Adapting lean methodology towards surgical tray rationalisation in inguinoscrotal day case surgery in the republic of Ireland

INTRODUCTION

Lean methodologies have been used successfully in both industry and healthcare to reduce waste. The operating room (OR) and central supplies department (CSD) are areas associated with high hospital costs. The aim of this study was to employ Lean methodologies to support the rationalisation of surgical trays in paediatric inguinoscrotal surgery in order to reduce instrument wastage, processing times and overall costs in a European setting.

METHODS

This was a prospective, pilot observation and implementation study using Lean methodology including DMAIC (Define, Measure, Analyse, Improve and Control) cycles. Relevant tray set-up included trays for boys ≥12 months age undergoing open elective inguinoscrotal surgery. A comparative analysis of two phases, pre and post-standardization was then carried out with respect to operating times, instrument set-up times, tray weights, and costs. Instruments that were used <40% of the time were eliminated from the surgical tray.

RESULTS

Rationalization of the inguinoscrotal tray led to a 34.7% reduction in tray size, with a concomitant time-reduction of >2 min per case. The average overall instrument utilisation rate increased from 56% to 80% across users. Cost savings were projected at €5380.40 per annum based on current changes. There were no differences in operative time, or adverse outcomes.

DISCUSSION

At the hospital level, the reduction in variation, and rationalisation of this single surgical tray could lead to both operational (Tray assembly process; Operating rooms; Ergonomic functionality) as well as economic (Sterilisation; Instrument repair; Purchases) financial and ergonomic improvements for the healthcare system. The reduction in time taken to count and sterilise instruments can lead to a potential manpower saving involving a redistribution of activities to other areas which may require them.

CONCLUSION

Surgical tray rationalisation is emerging Lean concept with overlap across a number of specialities, and represents a technique by which to manage costs, and improve supply chain efficiency without any adverse effect in patient healthcare outcomes.

Comparison of Three Anaesthetic Options to Reduce Acute Pain Response in Kid Goats

Three options for anesthetizing the skin around the horn bud of dairy goat kids were explored. Forty-five <10-day-old Saanen goat kids from were randomly split into five treatment groups (topical anesthetic cream (TA), vapocoolant spray (VS), local anesthetic applied by jet injector (JI), control - no treatment but painful stimulus applied (C), sham - no treatment and touching sites with a finger. The painful stimulus was multiple needle pricks on the skin around the horn bud. The outcome variables measured were heart rate movement, and vocalization during treatment application and administration of a painful stimulus around the horn bud. Heart rates were greater during application of a VS compared to TA.Neither the TA nor the VS appeared to have any effect on the response to the painful stimulus. Kids in the JI group had a 96% reduced odds of expressing a marked pain response in comparison to TA group and an 83% reduction in the odds of a high movement grade during a painful procedure in comparison to the combined results of the other three treatment groups.

0025 Circadian Dysregulation of Human DNA Repair Genes and Elevated DNA Damage in Simulated Night Shift Schedule

Introduction

Circadian misalignment from night shift (NS) work is associated with increased risk of cancer. In a simulated NS study, we sought to investigate the potential role of circadian disruption of cancer hallmark pathway genes.

Methods

N=14 healthy adults (aged 22-34) participated in a laboratory study. Seven were assigned to a simulated day shift (DS) schedule involving 3 days of daytime wakefulness (06:00-22:00); the other seven were assigned to a simulated NS schedule involving 3 days of nighttime wakefulness (18:00-10:00). Subjects then underwent a 24-hour constant routine protocol, during which blood was collected at 3-hour intervals. Leukocytes extracted from blood were subjected to transcriptomics using the NanoString nCounter PanCancer Pathways panel augmented with canonical clock genes. Statistical analysis involved mixed-effects cosinor analysis followed by functional enrichment analysis of rhythmic genes. Leukocytes were also subjected to endogenous DNA damage assessment through alkaline comet and immunofluorescence assays. Furthermore, exogenous DNA damage from exposure to ionizing radiation was investigated for blood collected at opposite times of day (07:30 and 19:30) based on DNA damage biomarkers assessed with immunofluorescence and immunoblot assays.

Results

Transcriptomics data showed that the simulated NS schedule, as compared to the simulated DS schedule, significantly altered the endogenous circadian rhythmicity of genes involved in cancer hallmark pathways, as measured under constant routine. A DNA repair pathway showed enrichment of rhythmic genes following the DS schedule (P&lt;0.05), but not following the NS schedule. Functional assessments revealed that the NS schedule was associated with increased endogenous DNA damage, as evidenced by alkaline comet assay (P&lt;0.001) and increased BRCA1 foci (P&lt;0.01) and γH2AX foci by immunofluorescence assay (P&lt;0.001). After exposure to ionizing radiation, there were increased BRCA1 foci (P&lt;0.01) and γH2AX foci by immunofluorescence assay (P&lt;0.005) and elevated DNA damage response signaling biomarkers by immunoblot assay, especially in the samples collected at 19:30.

Conclusion

These results suggest that a NS schedule causes circadian dysregulation of DNA repair genes and increases DNA damage – a primary hallmark of carcinogenesis – which may underlie the elevated cancer risk in NS workers.

Support (If Any)

WSU, CHHE P30ES025128, USAMRDC W81XWH-18-1-0100, NIH R01ES030113 and R21CA227381, CDMRP CA171123, DOE BRAVE DE-AC05-76RL01830.

Abstract 197: Proteomic Characterization Of Human Brain Lipoproteins Speciated By Size Exclusion Chromatography

Like plasma, the cerebrospinal fluid (CSF) contains lipid-protein complexes called lipoproteins tasked with transporting lipids and protecting against cerebrovascular dysfunction. These brain lipoproteins (BLps) are generated de novo in the central nervous system (CNS), but little is known about them, because they exist in CSF at <0.5% the concentration of lipoproteins in plasma making them difficult to study. BLps are thought to resemble plasma high-density lipoproteins (HDL), a heterogenous population of compositionally distinct particles important for transporting lipid, protecting against oxidative stress, and modulating immune and inflammatory responses in the periphery. Mass spectrometry (LC-MS/MS) studies have shown that 260 different proteins can interact with different HDLs in the periphery and specific combinations of these proteins cluster on the lipid surface to govern particle function. In the current study, we developed a lipoprotein profiling technology that overcomes the BLp abundance problem in CSF to capture BLp subspecies with unprecedented sensitivity and resolution. Using high-resolution size exclusion chromatography, we identified at least 10 distinctly sized BLp populations in human CSF with a majority of the particles eluting in size ranges between plasma low-density lipoproteins (LDL) and HDL. BLps were isolated from fractionated CSF using a lipid-binding resin. Proteomic analysis of the particles using LC-MS/MS identified 299 different lipid-associated proteins across fractions with 189 of those proteins not currently reported on the human HDL Proteome Watch. Co-migration analysis further revealed at least 27 unique protein communities across the fractions indicating that multiple distinct subspecies exist within the same sized subfractions. DAVID functional analysis shows that the communities are highly enriched in proteins important in the immune response and neurometabolic functions such as neuron generation and development. In summary, our study shows that similar to plasma HDL, BLps are a highly speciated population of compositionally distinct particles but are enriched in CNS-derived proteins that are essential for maintaining cognitive health.

139 OLDER PERSONS REHABILITATION: A SIX MONTH PATIENT PROFILE

Background

For quality improvement to be assessed in a healthcare setting, understanding the specific patient profile is vital. Only then can system performance and service development be reviewed accurately. The purpose of this review was to analyse the patient profile of a 20 bed older persons rehabilitation unit.

Methods

Data was collected weekly for patients admitted and discharged to a sub-acute rehabilitation unit over a six month period (January to June 2021) by a multi-disciplinary team (MDT). Information collected included; age, clinical frailty scale (CFS, revised 2008, Rockwood et al., 2005), MDT involvement, care needs on discharge, onward community referrals and length of stay.

Results

62 patients were included (25 males and 37 females) with an average age of 81 (range 61–99). The CFS was measured for 58 patients and ranged from 1 to 7. On examination, 9% of patients had a CFS of 1–2, 38% a CFS of 3–4, 46% a CFS of 5–6 and 7% a CFS of 7.

Of the 62 patients included, all received physiotherapy and occupational therapy, 28 speech and language therapy, 25 dietetics and 48 medical social work.

The average length of stay was 42 days (range 10–162).

On discharge 42% of patients went home with existing supports, 50% went home with increased supports and 8% went to a residential care facility. Referrals to community services were sent for 65% of patients.

Conclusion

53% of patients admitted to an older person rehabilitation unit had a CFS of 5 or more, indicating they were at least mildly frail. The average length of stay was six weeks and all patients required a minimum of two MDT members during their stay. This highlights the presence of frailty and the importance of effective MDT working in the sub-acute rehabilitation setting.

151 THERAPY OUTCOME MEASURES IN AN OLDER PERSONS REHABILITATION UNIT

Background

The mission of an older person’s sub-acute rehabilitation unit is to improve the individual’s function and quality of life. This is achieved through patient and multidisciplinary team (MDT) collaboration. The MDT collect Therapy Outcome Measure (TOM) (Enderby and John 2015) data to measure the effectiveness of rehabilitation and facilitate analysis of patient and service outcomes. This abstract will present 6 months of data collection with the aim of evaluating the impact of MDT intervention from January 2021.

Methods

The MDT meet weekly to jointly record patient TOM scores on admission and discharge. The TOM scales used are; multifactorial conditions, stroke and neurological disorder. The patient is scored from 0–5 in four domains; impairment, activity, participation and well-being. There are 11 parts to the scale with 0.5 scores permitted (Enderby and John 2015).

Results

Data was analysed on 62 patients. Across an episode of rehabilitation an increase of 0.5 or more on the TOM is a clinically significant (positive) change. 84% of patients had an overall improvement in the total TOM score. There was an average overall increase of 2.6 points on the scale which equates to a 25% overall change. 63% improved in the domain of impairment, 77% in activity, 73% in participation and 66% in wellbeing. 100% of patients post-stroke, 81% with multifactorial conditions and 75% with neurological conditions experienced an overall improvement.

Conclusion

The data objectively shows positive patient outcomes in older persons rehabilitation. Individuals experienced the most positive change in their activity and participation function and high levels of change are also evident in impairment levels and well-being. Overall, TOM is a very useful MDT outcome measure tool. It has been successfully implemented and maintained in the service and facilitates the ongoing analysis of individual and service outcomes to understand the impact of intervention.

An Evaluation of the Keeping Well at Home Booklet

Background

In the first wave of COVID-19, the UK Government relied heavily on digital channels to provide information to the public. This disproportionately excluded older people - one of the groups with least access to (or experience of) using the internet. Approximately 11.5 million people in the UK lack digital skills and 4.8 million people never go online, with around half (51%) of these being aged over 65. The Greater Manchester (GM) response was to work collaboratively with a number of key Ageing groups to develop Keeping Well at Home, a booklet providing evidence based health and wellbeing information and advice for older people during COVID-19 restrictions.

Methods

An evaluation of the booklet was undertaken during summer 2020 by the Healthy Ageing team at the Applied Research Collaboration GM. As national restrictions on movement remained in place at the time, a postal questionnaire was distributed to a sample of older adults in GM.

Results

Nearly 500 questionnaires were returned. The response was overwhelmingly positive; 92% found the information helpful; 90% agreed the booklet would help older people stay healthy during lockdown; 74% had used the home exercises section; 78% found the tips for keeping their mind well helpful. Around 50% of respondents did not have internet access. Paper based resources was the preferred choice for 92% of respondents with only 6% opting for digital versions.

Conclusions

The evidence from the evaluation challenges the growing trend towards communicating just through digital channels, and emphasises the need for tailored paper-based materials for older adults. The Keeping Well at Home booklet also shows the value of working with older adults to ensure the content and design are inviting to readers. Information, support and services must be made available in an offline equivalent and proactively disseminated to reach those who otherwise would not have access to it.

Key messages

Print-based communications are preferred over digital for some groups; ensuring inclusivity is critical as the ‘digital by default’ approach excludes large numbers of our population.

Including target group representatives as co-editors to advise on content and stylistic design is key to ensure content is relevant and useful.

Abstract 5123: Proteogenomic characterization reveals mitotic kinase and replication stress implicated in ovarian high-grade serous cancer

High-grade serous cancer (HGSC), the most prevalent histotype of ovarian cancer, has the lowest survival rates and is the leading cause of gynecological cancer-related deaths in the developed world. HGSC is characterized by the presence of nearly universal TP53 mutations, diverse and widespread chromosomal instability, and a general shortage of targetable driving mutations. The major clinical needs in HGSC include the identification of alternative therapeutic targets and an improved understanding of the mechanisms driving chromosomal heterogeneity. We prospectively collected 83 new ovarian HGSC samples and 20 normal precursor tissue samples (Fallopian tube, FT) for deep characterization at the genomic, transcriptomic, proteomic, and phosphoproteomic levels. We were also able to obtain cytobrush samples of Fallopian tube epithelium and provide the first extensive comparison of HGSC and FT proteomes and phosphoproteomes that used surgical specimens rather than cell lines. The ability to compare tumor and normal precursor tissues provided new biological insights regarding the role of increased proliferation in promoting replication stress in a DNA repair-deficient background, potentially explaining the high degree of chromosomal instability associated with HGSC. Our collection protocols were specifically designed to minimize the effect of ischemia on protein phosphorylation, which has been identified as a significant confounding variable. Thus, we were able to identify novel signaling interactions that would have been lost in the background of ischemic stress, most notably the activation of CDK4 and CDK7. Widespread increases in protein phosphorylation and pathway activation in tumors compared to normal tissues, particularly in the proliferation-associated CDK/RB and AURKA pathways that are targetable by FDA-approved inhibitors, provide a rational basis for the use of these therapeutics in ovarian cancer. Phosphosite-specific analysis of CDKs and FANCD was consistent with an elevated response to replication stress, potentially induced by proliferative signals. Additionally, pathway-level observations from the retrospective TCGA cohort were conserved in the prospective cohort, including histone acetylation marks associated with homologous repair deficiency. In addition to confirming key features of HGSC from previous proteogenomic study, analysis of prospectively collected HGSC samples provided significant new insights stemming from direct comparisons to normal precursor tissues; deep phosphoproteomics revealed new insights regarding the potential role of proliferation-induced replication stress in promoting the characteristic chromosomal instability of HGSC and suggested novel therapeutic targets for use in precision medicine trials.

Citation Format: Jason McDermott, Osama Arshad, Vladislav Petyuk, Yi Fu, Marina Gritsenko, Chia-Feng Tsai, Samuel Payne, Mathangi Thiagarajan, Christopher Kinsinger, Ana Robles, Emily Boja, Henry Rodriguez, Daniel Chan, Bing Zhang, Zhen Zhang, Li Ding, Richard Smith, Tao Liu, Karin Rodland. Proteogenomic characterization reveals mitotic kinase and replication stress implicated in ovarian high-grade serous cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5123.

Effects of a topically applied anaesthetic on the behaviour, pain sensitivity and weight gain of dairy calves following thermocautery disbudding with a local anaesthetic

Aims: To compare the effect of a topically applied anaesthetic to no pain relief or meloxicam on the behavioural responses, pain sensitivity and weight gain of calves following disbudding with or without sedation. Methods: A total of 364, 2-6 week-old calves from three commercial farms were systematically allocated to one of six treatment groups. All calves received a cornual nerve block prior to disbudding, with half restrained in a crate and half sedated with xylazine. Within these groups one third received no further treatment (control), one third were treated with meloxicam >10 minutes prior to disbudding and one third received a topical anaesthetic applied to the horn bud wounds following disbudding. The frequency of ear flicks, head shakes, head scratches and pain sensitivity of the wound were recorded on up to eight occasions over 24 hours after disbudding. Calves were weighed before, and 7 and 28 days after, disbudding to determine average daily weight gain (ADG). Results: Compared to calves in the crate-control group, all other groups had reduced ear flicks at all times following disbudding (p < 0.01). Treatment with meloxicam and topical anaesthesia in addition to sedation reduced head scratches compared to calves in the crate-control group (p ≤ 0.013). At 22 hours after disbudding head shakes were reduced in sedated calves treated with topical anaesthetic compared to calves in the crate-control group (p < 0.001). Pain sensitivity was lower in all sedated calves than unsedated calves (p < 0.001). The ADG between Days 0-7 was 0.14 (95% CI = 0.015-0.274) kg/day greater in sedated calves treated with meloxicam than calves in the crate-control group (p = 0.03), and the ADG between Days 0-28 tended to be 0.06 (95% CI=-0.01-0.13) kg/day greater in sedated calves treated with topical anaesthetic than calves in the crate-control group (p = 0.09). Conclusion and clinical relevance: Sedation of calves for disbudding reduced the pain experienced in the following 24 hours. There was a benefit to providing calves with topical anaesthetic following disbudding on behavioural responses and pain sensitivity, which was similar to that of treating calves with meloxicam.

Pembrolizumab: PD-1 inhibition as a therapeutic strategy in cancer

Programmed cell death protein 1 (PD-1) and its ligands, programmed cell death 1 ligand 1 (PD-L1) and 2 (PD-L2) play an important role in regulating immune response through various mechanisms. This inhibitory action is thought to assist in immune evasion by cancer cells as PD-1, PD-L1 and PD-L2 have been found to be abnormally expressed by tumor cells and lymphocytes in the tumor microenvironment. Preclinical studies described PD-1 blockade resulting in tumor growth suppression and even decreased metastasis. This has led to the development of pembrolizumab (MK-3475), a highly selective, humanized monoclonal IgG4-kappa isotype antibody against PD-1. Early clinical trials have shown high tumor response rates and long duration of effect in previously treated advanced melanoma resulting in accelerated FDA approval for the drug in this situation. Pembrolizumab has also had success in non-small cell lung cancer and is being tested in multiple other tumor types. This review will discuss the development, preclinical data, pharmacokinetics and clinical efficacy to date of pembrolizumab.

Abstract OT2-01-10: A phase 1 study of RAD1901, a novel, orally available, selective estrogen receptor degrader, for the treatment of ER positive advanced breast cancer

The current NCCN treatment guidelines for ER+ breast cancer involves the use of approved agents such as fulvestrant, tamoxifen and aromatase inhibitors that either inhibit estrogen production or block estrogen receptor binding. While the initial treatment regimens with these selective estrogen receptor modulators (SERMs) and selective estrogen receptor degraders (SERDs) is often successful, many women eventually relapse with more aggressive forms of endocrine-resistant disease. To begin to overcome some of the challenges associated with current therapies including exposure limitations and intramuscular administration, we have developed RAD1901, a novel, non-steroidal, orally available SERD. Preclinical studies with RAD1901 have demonstrated potent dose dependent ER degradation consistent with a SERD mechanism of action, as well as potent inhibition of proliferation in vitro in breast cancer cell lines. RAD1901 also demonstrated significant anti-tumor efficacy in vivo, and notably single agent regressions in both MCF7 and a primary patient derived xenograft models harboring an ESR1 mutations.

A phase 1 monotherapy study conducted in healthy postmenopausal female volunteers evaluated forty four subjects treated once daily with RAD1901 with doses ranging from 200 mg/day up to 1000 mg/day for 7 days. All dose levels were generally well tolerated and pharmacokinetic analysis demonstrated plasma exposures consistent with preclinical efficacy in ER+ breast cancer models. Furthermore, 18F-estradiol positron emission tomography (FES-PET) was also performed at baseline and after 7 days of RAD1901 treatment, to evaluate estrogen receptor engagement. Standardized uptake values (SUV) pre- and post-treatment with RAD1901 demonstrated complete attenuation of FES-PET signal in ER+ tissues such as the uterus from the 200 mg/day dose level. Taken together, these results provide strong preclinical and clinical rationale for the development of RAD1901 as a potent and selective oral SERD for the treatment of hormone driven and hormone resistant ER + metastatic breast cancers.

RAD1901-005 is a Phase 1 study currently enrolling ER+ advanced metastatic breast cancer patients. The study consists of two parts: a monotherapy dose escalation followed by a safety expansion at the maximum tolerated dose (MTD). The dose escalation will follow a standard 3+3 design with once daily dosing to establish, safety, tolerability, and PK. Once the MTD for RAD1901 has been established, the safety expansion will further evaluate the safety, tolerability, biomarkers and preliminary efficacy at the recommended phase 2 dose (RP2D) following a continuous once daily schedule. Key inclusion criteria include post-menopausal women aged 18 years or older, with advanced ER positive, HER2 negative breast cancer, who have received ≤ 2 prior chemotherapy regimens in the metastatic setting and &gt; 6 months of prior endocrine therapy. Patient enrollment started in early 2015, and is currently ongoing.

ClinicalTrials.gov identifier: NCT02338349.

Citation Format: Harb W, Garner F, McDermott J, Zimmerman T, Williams G, Hattersley G, Purandare D. A phase 1 study of RAD1901, a novel, orally available, selective estrogen receptor degrader, for the treatment of ER positive advanced breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr OT2-01-10.

Regional deposition of mometasone furoate nasal spray suspension in humans

Nasal deposition studies can demonstrate whether nasal sprays treating allergic rhinitis and polyposis reach the ciliated posterior nasal cavity, where turbinate inflammation and other pathology occurs. However, quantifying nasal deposition is challenging, because in vitro tests do not correlate to human nasal deposition; gamma scintigraphy studies are thus used. For valid data, the radiolabel must distribute, as the drug, into different-sized droplets, remain associated with the drug in the formulation after administration, and not alter its deposition. Some nasal deposition studies have demonstrated this using homogenous solutions. However, most commercial nasal sprays are heterogeneous suspensions. Using mometasone furoate nasal suspension (MFS), we developed a technique to validate radiolabel deposition as a surrogate for nasal cavity drug deposition and characterized regional deposition and nasal clearance in humans. Mometasone furoate (MF) formulation was spiked with diethylene triamine pentacaetic acid. Both unlabeled and radiolabeled formulations (n = 3) were sprayed into a regionally divided nasal cast. Drug deposition was quantified by high pressure liquid chromatography within each region; radiolabel deposition was determined by gamma camera. Healthy subjects (n = 12) were dosed and imaged for six hours. Scintigraphic images were coregistered with magnetic resonance imaging scans to quantify anterior and posterior nasal cavity deposition and mucociliary clearance. The ratio of radiolabel to unlabeled drug was 1.05 in the nasal cast and regionally appeared to match, indicating that in vivo radiolabel deposition could represent drug deposition. In humans, MFS delivered 86% (9.2) of metered dose to the nasal cavity, approximately 60% (9.1) of metered dose to the posterior nasal cavity. After 15 minutes, mucociliary clearance removed 59% of the initial radiolabel in the nasal cavity, consistent with clearance rates from the ciliated posterior surface. MFS deposited significant drug into the posterior nasal cavity. Both nasal cast validation and mucociliary clearance confirm the radiolabel deposition distribution method accurately represented corticosteroid nasal deposition.

A comprehensive collection of systems biology data characterizing the host response to viral infection

The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archived at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). By comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.

Ibrutinib for the treatment of chronic lymphocytic leukemia and mantle cell lymphoma

Ibrutinib is a novel oral tyrosine kinase inhibitor that irreversibly binds and inhibits tyrosine-protein kinase BTK (Bruton tyrosine kinase). BTK has been found to be important in the function of B-cell receptor signaling and therefore in the maintenance and expansion of various B-cell malignancies including chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL). Targeting BTK with ibrutinib has been found to be an effective strategy in treating these malignancies. Phase I clinical testing in non-Hodgkin's lymphomas and CLL showed that the drug was extremely well tolerated with no major dose-limiting toxicities and a 54% overall response rate. Subsequently, two phase Ib/II studies were performed on patients with CLL, one in relapsed/refractory CLL and one in previously untreated elderly patients with CLL. Both of these studies continued to show good tolerability of the drug and an overall response rate of about 71% with extended duration of response. Another phase II study using ibrutinib in relapsed/refractory MCL was conducted and also showed that it was well tolerated with an overall response rate of 68% and extended duration of response. Due to these results, the U.S. Food and Drug Administration granted accelerated approval for ibrutinib in November 2013 for patients with MCL who had received at least one prior therapy and in February 2014 for patients with CLL who had received at least one prior therapy. This review will discuss the preclinical pharmacology, pharmacokinetics and clinical efficacy to date of ibrutinib in the treatment of CLL and MCL.

Belinostat for the treatment of peripheral T-cell lymphomas

Belinostat is a novel histone deacetylase (HDAC) inhibitor that is being developed in various solid tumors and hematologic malignancies. HDACs have been found to be important in the epigenetic regulation of cancer progression and inhibition of these molecules in preclinical studies induces cancer cell apoptosis and prevents tumor growth. Several HDAC molecules have been found to be overexpressed in peripheral T-cell lymphoma (PTCL) and therefore HDAC inhibition has been an important new target in treating these malignancies which have traditionally had poor outcomes and limited treatment response. Phase I studies were tested across a broad range of hematologic and solid tumors and showed stability of disease in various tumor types with low rates of adverse events. This made it acceptable to proceed with further testing in specific tumor types to further determine efficacy. Two phase II studies have been completed with belinostat given intravenously in the relapsed/refractory PTCL setting with at least 25% overall response and minimal toxicities. These findings have led to a request for accelerated approval to the U.S. Food and Drug Administration for belinostat in this setting. This review will discuss the preclinical pharmacology, pharmacokinetics and clinical efficacy to date of belinostat in the treatment of PTCL.

Biocellion: accelerating computer simulation of multicellular biological system models

MOTIVATION

Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming.

RESULTS

We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies.

AVAILABILITY AND IMPLEMENTATION

Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information.

Economics of brucellosis impact and control in low-income countries

Most data and evidence on the economic burden of brucellosis and the benefits of its control are from high-income and middle-income countries. However, the burden of brucellosis is greatest in low-income countries. This paper focuses on estimating the economic burdens of brucellosis in low-income countries in tropical Asia and Africa. The prospects for national, technically feasible, and economically viable, national brucellosis control programmes in most low-income countries are limited. However, some targeted control programmes will be beneficial and can probably be feasibly managed and provide good economic returns. More ambitious control will require a more general strengthening of Veterinary Services and livestock-sector capacity, using risk-management-based approaches.

Pretreatment of endothelial progenitor cells with osteopontin enhances cell therapy for peripheral vascular disease

Tissue necrosis resulting from critical limb ischemia (CLI) leads to amputation in a significant number of patients. Autologous cell therapy using angiogenic cells such as endothelial progenitor cells (EPCs) holds promise as a treatment for CLI but a limitation of this treatment is that the underlying disease etiology that resulted in CLI may also contribute to dysfunction of the therapeutic EPCs. This study aimed to elucidate the mechanism of EPC dysfunction using diabetes mellitus as a model and to determine whether correction of this defect in dysfunctional EPCs ex vivo would improve the outcome after cell transplantation in the murine hind limb ischemia model. EPC dysfunction was confirmed in a homogenous population of patients with type 1 diabetes mellitus and a microarray study was preformed to identify dysregulated genes. Notably, the secreted proangiogenic protein osteopontin (OPN) was significantly downregulated in diabetic EPCs. Furthermore, OPN-deficient mice showed impaired recovery following hind limb ischemia, suggesting a critical role for OPN in postnatal neovascularization. EPCs isolated from OPN KO mice showed decreased ability to adhere to endothelial cells as well as impaired angiogenic potential. However, this dysfunction was reversed upon exposure to recombinant OPN, suggesting that OPN may act in an autocrine manner on EPCs. Indeed, exposure of OPN knockout (KO) EPCs to OPN was sufficient to induce the secretion of angiogenic proteins (IL-6, TGF-α, and FGF-α). We also demonstrated that vascular regeneration following hind limb ischemia in OPN KO mice was significantly improved upon injection of EPCs preexposed to OPN. We concluded that OPN acts in an autocrine manner on EPCs to induce the secretion of angiogenic proteins, thereby playing a critical role in EPC-mediated neovascularization. Modification of cells by exposure to OPN may improve the efficacy of autologous EPC transplantation via the enhanced secretion of angiogenic proteins.

Antitumor activity of a small-molecule inhibitor of the histone kinase Haspin

The approval of histone deacetylase inhibitors for treatment of lymphoma subtypes has positioned histone modifications as potential targets for the development of new classes of anticancer drugs. Histones also undergo phosphorylation events, and Haspin is a protein kinase the only known target of which is phosphorylation of histone H3 at Thr3 residue (H3T3ph), which is necessary for mitosis progression. Mitotic kinases can be blocked by small drugs and several clinical trials are underway with these agents. As occurs with Aurora kinase inhibitors, Haspin might be an optimal candidate for the pharmacological development of these compounds. A high-throughput screening for Haspin inhibitors identified the CHR-6494 compound as being one promising such agent. We demonstrate that CHR-6494 reduces H3T3ph levels in a dose-dependent manner and causes a mitotic catastrophe characterized by metaphase misalignment, spindle abnormalities and centrosome amplification. From the cellular standpoint, the identified small-molecule Haspin inhibitor causes arrest in G2/M and subsequently apoptosis. Importantly, ex vivo assays also demonstrate its anti-angiogenetic features; in vivo, it shows antitumor potential in xenografted nude mice without any observed toxicity. Thus, CHR-6494 is a first-in-class Haspin inhibitor with a wide spectrum of anticancer effects that merits further preclinical research as a new member of the family of mitotic kinase inhibitors.

Field trial of a synthetic tsetse-repellent technology developed for the control of bovine trypanosomosis in Kenya

We conducted a field trial among Maasai cattle-keepers in Nkuruman and Nkineji areas of Kenya to evaluate the effectiveness of a synthetic tsetse-repellent technology developed for the control of trypanosomosis in cattle. The technology was a repellent (2-methoxy 4-methylphenol) emitted from dispensers attached to collars worn by cattle. Treatment was allocated at the herd level to ensure adequate protection of all the animals in a herd, with measurements of effectiveness conducted at the individual-animal level. The trial began in April 2005 and ran for 16 months including a baseline phase of 4 months. We recruited 12 herds in each area using a restricted random-sampling technique and distributed them equally into intervention (repellent) and control groups. Sample size was determined using a formal power calculation. Effectiveness or minimal worthwhile difference was defined as a 50% reduction in the incidence of trypanosome infection in the treated versus control group (effectiveness below which the technology was considered by experts as not viable compared to existing control techniques). All the animals in the recruited herds were screened monthly (buffy-coat technique) for trypanosome infections. The analysis followed the principle of intention-to-treat by which subjects are analysed according to their initial treatment assignment, regardless of the mechanical performance of the device. Crude and adjusted effects of the technology were 23% (p<0.001) and 18% (p=0.08) reduction in the infection incidence in the treatment compared to the control groups, respectively. The impact of the technology estimated in this study did not achieve the threshold of 50% reduction in the trypanosome infection incidence set a priori to indicate effectiveness (p<0.001). We therefore concluded that the prototype repellent technology package was not sufficiently effective in reducing trypanosome infection incidence under natural tsetse challenge to merit commercial development.

Expert and novice performance in solving physics problems

Although a sizable body of knowledge is prerequisite to expert skill, that knowledge must be indexed by large numbers of patterns that, on recognition, guide the expert in a fraction of a second to relevant parts of the knowledge store. The knowledge forms complex schemata that can guide a problem's interpretation and solution and that constitute a large part of what we call physical intuition.

Smart investments in sustainable food production: revisiting mixed crop-livestock systems

Farmers in mixed crop-livestock systems produce about half of the world's food. In small holdings around the world, livestock are reared mostly on grass, browse, and nonfood biomass from maize, millet, rice, and sorghum crops and in their turn supply manure and traction for future crops. Animals act as insurance against hard times and supply farmers with a source of regular income from sales of milk, eggs, and other products. Thus, faced with population growth and climate change, small-holder farmers should be the first target for policies to intensify production by carefully managed inputs of fertilizer, water, and feed to minimize waste and environmental impact, supported by improved access to markets, new varieties, and technologies.

Using the gene ontology to enrich biological pathways

Most current approaches to automatic pathway generation are based on a reverse engineering approach in which pathway plausibility is solely derived from gene expression data and not independently validated. Alternative approaches use prior biological knowledge to validate automatically inferred pathways, but the prior knowledge is usually not sufficiently tuned to the pathology of focus. We present a novel pathway generation approach that combines insights from the reverse engineering and knowledge-based approaches to increase the biological plausibility of automatically generated regulatory networks and describe an application of this approach to transcriptional data from a mouse model of neuroprotection during stroke.

A network inference workflow applied to virulence-related processes in Salmonella typhimurium

Inference of the structure of mRNA transcriptional regulatory networks, protein regulatory or interaction networks, and protein activation/inactivation-based signal transduction networks are critical tasks in systems biology. In this article we discuss a workflow for the reconstruction of parts of the transcriptional regulatory network of the pathogenic bacterium Salmonella typhimurium based on the information contained in sets of microarray gene-expression data now available for that organism and describe our results obtained by following this workflow. The primary tool is one of the network-inference algorithms deployed in the Software Environment for Biological Network Inference (SEBINI). Specifically, we selected the algorithm called context likelihood of relatedness (CLR), which uses the mutual information contained in the gene-expression data to infer regulatory connections. The associated analysis pipeline automatically stores the inferred edges from the CLR runs within SEBINI and, upon request, transfers the inferred edges into either Cytoscape or the plug-in Collective Analysis of Biological Interaction Networks (CABIN) tool for further postanalysis of the inferred regulatory edges. The following article presents the outcome of this workflow, as well as the protocols followed for microarray data collection, data cleansing, and network inference. Our analysis revealed several interesting interactions, functional groups, metabolic pathways, and regulons in S. typhimurium.

Prediction and integration of regulatory and protein-protein interactions

Knowledge of transcriptional regulatory interactions (TRIs) is essential for exploring functional genomics and systems biology in any organism. While several results from genome-wide analysis of transcriptional regulatory networks are available, they are limited to model organisms such as yeast ( 1 ) and worm ( 2 ). Beyond these networks, experiments on TRIs study only individual genes and proteins of specific interest. In this chapter, we present a method for the integration of various data sets to predict TRIs for 54 organisms in the Bioverse ( 3 ). We describe how to compile and handle various formats and identifiers of data sets from different sources and how to predict TRIs using a homology-based approach, utilizing the compiled data sets. Integrated data sets include experimentally verified TRIs, binding sites of transcription factors, promoter sequences, protein subcellular localization, and protein families. Predicted TRIs expand the networks of gene regulation for a large number of organisms. The integration of experimentally verified and predicted TRIs with other known protein-protein interactions (PPIs) gives insight into specific pathways, network motifs, and the topological dynamics of an integrated network with gene expression under different conditions, essential for exploring functional genomics and systems biology.

INTEGRATOR: interactive graphical search of large protein interactomes over the Web

Background

The rapid growth of protein interactome data has elevated the necessity and importance of network analysis tools. However, unlike pure text data, network search spaces are of exponential complexity. This poses special challenges for storing, searching, and navigating this data efficiently. Moreover, development of effective web interfaces has been difficult.

Results

We present Integrator, a web-integrated graphical search tool for protein-protein interaction networks across 50+ genomes.

Conclusion

Integrator provides single and multiple protein searches of the Bioverse database containing experimentally-derived and predicted protein-protein interactions. The interface provides animated local network views, rapid subgraph manipulation, and cross-referencing of functional annotations. Integrator is available at .

A heterogeneous population model for contagious bovine pleuropneumonia transmission and control in pastoral communities of East Africa

Pastoral cattle live in highly structured communities characterized by complex contact patterns. The present paper describes a spatially heterogeneous model for the transmission of contagious bovine pleuropneumonia (CBPP) developed specifically for pastoral communities of East Africa. The model is validated against serological data on the prevalence of CBPP infection in several communities of southern Sudan and against livestock owner information on community structure, livestock contact and cattle exchange. The model is used to assess the impact of alternative control strategies including mass and elective vaccination programmes, potential treatment regimes and the combination of vaccination and treatment in a single unified strategy. The results indicate that the eradication of CBPP using mass vaccination with currently available vaccines is unlikely to succeed. On the other hand, elective control programmes based on herd level vaccination, treatment of clinical cases or a combination of both vaccination and treatment enabled individual livestock owners to capture a large benefit in terms of reduced animal-level prevalence and mortality experience. The most promising intervention scenario was a programme which combined the vaccination of healthy animals with treatment of clinical cases.

A model of contagious bovine pleuropneumonia transmission dynamics in East Africa

The dynamics of contagious bovine pleuropneumonia (CBPP) transmission vary widely between livestock production systems. This paper describes the development of a homogeneous, stochastic, compartmental model for CBPP transmission in pastoral herds of East Africa. The model was built using parameter estimates based on data published in the literature and on observations of livestock owners obtained through participatory research. The basic reproduction number for CBPP in southern Sudan was estimated to range from 3.2 to 4.6. The homogeneous model indicates that the critical community size for the persistence of CBPP falls within the typical herd sizes for pastoral communities in East Africa suggesting that individual isolated herds are capable of maintaining infection indefinitely. Vaccination alone with currently available vaccines was unlikely to eradicate the disease.

Origin and evolution of new exons in rodents

Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new genes. Yet to be learned are the ways new exons originate and evolve, and how often new exons appear. To address these questions, we identified 2695 newly evolved exons in the mouse and rat by comparing the expressed sequences of 12,419 orthologous genes between human and mouse, using 743,856 pig ESTs as the outgroup. The new exon origination rate is about 2.71 x 10(-3) per gene per million years. These new exons have markedly accelerated rates both of nonsynonymous substitutions and of insertions/deletions (indels). A much higher proportion of new exons have K(a)/K(s) ratios >1 (where K(a) is the nonsynonymous substitution rate and K(s) is the synonymous substitution rate) than do the old exons shared by human and mouse, implying a role of positive selection in the rapid evolution. The majority of these new exons have sequences unique in the genome, suggesting that most new exons might originate through "exonization" of intronic sequences. Most of the new exons appear to be alternative exons that are expressed at low levels.

BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes

We have made a number of enhancements to the previously described Bioverse web server and computational biology framework (). In this update, we provide an overview of the new features available that include: (i) expansion of the number of organisms represented in the Bioverse and addition of new data sources and novel prediction techniques not available elsewhere, including network-based annotation; (ii) reengineering the database backend and supporting code resulting in significant speed, search and ease-of use improvements; and (iii) creation of a stateful and dynamic web application frontend to improve interface speed and usability. Integrated Java-based applications also allow dynamic visualization of real and predicted protein interaction networks.

Functional annotation from predicted protein interaction networks

MOTIVATION

Progress in large-scale experimental determination of protein-protein interaction networks for several organisms has resulted in innovative methods of functional inference based on network connectivity. However, the amount of effort and resources required for the elucidation of experimental protein interaction networks is prohibitive. Previously we, and others, have developed techniques to predict protein interactions for novel genomes using computational methods and data generated from other genomes.

RESULTS

We evaluated the performance of a network-based functional annotation method that makes use of our predicted protein interaction networks. We show that this approach performs equally well on experimentally derived and predicted interaction networks, for both manually and computationally assigned annotations. We applied the method to predicted protein interaction networks for over 50 organisms from all domains of life, providing annotations for many previously unannotated proteins and verifying existing low-confidence annotations.

AVAILABILITY

Functional predictions for over 50 organisms are available at http://bioverse.compbio.washington.edu and datasets used for analysis at http://data.compbio.washington.edu/misc/downloads/nannotation_data/.

SUPPLEMENTARY INFORMATION

A supplemental appendix gives additional details not in the main text. (http://data.compbio.washington.edu/misc/downloads/nannotation_data/supplement.pdf).

A model of lineage-1 and lineage-2 rinderpest virus transmission in pastoral areas of East Africa

The development of a stochastic, state-transition model of rinderpest transmission dynamics is described using parameter estimates obtained from both laboratory and participatory research. Using serological data, the basic reproduction numbers for lineage-1 rinderpest virus in southern Sudan and for lineage-2 rinderpest virus in Somali livestock were estimated as 4.4 and between 1.2 and 1.9, respectively. The model predictions for the inter-epidemic period in Sudan and Somalia (1.2 and 4.2 years, respectively) were in agreement with analysis of livestock-owner reports (1-2 years and 5 years, respectively).