Partial Response to Platinum Doublets in Refractory EGFR-Positive Non-Small Cell Lung Cancer Patients after RRx-001: Evidence of Episensitization.

RRx-001, an experimental systemically non-toxic epi-immunotherapeutic agent, which potentiates the resensitization of resistant cancer cells to formerly effective therapies, is under active investigation in several clinical trials that are based on sequential or concomitant rechallenge to resistant first- or second-line regimens. One of these trials is designated TRIPLE THREAT (NCT02489903), because it explores the conditioning or priming effect of RRx-001 on three tumor types - non-small cell lung cancer (NSCLC), small cell lung cancer and high-grade neuroendocrine tumors - prior to re-administration of platinum doublets. In follow-up to a recent case study, which describes early monotherapeutic benefit with RRx-001 in a refractory EGFR-mutated NSCLC tumor, we present subsequent evidence of a radiological partial response to reintroduced platinum doublets after RRx-001. For the 50% of patients with EGFR-mutated NSCLC who progress on EGFR-tyrosine kinase inhibitors (without evidence of a T790M mutations) as well as platinum doublets and pemetrexed/taxane, no other clinically established treatment options exist. A retrial of these therapies in EGFR-positive NSCLC patients via priming with epigenetic agents such as RRx-001 constitutes a strategy to 'episensitize' tumors (i.e. reverse resistance by epigenetic means) and to extend overall survival

Immune Reactivity and Pseudoprogression or Tumor Flare in a Serially Biopsied Neuroendocrine Patient Treated with the Epigenetic Agent RRx-001.

Neuroendocrine tumors (NETs) are grouped together as a single class on the basis of histologic appearance, immunoreactivity for the neuroendocrine markers chromogranin A and synaptophysin, and potential secretion of hormones, neurotransmitters, neuromodulators and neuropeptides. Nevertheless, despite these common characteristics, NETs differ widely in terms of their natural histories: high-grade NETs are clinically aggressive and, like small cell lung cancer, which they most closely resemble, tend to respond to cisplatin and etoposide. In contrast, low-grade NETs, which as a rule progress and behave indolently, do not. In either case, the treatment strategy, apart from potentially curative surgical resection, is very poorly defined. This report describes the case of a 28-year-old white male with a diagnosis of high-grade NET of undetermined primary site metastatic to the lymph nodes, skin and paraspinal soft tissues, treated with the experimental anticancer agent RRx-001, in the context of a phase II clinical trial called TRIPLE THREAT (NCT02489903); serial sampling of tumor material through repeat biopsies demonstrated an intratumoral inflammatory response, including the amplification of infiltrating T cells, which correlated with clinical and symptomatic benefit. This case suggests that pseudoprogression or RRx-001-induced enlargement of tumor lesions, which has been previously described for several RRx-001-treated patients, is the result of tumoral lymphocyte infiltration

Cosmological simulations of galaxy clusters with feedback from active galactic nuclei: profiles and scaling relations

We present results from a new set of 30 cosmological simulations of galaxy clusters, including the effects of radiative cooling, star formation, supernova feedback, black hole growth and AGN feedback. We first demonstrate that our AGN model is capable of reproducing the observed cluster pressure profile at redshift, z ≃ 0, once the AGN heating temperature of the targeted particles is made to scale with the final virial temperature of the halo. This allows the ejected gas to reach larger radii in higher mass clusters than would be possible had a fixed heating temperature been used. Such a model also successfully reduces the star formation rate in brightest cluster galaxies and broadly reproduces a number of other observational properties at low redshift, including baryon, gas and star fractions, entropy profiles outside the core and the X-ray luminosity–mass relation. Our results are consistent with the notion that the excess entropy is generated via selective removal of the densest material through radiative cooling; supernova and AGN feedback largely serve as regulation mechanisms, moving heated gas out of galaxies and away from cluster cores. However, our simulations fail to address a number of serious issues; for example, they are incapable of reproducing the shape and diversity of the observed entropy profiles within the core region. We also show that the stellar and black hole masses are sensitive to numerical resolution, particularly the gravitational softening length; a smaller value leads to more efficient black hole growth at early times and a smaller central galaxy

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean.

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad

The conference effect: National surgery meetings are associated with increased mortality at trauma centers without American College of Surgeons verification

BACKGROUND: Thousands of physicians attend scientific conferences each year. While recent data indicate that variation in staffing during such meetings impacts survival of non-surgical patients, the association between treatment during conferences and outcomes of a surgical population remain unknown. The purpose of this study was to examine mortality resulting from traumatic injuries and the influence of hospital admission during national surgery meetings. STUDY DESIGN: Retrospective analysis of in-hospital mortality using data from the Trauma Quality Improvement Program (2010-2011). Identified patients admitted during four annual meetings and compared their mortality with that of patients admitted during non-conference periods. Analysis included 155 hospitals with 12,256 patients admitted on 42 conference days and 82,399 patients admitted on 270 non-conference days. Multivariate analysis performed separately for hospitals with different levels of trauma center verification by state and American College of Surgeons (ACS) criteria. RESULTS: Patient characteristics were similar between meeting and non-meeting dates. At ACS level I and level II trauma centers during conference versus non-conference dates, adjusted mortality was not significantly different. However, adjusted mortality increased significantly for patients admitted to trauma centers that lacked ACS trauma verification during conferences versus non-conference days (OR 1.2, p = 0.008), particularly for patients with penetrating injuries, whose mortality rose from 11.6% to 15.9% (p = 0.006). CONCLUSIONS: Trauma mortality increased during surgery conferences compared to non-conference dates for patients admitted to hospitals that lacked ACS trauma level verification. The mortality difference at those hospitals was greatest for patients who presented with penetrating injuries

Integrated stratigraphy of the Waitakian-Otaian Stage boundary stratotype, Early Miocene, New Zealand

The base of the type section of the Otaian Stage at Bluecliffs, South Canterbury, is recognised as the stratotype for the boundary between the Waitakian and Otaian Stages. Principal problems with the boundary are the restriction of existing bioevent proxies to shelf and upper slope environments and its uncertain age. These topics are addressed by a multidisplinary study of a 125 m section about the boundary, which examines its lithostratigraphy, depositional setting, biostratigraphy, correlation, and geochronology. The lower siltstone lithofacies (0-38.5 m) was deposited at upper bathyal depths (200-600 m) in a marginal basin which was partially sheltered from fully oceanic circulation by a submarine high and islands. The site was covered by cool-temperate water and was probably adjacent to the Subtropical Convergence. This unit is succeeded by the banded lithofacies (38.5-106 m) and the upper siltstone lithofacies (basal 19 m studied). Paleodepth probably declined up-sequence, but deposition at shelf depths is not definitely indicated. A cyclic pattern of abundance spikes in benthic and planktonic foraminifera commences 9 m above base and extends to 73 m in the banded lithofacies. Oxygen isotope excursions (up to 2.08%) in Euuvigerina miozea and Cibicides novozelandicus are greatest within the interval containing the abundance spikes. The stage boundary occurs in the banded lithofacies at the highest abundance spike (73 m). Although condensed intervals might affect the completeness of the section, they are not associated with sedimentary discontinuities, and we consider that the section is suitable as a biostratigraphic reference. Spores, pollens, dinoflagellates, calcareous nannofossils, foraminifera, bryozoans, and ostracods are preserved near the boundary, but molluscs principally occur higher, in the shallower upper siltstone lithofacies. Siliceous microfossils are rare. There is considerable scope for further biostratigraphic research. The primary event marking the boundary at 73 m is the appearance of the benthic foraminifer Ehrenbergina marwicki. This is a distinctive and widely distributed event but is restricted to shelf and upper bathyal environments. Supplementary events in planktonic foraminifera and calcareous nannofossils were researched. Highest occurrences of Globigerina brazieri and G. euapertura are recorded at 47 and 58 m. There is a marked decline in relative abundance of Paragloborotalia spp. at 62 m. Helicosphaera carteri becomes more abundant than H. euphratis between 56 and 87 m. These events are not exact proxies for the boundary but they may usefully indicate proximity to it. They occur in the interval of prominent spikes in foraminiferal abundance. The Waitakian-Otaian boundary is dated at 21.7 Ma by strontium isotopes. Stable primary remanence could not be determined in a pilot paleomagnetic study of Bluecliffs specimens. However, specimens trended towards reversed polarity, and remagnetisation great circle analysis will allow directions to be calculated in future collections

The prosequence of procaricain forms an α-helical domain that prevents access to the substrate-binding cleft

AbstractBackground Cysteine proteases are involved in a variety of cellular processes including cartilage degradation in arthritis, the progression of Alzheimer's disease and cancer invasion: these enzymes are therefore of immense biological importance. Caricain is the most basic of the cysteine proteases found in the latex of Carica papaya. It is a member of the papain superfamily and is homologous to other plant and animal cysteine proteases. Caricain is naturally expressed as an inactive zymogen called procaricain. The inactive form of the protease contains an inhibitory proregion which consists of an additional 106 N-terminal amino acids; the proregion is removed upon activation.Results The crystal structure of procaricain has been refined to 3.2 å resolution; the final model consists of three non-crystallographically related molecules. The proregion of caricain forms a separate globular domain which binds to the C-terminal domain of mature caricain. The proregion also contains an extended polypeptide chain which runs through the substrate-binding cleft, in the opposite direction to that of the substrate, and connects to the N terminus of the mature region. The mature region does not undergo any conformational change on activation.Conclusions We conclude that the rate-limiting step in the in vitro activation of procaricain is the dissociation of the prodomain, which is then followed by proteolytic cleavage of the extended polypeptide chain of the proregion. The prodomain provides a stable scaffold which may facilitate the folding of the C-terminal lobe of procaricain

Granular clustering in a hydrodynamic simulation

We present a numerical simulation of a granular material using hydrodynamic equations. We show that, in the absence of external forces, such a system phase-separates into high density and low density regions. We show that this separation is dependent on the inelasticity of collisions, and comment on the mechanism for this clustering behavior. Our results are compatible with the granular clustering seen in experiments and molecular dynamic simulations of inelastic hard disks.Comment: 4 pages, 5 figure

Impact of the SPOP Mutant Subtype on the Interpretation of Clinical Parameters in Prostate Cancer.

Purpose: Molecular characterization of prostate cancer, including The Cancer Genome Atlas, has revealed distinct subtypes with underlying genomic alterations. One of these core subtypes, SPOP (speckle-type POZ protein) mutant prostate cancer, has previously only been identifiable via DNA sequencing, which has made the impact on prognosis and routinely used risk stratification parameters unclear. Methods: We have developed a novel gene expression signature, classifier (Subclass Predictor Based on Transcriptional Data), and decision tree to predict the SPOP mutant subclass from RNA gene expression data and classify common prostate cancer molecular subtypes. We then validated and further interrogated the association of prostate cancer molecular subtypes with pathologic and clinical outcomes in retrospective and prospective cohorts of 8,158 patients. Results: The subclass predictor based on transcriptional data model showed high sensitivity and specificity in multiple cohorts across both RNA sequencing and microarray gene expression platforms. We predicted approximately 8% to 9% of cases to be SPOP mutant from both retrospective and prospective cohorts. We found that the SPOP mutant subclass was associated with lower frequency of positive margins, extraprostatic extension, and seminal vesicle invasion at prostatectomy; however, SPOP mutant cancers were associated with higher pretreatment serum prostate-specific antigen (PSA). The association between SPOP mutant status and higher PSA level was validated in three independent cohorts. Despite high pretreatment PSA, the SPOP mutant subtype was associated with a favorable prognosis with improved metastasis-free survival, particularly in patients with high-risk preoperative PSA levels. Conclusion: Using a novel gene expression model and a decision tree algorithm to define prostate cancer molecular subclasses, we found that the SPOP mutant subclass is associated with higher preoperative PSA, less adverse pathologic features, and favorable prognosis. These findings suggest a paradigm in which the interpretation of common risk stratification parameters, particularly PSA, may be influenced by the underlying molecular subtype of prostate cancer

Tuberculosis infection control in a South African rural regional hospital emergency centre: Prioritisation for patients and healthcare workers

South Africa (SA) is in the midst of a tuberculosis (TB) epidemic and has one of the highest TB incidence rates globally. Despite increasing global commitment to eliminate TB, SA appears to be falling behind in this regard. This article examines key challenges to effective TB infection control from a rural regional hospital perspective. It uses the Eden District in Western Cape Province as an example to share lessons learnt. This quality-improvement project identifies four priorities for improving TB infection control in George Hospital and the Eden District: (i) prioritising TB infection control in local policy; (ii) improving the quality of TB screening in the emergency centre; (iii) increasing the number of TB patients followed up; and (iv) implementing TB infection control training for all staff. This project demonstrates the role of an emergency centre in TB screening, highlighting that this should not only be a priority for primary care, but also for secondary and tertiary care. Simple interventions, such as training of local healthcare workers in TB infection control and good-quality TB screening, can initiate a behavioural change. It also stresses the importance of good communication and co-ordination of care across primary and secondary care, ensuring that patients are not lost to follow-up. Local policy needs to reflect these straightforward interventions, empowering local healthcare workers and managers to increase responsibility and accountability for TB infection control.TB is preventable, and infection control needs to become a priority throughout SA primary, secondary and tertiary care. This project highlights that simple interventions, such as engaging local healthcare workers in a co-ordinated multisystem and multidisciplinary approach, could help to reduce the number of missing TB cases and bring SA’s TB epidemic under control