The Atlas of Protein-Protein Interactions in Cancer (APPIC)-a webtool to visualize and analyze cancer subtypes.

Cancer is a complex disease with heterogeneous mutational and gene expression patterns. Subgroups of patients who share a phenotype might share a specific genetic architecture including protein-protein interactions (PPIs). We developed the Atlas of Protein-Protein Interactions in Cancer (APPIC), an interactive webtool that provides PPI subnetworks of 10 cancer types and their subtypes shared by cohorts of patients.

Variant graph craft (VGC): a comprehensive tool for analyzing genetic variation and identifying disease-causing variants.

Background: The variant call format (VCF) file is a structured and comprehensive text file crucial for researchers and clinicians in interpreting and understanding genomic variation data. It contains essential information about variant positions in the genome, along with alleles, genotype calls, and quality scores. Analyzing and visualizing these files, however, poses significant challenges due to the need for diverse resources and robust features for in-depth exploration.

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.

Evaluating CH/N Separation Performances of Hundreds of Thousands of Real and Hypothetical MOFs by Harnessing Molecular Modeling and Machine Learning.

Considering the large abundance and diversity of metal-organic frameworks (MOFs), evaluating the gas adsorption and separation performance of the entire MOF material space using solely experimental techniques or brute-force computer simulations is impractical. In this study, we integrated high-throughput molecular simulations with machine learning (ML) to explore the potential of both synthesized, the real MOFs, and computer-generated, the hypothetical MOFs (hypoMOFs), for adsorption-based CH/N separation. CH/N mixture adsorption data obtained from molecular simulations were used to train the ML models that could accurately predict gas uptakes of 4612 real MOFs.

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

Capturing CO 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 CO/N, CO/CH, and CH/N separation performance of the composite were examined by volumetric gas adsorption measurements complemented by the density functional theory (DFT) calculations.

MMR Deficiency Defines Distinct Molecular Subtype of Breast Cancer with Histone Proteomic Networks.

Mismatch repair (MMR) alterations are important prognostic and predictive biomarkers in a variety of cancer subtypes, including colorectal and endometrial. However, in breast cancer (BC), the distinction and clinical significance of MMR are largely unknown. This may be due in part to the fact that genetic alterations in MMR genes are rare and only seen to occur in around 3% of BCs.

Integrating Molecular Simulations with Machine Learning Guides in the Design and Synthesis of [BMIM][BF]/MOF Composites for CO/N 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--butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF]) with a large variety of MOFs for CO and N adsorption.

Clinical features of patients with -deleted bladder cancer.

Advanced urothelial carcinoma continues to have a dismal prognosis despite several new therapies in the last 5 years. and 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.

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.

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.

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) complexes bound to metal-oxide supports because of their electron-donor/acceptor capacities. The combined effects of supports and ILs as ligands may pave the way to the tuning of the surrounding electronic properties to increase electron-donor/acceptor efficiency in metal-oxide supported Ir(CO) complexes. Herein, we have used Density Functional Theory to model Ir(CO) complexes bound to MgO supports with and without the presence of an IL to explain the role of ILs in modifying the electronic structure of the supported complex.

Protein interaction networks define the genetic architecture of preterm birth.

The likely genetic architecture of complex diseases is that subgroups of patients share variants in genes in specific networks sufficient to express a shared phenotype. We combined high throughput sequencing with advanced bioinformatic approaches to identify such subgroups of patients with variants in shared networks. We performed targeted sequencing of patients with 2 or 3 generations of preterm birth on genes, gene sets and haplotype blocks that were highly associated with preterm birth.

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.

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.

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

We incorporated a water-stable ionic liquid (IL), 1-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF], into a water-stable metal-organic framework (MOF), MIL-53(Al), to generate the [BMIM][PF]/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][PF] incorporation.

Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis.

has emerged as a frequent cause of invasive candidiasis with increasing evidence of unique biological features relative to As it adapts to conditions within a mammalian host, rapid changes in gene expression are necessary to facilitate colonization and persistence in this environment. Adhesion of the organism to biological surfaces is a key first step in this process and is the focus of this study. Building on previous observations showing the importance of a member of the gene family in adhesion, three clinical isolates were cultured under two conditions that mimic the mammalian host and promote adhesion, incubation at 37°C in tissue culture medium 199 or in human plasma.

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.

Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool.

We posit the likely architecture of complex diseases is that subgroups of patients share variants in genes in specific networks which are sufficient to give rise to a shared phenotype. We developed Proteinarium, a multi-sample protein-protein interaction (PPI) tool, to identify clusters of patients with shared gene networks. Proteinarium converts user defined seed genes to protein symbols and maps them onto the STRING interactome.

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--butyl-3-methylimidazolium methyl sulfate ([BMIM][MeSO]) into two different metal organic frameworks (MOFs), UiO-66, and its amino-functionalized counterpart, NH-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.

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

1--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).

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.

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.

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.