Equitable inclusion of diverse populations in oncology clinical trials: deterrents and drivers.

The burden of cancer exerts a disproportionate impact across different regions and population subsets. Disease-specific attributes, coupled with genetic and socioeconomic factors, significantly influence cancer treatment outcomes. Precision oncology promises the development of safe and effective options for specific ethnic phenotypes and clinicodemographic profiles. Currently, clinical trials are concentrated in resource-rich geographies with younger, healthier, white, educated, and empowered populations. Vulnerable and marginalized people are often deprived of opportunities to participate in clinical trials. Despite consistent endeavors by regulators, industry, and other stakeholders, factors including diversity in trial regulations and patient and provider-related cultural, logistic, and operational barriers limit the inclusiveness of clinical trials. Understanding and addressing these constraints by collaborative actions involving regulatory initiatives, industry, patient advocacy groups, community engagement in a culturally sensitive manner, and designing and promoting decentralized clinical trials are vital to establishing a clinical research ecosystem that promotes equity in the representation of population subgroups.

Insights into Metatranscriptome, and CAZymes of Buffalo Rumen Supplemented with Blend of Essential Oils.

The aim of this study was to investigate the rumen microbial diversity and functionality in buffaloes fed with a blend of essential oils (BEO) using LSD switch over design. The BEO consisting of blend of Trachyspermum copticum (Ajwain) oil, Cymbopogon citratus (lemon grass) oil and Syzygium aromaticum (clove bud) oleoresin mixed in equal proportion, was fed at the rate of 0, 0.75 and 1.5 ml/100 kg of body weight in 0 (control), 0.75 and 1.5 groups, respectively. The metatranscriptomic libraries of the rumen microbiome were represented by 7 domains, 84 phyla, 64 archeal genera and 663 bacterial genera with Bacteroidetes and Firmicutes constituting 80% of phyla abundance irrespective of feeding regime. Methanogenic archaea was represented by 22 phyla with Methanobrevibacter as the major genus. BEO feeding reduced the abundance of Methanococcus and Thermoplasma (P < 0.05) at all levels. The results revealed that the feeding of BEO shifted the archeal and bacterial population at very low magnitude. The study explored the vast diversity of buffalo rumen bacteria and archaea, and the diverse wealth of rumen enzymes (CAZymes), which revealed that a major part of CAZymes comes from the less known rumen microbes indicating alternative paths of fiber degradation along with the very well known ones.

Transcriptome analysis of Clarias magur brain and gonads suggests neuro-endocrine inhibition of milt release from captive GnRH-induced males.

Transcriptome analysis of Clarias magur brain and gonads at preparatory, mature, 6 and 16 h post-GnRH injection (hpi) stages yielded 9.5 GB data with 39,738 contigs. Sequences of 45 reproductive genes were identified for the first time in C. magur along with unique and differentially expressed genes. The expression of 20 genes was validated by qRT-PCR. Upregulation of Cyp11A1, Cyp17A1 and FTZF1 genes in the 16hpi testis accompanied by the 17ß-HSD3 expression indicates testosterone (T) synthesis in response to LH surge, while reduced expression of CYP11B1 suggests a high T: 11-KT ratio. It is evident by the gene expression analysis that the inhibitory neurotransmitter GABA, altered T: 11-KT, increased testicular bile acids, and oxytocin-like neuropeptide in the male brain, appear to be involved in arresting the pulsatile motion of testicular smooth muscles. The work generates important leads for an effective induced breeding strategy for silurid catfish.

Colchicine: Isolation, LC-MS QTof Screening, and Anticancer Activity Study of Gloriosa superba Seeds.

Colchicine was extracted from Gloriosa superba seeds using the Super Critical Fluid (CO2) Extraction (SCFE) technology. The seeds were purified upto 99.82% using column chromatography. Colchicine affinity was further investigated for anticancer activity in six human cancer cell lines, i.e., A549, MCF-7, MDA-MB231, PANC-1, HCT116, and SiHa. Purified colchicine showed the least cell cytotoxicity and antiproliferation and caused no G2/M arrest at clinically acceptable concentrations. Mitotic arrest was observed in only A549 and MDA-MB231 cell lines at 60nM concentration. Our finding indicated the possible use of colchicine at a clinically acceptable dose and provided insight into the science behind microtubule destabilization. However, more studies need to be conducted beforethese findings could be established.

Betatron radiation and emittance growth in plasma wakefield accelerators.

Beam-driven plasma wakefield acceleration (PWFA) has demonstrated significant progress during the past two decades of research. The new Facility for Advanced Accelerator Experimental Tests (FACET) II, currently under construction, will provide 10 GeV electron beams with unprecedented parameters for the next generation of PWFA experiments. In the context of the FACET II facility, we present simulation results on expected betatron radiation and its potential application to diagnose emittance preservation and hosing instability in the upcoming PWFA experiments. This article is part of the Theo Murphy meeting issue 'Directions in particle beam-driven plasma wakefield acceleration'.

Immunomodulation of IL-1, IL-6 and IL-8 cytokines by Prosopis juliflora alkaloids during bovine sub-clinical mastitis.

The current work is focused on establishing therapeutic protocol using unconventional drugs of herbal origin and studying their mechanism of action at molecular level in the treatment of bovine sub-clinical mastitis. It explores the potential of different cytokines which can be used for diagnosis, prognosis and monitoring of bovine sub-clinical mastitis. Prosopis juliflora alkaloids was administered intramammarily in 24 sub-clinically affected quarters once a day for 5 consecutive days at the rate of 10 ml of 1% formulation. In 18 disease control quarters, sterile normal saline was infused. The bacterial cultural examination, somatic cell count (SCC) and cytokines (IL-1ß, IL-6, IL-8, IL-12, GM-CSF, IFN-γ, TNF-α) expression by real-time PCR were evaluated on day 7, 14, 21 and 28 post-last treatment from milk samples. Around 75.0% of treatment group quarters showed significant (p < 0.05) reduction in SCC on day 28 post-last treatment, whereas 94.4% control group quarters did not show any significant decline in SCC. 58.3% of treated quarters showed both bacteriological cure as well as significant (p < 0.05) reduction in SCC on day 28 post-last treatment. While, among control group quarters, 83.3% quarters not only remained bacteriological positive, they also did not show any significant decline in SCC. The in vitro antimicrobial activity of alkaloids of P. juliflora was evaluated. Lower concentrations of alkaloids (0.25% and 0.50%) dissolved in normal saline showed zone of inhibition against 12 out of 15 isolates, however higher concentration (1, 1.5, 2, 2.5 and 5%) showed zone of inhibition against all 15 bacterial isolates. The gene expression level of IL-1ß, IL-8 and IFN-γ cytokines exhibited significant difference between healthy and sub-clinically affected quarters highlighting the potential of these cytokines in the diagnosis of bovine sub-clinical mastitis. Down-regulation of IL-1, IL-6, IL-8 and IFN-γ cytokines in treated quarters can be explored for making the prognosis and monitoring post-treatment disease progression of bovine sub-clinical mastitis. The P. juliflora alkaloid demonstrated strong in vitro and in vivo antibacterial activity, along with causing immunomodulation by enhancing post-treatment gene expression of IL-1, IL-6 and IL-8 cytokines. Therefore, P. juliflora alkaloids hold a strong claim as an effective alternative herbal therapy in bovine sub-clinical mastitis.

Observation of Betatron X-Ray Radiation in a Self-Modulated Laser Wakefield Accelerator Driven with Picosecond Laser Pulses.

We investigate a new regime for betatron x-ray emission that utilizes kilojoule-class picosecond lasers to drive wakes in plasmas. When such laser pulses with intensities of ∼5×10^{18} W/cm^{2} are focused into plasmas with electron densities of ∼1×10^{19} cm^{-3}, they undergo self-modulation and channeling, which accelerates electrons up to 200 MeV energies and causes those electrons to emit x rays. The measured x-ray spectra are fit with a synchrotron spectrum with a critical energy of 10-20 keV, and 2D particle-in-cell simulations were used to model the acceleration and radiation of the electrons in our experimental conditions.

Transcriptomic comparison of primary bovine horn core carcinoma culture and parental tissue at early stage.

AIM: Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Comparison of gene expression in between horn's SCC tissue and its early passage primary culture using next generation sequencing was the aim of this study. MATERIALS AND METHODS: Whole transcriptome sequencing of horn's SCC tissue and its early passage cells using Ion Torrent PGM were done. Comparative expression and analysis of different genes and pathways related to cancer and biological processes associated with malignancy, proliferating capacity, differentiation, apoptosis, senescence, adhesion, cohesion, migration, invasion, angiogenesis, and metabolic pathways were identified. RESULTS: Up-regulated genes in SCC of horn's early passage cells were involved in transporter activity, catalytic activity, nucleic acid binding transcription factor activity, biogenesis, cellular processes, biological regulation and localization and the down-regulated genes mainly were involved in focal adhesion, extracellular matrix receptor interaction and spliceosome activity. CONCLUSION: The experiment revealed similar transcriptomic nature of horn's SCC tissue and its early passage cells.

Physical Mechanism of the Transverse Instability in Radiation Pressure Ion Acceleration.

The transverse stability of the target is crucial for obtaining high quality ion beams using the laser radiation pressure acceleration (RPA) mechanism. In this Letter, a theoretical model and supporting two-dimensional (2D) particle-in-cell (PIC) simulations are presented to clarify the physical mechanism of the transverse instability observed in the RPA process. It is shown that the density ripples of the target foil are mainly induced by the coupling between the transverse oscillating electrons and the quasistatic ions, a mechanism similar to the oscillating two stream instability in the inertial confinement fusion research. The predictions of the mode structure and the growth rates from the theory agree well with the results obtained from the PIC simulations in various regimes, indicating the model contains the essence of the underlying physics of the transverse breakup of the target.

High-field plasma acceleration in a high-ionization-potential gas.

Plasma accelerators driven by particle beams are a very promising future accelerator technology as they can sustain high accelerating fields over long distances with high energy efficiency. They rely on the excitation of a plasma wave in the wake of a drive beam. To generate the plasma, a neutral gas can be field-ionized by the head of the drive beam, in which case the distance of acceleration and energy gain can be strongly limited by head erosion. Here we overcome this limit and demonstrate that electrons in the tail of a drive beam can be accelerated by up to 27 GeV in a high-ionization-potential gas (argon), boosting their initial 20.35 GeV energy by 130%. Particle-in-cell simulations show that the argon plasma is sustaining very high electric fields, of ∼150 GV m(-1), over ∼20 cm. The results open new possibilities for the design of particle beam drivers and plasma sources.

Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing.

The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM. Data obtained were analysed using DNASTAR software package and case control analysis using SAS software. We found SNP present in BPIFA1 gene of B. indicus shows association with event of HC which reflects its potential to be a genetic marker. Bioinformatic analysis to detect structural and functional impact nsSNP of BPIFA1 added another layer of confirmation to our result. We successfully identified SNP associated with HC as well as demonstrated efficient approach for limited number of SNP discovery and validation in targeted genomics regions in large number of samples combining PCR amplification and Ion Torrent PGM sequencing which suits small-scale laboratories with limited budget.

Comprehensive transcriptome profiling of squamous cell carcinoma of horn in Bos indicus.

Squamous cell carcinoma (SCC) of horn is frequently observed in Bos indicus affecting 1% of cattle population and accounting 83.34% of total tumours found. The transcriptome profile of horn cancer (HC) tissue and the matched normal (HN) tissue were analysed by RNA-seq using Roche 454 sequencing. A total of 1 504 900 reads comprising of 612 MB data were used to identify differentially expressed genes using CLC Genomic Workbench. These include up-regulation of KRT6A, KRT6B, KRT6C, KRT14, SFN, KRT84, PI3, COL17A1, ANLN, SERPINB5 and down-regulation of BOLA, SCGB1A1, CXCL17, KRT19, BPIFB1, NR4A1 and TFF3 in HC, which are involved in regulation of gene transcription, cell proliferation, apoptosis, cell survival and metabolic pathways. The qPCR analysis of several targets suggested concordance of gene expression profile with RNA-seq analysis. The present findings would provide basis for further screening of genes and identification of markers for early diagnosis and therapeutic intervention of HC.

Poster - Thur Eve - 34: Evaluation of 4DCT on the GE lightspeed RT16 using a respiratory motion phantom.

PURPOSE: This study encompasses several quality assurance tests performed during the commissioning of the 4DCT technique on the GE Lightspeed RT16 CT scanner for SBRT at the Cancer Centre of Southeastern Ontario. The main purpose is to assess geometric position and volumetric delineation accuracy. A limited assessment of the image quality and dose was performed. METHODS: The Quasar Respiratory Motion with a modified cylindrical moving insert was used. Clinically relevant breathing motion patterns analyzed were: sinusoidal with amplitudes of 5 and 15 mm, and periods of 3 s and 6 s; and a typical respiratory breathing motion of amplitude of 10 mm and period of 4 s. RESULTS: Couch position errors were ≤ 1mm for maximum inspiration (Ph 0%) and expiration (Ph 50%) phases. errors were greater for mid-phases, the largest being 8.1 mm (Ph 20%) for the typical respiratory pattern. MIP volume deviations ranged from -0.3 to -3.2 cm3 ; the greater deviations corresponding to larger amplitudes and shorter periods, where image distortion is also more severe. SUP and INF position error of MIP on coronal views for the lung window and level used in our centre ranged from -0.07 to 1.4 mm and from -0.04 to 1 mm on the SUP and INF direction respectively. The dose from a 4DCT acquisition was 2.8 times higher than in a free breading scan, while the noise was comparable. CONCLUSIONS: Although higher doses are obtained, 4DCT is a sufficiently accurate approach that could be used safely to account for breathing motion.

Immobilization and catheter guidance for breast brachytherapy.

PURPOSE: Brachytherapy is an important mode of breast cancer treatment; however, improvements in both treatment planning and delivery are needed. In order to meet these specific needs, integration of pre-operative imaging, supplemented by computerized surgical planning and mathematical optimization were used to develop and test an intra-operative immobilization and catheter guidance system. METHOD: A custom template specific to each patient with optimally placed guide holes for catheter insertion was designed and fabricated. Creation of the template is based on a virtual reality reconstruction of the patient's anatomy from computed tomography imaging. The template fits on the patient's breast, immobilizing the soft tissue, and provides pre-planned catheter insertion holes for guidance to the tumor site. Agar-based phantom and target models were used for quantitative validation of the template by ascertaining the precision and accuracy of the templates. RESULTS: Tests were performed on agar-based tissue models using computed tomography imaging for template planning and validation. Planned catheter tracks were compared to post-insertion image data and distance measurements from target location were used to create an error measure. Initial results yielded an average error of 4.5mm. Once the workflow and template design were improved, an average error of 2.6mm was observed, bringing the error close to a clinically acceptable range. CONCLUSION: Use of a patient-specific template for breast brachytherapy is feasible and may improve the procedure accuracy and outcome.

Dasytricha dominance in Surti buffalo rumen revealed by 18S rRNA sequences and real-time PCR assay.

The genetic diversity of protozoa in Surti buffalo rumen was studied by amplified ribosomal DNA restriction analysis, 18S rDNA sequence homology and phylogenetic and Real-time PCR analysis methods. Three animals were fed diet comprised green fodder Napier bajra 21 (Pennisetum purpureum), mature pasture grass (Dicanthium annulatum) and concentrate mixture (20% crude protein, 65% total digestible nutrients). A protozoa-specific primer (P-SSU-342f) and a eukarya-specific primer (Medlin B) were used to amplify a 1,360 bp fragment of DNA encoding protozoal small subunit (SSU) ribosomal RNA from rumen fluid. A total of 91 clones were examined and identified 14 different 18S RNA sequences based on PCR-RFLP pattern. These 14 phylotypes were distributed into four genera-based 18S rDNA database sequences and identified as Dasytricha (57 clones), Isotricha (14 clones), Ostracodinium (11 clones) and Polyplastron (9 clones). Phylogenetic analyses were also used to infer the makeup of protozoa communities in the rumen of Surti buffalo. Out of 14 sequences, 8 sequences (69 clones) clustered with the Dasytricha ruminantium-like clone and 4 sequences (13 clones) were also phylogenetically placed with the Isotricha prostoma-like clone. Moreover, 2 phylotypes (9 clones) were related to Polyplastron multivesiculatum-like clone. In addition, the number of 18S rDNA gene copies of Dasytricha ruminantium (0.05% to ciliate protozoa) was higher than Entodinium sp. (2.0 × 10(5) vs. 1.3 × 10(4)) in per ml ruminal fluid.

Molecular identification of methanogenic archaea from Surti buffaloes (bubalus bubalis), reveals more hydrogenotrophic methanogens phylotypes

Methane emissions from ruminant livestock are considered to be one of the more potent forms of greenhouses gases contributing to global warming. Many strategies to reduce emissions are targeting the methanogens that inhabit the rumen, but such an approach can only be successful if it targets all the major groups of ruminant methanogens. Therefore, a thorough knowledge of the diversity of these microbes in breeds of buffaloes, as well as in response to geographical location and different diets, is required. Therefore, molecular diversity of rumen methanogens in Surti buffaloes was investigated using 16S rRNA gene libraries prepared from pooled rumen contents from three Surti buffaloes. A total of 171 clones were identified revealing 23 different sequences (phylotypes). Of these 23 sequences, twelve sequences (12 OTUs, 83 clones) and 10 sequences (10 OTUs, 83 clones) were similar to methanogens belonging to the orders Methanomicrobiales and Methanobacteriales, and the remaining 1 phylotype (5 clones) were similar to Methanosarcina barkeri. These unique sequences clustered within a distinct and strongly supported phylogenetic group. Further studies and effective strategies can be made to inhibit the growth of Methanomicrobiales and Methanobacteriales phylotypes to reduce the methane emission from rumen and thus help in preventing global warming.

Positron injection and acceleration on the wake driven by an electron beam in a foil-and-gas plasma.

A novel approach for generating and accelerating positron bunches in a plasma wake is proposed and modeled. The system consists of a plasma with an embedded thin foil into which two electron beams are shot. The first beam creates a region for accelerating and focusing positrons and the second beam provides positrons to be accelerated. Monte Carlo and 3D PIC simulations show a large number of positrons (10(7) approximately 10(8)) are trapped and accelerated to approximately 5 GeV over 1 m with relatively narrow energy spread and low emittance.

Genetic characterization of Indian peste des petits ruminants virus (PPRV) by sequencing and phylogenetic analysis of fusion protein and nucleoprotein gene segments.

Peste des petits ruminants (PPR) is an important viral disease of sheep and goats, endemic in India. The study was undertaken to characterize the local PPRV by sequencing fusion (F) protein and nucleoprotein (N) gene segments and phylogenetic analysis, so as to focus on genetic variation in the field viruses. Selected regions of PPRV genome were amplified from clinical samples collected from 32 sheep and goats by RT-PCR and the resulting amplicons were sequenced for phylogenetic analysis. The phylogenetic tree based on the 322bp F gene sequences of PPRV from five different locations clustered them into lineage 4 along with other Asian isolates. While the 425bp N gene sequences revealed a different pattern of branching, yielding three distinct clusters for Nigerian, Turkey and Indian isolates. Thus, classification of PPRV into lineages based on the N gene sequences appeared to yield better picture of molecular epidemiology for PPRV.

Poster - Thurs Eve-15: Comparison of Cobalt-60 and 6 MV linac based tomotherapy: A prostate case study.

Previous work reported by us has shown the potential for Cobalt-60 (Co-60) tomotherapy for sites with small separations such as in head and neck site. In this work we extend our investigations by comparing tomotherapy plans for the treatment of a typical prostate cancer obtained for 6 MV and Co-60 beams. Beam collimation was provided by the MIMiC® (NOMOS Corporation, Sewickly, PA) multi-leaf collimator (MLC). Both plans used 21 beam angles, each utilizing the central 10 leaf-pairs of the MLC for intensity modulation. An in-house inverse treatment planning program, based on the active-set conjugate gradient method, was used for dose-volume optimization. BEAMnrc and DOSXYZnrc Monte Carlo simulated beam and dose data, including inhomogeneity corrections, were used to calculate the optimized tomotherapy dose distributions. Prostate, rectum, and external body contours were outlined and dose-volume optimization objectives were set to deliver a minimum of 95% and a maximum of 105% of the 76 Gy dose prescription to the prostate and limiting only 20% of the rectum volume to receive ⩾ 70 Gy. A quantitative analysis of the dose distributions and dose-area histograms show that both Co-60 and 6 MV plans achieve the initial objectives for target (prostate) and organ at risk (rectum). Although the dose to the body and rectum for Co-60 is slightly higher than that for 6 MV, it satisfies the plan objectives based on the clinical dose tolerance. Our results demonstrate that Co-60 based tomotherapy can provide clinically competitive dose distributions for the treatment of prostate cancer.

Hose instability and wake generation by an intense electron beam in a self-ionized gas.

The propagation of an intense relativistic electron beam through a gas that is self-ionized by the beam's space charge and wakefields is examined analytically and with 3D particle-in-cell simulations. Instability arises from the coupling between a beam and the offset plasma channel it creates when it is perturbed. The traditional electron hose instability in a preformed plasma is replaced with this slower growth instability depending on the radius of the ionization channel compared to the electron blowout radius. A new regime for hose stable plasma wakefield acceleration is suggested.