Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network.

Although our understanding of how life emerged on Earth from simple organic precursors is speculative, early precursors likely included amino acids. The polymerization of amino acids into peptides and interactions between peptides are of interest because peptides and proteins participate in complex interaction networks in extant biology. However, peptide reaction networks can be challenging to study because of the potential for multiple species and systems-level interactions between species. We developed and employed a computational network model to describe reactions between amino acids to form di-, tri-, and tetra-peptides. Our experiments were initiated with two of the simplest amino acids, glycine and alanine, mediated by trimetaphosphate-activation and drying to promote peptide bond formation. The parameter estimates for bond formation and hydrolysis reactions in the system were found to be poorly constrained due to a network property known as sloppiness. In a sloppy model, the behavior mostly depends on only a subset of parameter combinations, but there is no straightforward way to determine which parameters should be included or excluded. Despite our inability to determine the exact values of specific kinetic parameters, we could make reasonably accurate predictions of model behavior. In short, our modeling has highlighted challenges and opportunities toward understanding the behaviors of complex prebiotic chemical experiments.

Enhancement of Prebiotic Peptide Formation in Cyclic Environments.

The dynamic behaviors of prebiotic reaction networks may be critically important to understanding how larger biopolymers could emerge, despite being unfavorable to form in water. We focus on understanding the dynamics of simple systems, prior to the emergence of replication mechanisms, and what role they may have played in biopolymer formation. We specifically consider the dynamics in cyclic environments using both model and experimental data. Cyclic environmental conditions prevent a system from reaching thermodynamic equilibrium, improving the chance of observing interesting kinetic behaviors. We used an approximate kinetic model to simulate the dynamics of trimetaphosphate (TP)-activated peptide formation from glycine in cyclic wet-dry conditions. The model predicts that environmental cycling allows trimer and tetramer peptides to sustain concentrations above the predicted fixed points of the model due to overshoot, a dynamic phenomenon. Our experiments demonstrate that oscillatory environments can shift product distributions in favor of longer peptides. However, experimental validation of certain behaviors in the kinetic model is challenging, considering that open systems with cyclic environmental conditions break many of the common assumptions in classical chemical kinetics. Overall, our results suggest that the dynamics of simple peptide reaction networks in cyclic environments may have been important for the formation of longer polymers on the early Earth. Similar phenomena may have also contributed to the emergence of reaction networks with product distributions determined not by thermodynamics, but rather by kinetics.

"It's just another tool on my toolbelt": New York state law enforcement officer experiences administering naloxone.

BACKGROUND: Although naloxone is widely acknowledged as a life-saving intervention and a critical tool for first responders, there remains a need to explore how law enforcement officers have adapted to a shifting scope of work. Past research has focused mainly on officer training, their abilities to administer naloxone, and to a lesser extent on their experiences and interactions working with people who use drugs (PWUD). METHODS: A qualitative approach was used to explore officer perspectives and behaviors surrounding responses to incidents of suspected opioid overdose. Between the months of March and September 2017, semi-structured interviews were conducted with 38 officers from 17 counties across New York state (NYS). RESULTS: Analysis of in-depth interviews revealed that officers generally considered the additional responsibility of administering naloxone to have become "part of the job". Many officers reported feeling as though they are expected to wear multiple hats, functioning as both law enforcement and medical personnel and at times juggling contradictory roles. Evolving views on drugs and drug use defined many interviews, as well as the recognition that a punitive approach to working with PWUD is not the solution, emphasizing the need for cohesive, community-wide support strategies. Notable differences in attitudes toward PWUD appeared to be influenced by an officer's connection to someone who uses drugs and/or due to a background in emergency medical services. CONCLUSION: Law enforcement officers in NYS are emerging as an integral part of the continuum of care for PWUD. Our findings are capturing a time of transition as more traditional approaches to law enforcement appear to be shifting toward those prioritizing prevention and diversion. Widespread adoption of naloxone administration by law enforcement officers in NYS is a powerful example of the successful integration of a public health intervention into police work.

Mathematical modeling of the lower urinary tract: A review.

AIMS: Understand what progress has been made toward a functionally predictive lower urinary tract (LUT) model, identify knowledge gaps, and develop from them a path forward. METHODS: We surveyed prominent mathematical models of the basic LUT components (bladder, urethra, and their neural control) and categorized the common modeling strategies and theoretical assumptions associated with each component. Given that LUT function emerges from the interaction of these components, we emphasized attempts to model their connections, and highlighted unmodeled aspects of LUT function. RESULTS: There is currently no satisfactory model of the LUT in its entirety that can predict its function in response to disease, treatment, or other perturbations. In particular, there is a lack of physiologically based mathematical descriptions of the neural control of the LUT. CONCLUSIONS: Based on our survey of the work to date, a potential path to a predictive LUT model is a modular effort in which models are initially built of individual tissue-level components using methods that are extensible and interoperable, allowing them to be connected and tested in a common framework. A modular approach will allow the larger goal of a comprehensive LUT model to be in sight while keeping individual efforts manageable, ensure new models can straightforwardly build on prior research, respect potential interactions between components, and incentivize efforts to model absent components. Using a modular framework and developing models based on physiological principles, to create a functionally predictive model is a challenge that the field is ready to undertake.

Glycine to Oligoglycine via Sequential Trimetaphosphate Activation Steps in Drying Environments.

Polyphosphate-mediated peptide bond formation is central to protein synthesis in modern organisms, but a simpler form of activation likely preceded the emergence of proteins and RNA. One suggested scenario involves trimetaphosphate (TP), an inorganic phosphate that promotes peptide condensation. Peptide bond formation can also be promoted by high pH and drying, but the interaction of these factors with TP has yet to be characterized kinetically. We studied the formation of glycine oligomers formed under initially alkaline conditions in the presence of TP during the process of drying. Oligopeptide products sampled over 24 h were analyzed by functionalization and high-performance liquid chromatography with ultraviolet absorption (UV-HPLC). As they dried, two different pH-dependent mechanisms dominated during different stages of the process. The first mechanism occurs in alkaline solutions and activates monomer amino acids to form dimers while reducing the pH. Our results then become consistent with a second mechanism that proceeds at neutral pH and consumes dimers to form longer products. The possibility that a series of reactions might occur where the first reaction changes the environment to favor the second, and so on, may have broader implications for prebiotic polymerization. Studying how the environment changes during time-varying conditions, like drying, could help us understand how organic polymers formed during the origin of life.

Naloxone administration by law enforcement officers in New York State (2015-2020).

BACKGROUND: The COVID-19 pandemic has amplified the need for wide deployment of effective harm reduction strategies in preventing opioid overdose mortality. Placing naloxone in the hands of key responders, including law enforcement officers who are often first on the scene of a suspected overdose, is one such strategy. New York State (NYS) was one of the first states to implement a statewide law enforcement naloxone administration program. This article provides an overview of the law enforcement administration of naloxone in NYS between 2015 and 2020 and highlights key characteristics of over 9000 opioid overdose reversal events. METHODS: Data in naloxone usage report forms completed by police officers were compiled and analyzed. Data included 9133 naloxone administration reports by 5835 unique officers located in 60 counties across NYS. Descriptive statistics were used to examine attributes of the aided individuals, including differences between fatal and non-fatal incidents. Additional descriptive analyses were conducted for incidents in which law enforcement officers arrived first at the scene of suspected overdose. Comparisons were made to examine year-over-year trends in administration as naloxone formulations were changed. Quantitative analysis was supplemented by content analysis of officers' notes (n = 2192). RESULTS: In 85.9% of cases, law enforcement officers arrived at the scene of a suspected overdose prior to emergency medical services (EMS) personnel. These officers assessed the likelihood of an opioid overdose having occurred based on the aided person's breathing status and other information obtained on the scene. They administered an average of 2 doses of naloxone to aided individuals. In 36.8% of cases, they reported additional administration of naloxone by other responders including EMS, fire departments, and laypersons. Data indicated the aided survived the suspected overdose in 87.4% of cases. CONCLUSIONS: With appropriate training, law enforcement personnel were able to recognize opioid overdoses and prevent fatalities by administering naloxone and carrying out time-sensitive medical interventions. These officers provided life-saving services to aided individuals alongside other responders including EMS, fire departments, and bystanders. Further expansion of law enforcement naloxone administration nationally and internationally could help decrease opioid overdose mortality.

Reducing Disparities: A Virtual Quality Improvement Collaborative Resulted in Better Health Outcomes for 4 Target Populations Disproportionately Affected by HIV.

CONTEXT: Although viral suppression rates have recently increased among people with HIV, specific populations still experience disparities in health outcomes, a priority in the national response to end the HIV epidemic. PURPOSE: The end+disparities ECHO Collaborative, a quality improvement initiative among HIV providers in the United States from June 2018 to December 2019, created virtual communities of practice to measurably increase viral suppression rates in populations disproportionately affected by HIV: men who have sex with men of color, Black/African American and Latina women, youth aged 13 to 24 years, and transgender people. METHODS: Participating Ryan White HIV/AIDS Program-funded providers prioritized their improvement efforts to focus on one target population and joined virtual affinity sessions with other providers focused on that population for guidance by subject matter experts and exchanges with peer providers. During 9 submission cycles, providers reported their viral suppression data for the preceding 12 months. MAIN OUTCOME MEASURES: The principal outcome measures were changes in viral suppression rates among 4 target populations and changes in viral suppression gaps compared with the rest of HIV-infected patients served by the same agency. RESULTS: A total of 90 providers were included in the data analyses with an average of 110 775 reported patients, out of which 19 442 represented the targeted populations. The average viral suppression rates for agency-selected populations increased from 79.2% to 82.3% (a 3.9% increase), while the remaining caseload increased at a lower rate from 84.9% to 86.1% (a 1.4% increase). The viral suppression gap was reduced from 5.7% to 3.8%, a 33.5% reduction. Improvements were found across all target populations. CONCLUSIONS: The collaborative demonstrated improved health outcomes and reductions in HIV-related health disparities, moving toward ending the HIV epidemic. The model of utilizing low-cost videoconferencing technologies to create virtual communities of learning is well suited to mitigate other disease-related disparities, nationally and abroad.

Kinetics of Asian and African Zika virus lineages over single-cycle and multi-cycle growth in culture: Gene expression, cell killing, virus production, and mathematical modeling.

Since 2014, an Asian lineage of Zika virus has caused outbreaks, and it has been associated with neurological disorders in adults and congenital defects in newborns. The resulting threat of the Zika virus to human health has prompted the development of new vaccines, which have yet to be approved for human use. Vaccines based on the attenuated or chemically inactivated virus will require large-scale production of the intact virus to meet potential global demands. Intact viruses are produced by infecting cultures of susceptible cells, a dynamic process that spans from hours to days and has yet to be optimized. Here, we infected Vero cells adhesively cultured in well-plates with two Zika virus strains: a recently isolated strain from the Asian lineage, and a cell-culture-adapted strain from the African lineage. At different time points post-infection, virus particles in the supernatant were quantified; further, microscopy images were used to quantify cell density and the proportion of cells expressing viral protein. These measurements were performed across multiple replicate samples of one-step infections every four hours over 60 h and for multi-step infections every four to 24 h over 144 h, generating a rich data set. For each set of data, mathematical models were developed to estimate parameters associated with cell infection and virus production. The African-lineage strain was found to produce a 14-fold higher yield than the Asian-lineage strain in one-step growth and a sevenfold higher titer in multi-step growth, suggesting a benefit of cell-culture adaptation for developing a vaccine strain. We found that image-based measurements were critical for discriminating among different models, and different parameters for the two strains could account for the experimentally observed differences. An exponential-distributed delay model performed best in accounting for multi-step infection of the Asian strain, and it highlighted the significant sensitivity of virus titer to the rate of viral degradation, with implications for optimization of vaccine production. More broadly, this study highlights how image-based measurements can contribute to the discrimination of virus-culture models for the optimal production of inactivated and attenuated whole-virus vaccines.

Toward Molecular Cooperation by De Novo Peptides.

Theoretical models of the chemical origins of life depend on self-replication or autocatalysis, processes that arise from molecular interactions, recruitment, and cooperation. Such models often lack details about the molecules and reactions involved, giving little guidance to those seeking to detect signs of interaction, recruitment, or cooperation in the laboratory. Here, we develop minimal mathematical models of reactions involving specific chemical entities: amino acids and their condensation reactions to form de novo peptides. Reactions between two amino acids form a dipeptide product, which enriches linearly in time; subsequent recruitment of such products to form longer peptides exhibit super-linear growth. Such recruitment can be reciprocated: a peptide contributes to and benefits from the formation of one or more other peptides; in this manner, peptides can cooperate and thereby exhibit autocatalytic or exponential growth. We have started to test these predictions by quantitative analysis of de novo peptide synthesis conducted by wet-dry cycling of a five-amino acid mixture over 21 days. Using high-performance liquid chromatography, we tracked abundance changes for >60 unique peptide species. Some species were highly transient, with the emergence of up to 17 new species and the extinction of nine species between samplings, while other species persisted across many cycles. Of the persisting species, most exhibited super-linear growth, a sign of recruitment anticipated by our models. This work shows how mathematical modeling and quantitative analysis of kinetic data can guide the search for prebiotic chemistries that have the potential to cooperate and replicate.

ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization.

MOTIVATION: Evolutionary histories can change from one part of the genome to another. The potential for discordance between the gene trees has motivated the development of summary methods that reconstruct a species tree from an input collection of gene trees. ASTRAL is a widely used summary method and has been able to scale to relatively large datasets. However, the size of genomic datasets is quickly growing. Despite its relative efficiency, the current single-threaded implementation of ASTRAL is falling behind the data growth trends is not able to analyze the largest available datasets in a reasonable time. RESULTS: ASTRAL uses dynamic programing and is not trivially parallel. In this paper, we introduce ASTRAL-MP, the first version of ASTRAL that can exploit parallelism and also uses randomization techniques to speed up some of its steps. Importantly, ASTRAL-MP can take advantage of not just multiple CPU cores but also one or several graphics processing units (GPUs). The ASTRAL-MP code scales very well with increasing CPU cores, and its GPU version, implemented in OpenCL, can have up to 158× speedups compared to ASTRAL-III. Using GPUs and multiple cores, ASTRAL-MP is able to analyze datasets with 10 000 species or datasets with more than 100 000 genes in <2 days. AVAILABILITY AND IMPLEMENTATION: ASTRAL-MP is available at https://github.com/smirarab/ASTRAL/tree/MP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Immunogenetic effects of low dose (CEM43 30) magnetic nanoparticle hyperthermia and radiation in melanoma cells.

Objective: In this in vitro study we have used an RNA quantification technique, nanoString, and a conventional protein analysis technique (Western Blot) to assess the genetic and protein expression of B16 murine melanoma cells following a modest magnetic nanoparticle hyperthermia (mNPH) dose equivalent to 30 minutes @ 43°C (CEM43 30) and/or a clinically relevant 8 Gy radiation dose.Methods: Melanoma cells with mNPs(2.5 µg Fe/106 cells) were pelleted and exposed to an alternating magnetic field (AMF) to generate the targeted thermal dose. Thermal dose was accurately monitored by a fiber optic probe and automatically maintained at CEM43 30. All cells were harvested 24 hours after treatment.Results: The mNPH dose demonstrated notable elevations in the thermotolerance/immunogenic HSP70 gene and a number of chemoattractant and toll-like receptor gene pathways. The 8 Gy dose also upregulated a number of important immune and cytotoxic genetic and protein pathways. However, the mNPH/radiation combination was the most effective stimulator of a wide variety of immune and cytotoxic genes including HSP70, cancer regulating chemokines CXCL10, CXCL11, the T-cell trafficking chemokine CXCR3, innate immune activators TLR3, TLR4, the MDM2 and mTOR negative regulator of p53, the pro-apoptotic protein PUMA, and the cell death receptor Fas. Importantly a number of the genetic changes were accurately validated by protein expression changes, i.e., HSP70, p-mTOR, p-MDM2.Conclusion: These results not only show that low dose mNPH and radiation independently increase the expression of important immune and cytotoxic genes but that the effect is greatly enhanced when they are used in combination.

Differential Disruption of Nucleocytoplasmic Trafficking Pathways by Rhinovirus 2A Proteases.

The RNA rhinoviruses (RV) encode 2A proteases (2Apro) that contribute essential polyprotein processing and host cell shutoff functions during infection, including the cleavage of Phe/Gly-containing nucleoporin proteins (Nups) within nuclear pore complexes (NPC). Within the 3 RV species, multiple divergent genotypes encode diverse 2Apro sequences that act differentially on specific Nups. Since only subsets of Phe/Gly motifs, particularly those within Nup62, Nup98, and Nup153, are recognized by transport receptors (karyopherins) when trafficking large molecular cargos through the NPC, the processing preferences of individual 2Apro predict RV genotype-specific targeting of NPC pathways and cargos. To test this idea, transformed HeLa cell lines were created with fluorescent cargos (mCherry) for the importin α/ß, transportin 1, and transportin 3 import pathways and the Crm1-mediated export pathway. Live-cell imaging of single cells expressing recombinant RV 2Apro (A16, A45, B04, B14, B52, C02, and C15) showed disruption of each pathway with measurably different efficiencies and reaction rates. The B04 and B52 proteases preferentially targeted Nups in the import pathways, while B04 and C15 proteases were more effective against the export pathway. Virus-type-specific trends were also observed during infection of cells with A16, B04, B14, and B52 viruses or their chimeras, as measured by NF-κB (p65/Rel) translocation into the nucleus and the rates of virus-associated cytopathic effects. This study provides new tools for evaluating the host cell response to RV infections in real time and suggests that differential 2Apro activities explain, in part, strain-dependent host responses and diverse RV disease phenotypes.IMPORTANCE Genetic variation among human rhinovirus types includes unexpected diversity in the genes encoding viral proteases (2Apro) that help these viruses achieve antihost responses. When the enzyme activities of 7 different 2Apro were measured comparatively in transformed cells programed with fluorescent reporter systems and by quantitative cell imaging, the cellular substrates, particularly in the nuclear pore complex, used by these proteases were indeed attacked at different rates and with different affinities. The importance of this finding is that it provides a mechanistic explanation for how different types (strains) of rhinoviruses may elicit different cell responses that directly or indirectly lead to distinct disease phenotypes.

Trimetaphosphate Activates Prebiotic Peptide Synthesis across a Wide Range of Temperature and pH.

The biochemical activation of amino acids by adenosine triphosphate (ATP) drives the synthesis of proteins that are essential for all life. On the early Earth, before the emergence of cellular life, the chemical condensation of amino acids to form prebiotic peptides or proteins may have been activated by inorganic polyphosphates, such as tri metaphosphate (TP). Plausible volcanic and other potential sources of TP are known, and TP readily activates amino acids for peptide synthesis. But de novo peptide synthesis also depends on pH, temperature, and processes of solvent drying, which together define a varied range of potential activating conditions. Although we cannot replay the tape of life on Earth, we can examine how activator, temperature, acidity and other conditions may have collectively shaped its prebiotic evolution. Here, reactions of two simple amino acids, glycine and alanine, were tested, with or without TP, over a wide range of temperature (0-100 °C) and acidity (pH 1-12), while open to the atmosphere. After 24 h, products were analyzed by HPLC and mass spectrometry. In the absence of TP, glycine and alanine readily formed peptides under harsh near-boiling temperatures, extremes of pH, and within dry solid residues. In the presence of TP, however, peptides arose over a much wider range of conditions, including ambient temperature, neutral pH, and in water. These results show how polyphosphates such as TP may have enabled the transition of peptide synthesis from harsh to mild early Earth environments, setting the stage for the emergence of more complex prebiotic chemistries.

High-Throughput Single-Cell Kinetics of Virus Infections in the Presence of Defective Interfering Particles.

UNLABELLED: Defective interfering particles (DIPs) are virus mutants that lack essential genes for growth. In coinfections with helper virus, the diversion of viral proteins to the replication and packaging of DIP genomes can interfere with virus production. Mounting cases of DIPs and DIP-like genomes in clinical and natural isolates, as well as growing interest in DIP-based therapies, underscore a need to better elucidate how DIPs work. DIP activity is primarily measured by its inhibition of virus infection yield, an endpoint that masks the dynamic and potentially diverse individual cell behaviors. Using vesicular stomatitis virus (VSV) as a model, we coinfected BHK cells with VSV DIPs and recombinant helper virus carrying a gene encoding a red fluorescent protein (RFP) whose expression correlates with the timing and level of virus release. For single cells within a monolayer, 10 DIPs per cell suppressed the reporter expression in only 1.2% of the cells. In most cells, it slowed and reduced viral gene expression, manifested as a shift in mean latent time from 4 to 6 h and reduced virus yields by 10-fold. For single cells isolated in microwells, DIP effects were more pronounced, reducing virus yields by 100-fold and extending latent times to 12 h, including individual instances above 20 h. Together, these results suggest that direct or indirect cell-cell interactions prevent most coinfected cells from being completely suppressed by DIPs. Finally, a gamma distribution model captures well how the infection kinetics quantitatively depends on the DIP dose. Such models will be useful for advancing a predictive biology of DIP-associated virus growth and infection spread. IMPORTANCE: During the last century, basic studies in virology have focused on developing a molecular mechanistic understanding of how infectious viruses reproduce in their living host cells. However, over the last 10 years, the advent of deep sequencing and other powerful technologies has revealed in natural and patient infections that viruses do not act alone. Instead, viruses are often accompanied by defective virus-like particles that carry large deletions in their genomes and fail to replicate on their own. Coinfections of viable and defective viruses behave in unpredictable ways, but they often interfere with normal virus growth, potentially enabling infections to evade host immune surveillance. In the current study, controlled levels of defective viruses are coinfected with viable viruses that have been engineered to express a fluorescent reporter protein during infection. Unique profiles of reporter expression acquired from thousands of coinfected cells reveal how interference acts at multiple stages of infection.

Spatial-Temporal Patterns of Viral Amplification and Interference Initiated by a Single Infected Cell.

UNLABELLED: When viruses infect their host cells, they can make defective virus-like particles along with intact virus. Cells coinfected with virus and defective particles often exhibit interference with virus growth caused by the competition for resources by defective genomes. Recent reports of the coexistence and cotransmission of such defective interfering particles (DIPs) in vivo, across epidemiological length and time scales, suggest a role in viral pathogenesis, but it is not known how DIPs impact infection spread, even under controlled culture conditions. Using fluorescence microscopy, we quantified coinfections of vesicular stomatitis virus (VSV) expressing a fluorescent reporter protein and its DIPs on BHK-21 host cell monolayers. We found that viral gene expression was more delayed, infections spread more slowly, and patterns of spread became more "patchy" with higher DIP inputs to the initial cell. To examine how infection spread might depend on the behavior of the initial coinfected cell, we built a computational model, adapting a cellular automaton (CA) approach to incorporate kinetic data on virus growth for the first time. Specifically, changes in observed patterns of infection spread could be directly linked to previous high-throughput single-cell measures of virus-DIP coinfection. The CA model also provided testable hypotheses on the spatial-temporal distribution of the DIPs, which remain governed by their predator-prey interaction. More generally, this work offers a data-driven computational modeling approach for better understanding of how single infected cells impact the multiround spread of virus infections across cell populations. IMPORTANCE: Defective interfering particles (DIPs) compete with intact virus, depleting host cell resources that are essential for virus growth and infection spread. However, it is not known how such competition, strong or weak, ultimately affects the way in which infections spread and cause disease. In this study, we address this unmet need by developing an integrated experimental-computational approach, which sheds new light on how infections spread. We anticipate that our approach will also be useful in the development of DIPs as therapeutic agents to manage the spread of viral infections.

Neucode Labels for Multiplexed, Absolute Protein Quantification.

We describe a new method to accomplish multiplexed, absolute protein quantification in a targeted fashion. The approach draws upon the recently developed neutron encoding (NeuCode) metabolic labeling strategy and parallel reaction monitoring (PRM). Since PRM scanning relies upon high-resolution tandem mass spectra for targeted protein quantification, incorporation of multiple NeuCode labeled peptides permits high levels of multiplexing that can be accessed from high-resolution tandem mass spectra. Here we demonstrate this approach in cultured cells by monitoring a viral infection and the corresponding viral protein production over many infection time points in a single experiment. In this context the NeuCode PRM combination affords up to 30 channels of quantitative information in a single MS experiment.

Response to ruxolitinib in patients with intermediate-1-, intermediate-2-, and high-risk myelofibrosis: results of the UK ROBUST Trial.

Myelofibrosis is characterized by splenomegaly and debilitating constitutional symptoms that negatively impact patients' quality of life. ROBUST, a UK, open-label, phase II study, evaluated the safety and efficacy of ruxolitinib in patients with myelofibrosis (N = 48), including intermediate-1 risk patients. The primary composite endpoint was the proportion of patients achieving treatment success [≥ 50% reduction in palpable spleen length and/or a ≥ 50% decrease in Myelofibrosis Symptom Assessment Form Total Symptom Score (MF-SAF TSS)] at 48 weeks. This was the first time that efficacy of ruxolitinib in myelofibrosis has been evaluated based on these criteria and the first time the MF-SAF was used in a population of patients solely from the United Kingdom. Overall, 50% of patients and 57% of intermediate-1 risk patients, achieved treatment success; reductions in spleen length and symptoms were observed in all risk groups. The majority of patients (66.7%) experienced ≥ 50% reductions from baseline in spleen length at any time. Improvements in MF-SAF TSS were seen in 80.0%, 72.7%, and 72.2% of intermediate-1, intermediate-2, and high-risk patients, respectively. Consistent with other studies of ruxolitinib, the most common haematological adverse events were anaemia and thrombocytopenia. Results indicate that most patients with myelofibrosis, including intermediate-1 risk patients, may benefit from ruxolitinib treatment.

Quantitative characterization of defective virus emergence by deep sequencing.

UNLABELLED: Populations of RNA viruses can spontaneously produce variants that differ in genome size, sequence, and biological activity. Defective variants that lack essential genes can nevertheless reproduce by coinfecting cells with viable virus, a process that interferes with virus growth. How such defective interfering particles (DIPs) change in abundance and biological activity within a virus population is not known. Here, a prototype RNA virus, vesicular stomatitis virus (VSV), was cultured for three passages on BHK host cells, and passages were subjected to Illumina sequencing. Reads from the initial population, when aligned to the full-length viral sequence (11,161 nucleotides [nt]), distributed uniformly across the genome. However, during passages two plateaus in read counts appeared toward the 5' end of the negative-sense viral genome. Analysis by normalization and a simple sliding-window approach revealed plateau boundaries that suggested the emergence and enrichment of at least two truncated species having medium (∼5,900 nt) and short (∼4,000 nt) genomes. Relative measures of full-length and truncated species based on read counts were validated by quantitative reverse transcription-PCR (qRT-PCR). Limit-of-detection analysis suggests that deep sequencing can be more sensitive than complementary measures for detecting and quantifying defective particles in a population. Further, particle counts from transmission electron microscopy, coupled with infectivity assays, linked the rise in smaller genomes with an increase in truncated particles and interference activity. In summary, variation in deep sequencing coverage simultaneously shows the size, location, and relative level of truncated-genome variants, revealing a level of population heterogeneity that is masked by other measures of viral genomes and particles. IMPORTANCE: We show how deep sequencing can be used to characterize the emergence, diversity, and relative abundance of truncated virus variants in virus populations. Adaptation of this approach to natural isolates may elucidate factors that influence the stability and persistence of virus populations in nature.

Clofarabine doubles the response rate in older patients with acute myeloid leukemia but does not improve survival.

Better treatment is required for older patients with acute myeloid leukemia (AML) not considered fit for intensive chemotherapy. We report a randomized comparison of low-dose Ara-C (LDAC) vs the novel nucleoside, clofarabine, in untreated older patients with AML and high-risk myelodysplastic syndrome (MDS). A total of 406 patients with de novo (62%), secondary disease (24%), or high-risk MDS (>10% marrow blasts) (15%), median age 74 years, were randomized to LDAC 20 mg twice daily for 10 days every 6 weeks or clofarabine 20 mg/m(2) on days 1 to 5, both for up to 4 courses. These patients had more adverse demographics than contemporaneous intensively treated patients. The overall remission rate was 28%, and 2-year survival was 13%. Clofarabine significantly improved complete remission (22% vs 12%; hazard ratio [HR] = 0.47 [0.28-0.79]; P = .005) and overall response (38% vs 19%; HR = 0.41 [0.26-0.62]; P < .0001), but there was no difference in overall survival, explained by poorer survival in the clofarabine patients who did not gain complete remission and also following relapse. Clofarabine was more myelosuppressive and required more supportive care. Although clofarabine doubled remission rates, overall survival was not improved overall or in any subgroup. The treatment of patients of the type treated here remains a major unmet need.

Paliperidone Palmitate Long-Acting Injectable Given Intramuscularly in the Deltoid Versus the Gluteal Muscle: Are They Therapeutically Equivalent?

Paliperidone palmitate long-acting injectable is a second-generation antipsychotic indicated for the treatment of schizophrenia. According to the product monograph, the monthly maintenance dose of paliperidone palmitate can be given in either the deltoid or gluteal muscle. Unfortunately, many clinicians may misinterpret these directions to mean that these intramuscular sites are interchangeable, and thus therapeutically equivalent. Currently, the literature on this topic is sparse, but the published pharmacokinetic studies and Food and Drug Administration submission data on paliperidone palmitate show discrepancies in the elimination half-life, peak plasma concentration, and absorption rate that are dependent on the site of injection. The degree of shifts in pharmacokinetic parameters suggests that paliperidone palmitate injections via the deltoid and gluteal muscle are not bioequivalent and therefore are not therapeutically equivalent. Thus, using the same maintenance dosing regimen at both sites or switching between sites of injection may result in unforeseen consequences in patient outcomes.