately. The crystal structure and the total degree of unsaturation were found to be the effective user-defined descriptors, whereas the pore volume and maximum pore diameter, as structural properties, were sufficient to determine the MOFs having high CH₄-storage capacity. Moreover, a high pore volume is always required, as expected. In ANN analyses, models were also developed by using user-defined descriptors and structural properties separately. It was observed that the user-defined descriptors were not sufficient to describe the CH₄-storage capacities of MOFs, whereas the structural properties in particular led to accurate CH₄-storage predictions with an RMSE of 26.8 and an R² of 0.92 for testing.

Controlling catalytic activity and selectivity for partial hydrogenation by tuning the environment around active sites in iridium complexes bonded to supports

Single-site Ir(CO)2 complexes bonded to high-surface-area metal oxide supports, SiO2, TiO2, Fe2O3, CeO2, MgO, and La2O3, were synthesized by chemisorption of Ir(CO)2(acac) (acac = acetylacetonate) followed by coating with each of the following ionic liquids (ILs): 1-n-butyl-3-methylimidazolium tetrafluoroborate, [BMIM][BF4], 1-n-butyl-3-methylimidazolium acetate, [BMIM][Ac], and 1-(3-cyanopropyl)-3-methylimidazolium dicyanamide, [CPMIM][DCA]. Extended X-ray absorption fine structure spectroscopy showed that site-isolated iridium was bonded to oxygen atoms of the support. Electron densities on the iridium enveloped by each IL sheath/support combination were characterized by carbonyl infrared spectroscopy of the iridium gem-dicarbonyls and by X-ray absorption near-edge structure data. The electron-donor/acceptor tendencies of both the support and IL determine the activity and selectivity of the catalysts for the hydrogenation of 1,3-butadiene, with electron-rich iridium being selective for partial hydrogenation. The results resolve the effects of the IL and support as ligands; for example, the effect of the IL becomes dominant when the support has a weak electron-donor character. The combined effects of supports and ILs as ligands offer broad opportunities for tuning catalytic properties of supported metal catalysts.

Machine learning approach to literature mining for the genetics of complex diseases

To generate a parsimonious gene set for understanding the mechanisms underlying complex diseases, we reasoned it was necessary to combine the curation of public literature, review of experimental databases and interpolation of pathway-associated genes. Using this strategy, we previously built the following two databases for reproductive disorders: The Database for Preterm Birth (dbPTB) and The Database for Preeclampsia (dbPEC). The completeness and accuracy of these databases is essential for supporting our understanding of these complex conditions. Given the exponential increase in biomedical literature, it is becoming increasingly difficult to manually maintain these databases. Using our curated databases as reference data sets, we implemented a machine learning-based approach to optimize article selection for manual curation. We used logistic regression, random forests and neural networks as our machine learning algorithms to classify articles. We examined features derived from abstract text, annotations and metadata that we hypothesized would best classify articles with genetically relevant content associated to the disorder of interest. Combinations of these features were used build the classifiers and the performance of these feature sets were compared to a standard 'Bag-of-Words'. Several combinations of these genetic based feature sets outperformed 'Bag-of-Words' at a threshold such that 95% of the curated gene set obtained from the original manual curation of all articles were extracted from the articles classified by machine learning as 'considered'. The performance was superior in terms of the reduction of required manual curation and two measures of the harmonic mean of precision and recall. The reduction in workload ranged from 0.814 to 0.846 for the dbPTB and 0.301 to 0.371 for the dbPEC. Additionally, a database of metadata and annotations is generated which allows for rapid query of individual features. Our results demonstrate that machine learning algorithms can identify articles with relevant data for databases of genes associated with complex diseases.

Effect of methylation of ionic liquids on the gas separation performance of ionic liquid/metal-organic framework composites

1-N-Butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF6], and its methylated form, 1-N-butyl-2,3-dimethylimidazolium hexafluorophosphate, [BMMIM][PF6], were incorporated into CuBTC to examine the effect of methylation of ionic liquids (ILs) on the gas separation performance of the corresponding IL/metal-organic framework (MOF) composites. Spectroscopic analysis revealed that the interactions of the methylated ILs with CuBTC were weaker compared to those of its non-methylated counterpart. Gas uptake measurements illustrated that this difference in the interactions influences the gas separation performance of the composites. Accordingly, the CO2/N2: 15/85 and CH4/N2: 50/50 selectivities increased by 37% and 60% for [BMMIM][PF6]/CuBTC and 34% and 50% for [BMIM][PF6]/CuBTC, respectively, compared to the corresponding selectivities of pristine CuBTC at 1000 mbar. The results revealed another structural parameter controlling the performance of the IL/MOF composites, a novel type of material with rapidly expanding application areas.

An Extremely Rare Side Effect of Ranitidine: Junctional Rhythm

Ranitidine is a H2 receptor blocker and rarely cause bradycardia. A 28 years old male patient attended the emergency department for urticaria. He was given 45 mg of phenyramine and 50 mg of ranitidine intravenously. He then complained of dizziness and developed bradycardia and hypotension. Electrocardiogram detected junctional bradycardia rhythm. He was given 0.5 mg atropine intravenously and his rhythm then returned to normal. His symptoms subsided and the blood pressure improved. Ranitidine is a frequently used medication and this case illustrated a rare but serious side-effect of the medication.

Toward Rational Design of Ionic Liquid/Metal-Organic Framework Composites: Effects of Interionic Interaction Energy

One of the structural factors controlling the extent of interactions between ionic liquids (ILs) and metal-organic frameworks (MOFs) in IL/MOF composites is elucidated. Results showed that the thermal stability limits and adsorption performances of the IL/MOF composites can be tuned by the interionic interaction energy of bulk ILs, which can be probed spectroscopically via C2H infrared stretching frequency.

A novel, de novo mutation in the PRKAG2 gene: infantile-onset phenotype and the signaling pathway involved

PRKAG2 encodes the γ2-subunit isoform of 5'-AMP-activated protein kinase (AMPK), a heterotrimeric enzyme with major roles in the regulation of energy metabolism in response to cellular stress. Mutations in PRKAG2 have been implicated in a unique hypertrophic cardiomyopathy (HCM) characterized by cardiac glycogen overload, ventricular preexcitation, and hypertrophy. We identified a novel, de novo PRKAG2 mutation (K475E) in a neonate with prenatal onset of HCM. We aimed to investigate the cellular impact, signaling pathways involved, and therapeutic options for K475E mutation using cells stably expressing human wild-type (WT) or the K475E mutant. In human embryonic kidney-293 cells, the K475E mutation induced a marked increase in the basal phosphorylation of T172 and AMPK activity, reduced sensitivity to AMP in allosteric activation, and a loss of response to phenformin. In H9c2 cardiomyocytes, the K475E mutation induced inhibition of AMPK and reduced the response to phenformin and increases in the phosphorylation of p70S6 kinase (p70S6K) and eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1). Primary fibroblasts from the patient with the K475E mutation also showed marked increases in the phosphorylation of p70S6K and 4E-BP1 compared with those from age-matched, nondiseased controls. Moreover, overexpression of K475E induced hypertrophy in H9c2 cells, which was effectively reversed by treatment with rapamycin. Taken together, we have identified a novel, de novo infantile-onset PRKAG2 mutation causing HCM. Our study suggests the K475E mutation induces alteration in basal AMPK activity and results in a hypertrophy phenotype involving the mechanistic target of rapamycin signaling pathway, which can be reversed with rapamycin.NEW & NOTEWORTHY We identified a novel, de novo PRKAG2 mutation (K475E) in the cystathionine β-synthase 3 repeat, a region critical for AMP binding but with no previous reported mutation. Our data suggest the mutation affects AMP-activated protein kinase activity, activates cell growth pathways, and results in cardiac hypertrophy, which can be reversed with rapamycin.

Ionic Liquid/Metal-Organic Framework Composites: From Synthesis to Applications

Metal-organic frameworks (MOFs) have been widely studied for different applications owing to their fascinating properties such as large surface areas, high porosities, tunable pore sizes, and acceptable thermal and chemical stabilities. Ionic liquids (ILs) have been recently incorporated into the pores of MOFs as cavity occupants to change the physicochemical properties and gas affinities of MOFs. Several recent studies have shown that IL/MOF composites show superior performances compared with pristine MOFs in various fields, such as gas storage, adsorption and membrane-based gas separation, catalysis, and ionic conductivity. In this review, we address the recent advances in syntheses of IL/MOF composites and provide a comprehensive overview of their applications. Opportunities and challenges of using IL/MOF composites in many applications are reviewed and the requirements for the utilization of these composite materials in real industrial processes are discussed to define the future directions in this field.