DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples.

Personalized cancer care requires molecular characterization of neoplasms. While the research community accepts frozen tissues as the gold standard analyte for molecular assays, the source of tissue for testing in clinical cancer care comes almost universally from formalin-fixed, paraffin-embedded tissue (FFPE). As newer technologies emerge for DNA characterization that requires higher molecular weight DNA, it was necessary to compare the quality of DNA in terms of DNA length between FFPE and cryopreserved samples. We hypothesized that cryopreserved samples would yield higher quantity and superior quality DNA compared to FFPE samples. We analyzed DNA metrics by performing a head-to-head comparison between FFPE and cryopreserved samples from 38 human tumors representing various cancer types. DNA quantity and purity were measured by UV spectrophotometry, and DNA from cryopreserved tissue demonstrated a 4.2-fold increase in DNA yield per mg of tissue (p-value < 0.001). DNA quality was measured on a fragment microelectrophoresis analyzer, and again, DNA from cryopreserved tissue demonstrated a 223% increase in the DNA quality number and a 9-fold increase in DNA fragments > 40,000 bp (p-value < 0.0001). DNA from the cryopreserved tissues was superior to the DNA from FFPE samples in terms of DNA yield and quality.

IsoVis - a webserver for visualization and annotation of alternative RNA isoforms.

Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Making sense of the plethora of known and novel RNA isoforms being identified by transcriptomic approaches requires a user-friendly way to visualize gene isoforms and how they differ in exonic content, expression levels and potential functions. Here we introduce IsoVis, a freely available webserver that accepts user-supplied transcriptomic data and visualizes the expressed isoforms in a clear, intuitive manner. IsoVis contains numerous features, including the ability to visualize all RNA isoforms of a gene and their expression levels; the annotation of known isoforms from external databases; mapping of protein domains and features to exons, allowing changes to protein sequence and function between isoforms to be established; and extensive species compatibility. Datasets visualised on IsoVis remain private to the user, allowing analysis of sensitive data. IsoVis visualisations can be downloaded to create publication-ready figures. The IsoVis webserver enables researchers to perform isoform analyses without requiring programming skills, is free to use, and available at https://isomix.org/isovis/.

Investigation into a Conformationally Locked (Z)-Azidoxime.

High nitrogen compounds find wide use in the development of new propellants and explosives as well as pharmaceutical chemistry as bioisosteres, bacterial stains, and antifungal agents. A class of underexplored high-nitrogen materials includes azidoximes and their 1-hydroxytetrazole isomers. Azidoximes possess an energetic azide group and are quite sensitive to impact, spark, and friction. Therefore, these materials are generated in situ and cyclized under mild acidic conditions to their 1-hydroxytetrazole isomers. Recently, we synthesized a novel 1,2,4-triazine-derived azidoxime; however, upon subjecting this material to established cyclization conditions, no reaction was observed, even after prolonged reaction times with heating. Additional 1,2,4-triazine-derived azidoximes also displayed a similar lack of reactivities. This observation led us to probe the reactivity of these materials with both a DFT investigation and crystallographically based electrostatic potential mapping. In all, the lack of reactivity toward cyclization was found to be due to an inability of 1,2,4-triazine-based azidoximes to isomerize into the reactive (E)-conformation, requiring an activation energy of 26.4 kcal mol-1.

A dynamic actin cytoskeleton is required to prevent constitutive VDAC-dependent MAPK signalling and aberrant lipid homeostasis.

The dynamic nature of the actin cytoskeleton is required to coordinate many cellular processes, and a loss of its plasticity has been linked to accelerated cell aging and attenuation of adaptive response mechanisms. Cofilin is an actin-binding protein that controls actin dynamics and has been linked to mitochondrial signaling pathways that control drug resistance and cell death. Here we show that cofilin-driven chronic depolarization of the actin cytoskeleton activates cell wall integrity mitogen-activated protein kinase (MAPK) signalling and disrupts lipid homeostasis in a voltage-dependent anion channel (VDAC)-dependent manner. Expression of the cof1-5 mutation, which reduces the dynamic nature of actin, triggers loss of cell wall integrity, vacuole fragmentation, disruption of lipid homeostasis, lipid droplet (LD) accumulation, and the promotion of cell death. The integrity of the actin cytoskeleton is therefore essential to maintain the fidelity of MAPK signaling, lipid homeostasis, and cell health in S. cerevisiae.

Pseudomonas aeruginosa increases the susceptibility of Candida albicans to amphotericin B in dual-species biofilms.

BACKGROUND: Biofilms are the leading cause of nosocomial infections and are hard to eradicate due to their inherent antimicrobial resistance. Candida albicans is the leading cause of nosocomial fungal infections and is frequently co-isolated with the bacterium Pseudomonas aeruginosa from biofilms in the cystic fibrosis lung and severe burn wounds. The presence of C. albicans in multispecies biofilms is associated with enhanced antibacterial resistance, which is largely mediated through fungal extracellular carbohydrates sequestering the antibiotics. However, significantly less is known regarding the impact of polymicrobial biofilms on antifungal resistance. RESULTS: Here we show that, in dual-species biofilms, P. aeruginosa enhances the susceptibility of C. albicans to amphotericin B, an effect that was biofilm specific. Transcriptional analysis combined with gene ontology enrichment analysis identified several C. albicans processes associated with oxidative stress to be differentially regulated in dual-species biofilms, suggesting that P. aeruginosa exerts oxidative stress on C. albicans, likely through the secretion of phenazines. However, the mitochondrial superoxide dismutase SOD2 was significantly down-regulated in the presence of P. aeruginosa. Monospecies biofilms of the sod2Δ mutant were more susceptible to amphotericin B, and the susceptibility of these biofilms was further enhanced by exogenous phenazines. CONCLUSIONS: We propose that in dual-species biofilms, P. aeruginosa simultaneously induces mitochondrial oxidative stress, while down-regulating key detoxification enzymes, which prevents C. albicans mounting an appropriate oxidative stress response to amphotericin B, leading to fungal cell death. This work highlights the importance of understanding the impact of polymicrobial interactions on antimicrobial susceptibility.

Halogenated PETN derivatives: interplay between physical and chemical factors in explosive sensitivity.

Determining the factors that influence and can help predict energetic material sensitivity has long been a challenge in the explosives community. Decades of literature reports identify a multitude of factors both chemical and physical that influence explosive sensitivity; however no unifying theory has been observed. Recent work by our team has demonstrated that the kinetics of "trigger linkages" (i.e., the weakest bonds in the energetic material) showed strong correlations with experimental drop hammer impact sensitivity. These correlations suggest that the simple kinetics of the first bonds to break are good indicators for the reactivity observed in simple handling sensitivity tests. Herein we report the synthesis of derivatives of the explosive pentaerythritol tetranitrate (PETN) in which one, two or three of the nitrate ester functional groups are substituted with an inert group. Experimental and computational studies show that explosive sensitivity correlates well with Q (heat of explosion), due to the change in the number of trigger linkages removed from the starting material. In addition, this correlation appears more significant than other observed chemical or physical effects imparted on the material by different inert functional groups, such as heat of formation, heat of explosion, heat capacity, oxygen balance, and the crystal structure of the material.

Binding of Nitriles and Isonitriles to V(III) and Mo(III) Complexes: Ligand vs Metal Controlled Mechanism.

The synthesis and structures of nitrile complexes of V(N[tBu]Ar)3, 2 (Ar = 3,5-Me2C6H3), are described. Thermochemical and kinetic data for their formation were determined by variable temperature Fourier transform infrared (FTIR), calorimetry, and stopped-flow techniques. The extent of back-bonding from metal to coordinated nitrile indicates that electron donation from the metal to the nitrile plays a less prominent role for 2 than for the related complex Mo(N[tBu]Ar)3, 1. Kinetic studies reveal similar rate constants for nitrile binding to 2, but the activation parameters depend critically on the nature of R in RCN. Activation enthalpies range from 2.9 to 7.2 kcal·mol-1, and activation entropies from -9 to -28 cal·mol-1·K-1 in an opposing manner. Density functional theory (DFT) calculations provide a plausible explanation supporting the formation of a π-stacking interaction between a pendant arene of the metal anilide of 2 and the arene substituent on the incoming nitrile in favorable cases. Data for ligand binding to 1 do not exhibit this range of activation parameters and are clustered in a small area centered at ΔH‡ = 5.0 kcal·mol-1 and ΔS‡ = -26 cal·mol-1·K-1. Computational studies are in agreement with the experimental data and indicate a stronger dependence on electronic factors associated with the change in spin state upon ligand binding to 1.

Evolution of cisplatin resistance through coordinated metabolic reprogramming of the cellular reductive state.

BACKGROUND: Cisplatin (CDDP) is a mainstay treatment for advanced head and neck squamous cell carcinomas (HNSCC) despite a high frequency of innate and acquired resistance. We hypothesised that tumours acquire CDDP resistance through an enhanced reductive state dependent on metabolic rewiring. METHODS: To validate this model and understand how an adaptive metabolic programme might be imprinted, we performed an integrated analysis of CDDP-resistant HNSCC clones from multiple genomic backgrounds by whole-exome sequencing, RNA-seq, mass spectrometry, steady state and flux metabolomics. RESULTS: Inactivating KEAP1 mutations or reductions in KEAP1 RNA correlated with Nrf2 activation in CDDP-resistant cells, which functionally contributed to resistance. Proteomics identified elevation of downstream Nrf2 targets and the enrichment of enzymes involved in generation of biomass and reducing equivalents, metabolism of glucose, glutathione, NAD(P), and oxoacids. This was accompanied by biochemical and metabolic evidence of an enhanced reductive state dependent on coordinated glucose and glutamine catabolism, associated with reduced energy production and proliferation, despite normal mitochondrial structure and function. CONCLUSIONS: Our analysis identified coordinated metabolic changes associated with CDDP resistance that may provide new therapeutic avenues through targeting of these convergent pathways.

Chemical Descriptors for a Large-Scale Study on Drop-Weight Impact Sensitivity of High Explosives.

The drop-weight impact test is an experiment that has been used for nearly 80 years to evaluate handling sensitivity of high explosives. Although the results of this test are known to have large statistical uncertainties, it is one of the most common tests due to its accessibility and modest material requirements. In this paper, we compile a large data set of drop-weight impact sensitivity test results (mainly performed at Los Alamos National Laboratory), along with a compendium of molecular and chemical descriptors for the explosives under test. These data consist of over 500 unique explosives, over 1000 repeat tests, and over 100 descriptors, for a total of about 1500 observations. We use random forest methods to estimate a model of explosive handling sensitivity as a function of chemical and molecular properties of the explosives under test. Our model predicts well across a wide range of explosive types, spanning a broad range of explosive performance and sensitivity. We find that properties related to explosive performance, such as heat of explosion, oxygen balance, and functional group, are highly predictive of explosive handling sensitivity. Yet, models that omit many of these properties still perform well. Our results suggest that there is not one or even several factors that explain explosive handling sensitivity, but that there are many complex, interrelated effects at play.

Allergenicity reduction of the bio-elicited peanut sprout powder (BPSP) and toxicological acceptance of BPSP-supplemented diets assessed with ICR mice.

The allergenic and toxicological acceptances of the bio-elicited peanut sprout powder (BPSP) have not been assessed. BPSP was generated from peanut kernels germinated at 26-28 °C for 72 h (designated as 72 h-NGS). The 72 h-NGS were subsequently sliced, incubated, dried, defatted and pulverized to generate bio-elicited peanut sprout powder (BPSP). Protein solubility of BPSP increased 2.6-fold compared to 72 h-NGS. SDS-PAGE analysis revealed BPSP production triggered extensive degradation of the high-molecular weight peanut allergic proteins, mainly Ara h 1 and Ara h 3. Western blotting detected with peanut allergic patients' IgE indicated decreased in vitro reactivity. Food safety assessment of BPSP was performed with ICR mice fed with basal (control) and three doses of formulated BPSP-supplemented diets containing 0.11 g (normal), 2.5 g (high) and 25 g (super high) BPSP /kg BW. Animals appeared healthy with steady body weight gain in all groups during the entire 35-day dietary intervention. Hematological and serum biochemical analyses revealed no significant difference among groups. Histopathological examination on the tissue sections of primary organs further supported safety with no pathologies. The in vitro allergic reduction and toxicological safety in the BPSP-supplemented dietary intervention in the ICR mice study, support moving forward with BPSP-involved product development. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-022-05537-7.

Nonwoven Membranes with Infrared Light-Controlled Permeability.

This study presents the development of the first composite nonwoven fiber mats (NWFs) with infrared light-controlled permeability. The membranes were prepared by coating polypropylene NWFs with a photothermal layer of poly(N-isopropylacrylamide) (PNIPAm)-based microgels impregnated with graphene oxide nanoparticles (GONPs). This design enables "photothermal smart-gating" using light dosage as remote control of the membrane's permeability to electrolytes. Upon exposure to infrared light, the GONPs trigger a rapid local increase in temperature, which contracts the PNIPAm-based microgels lodged in the pore space of the NWFs. The contraction of the microgels can be reverted by cooling from the surrounding aqueous environment. The efficient conversion of infrared light into localized heat by GONPs coupled with the phase transition of the microgels above the lower critical solution temperature (LCST) of PNIPAm provide effective control over the effective porosity, and thus the permeability, of the membrane. The material design parameters, namely the monomer composition of the microgels and the GONP-to-microgel ratio, enable tuning the permeability shift in response to IR light; control NWFs coated with GONP-free microgels displayed thermal responsiveness only, whereas native NWFs showed no smart-gating behavior at all. This technology shows potential toward processing temperature-sensitive bioactive ingredients or remote-controlled bioreactors.

A genetic probe into the ancient and medieval history of Southern Europe and West Asia.

Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia.

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.

The genetic history of the Southern Arc: A bridge between West Asia and Europe.

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

COVID-19-A Qualitative Orthopaedic Nurse Perspective.

In response to a March 2020, New York State mandate, our elective surgery center began a physical and operational transformation to provide inpatient care to COVID-19 patients. Research study aims included (1) a description of the orthopaedic nurses' experience during the pandemic, and (2) tactics used to cope with related stress. Researchers used a descriptive, qualitative design to achieve study aims. During April to December 2020, nine nurses responded to seven open-ended, study prompts asking them to journal their thoughts about the pandemic. The majority (66%) of participants were experienced nurses and all provided direct patient care. Nurses provided 51 journal entries that generated 12 themes, which encapsulated their experience living through the pandemic: (1) Whirlwind, (2) War, (3) Control, (4) Death and Dying, (5) Staying Safe, (6) Loss, (7) Looking for Meaning, (8) Whatever It Takes, (9) Adaptability and Resilience, (10) What I Have Learned, (11) The New Normal, and (12) When Will This Be Over? Orthopaedic nurses in this study pivoted to the needs of patients requiring them to draw on all their training and resources. Nurses described the enormity and taxing nature of the viral threat and their ability to manage their well-being while caring for patients and loved ones, amidst social distancing and need for aggressive infection control. Support from peers and leadership were paramount factors in nurse coping. Positive thinking and personal resilience were considered essential. Most participants described personal growth; however, decreased participation in journal responses overtime, suggested emotional strain. Future studies should examine nurses' observations about the impact of changes to their practice brought on by the pandemic, and reliance on technology.

Mental Health Surveillance Among Children - United States, 2013-2019.

Mental health encompasses a range of mental, emotional, social, and behavioral functioning and occurs along a continuum from good to poor. Previous research has documented that mental health among children and adolescents is associated with immediate and long-term physical health and chronic disease, health risk behaviors, social relationships, education, and employment. Public health surveillance of children's mental health can be used to monitor trends in prevalence across populations, increase knowledge about demographic and geographic differences, and support decision-making about prevention and intervention. Numerous federal data systems collect data on various indicators of children's mental health, particularly mental disorders. The 2013-2019 data from these data systems show that mental disorders begin in early childhood and affect children with a range of sociodemographic characteristics. During this period, the most prevalent disorders diagnosed among U.S. children and adolescents aged 3-17 years were attention-deficit/hyperactivity disorder and anxiety, each affecting approximately one in 11 (9.4%-9.8%) children. Among children and adolescents aged 12-17 years, one fifth (20.9%) had ever experienced a major depressive episode. Among high school students in 2019, 36.7% reported persistently feeling sad or hopeless in the past year, and 18.8% had seriously considered attempting suicide. Approximately seven in 100,000 persons aged 10-19 years died by suicide in 2018 and 2019. Among children and adolescents aged 3-17 years, 9.6%-10.1% had received mental health services, and 7.8% of all children and adolescents aged 3-17 years had taken medication for mental health problems during the past year, based on parent report. Approximately one in four children and adolescents aged 12-17 years reported having received mental health services during the past year. In federal data systems, data on positive indicators of mental health (e.g., resilience) are limited. Although no comprehensive surveillance system for children's mental health exists and no single indicator can be used to define the mental health of children or to identify the overall number of children with mental disorders, these data confirm that mental disorders among children continue to be a substantial public health concern. These findings can be used by public health professionals, health care providers, state health officials, policymakers, and educators to understand the prevalence of specific mental disorders and other indicators of mental health and the challenges related to mental health surveillance.

Understanding Explosive Sensitivity with Effective Trigger Linkage Kinetics.

We present a simple linear model for ranking the drop weight impact sensitivity of organic explosives that is based explicitly on chemical kinetics. The model is parameterized to specific heats of explosion, Q, and Arrhenius kinetics for the onset of chemical reactions that are obtained from gas-phase Born-Oppenheimer molecular dynamics simulations for a chemically diverse set of 24 molecules. Reactive molecular dynamics simulations sample all possible decomposition pathways of the molecules with the appropriate probabilities to provide an effective reaction barrier. In addition, the calculations of effective trigger linkage kinetics can be accomplished without prior physical intuition of the most likely decomposition pathways. We found that the specific heat of explosion tends to reduce the effective barrier for decomposition in accordance with the Bell-Evans-Polanyi principle, which accounts naturally for the well-known correlations between explosive performance and sensitivity. Our model indicates that sensitive explosives derive their properties from a combination of weak trigger linkages that react at relatively low temperatures and large specific heats of explosion that further reduce the effective activation energy.

High-resolution within-sewer SARS-CoV-2 surveillance facilitates informed intervention.

To assist in the COVID-19 public health guidance on a college campus, daily composite wastewater samples were withdrawn at 20 manhole locations across the University of Colorado Boulder campus. Low-cost autosamplers were fabricated in-house to enable an economical approach to this distributed study. These sample stations operated from August 25th until November 23rd during the fall 2020 semester, with 1512 samples collected. The concentration of SARS-CoV-2 in each sample was quantified through two comparative reverse transcription quantitative polymerase chain reactions (RT-qPCRs). These methods were distinct in the utilization of technical replicates and normalization to an endogenous control. (1) Higher temporal resolution compensates for supply chain or other constraints that prevent technical or biological replicates. (2) The data normalized by an endogenous control agreed with the raw concentration data, minimizing the utility of normalization. The raw wastewater concentration values reflected SARS-CoV-2 prevalence on campus as detected by clinical services. Overall, combining the low-cost composite sampler with a method that quantifies the SARS-CoV-2 signal within six hours enabled actionable and time-responsive data delivered to key stakeholders. With daily reporting of the findings, wastewater surveillance assisted in decision making during critical phases of the pandemic on campus, from detecting individual cases within populations ranging from 109 to 2048 individuals to monitoring the success of on-campus interventions.

Army Nurse Corps Coronavirus Disease (COVID-19) Lessons Learned.

A new strain of coronavirus (COVID-19) emerged in 2020 changing the way the nation looked, worked and lived. In response to this unprecedented COVID-19 pandemic, the Army Nurse Corps (ANC) reexamined our capabies and agility to respond to a new and rapidly evolving environment. Maintaining the pivot to readiness, providing sustainable support and protecting our most valuable asset-our people-were and continues to be in the forefront of leaders' thoughts as we faced this invisible adversary. With every new challenge, lessons learned provide an opportunity to re-examine challenges and successes of the response to COVID-19. Organizational restructuring, balancing risks, expanding capabilities and educational platforms were reassessed and adjusted to fill the needs of the environment as they evolved. The year 2020 will stand throughout history as another example where our readiness, resilience, and flexibility as an Army Nurse Corps was tried and tested. We demonstrated our ability to adapt and overcome-displaying our willingness to stand up as part of the Army Medicine Team and face an unknown adversary to protect the nation we vowed to serve.