Controlling Phalaris Minor in the Indian Rice-Wheat Belt

The ACIAR-managed project CS1/1996/013, Herbicide-resistant weeds of wheat in India and Australia: integrated management, was designed to find a long-term method of control of Phalaris minor, a problem weed of the rice–wheat cropping system of north-western India. By 1993, the weed had developed resistance to isoproturon, a herbicide which had delivered effective weed control for 15 years. The short-term solution, implemented before the ACIAR project commenced, involved identification and registration of a new set of herbicides. But these new herbicides were expensive. To ensure high adoption they needed to be combined with changes in wheat-growing techniques that would provide cost savings to help farmers pay for them. And to avoid the re-emergence of chemical resistance, they needed to be used sparingly as one element in a broader approach to weed management. The project team used these circumstances to field-test and encourage adoption of zero tillage, a technology that agronomists had been advocating for many years, but which had failed to capture the interest of Indian farmers. Zero tillage has the potential to deliver big cost savings. In addition, it provides prospects for yield increases by allowing early sowing of wheat and avoiding soil degradation. Project research established that zero tillage also provided effective weed control with only a moderate reliance on chemicals, making the re-emergence of herbicide resistance remote. We calculate a gain to the Indian economy of around $1800 million in net present value terms over the next 30 years from the adoption of zero tillage to control Phalaris minor infestation in the rice–wheat areas of north-western India. This leads to an extremely high ratio of benefits to project costs. Zero tillage by itself is clearly a profitable technology. It does not need a weed problem to justify its introduction. Without the ACIAR project, zero tillage would have been introduced to the region, though somewhat later than what has occurred. On the assumption that the ACIAR project has advanced the adoption profile of zero tillage by 3 years, we calculate gains that can be attributed to ACIAR’s role of$238 million in net present value terms over the next 30 years. This gain has been achieved with total expenditures on the ACIAR-managed project amounting to only $1.3 million in present values.herbicide-resistant weeds, wheat, weed, India, Australia, integrated management, phalaris minor, rice-wheat cropping systems, chemical resistance, weed management, zero tillage, cost saving, net present economy, high benefits, profitable technology, Agribusiness, Crop Production/Industries, Farm Management, Food Consumption/Nutrition/Food Safety, International Development, Production Economics,

TmaDB: a repository for tissue microarray data

Background: Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical specimens in a single experiment thereby permitting the parallel analysis of molecular alterations ( at the DNA, RNA, or protein level) in thousands of tissue specimens. As a vast quantity of data can be generated in a single TMA experiment a systematic approach is required for the storage and analysis of such data. Description: To analyse TMA output a relational database ( known as TmaDB) has been developed to collate all aspects of information relating to TMAs. These data include the TMA construction protocol, experimental protocol and results from the various immunocytological and histochemical staining experiments including the scanned images for each of the TMA cores. Furthermore the database contains pathological information associated with each of the specimens on the TMA slide, the location of the various TMAs and the individual specimen blocks ( from which cores were taken) in the laboratory and their current status i.e. if they can be sectioned into further slides or if they are exhausted. TmaDB has been designed to incorporate and extend many of the published common data elements and the XML format for TMA experiments and is therefore compatible with the TMA data exchange specifications developed by the Association for Pathology Informatics community. Finally the design of the database is made flexible such that TMA experiments from several types of cancer can be stored in a single database, which incorporates the national minimum data set required for pathology reports supported by the Royal College of Pathologists (UK). Conclusion: TmaDB will provide a comprehensive repository for TMA data such that a large number of results from the numerous immunostaining experiments can be efficiently compared for each of the TMA cores. This will allow a systematic, large-scale comparison of tumour samples to facilitate the identification of gene products of clinical importance such as therapeutic or prognostic markers. In addition this work will contribute to the establishment of a standard for reporting TMA data analogous to MIAME in the description of microarray dat

Association between family history and mismatch repair in colorectal cancer

BACKGROUND AND AIMS: Germline mutations in mismatch repair (MMR) genes cause a greatly increased risk of cancer of the gastrointestinal and female reproductive tracts (hereditary non-polyposis colorectal cancer (HNPCC)). Loss of MMR expression is common in colorectal cancer (CRC) overall. Such loss is assumed to be acquired predominantly, although a population of CRC cases will include individuals with unrecognised MMR mutations. This study examines the association between MMR gene expression and family history of cancer among the CRC population. METHODS: Individuals with CRC were identified from two well characterised populations: (1) consecutive hospital patients (n = 644) and (2) a population based cases series (n = 249). CRC was examined for expression of hMLH1 and hMSH2 using immunohistochemistry, and expression was related to family history using logistic regression. RESULTS: hMLH1 and hMSH2 expression was assessed in 732 CRCs with 8% showing loss of expression. No association was seen overall for hMLH1 or hMSH2 expression and family history of CRC. Loss of hMSH2 was predicted by family history of extracolonic cancer (odds ratio (OR) 5.78 (95% confidence interval (CI) 0.95–35.18)) and family history suggestive of HNPCC (OR 27.84 (95% CI 4.37–177.56)). Loss of hMLH1 was not predicted by family history of extracolonic cancer or a family history suggestive of HNPCC but was for a family history of at least two affected relatives (OR 4.88 (95% CI 1.25–19.03)). CONCLUSIONS: Individuals with hMSH2 deficient CRC in the general population exhibit a family history and other characteristics suggestive of HNPCC, and may carry germline MMR mutations. Loss of hMLH1 is only associated with a strong family history of extracolonic cancer at older ages, suggesting a novel mechanism of susceptibility

Impact of admission screening for methicillin-resistant Staphylococcus aureus on the length of stay in an emergency department.

Preventing and controlling methicillin-resistant Staphylococcus aureus (MRSA) includes early detection and isolation. In the emergency department (ED), such measures have to be balanced with the requirement to treat patients urgently and transfer quickly to an acute hospital bed. We assessed, in a busy and overcrowded ED, the contribution made to a patient\u27s stay by previous MRSA risk group identification and by selective rescreening of those patients who were previously documented in the research hospital as being MRSA positive. Patients with a previous diagnosis of MRSA colonisation were flagged automatically as \u27risk group\u27 (RG) on their arrival in the ED and were compared with \u27non-risk group\u27 (NRG), i.e. not previously demonstrated in the research hospital to be infected or colonised with MRSA. Over an 18 month period, there were 16 456 admissions via the ED, of which 985 (6%) were RG patients. The expected median times to be admitted following a request for a ward bed for NRG and RG patients were 10.4 and 12.9h, respectively. Female sex, age \u3e65 years, and RG status all independently predicted a statistically significantly longer stay in the ED following a request for a hospital bed. We consider that national and local policies for MRSA need to balance the welfare of patients in the ED with the need to comply with best practice, when there are inadequate ED and inpatient isolation facilities. Patients with MRSA requiring emergency admission must have a bed available for them

Leveraging wall-sized high-resolution displays for comparative genomics analyses of copy number variation

The scale of comparative genomics data frequently overwhelms current data visualization methods on conventional (desktop) displays. This paper describes two types of solution that take advantage of wall-sized high-resolution displays (WHirDs), which have orders of magnitude more display real estate (i.e., pixels) than desktop displays. The first allows users to view detailed graphics of copy number variation (CNV) that were output by existing software. A WHirD's resolution allowed a 10× increase in the granularity of bioinformatics output that was feasible for users to visually analyze, and this revealed a pattern that had previously been smoothed out from the underlying data. The second involved interactive visualization software that was innovative because it uses a music score metaphor to lay out CNV data, overcomes a perceptual distortion caused by amplification/deletion thresholds, uses filtering to reduce graphical data overload, and is the first comparative genomics visualization software that is designed to leverage a WHirD's real estate. In a field evaluation, a clinical user discovered a fundamental error in the way their data had been processed, and established confidence in the software by using it to 'find' known genetic patterns in hepatitis C-driven hepatocellular cancer

Equilibrium Simulation of the Slip Coefficient in Nanoscale Pores

Accurate prediction of interfacial slip in nanoscale channels is required by many microfluidic applications. Existing hydrodynamic solutions based on Maxwellian boundary conditions include an empirical parameter that depends on material properties and pore dimensions. This paper presents a derivation of a new expression for the slip coefficient that is not based on the assumptions concerning the details of solid-fluid collisions and whose parameters are obtainable from \textit{equilibrium} simulation. The results for the slip coefficient and flow rates are in good agreement with non-equilibrium molecular dynamics simulation.Comment: 11 pages, 4 figures, submitted to Phys Rev Let