Blood flow restriction attenuates surface mechanomyography lateral and longitudinal, but not transverse oscillations during fatiguing exercise.

Objective. Surface mechanomyography (sMMG) can measure oscillations of the activated muscle fibers in three axes (i.e.X,Y, andZ-axes) and has been used to describe motor unit activation patterns (X-axis). The application of blood flow restriction (BFR) is common in exercise studies, but the cuff may restrict muscle fiber oscillations. Therefore, the purpose of this investigation was to examine the acute effects of submaximal, fatiguing exercise with and without BFR on sMMG amplitude in theX,Y, andZ-axes among female participants.Approach. Sixteen females (21 ± 1 years) performed two separate exercise bouts to volitional exhaustion that consisted of unilateral, submaximal (50% maximal voluntary isometric contraction [MVIC]) intermittent, isometric, leg extensions with and without BFR. sMMG was recorded and examined across percent time to exhaustion (%TTE) in 20% increments. Separate 2-way repeated measures ANOVA models were constructed: (condition [BFR, non-BFR]) × (time [20, 40, 60, 80, and 100% TTE]) to examine absolute (m·s-2) and normalized (% of pretest MVIC) sMMG amplitude in theX-(sMMG-X),Y-(sMMG-Y), andZ-(sMMG-Z) axes.Main results. The absolute sMMG-X amplitude responses were attenuated with the application of BFR (mean ± SD = 0.236 ± 0.138 m·s-2) relative to non-BFR (0.366 ± 0.199 m·s-2, collapsed across time) and for sMMG-Y amplitude at 60%-100% of TTE (BFR range = 0.213-0.232 m·s-2versus non-BFR = 0.313-0.445 m·s-2). Normalizing sMMG to pretest MVIC removed most, but not all the attenuation which was still evident for sMMG-Y amplitude at 100% of TTE between BFR (72.9 ± 47.2%) and non-BFR (98.9 ± 53.1%). Interestingly, sMMG-Z amplitude was not affected by the application of BFR and progressively decreased across %TTE (0.332 ± 0.167 m·s-2to 0.219 ± 0.104 m·s-2, collapsed across condition.)Significance. The application of BFR attenuated sMMG-X and sMMG-Y amplitude, although normalizing sMMG removed most of this attenuation. Unlike theXandY-axes, sMMG-Z amplitude was not affected by BFR and progressively decreased across each exercise bout potentially tracking the development of muscle fatigue.

Response surface methodology optimizes selenium inhibition of prostate cancer PC-3 cell viability.

BACKGROUND: The rising incidence of prostate cancer in the U.S. necessitates innovative therapeutic approaches to this disease. Though extensive research has studied Selenium as an anticarcinogen against prostate cancer, results have varied due to overlooked experimental confounds. Recent studies have identified differential effects of various selenium compounds on prostate cancer cells. This study leverages Mixture Design Response Surface Methodology to characterize the ideal combination of select Se forms against the PC-3 prostate cancer cell line. METHODS: The PC-3 cell line was chosen as a model for its representation of advanced-stage malignancy. Three Se compounds-sodium selenite, methylseleninic acid, and nano-selenium-were selected for their promising antineoplastic potential. Nano-Se particles were synthesized and subsequently characterized by transmission electron microscopy. Cells were cultured, treated with Se compounds, and assessed for viability using an Alamar Blue Assay. IC50 values of individual Se compounds were determined, and treatment combinations evaluated. In collaboration with statical modeling experts, MDRSM was utilized to optimize Se compound combinations. RESULTS: Absolute IC50 values were identified for methylseleninic acid (5.01 µmol/L), sodium selenite (13.8 µmol/L), and nano-selenium (14.6 µmol/L). Combining methylseleninic acid and sodium selenite resulted in only 5% PC-3 cell viability, whereas individual treatments reduced viability by approximately 45%. Among the tested mixtures, the 50:50 combination of MSA and sodium selenite most effectively decreased PC-3 cell viability. Regression analysis indicated the special cubic model had a strong fit (multiple r² = 0.9853), predicting maximum cell viability reduction from the methylseleninic acid and selenite mixture. CONCLUSION: The specific form of Selenium plays a pivotal role in determining its physiological effects and therapeutic potential against prostate cancer. All three selenium compounds showed variable antineoplastic effects, with a 50:50 mixture of methylseleninic acid and selenite exhibiting optimal results. Nano-selenium, when combined with selenite, showed no additive effect, implying a shared mechanism of action. Our research underscores the critical need to consider Se compound forms as distinct entities in prostate cancer treatment and encourages further exploration of Se compounds against prostate cancer.

Acute Effects of Sprint Interval Training and Blood Flow Restriction on Neuromuscular and Muscle Function.

BFR) applied during sprint interval training (SIT) on performance and neuromuscular function. METHODS: Fifteen men completed a randomized bout of SIT with CBFR, IBFR, and without BFR (No-BFR), consisting of 2, 30-s maximal sprints on a cycle ergometer with a resistance of 7.5% of body mass. Concentric peak torque (CPT), maximal voluntary isometric contraction (MVIC) torque, and muscle thickness (MT) were measured before and after SIT, including surface electromyography (sEMG) recorded during the strength assessments. Peak and mean revolutions per minute (RPM) were measured during SIT and power output was examined relative to physical working capacity at the fatigue threshold (PWCFT). RESULTS: CPT and MVIC torque decreased from pre-SIT (220.3±47.6 Nm and 355.1±72.5 Nm, respectively) to post-SIT (147.9±27.7 Nm and 252.2±45.5 Nm, respectively, all P<0.05), while MT increased (1.77±0.31 cm to 1.96±0.30 cm). sEMG mean power frequency decreased during CPT (-12.8±10.5%) and MVIC (-8.7±10.2%) muscle actions. %PWCFT was greater during No-BFR (414.2±121.9%) than CBFR (375.9±121.9%). CONCLUSION: SIT with or without BFR induced comparable alterations in neuromuscular fatigue and sprint performance across all conditions, without affecting neuromuscular function.

Blood flow restriction increases necessary muscle excitation of the elbow flexors during a single high-load contraction.

PURPOSE: To investigate the effects of blood flow restriction (BFR) on electromyographic amplitude (EMGRMS)-force relationships of the biceps brachii (BB) during a single high-load muscle action. METHODS: Twelve recreationally active males and eleven recreationally active females performed maximal voluntary contractions (MVCs), followed by an isometric trapezoidal muscle action of the elbow flexors at 70% MVC. Surface EMG was recorded from the BB during BFR and control (CON) visits. For BFR, cuff pressure was 60% of the pressure required to completely occlude blood at rest. Individual b (slope) and a terms (gain) were calculated from the log-transformed EMGRMS-force relationships during the linearly increasing and decreasing segments of the trapezoid. EMGRMS during the steady force segment was normalized to MVC EMGRMS. RESULTS: For BFR, the b terms were greater during the linearly increasing segment than the linearly decreasing segment (p < 0.001), and compared to the linearly increasing segment for CON (p < 0.001). The a terms for BFR were greater during the linearly decreasing than linearly increasing segment (p = 0.028). Steady force N-EMGRMS was greater for BFR than CON collapsed across sex (p = 0.041). CONCLUSION: BFR likely elicited additional recruitment of higher threshold motor units during the linearly increasing- and steady force-segment. The differences between activation and deactivation strategies were only observed with BFR, such as the b terms decreased and the a terms increased for the linearly decreasing segment in comparison to the increasing segment. However, EMGRMS-force relationships during the linearly increasing- and decreasing-segments were not different between sexes during BFR and CON.

Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data.

Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure-function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient-weighted Class Activation Mapping for graphs (Graph Grad-CAM) to automatically identify structurally important residues and residue-residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad-CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well-known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad-CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub-classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high-throughput identification of protein structure-function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.

Repeat testing enhances long-term verbal memory in children with epilepsy.

To (i) determine whether accelerated long-term forgetting (ALF) can be found using standardized verbal memory test materials in children with genetic generalized epilepsy (GGE) and temporal lobe epilepsy (TLE), and (ii) to establish whether ALF is impacted by executive skills and repeat testing over long delays. One hundred and twenty-three children aged 8 to 16, (28 with GGE, 23 with TLE, and 72 typically developing; TD) completed a battery of standardized tests assessing executive functioning and memory for two stories. Stories were recalled immediately and after a 30-min delay. To examine whether repeat testing impacts long-term forgetting, one story was tested via free recall at 1-day and 2-weeks, and the other at 2-weeks only. Recognition was then tested for both stories at 2-weeks. Children with epilepsy recalled fewer story details, both immediately and after 30-min relative to TD children. Compared to TD children, the GGE group, but not the TLE group, showed ALF, having significantly poorer recall of the story tested only at the longest delay. Poor executive skills were significantly correlated with ALF for children with epilepsy. Standard story memory materials can detect ALF in children with epilepsy when administered over long delays. Our findings suggest that (i) ALF is related to poor executive skills in children with epilepsy, and (ii) repeated testing may ameliorate ALF in some children.

Computational Design of Low Melting Eutectics of Molten Salts: A Combined Machine Learning and Thermodynamic Modeling Approach.

We develop a computational framework combining thermodynamic and machine learning models to predict the melting temperatures of molten salt eutectic mixtures (Teut). The model shows an accuracy of ∼6% (mean absolute percentage error) over the entire data set. Using this approach, we screen millions of combinatorial eutectics ranging from binary to hexanary, predict new mixtures, and propose design rules that lead to low Teut. We show that heterogeneity in molecular sizes, quantified by the molecular volume of the components, and mixture configurational entropy, quantified by the number of mixture components, are important factors that can be exploited to design low Teut mixtures. While predicting eutectic composition with existing techniques had proved challenging, we provide some preliminary models for estimating the compositions. The high-throughput screening technique presented here is essential to design novel mixtures for target applications and efficiently navigate the vast design space of the eutectic mixtures.

Microstructural mechanisms of hysteresis and transformation width in NiTi alloy from molecular dynamics simulations.

Martensitic transformations in shape memory alloys are often accompanied by thermal hysteresis, and engineering this property is of prime scientific interest. The martensitic transformation can be characterized as thermoelastic, where the extent of the transformation is determined by a balance between thermodynamic driving force and stored elastic energy. Here we used molecular dynamics simulations of the NiTi alloy to explore hysteresis-inducing mechanisms and thermoelastic behavior by progressively increasing microstructural constraints from single crystals to bi-crystals to polycrystals. In defect-free single crystals, the austenite-martensite interface moves unimpeded with a high velocity. In bi-crystals, grain boundaries act as significant obstacles to the transformation and produce hysteresis by requiring additional nucleation events. In polycrystals, the transformation is further limited by the thermoelastic balance. The stored elastic energy can be converted to mechanisms of non-elastic strain accommodation, which also produce hysteresis. We further demonstrated that the thermoelastic behavior can be controlled by adjusting microstructural constraints.

Acute effects of low load blood flow restricted and non restricted exercise on muscle excitation, neuromuscular efficiency, and average torque.

OBJECTIVES: The purpose of this investigation was to examine the acute effects of low-load blood flow restriction (LLBFR) and low-load (LL) resistance exercise on muscle excitation, neuromuscular efficiency, and average torque. METHODS: Eleven men (age±SD=22±3yrs) randomly performed LLBFR and LL that consisted of 30 unilateral leg extensions at 30% of one-repetition maximum while surface electromyography (sEMG) and torque were simultaneously assessed. Polynomial regression analyses and slope comparisons were performed to examine patterns of responses and rates of change. RESULTS: sEMG amplitude increased for LLBFR (9 of 11) and LL (8 of 11) and between composite responses (R2=0.939-0.981). For LLBFR, sEMG amplitude increased to a greater extent for 5 of the 11 individual and for the composite responses. Similarly, neuromuscular efficiency decreased for LLBFR (8 of 11) and LL (5 of 11) as well as the composite responses r2=0.902-0.929, but the decrease was larger for LLBFR than LL for the individual (4 of 11) responses. For average submaximal concentric torque, there were individual increases, decreases, and no changes for the composite responses (R2=0.198-0.325). CONCLUSION: LLBFR elicited greater fatigue-induced increases in muscle excitation and decreases in neuromuscular efficiency than LL, but neither LLBFR nor LL affected average submaximal concentric torque.

A 3D printable alloy designed for extreme environments.

Multiprincipal-element alloys are an enabling class of materials owing to their impressive mechanical and oxidation-resistant properties, especially in extreme environments1,2. Here we develop a new oxide-dispersion-strengthened NiCoCr-based alloy using a model-driven alloy design approach and laser-based additive manufacturing. This oxide-dispersion-strengthened alloy, called GRX-810, uses laser powder bed fusion to disperse nanoscale Y2O3 particles throughout the microstructure without the use of resource-intensive processing steps such as mechanical or in situ alloying3,4. We show the successful incorporation and dispersion of nanoscale oxides throughout the GRX-810 build volume via high-resolution characterization of its microstructure. The mechanical results of GRX-810 show a twofold improvement in strength, over 1,000-fold better creep performance and twofold improvement in oxidation resistance compared with the traditional polycrystalline wrought Ni-based alloys used extensively in additive manufacturing at 1,093 °C5,6. The success of this alloy highlights how model-driven alloy designs can provide superior compositions using far fewer resources compared with the 'trial-and-error' methods of the past. These results showcase how future alloy development that leverages dispersion strengthening combined with additive manufacturing processing can accelerate the discovery of revolutionary materials.

IBA Delivery Technique and Media Salts Affected In Vitro Rooting and Acclimatization of Eight Prunus Genotypes.

Difficult-to-root plants often perform poorly during acclimatization and in vitro rooting can increase the survival and quality of plants. The influence of auxin application and mineral nutrition on in vitro rooting and subsequent effects on plant quality in eight Prunus genotypes were investigated. Microshoots were rooted in vitro on Murashige and Skoog (MS), ½ MS, Driver and Kuniyuki (DKW), or New Prunus Medium (NPM) media formulations in combination with 15 µM indole-3-butyric acid (IBA), 4-day 15 µM IBA pulse, 1 mM 30 s quick-dip, or IBA-free treatments. Shoots were observed pre- and post-acclimatization to determine rooting methods to maximize quality and minimize labor. A genotype-specific response to auxin application was observed with seven of eight genotypes achieving 100% survival when paired with the recommended IBA treatment. Peaches performed best when treated with 4-day IBA pulse or 30 s quick-dip. Rooting of P. cerasifera, it's hybrid to P. persica, and P. munsoniana all benefitted from IBA application. Shoots rooted with 15 µM IBA were smaller and lower quality in most genotypes. DKW maximized size and quality in six genotypes. Better shoots and larger root systems during in vitro rooting produced better plants in the greenhouse with no detrimental effect of callus growth. Rooting techniques to maximize plant quality while reducing labor are specified.

Modeling Singlet Oxygen-Induced Degradation Pathways Including Environmental Effects of 1,2-Dimethoxyethane in Li-O2 Batteries through Density Functional Theory.

We employ density functional theory (DFT) to examine reaction mechanisms involving singlet oxygen 1Δg (1O2) and 1,2-dimethoxyethane (DME) to probe potential parasitic reactions occurring in Li-O2 batteries. First, we investigate the attack of 1O2 on the ethylene group (-CH2-CH2-) to form H2O2 and a C-C double bond in a single step. Second, we look at hydroperoxide formation that occurs via a two-step mechanism. We employ an implicit solvent model, Li+ coordination, and external electric fields to model the complex electrolyte environment near the cathode of a Li-O2 battery. The initial barriers for these reactions are decreasing functions of the dielectric constant of the implicit solvent model as well as the strength of the electric field. These initial barriers range between 17 and 26 kcal mol-1 for large dielectric constants and in the presence of electric fields. We discuss the implications of these results on ether-based electrolytes for Li-O2 batteries.

Nature of the Electrical Double Layer on Suspended Graphene Electrodes.

The structure of interfacial water near suspended graphene electrodes in contact with aqueous solutions of Na2SO4, NH4Cl, and (NH4)2SO4 has been studied using confocal Raman spectroscopy, sum frequency vibrational spectroscopy, and Kelvin probe force microscopy. SO42- anions were found to preferentially accumulate near the interface at an open circuit potential (OCP), creating an electrical field that orients water molecules below the interface, as revealed by the increased intensity of the O-H stretching peak of H-bonded water. No such increase is observed with NH4Cl at the OCP. The intensity of the dangling O-H bond stretching peak however remains largely unchanged. The degree of orientation of the water molecules as well as the electrical double layer strength increased further when positive voltages are applied. Negative voltages on the other hand produced only small changes in the intensity of the H-bonded water peaks but affected the intensity and frequency of dangling O-H bond peaks. The TOC figure is an oversimplified representation of the system in this work.

Predicting the Ion Desolvation Pathway of Lithium Electrolytes and Their Dependence on Chemistry and Temperature.

To better understand the influence of electrolyte chemistry on the ion-desolvation portion of charge-transfer beyond the commonly applied techniques, we apply free-energy sampling to simulations involving diethyl ether (DEE) and 1,3-dioxoloane/1,2-dimethoxyethane (DOL/DME) electrolytes, which display bulk solvation structures dominated by ion-pairing and solvent coordination, respectively. This analysis was conducted at a pristine electrode with and without applied bias at 298 and 213 K to provide insights into the low-temperature charge-transfer behavior, where it has been proposed that desolvation dominates performance. We find that, to reach the inner Helmholtz layer, ion-paired structures are advantageous and that the Li+ ion must reach a total coordination number of 3, which requires the shedding of 1 species in the DEE electrolyte or 2-3 species in DOL/DME. This work represents an effort to predict the distinct thermodynamic states as well as the most probable kinetic pathways of ion desolvation relevant for the charge transfer at electrochemical interphases.

GenomicDistributions: fast analysis of genomic intervals with Bioconductor.

BACKGROUND: Epigenome analysis relies on defined sets of genomic regions output by widely used assays such as ChIP-seq and ATAC-seq. Statistical analysis and visualization of genomic region sets is essential to answer biological questions in gene regulation. As the epigenomics community continues generating data, there will be an increasing need for software tools that can efficiently deal with more abundant and larger genomic region sets. Here, we introduce GenomicDistributions, an R package for fast and easy summarization and visualization of genomic region data. RESULTS: GenomicDistributions offers a broad selection of functions to calculate properties of genomic region sets, such as feature distances, genomic partition overlaps, and more. GenomicDistributions functions are meticulously optimized for best-in-class speed and generally outperform comparable functions in existing R packages. GenomicDistributions also offers plotting functions that produce editable ggplot objects. All GenomicDistributions functions follow a uniform naming scheme and can handle either single or multiple region set inputs. CONCLUSIONS: GenomicDistributions offers a fast and scalable tool for exploratory genomic region set analysis and visualization. GenomicDistributions excels in user-friendliness, flexibility of outputs, breadth of functions, and computational performance. GenomicDistributions is available from Bioconductor ( https://bioconductor.org/packages/release/bioc/html/GenomicDistributions.html ).

Efficacy and safety of cannabidivarin treatment of epilepsy in girls with Rett syndrome: A phase 1 clinical trial.

OBJECTIVE: Rett syndrome (RTT), commonly caused by methyl-CpG-binding protein 2 (MECP2) pathogenic variants, has many comorbidities. Fifty to ninety percent of children with RTT have epilepsy, which is often drug-resistant. Cannabidivarin (CBDV), a non-hallucinogenic phytocannabinoid, has shown benefit in MECP2 animal models. This phase 1 trial assessed the safety and tolerability of CBDV in female children with RTT and drug-resistant epilepsy, as well as the effect on mean monthly seizure frequency (MMSF), the electroencephalogram (EEG), and non-epilepsy comorbid symptoms. METHODS: Five female children with drug-resistant epilepsy and a pathogenic MECP2 variant were enrolled. Baseline clinical and laboratory assessments, including monthly seizure frequency, were recorded. CBDV oral solution (50 mg/ml) was prescribed and titrated to 10 mg/kg/day. Data collected included pharmacokinetics, seizure type and frequency, adverse events, EEG, and responses to the Rett Syndrome Behaviour Questionnaire and Rett Syndrome Symptom Severity Index, and were compared to baseline data. RESULTS: All five children reached the maximum CBDV dose of 10 mg/kg/day and had a reduction in MMSF (median = 79% reduction). Three children had MMSF reduction > 75%. This corresponded to an overall reduction in seizure frequency from 32 to 7.2 seizures per month. Ninety-one percent of adverse events were mild or moderate, and none required drug withdrawal. Sixty-two percent were judged to be unrelated to CBDV. Thirty-one percent of adverse events were identified as possibly related, of which nearly all were mild, and the remainder were later assessed as RTT symptoms. Hypersomnolence and drooling were identified as related to CBDV. No serious adverse events reported were related to CBDV. No significant change was noted in EEG or non-epilepsy-related symptoms of RTT. SIGNIFICANCE: A dose of 10 mg/kg/day of CBDV is safe and well tolerated in a pediatric RTT cohort and suggests improved seizure control in children with MECP2-related RTT.

Expert advice for prescribing cannabis medicines for patients with epilepsy-drawn from the Australian clinical experience.

There is international interest for consensus advice for prescribers working in the field of drug resistant epilepsy intending to trial potential therapies that are nonregistered or off-label. Cannabinoids are one such therapy. In 2017, the New South Wales State Government (Australia) set up a cannabinoid prescribing guidance service for a wide variety of indications, based on known pharmacology together with the relevant new literature as it became available. Increasing interest in cannabis medicines use outside this State over the following 5 years together with a paucity of registration-standard clinical trials, lack of information around dosing issues, drug interactions and biological plausibility meant there remained a large unmet need for such advice. To address the unmet need in epilepsy, and until medicines were registered or regulator quality data were available, it was agreed to bring together a working group comprising paediatric and adult epilepsy specialists, clinical pharmacists., clinical pharmacologists and cannabis researchers from across Australia to develop interim consensus advice for prescribers. Although interim, this consensus advice addresses much of the current practice gap by providing an informed overview of the different cannabis medicines currently available for use in the treatment of epilepsy in paediatric and adult settings, with information on dose, drug interactions, toxicity, type of seizure and frequency of symptom relief. As such it supplements the limited evidence currently available from clinical trials with experience from front-line practice. It is expected that this consensus advice will be updated as new evidence emerges and will provide guidance for a subsequent Guideline.

Accelerated long-term forgetting in children with temporal lobe epilepsy: A timescale investigation of material specificity and executive skills.

Recently, children with temporal lobe epilepsy (TLE) were found to be at risk of accelerated long-term forgetting (ALF). In this study, we examined the temporal trajectory of ALF, while exploring the relationship between ALF, executive skills, and epilepsy variables. Fifty-one children, (23 with TLE and 28 typically developing) completed a battery of neuropsychological tests of verbal and visual memory, executive skills, and two experimental memory tasks (verbal and visual) involving recall after short (30-min) and extended (1-day and 2-week) delays. Side of seizure focus and hippocampal integrity were considered. On the visual task (Scene Memory), children with TLE performed comparably to typically developing children following a 30-min and 1-day delay, although worse than typically developing children at 2 weeks: ALF was observed in children with right TLE focus. The two groups did not differ on the experimental verbal memory task. Children with TLE also had worse performance than typically developing children on standardized verbal memory test and on tests of executive skills (i.e., verbal generativity, inhibition, working memory, complex attention). Only complex attention was associated with visual ALF. ALF was present for visuo-spatial materials in children with TLE at two weeks, and children with right TLE were most susceptible. A relationship was identified between complex attention and long-term forgetting. The findings extend our understanding of difficulties in long-term memory formation experienced by children with TLE.

Detecting molecular subtypes from multi-omics datasets using SUMO.

We present a data integration framework that uses non-negative matrix factorization of patient-similarity networks to integrate continuous multi-omics datasets for molecular subtyping. It is demonstrated to have the capability to handle missing data without using imputation and to be consistently among the best in detecting subtypes with differential prognosis and enrichment of clinical associations in a large number of cancers. When applying the approach to data from individuals with lower-grade gliomas, we identify a subtype with a significantly worse prognosis. Tumors assigned to this subtype are hypomethylated genome wide with a gain of AP-1 occupancy in demethylated distal enhancers. The tumors are also enriched for somatic chromosome 7 (chr7) gain, chr10 loss, and other molecular events that have been suggested as diagnostic markers for "IDH wild type, with molecular features of glioblastoma" by the cIMPACT-NOW consortium but have yet to be included in the World Health Organization (WHO) guidelines.

Coarse-Grained Dynamically Accurate Simulations of Ionic Liquids: [pyr14][TFSI] and [EMIM][BF4].

In this work, coarse-grained (CG) models for two different sets of ionic liquids were developed from atomistic molecular dynamics (MD) reference systems, expanding their system size and time duration capabilities. The bonded force field of the CG systems was built using harmonic oscillator potential (HOP) fitting, while the nonbonded force field was generated with the multiscale coarse-graining (MS-CG) approach based on force matching. The dynamics of each system were corrected using the probability distribution function-based coarse-grained molecular dynamics (PDF-based CGMD) method. The structure and dynamics of each system were proven to match reference system data at two temperature scales. CG models and force fields for these liquids were developed to exemplify a general purpose methodology for producing MD results of ionic liquids and other fluids with accurate structural as well as dynamic properties. As an application, developed ionic liquids CG models were then applied to study vacuum-interface interaction. Density profile results of vacuum-interface exposure show significant deviation from bulk behavior. At the interface, multilayer ordering of ionic liquids is predicted to be similar to those observed from an experimental work. This ordering is intensified by decreasing temperature and use of the PDF-based CGMD method as opposed to conventional CG methods.