bluuebunny/crossref_metadata_2025 huggingface dataset:
Explanation of IceCube spectrum with ν → 3ν neutrino splitting in a ν2HDM model
Authors: Mohanty Subhendra , Sadhukhan Soumya
Published: October 2018

Abstract

A single power law flux spectrum of high energy neutrinos does not adequately explain the entire 60 TeV to 10 PeV event spectrum observed at IceCube, specially the excess of PeV events and the lack of Glashow resonance events expected at 6.3 PeV cannot be simultaneously explained by a single power law source neutrino flux. Here we consider a model of neutrino splitting ν → 3ν over cosmological distances. Starting from a single power-law spectrum expected from the astrophysical sources, we show that by adjusting the decay length and spectral index one can give a better fit to the observed IceCube events over the entire 1 TeV-6 PeV, compared to that from a single power spectrum. For ν → 3ν neutrino splitting, the flavor ratios of the daughter neutrinos are different from the standard oscillation or invisible decay cases and can be used as a test of this scenario. We propose a ν2HDM where a light Higgs (∼0.1 eV) mediates neutrino splitting via a one-loop box diagram. The split in the masses of the scalars in the doublet gives a large contribution to the oblique T parameter which is severely constrained. This constraint from the S,T,U oblique parameters can be evaded by the introduction of an extra vector lepton doublet and with mass ∼ 200 GeV.
The Identification of Malnutrition in Heart Failure Patients
Authors: Nicol Sandra M. , Carroll Diane L. , Homeyer Carol M. , Zamagni Colleen M.
Published: October 2018

Heart failure (HF) is the only cardiovascular disease that is increasing in incidence, prevalence, and mortality. One of the major complications associated with HF is malnutrition. Fluctuations due to fluid make weight measurement an inaccurate parameter to identify malnutrition. Therefore, the purpose of this study is to assess clinical parameters that could assist in the recognition of malnutrition in HF patients. A convenience sample of 50 HF patients had anthropometric measurements, a review of their serum chemistry levels, a collection of standard hemodynamic measures plus electrical bioimpedance, and, each subject completed a gastrointestinal symptoms assessment with two meals. Eighteen (36%) subjects were classified as malnourished based on the selected criteria of a serum albumin <3.0 g/dl and/or being less than 90% of ideal body weight. Within this sample of malnourished subjects, 44% of the subjects were found to be obese based on skinfold measurement. A comparison between malnourished/not malnourished groups found that the mean heart rate was higher in the malnourished group (85 vs. 73 beats/min; P<0.017). There were no other parameters that differentiated between these groups. These results demonstrate the need for further research to identify predictive clinical parameters for malnutrition in this vulnerable population.
Self-Reported Behavioural and Medical Changes in Women after Their First Myocardial Infarction: A 4-Year Comparison Between Participation and Non-Participation in a Cardiac Rehabilitation Programme
Authors: Winberg Birgitta , Fridlund Bengt
Published: October 2018

Background: Women's recovery following a myocardial infarction (MI) has not yet been studied in a thorough manner. Aim: Therefore, the aim of this study was to compare women's self-reported behavioural and medical changes, both in those women who voluntarily participated and those women who did not participate in a cardiac rehabilitation programme (CRP). Methods: A non-randomised comparative study design, including pre- (baseline) and post-tests (1 and 4 years after), was implemented in 18 hospitals in Sweden. Consecutively chosen women suffering their first MI ( N=240) completed a questionnaire regarding behavioural and medical factors. Results: At baseline, significant differences existed between the groups regarding time stress (increased in the CRP group) and hypertension (increased in the non-CRP group). The behavioural factors improved, irrespective of CRP participation or not, with the exception of time stress, which was consistently high in the CRP group both 1- and 4-years after the MI. Regarding the medical factors, the significant difference in hypertension disappeared after 1 year. Four years after the MI, the CRP group reported significantly less rehospitalisation and more interventive cardiology compared to the non-CRP group. Conclusion: The women benefited from CRP participation in relation to medical factors, but not at all in relation to behavioural factors. Accordingly, randomised clinical trials are necessary to perform in order to determine the effects of a long-term individual-based supportive CRP, performed by well-educated healthcare professionals.
Normal Fluctuations in Pulmonary Artery Pressures and Cardiac Output in Patients with Severe Left Ventricular Dysfunction
Authors: Moser Debra K. , Frazier Susan K. , Woo Mary A. , Daley Linda K.
Published: October 2018

Background: One barrier to accurate interpretation of changes in hemodynamic pressures and cardiac output is lack of data about what constitutes a normal fluctuation. Few investigators have examined normal fluctuations in these parameters and none have done so in patients with left ventricular dysfunction. Aims: To describe normal fluctuations in pulmonary artery pressures and cardiac output in patients with left ventricular dysfunction. Methods: Hemodynamically stable advanced heart failure patients ( N=39; 55±6 years old; 62% male) with left ventricular dysfunction (mean ejection fraction 22±5%) were studied. Cardiac output and pulmonary artery pressures were measured every 15 min for 2 h. Results: Mean±standard deviation fluctuations were as follows: pulmonary artery systolic pressure=7±4 mmHg; pulmonary artery diastolic pressure=6±3 mmHg; pulmonary capillary wedge pressure=5±3 mmHg; cardiac output=0.7±0.3 l/min. The coefficient of variation for fluctuations in pulmonary artery systolic pressure was 6.7%, in pulmonary artery diastolic pressure was 9.3%, in pulmonary capillary wedge pressure was 9.2%, and in cardiac output was 7.2%. Conclusions: Values that vary <8% for pulmonary artery systolic pressure, <11% for pulmonary artery diastolic pressure, <12% for pulmonary capillary wedge pressure, and <9% for cardiac output from baseline represent normal fluctuations in these parameters in patients with left ventricular dysfunction.
Advancing Parallel Solution Phase Library Synthesis through Efficient Purification, Quantitation, and Characterization Techniques
Authors: Noonan Jeffrey W. , Brown Joe N. , Kershaw Mark T. , Lew Richard M. , Lombardi Christopher J. , Mach Christopher J. , Shaw Kenneth R. , Sogge Scott R. , Virdee Susan
Published: October 2018

Historically, access to large numbers of quality compounds in a parallel solution phase library synthesis environment has been hindered by the inability to rapidly purify, quantitate, and characterize solution phase libraries in an efficient and cost effective manner. At Neurogen Corporation, we overcome these barriers by employing a collection of novel workstations in the High Speed Synthesis (HSS) group that are tightly integrated into our informatics architecture. This approach supports rapid and reliable instrument operation, rapid interpretation of results, and decision analysis for further downstream tasks and processing. Our movement of library samples and data from workstation to workstation facilitates synthesis throughput and the utilization of equipment, creating a cost-effective library production environment.
Evaluation of Automated Cell Culture Incubators
Authors: Triaud Frederique , Clenet Diane-Helene , Cariou Yves , Le Neel Tanguy , Morin Delphine , Truchaud Alain
Published: October 2018

Automated cell culture incubators generally are considered primary components of fully automated cell culture systems, which are able to monitor cell growth without human interaction. This tutorial is focused on automated cell culture incubators. It emphasizes the impact of automation on throughput and environmental controls (temperature, humidity, and CO2) and proposes some basic protocols to check these functions. In addition, it details practical aspects for switching from manual to automated cell culture incubators.
Systems Development Strategy: A Component-Based Approach, the Prototype
Authors: Thakur Dinesh S. , Chen Vincent W. , Leister Kirk J.
Published: October 2018

This presentation provides a concrete example of an application developed using the component-based framework [1]. A sample inventory and control system was developed for the purpose of aliquoting, distributing and tracking biologic molecules in pharmaceutical drug development. This presentation will provide an overview of the workflow involved, a description of the detailed functional implementation of the robotic aliquoting system, and a demonstration of the application with a real world implementation of the component-based framework.
Systems Development Strategy: A Component Based Approach, the Architecture
Authors: Chen Vincent W. , Thakur Dinesh S. , Leister Kirk J.
Published: October 2018

An architecture for building laboratory automation systems was developed using the component-based framework [1]. The requirements to build a flexible and adaptable automation system were exemplified through the architectural design process. Existing tools and technologies facilitated the development of this scalable architecture. Several design patterns were used to model this architecture. The influence of these patterns on systems design and the impact of Unified Modeling Language on component and interface design was explored. Integration of the system components with the peripheral components to build an automated system is discussed with emphasis on run-time configuration and component reuse.
Novel Electrochemiluminescent Assays for Drug Discovery
Authors: Kibbey Maura C. , MacAllan David , Karaszkiewicz James W.
Published: October 2018

IGEN's ORIGEN® technology, which is based on electrochemiluminescence, has been adopted by a number of research and bioanalytical laboratories who have recognized its exquisite sensitivity, high precision, wide dynamic range, and flexibility in formatting a wide variety of applications. IGEN's M-SERIES™ marks the introduction of the second generation of detection systems employing the ORIGEN technology specifically repackaged to address the needs of the high throughput laboratories involved in drug discovery. Assays are formatted without wash steps. Users realize the high performance of a heterogeneous technology with the convenience of a homogeneous format. The M-SERIES platform can address enzymatic assays (kinases, proteases, helicases, etc.), receptor-ligand or protein-protein assays, immunoassays, quantitation of nucleic acids, as well as other applications. Recent assay formats will be explored in detail.
Performance of Low Output Impedance Composite pH Glass Electrodes
Authors: Veress Elisabeta , Végh Peter
Published: October 2018

Low output impedance composite pH sensors were constructed by direct attachment of an impedance converter to laboratory purpose combined pH glass electrodes. The signal was transmitted in analog form by unshielded electric cable. The performance of new and aged composite pH sensors was determined by the multiple-point calibration method. In case of new electrodes, the slope and the response time, as well as the reproducibility, were insignificantly influenced by the converter attached (the mean slope values calculated for the six electrode group studied were 57.80 mV/pH for unmodified electrodes and 57.97 mV/pH for modified electrodes). The electrode response was not affected by the presence of various electromagnetic noise sources or by the input impedance value of the measuring instrument. The slope and the response time of aged sensors were considerably improved using the impedance converter. The response time decreased from about 150–180 sec to about 30 sec and the average slope value increased from 54.94 mV/pH, calculated for unmodified electrodes, to 56.96 mV/pH, for modified electrodes.
The Wiggleometer: Measuring Larval Movement in a 96 Well Format
Authors: Solomon Fredric , Michael Bruce , Hamelin Michel , Smith McHardy
Published: October 2018

There has been relatively little progress in the area of high throughput screening for antiparasitic animal health targets, which involve whole organisms such as Haemonchus contortus and Caenorhabditis elegans. Most assays involve identifying compounds that can paralyze and/or kill the organism. A major impediment has been the lack of instrumentation suitable for automating the read-out of these assays. We have developed an automated reader that makes analysis of antiparasitic animal health assays possible. This reader uses computer vision techniques to determine whether or not there is larval motion in each well. The system has been validated by measuring the dose-response relationships for several nematocidal agents and by examining 1040 wells of H. contortus, with a 94.6%/94% concordance rate with a human reader with less than a 0.3% false negative rate.
Dealing with the Data Deluge in High Throughput Screening
Authors: Skehan Philip
Published: October 2018

Numerical taxonomy and pattern recognition analysis offer powerful tools that can greatly reduce the information burden of multiple-assay screening programs. These methods can be used to rationally design prescreens, identify assays with similar chemical response patterns, select reporter assays for chemical response groups, evaluate drug selectivity, and predict a drug's likely mechanism of action. When combined with assays designed to identify lead compounds with characteristics likely to cause failure at a later and more expensive stage of development, a simple 3-stage primary discovery process consisting of a rational prescreen, reporters, and clinical failure assay can reduce the number of required culture wells by more than 20-fold and can eliminate all but 1–2 drugs per 1,000 tested as leads for further evaluation and development.
The Planning and Establishment of a Sample Preparation Laboratory for Drug Discovery
Authors: Dufresne Claude
Published: October 2018

Nature has always been a productive source of new drugs. With the advent of HTS, it has now become possible to rapidly screen large sample collections. In addition to seeking greater diversity from natural products sources (microorganisms, plants, etc.), fractionation of the crude extracts prior to screening is becoming a more important part of our efforts.

As sample preparation protocols become more involved, automation can help achieve and maintain a desired sample throughput. To address the needs of our screening program, two robotic systems were designed.

The first system processes crude extracts all the way to 96-well plates, containing solutions suitable for screening in biological and biochemical assays. The system can dissolve crude extracts, fractionate them on SPE cartridges, dry and weigh each fraction, redissolve them to a known concentration, and prepare mother plates. The second system replicates mother plates into a number of daughter plates.
Finding the Discrepancy of MRI Images Using the Second Moment and Geometric Comparison Techniques
Authors: Su Ching-Liang
Published: October 2018

This research investigates the technique of image subtraction to find the discrepancy between healthy and illness MRI images. The technique developed in this research moves the healthy MRI image to overlap with the illness MRI image. Then, the two MRI images are aligned to the same orientation. After the healthy MRI image is overlapped with the illness MRI image, the illness MRI image is subtracted from the healthy MRI image. If there is discrepancy in the illness MRI image after the image subtraction, the discrepancy will remain in the subtracted result. The machine does the entire inspection automatically. There is no further human effort involved. The technique developed in this research can accurately find the discrepancy between healthy and illness images. This paper explains the method using the second moment to find the orientations of the MRI images. Using the orientations of the MRI images, the healthy MRI image and the illness MRI image can be aligned to the same orientation. The detailed process of image rotation is addressed in this paper.
The Incredibly Shrinking Laboratory Reactions, Separations and Detections
Authors: Sanders Giles H.W. , Manz Andreas
Published: October 2018

Microfluidic systems are developing in application and importance in many aspects of chemistry. This short review aims to provide a simple introduction to some of the concepts and instrumentation involved in this field. In particular, a number of systems for reactions, detections and analysis that have arisen from the research of our group are illustrated.
Tools for Analyzing Microarray Expression Data
Authors: Grewal Anoop , Conway Andrew
Published: October 2018

Microarray technologies have emerged as key tools for genomic expression analysis for the purposes of studying disease states, identifying drug targets, and profiling time-, tissue- or stage-dependent changes. The resulting volume of data generated necessitates the use of bioinformatics tools to find interesting gene expression patterns, to identify statistically significant changes across experiments, and to provide additional tools relevant to data mining.

We have developed a comprehensive workbench solution, GeneSpring™, which (1) comes with an intuitive interface incorporating organized file management, (2) handles data from multiple array formats, (3) includes multiple data display formats, (4) includes a suite of statistical clustering tools, and (5) incorporates automated annotation and cross-referencing.

We will discuss the set of algorithms collectively designed to facilitate gene function identification from large scale genomic expression experiments.
Software Implementation of Biological Repository for Human Genetic Material
Authors: Graves B. Sean , Mifflin Theodore AE , Kell Steve , Gunderson Jim , Geddy Sarah , Felder Robin A.
Published: October 2018

To provide biological specimens for scientific studies, the Medical Automation Research Center (MARC) designed and constructed a large-scale device that emphasizes the use of robotics and automation to integrate many associated laboratory operations. These included analysis, dilution, archival storage, and retrieval of purified human-derived specimens. Designers of automated biological repositories are challenged by complex engineering problems. In this paper, we present an overview of the biological repository (biorepository) and give details of the software architecture.
NetBookingLIMS: Automation of Workflow within Core Genetics Laboratories Using a Novel Internet-Based Information Management System
Authors: Hamoudi Rifat
Published: October 2018

NetBookingLIMS is Internet-based software used for the total automation of workflow within core diagnostic or genetics laboratories. NetBookingLIMS organises all data incoming into the laboratory in a flat file and converts it to a relational database that can be used to generate auditing, billing, troubleshooting and usage reports. Also, it generates instrument compatible data and organises the day-to-day management of the laboratory in an efficient and structured manner. It is written using Perl5 and C and designed to run solely using an Internet browser. NetBookingLIMS software as well as a user manual and documentation are available at http://dcs.bbk.ac.uk/∼ahamo01/nblfrontpage.cgi .
Automated Lead Discovery and Development in HTS Datasets
Authors: Nicolaou Christos A.
Published: October 2018

The analysis of biological screening results has traditionally been a labor intensive process. Scientists familiar with the biological data under investigation would visually inspect the results, evaluate the quality and promise of active data points and identify leads. The introduction and widespread use of high throughput screening systems has increased the size of biological datasets immensely thus pushing the traditional analysis method to its limits. In this presentation we describe a new automated approach that emulates the decision making process of human experts. This approach combines knowledge-based techniques with human expertise to enable rapid identification, characterization and prioritization of lead candidates.
A Fully Automated Process Using a Magnetic Particle Based Kit for Removal of Dye Terminators from Sequencing Reactions
Authors: Spicer Douglas A. , Booth Lisa R. , Hughes Karin A. , Kaiser Robert J. , Springer Amy L.
Published: October 2018

Prolinx,® Inc. of Bothell, WA has developed the RapXtract™ 384 Dye Terminator Removal Kit for full automation of DNA sequencing reaction purification. The RapXtract product line is based upon proprietary superparamagnetic particle technology that eliminates the need for centrifugation, vacuum filtration, or modified primers to achieve purification of sequencing reactions. The kit described here is pre-dispensed in a 384-well microtiter plate and run on the TECAN GENESIS Workstation 150 (Tecan U.S. Inc., Research Triangle Park, NC). This system enables rapid purification of up to 384 sequencing reactions in a single run.

As the completion of the Human Genome Project nears, it is imperative for biotechnology and pharmaceutical companies to increase throughput of DNA sequencing in order to be competitive in the drug discovery and validation process. The “race to market” requires a shift from standard DNA sequencing processes-including DNA sequencing reaction purification-towards complete walk-away automation for all steps.

Existing sequencing reaction purification methods (Table 1) require considerable resources including: plastic and other laboratory consumables; specialized equipment, such as high-speed centrifuges or vacuum filtration apparatus; and labor-intensive protocols requiring large amounts of technician time. As a result, walk-away automation of standard purification methods is difficult and expensive.
Determining Feasibility and Parameter Values for Compound Orders Based on Transfer Amounts, Liquid Handler Capabilities, and Container Volume Capacities
Authors: Russo Mark F. , Hoffman Steven L.
Published: October 2018

An algorithm is described for determining feasibility and calculating parameter values for one or more compound processing orders. Feasibility is determined primarily by applying a series of inequality constraints that result in a valid target concentration range within which orders can be processed. These inequality constraints are obtained from initial compound amounts, source and destination container volume capacities, the liquid handler transfer volume range, and the amount of compound to be processed. If feasible, calculated parameter values include the dilution, transfer and top-off volumes necessary to fulfill the order. Sample code implementing the algorithm is given in Microsoft Visual Basic®d.
Microfluidic Devices Made of Glass
Authors: Freitag A. , Vogel D. , Scholz R. , Dietrich T. R.
Published: October 2018

Mikroglas is a young, innovative and highly-specialized enterprise, which has special know-how in the development of microstructured glass components. Due to its unique properties, glass plays an important role in the field of microtechnology. Most important for many of these new applications are:

• its optical transparency and good fluorescence properties, allowing the user to carry out in-situ-measurements, e.g., to detect products after a chemical reaction directly in the device • its stability at high temperatures so that reactions can be influenced by heating different zones of the device • its chemical resistivity, e.g., to handle aggressive substances • its high electrical resistivity, e.g., to transport liquids by electrophoresis or to carry out electrical measurements • its good biological compatibility which is necessary for medical and biological applications

The process of structuring FOTURAN will be described. With this technology different microfluidic devices have been manufactured. The channels have a width and depth of 50 μm up to 1 mm and a length of 20 mm up to 280 mm. Various parameters have been measured, e. g., the heat exchange and transfer coefficient for pure water as a function of the temperature. Also optical and thermal analysis techniques have been used to characterize the fluidic components. The results combined with advanced computational fluidic simulations lead to new solutions for different tasks.
Laboratory Automation in a Supplemental Newborn Screening Laboratory
Authors: Paszko Christine , Kolva Don , Miller Tom , Ashcraft Paula , Walters Bonnie , Sweetman Larry
Published: October 2018

The Institute of Metabolic Disease performs Supplemental Newborn screening for genetic biochemical abnormalities. A challenge facing many specialized high throughput-screening laboratories is fast, efficient data management, instrument integration, reporting, and invoicing. The Supplemental Screening laboratory operates three tandem mass spectrometry analyzers and screens samples for compounds that are not examined by typical newborn screening laboratories. The Institute of Metabolic Disease implemented NeoMate™ LIMS (Laboratory Information Management System) to streamline sample demographic entry, data entry (manual, for more specialized tests and automated entry from instruments), automatic result reporting, follow-up and invoicing. The Institute consists of six departments which include; Supplemental Screening, Tissue Culture, Molecular Diagnostics, Neuropharmacology, Neurochemistry and Mass Spectrometry. These departments have unique requirements that differed from the high-throughput supplemental screening department. This required a system that offered the flexibility to provide custom interpretations, maintaining patient histories, sample storage, and graphing of patient results. This paper will focus on the process of implementing automation from project initiation, flow charting through software installation, instrument integration, system integration and going live.
Multistep Solution Phase Synthesis of 1,2-Diarylbenzimidazoles on the Trident™System
Authors: Vo Lanchi , Yun Young K. , Wright Peter , Labadie Jeff , Swienty-Busch Juergen
Published: October 2018

High throughput parallel organic synthesis is now a common practice in discovery chemistry research. Argonaut's modular reaction cassette technology is aimed at parallel synthesis of focused small molecule libraries. The Trident™ automated platform has been designed to perform high throughput organic synthesis using this modular reaction cassette under truly inert conditions and in a robust, reproducible manner. This enables one to generate high quality libraries of small molecules and to access chemistry not normally amenable to automation.

Recently we have introduced a Sample Processing Station (SPS), which enhances the upstream and downstream sample handling capabilities of the Trident™ platform. Enhanced software capabilities also provide the Trident™ synthesizer with powerful reaction development and optimization capabilities. Application of this technology in the synthesis of a small library of 1,2-diarylbenzimidazoles using solution-phase chemistry is presented. A number of product purification and isolation protocols using polymer-bound scavengers are discussed.
Clinical Biochemistry Automation a Report from a UK District General Hospital
Authors: Frowen Colin , Firth Gary
Published: October 2018

We describe the planning, selection and implementation of an advanced clinical analysis automated system into a United Kingdom National Health Service District General Hospital.
A Novel Three-Dimensional Hydrogel-Based Microarray Platform
Authors: Gurevitch Douglas , Dongs X. Fan , Pircher Tony J. , Matsumoto Sandra S. , Roycroft Pat , Tsinberg Pavel , Falcovitz Yehudit H. , Hahn Soonkap
Published: October 2018

Three dimensional (3D) microarrays utilizing hydrogel matrixes are becoming increasingly attractive as a desired format for bio-analysis. These materials offer significant advantages as a scaffolding for capture agents over more conventional two dimensional (2D) printed formats in both captures per site and the ability to provide an environment more closely resembling that of a free solution. Biocept has developed a flexible three dimensional polyethylene glycol (PEG) polymer based platform suitable for a variety of biological assays. This novel approach is simple, biocompatible and provides a high degree of reproducibility and very low variability in the final array.
The Use of Flying Null Technology in the Tracking of Labware in Laboratory Automation
Authors: Karsten Robert P
Published: October 2018

This paper examines the merit of tracking and tracing Labware in laboratory automation. It will review and assess the existing technologies for tracking and tracing Labware in the HTS environment. Finally it will conclude with a description and analysis of Flying Null technology and its application in tracking and tracing in Laboratory Automation.
A Cross-Functional Team Approach to Implementing and Managing Laboratory Automation in the Quality Control Laboratory
Authors: Reilly Timothy
Published: October 2018

Poorly defined project goals and an inadequate infrastructure have hindered previous attempts to initiate automation projects in the Novartis Quality Control laboratory. This haphazard approach has been replaced with well-defined project expectations and agreement among the functional groups that make up the project infrastructure to aggressively support the automation project goals.
Optimizing Reaction Conditions of the NanoOrange® Protein Quantitation Method for Use with Microplate-based Automation
Authors: Silberblatt Sarah , Felder Robin A. , Mifflin Theodore E.
Published: October 2018

Because of the rapidly expanding need for higher sample throughput in drug discovery, automation of corresponding biochemical analyses is desirable. In particular, automation of protein quantitation is crucial since its results are used extensively. Recently, a single-reagent fluorescent protein quantitation method (NanoOrange®) with attractive performance attributes has become available. While it can potentially be automated with liquid handling workstations, several of this method's reaction parameters need to be optimized.

We studied the time and a temperature dependence of the NanoOrange protein quantitation reaction in ninety-six well black microplates using either a temperature-regulated hot block or a microwave oven as heat sources. Fluorescence of the NanoOrange reaction was quantified with a multimode microplate spectral scanner.

Time-dependent heating profiles of filled microplates placed on hot blocks at fixed temperatures (45, 55, 65, 75, and 95°C) revealed temperature differences of 4–7°C cooler for the outside wells compared to the inner wells, however the maximum well temperature did not exceed 65°C. Similar time-temperature studies of microwave-heated microplates revealed an equilibrium temperature of 45–49°C that was 10–16°C lower than microplates that were block heated.

The bovine serum albumin (BSA): NanoOrange standard curves created using a hot block increased in slope from 45°C to 55°C, but then remained constant from 65 to 85°C. Fluorescence of the BSA: NanoOrange standard curve created using a microwave oven was about half the magnitude of the hot block-derived curves, possible reflecting a lower energy transfer rate of the microwave oven. We conclude that the NanoOrange protein quantitation method can be automated if a microplate-compatible hot block with a 65–85°C surface can heat the microplate for minimum of 15 min prior to quantifying the reaction's fluorescence.
An Optical Readout Scheme Providing High Spatial Resolution for the Evaluation of Combinatorial Libraries on Optical Fibers
Authors: Prince Barry J. , Schwabacher Alan W. , Geissinger Peter
Published: October 2018

We have developed a novel method for combinatorial chemistry that allows for fully parallel synthesis and full library analysis. The key feature is the use of linear supports for synthesis, where the position of a compound along the support encodes its synthetic history. Use of an optical fiber as the linear support allows for the optical evaluation of libraries: the location of an emitting fluorophore can be determined using fluorescent optical time domain reflectometry. We have demonstrated that limitations on the spatial resolution imposed by the fluorescence lifetimes are overcome by using a second fiber as an optical delay.
Automation of Chemical Reaction Kinetics and Product Distribution Studies in Pharmaceutical Development
Authors: Fermier Adam M. , Oyler Alan R. , Armstrong Barbara L. , Weber Bruce A. , Rodríguez Ramón L. , Weber James V. , Nalasco James A.
Published: October 2018

An automated instrument was designed and constructed to facilitate the performance of pharmaceutical degradation studies. A brief theoretical background on degradation kinetics is given to rationalize the design of the instrument and representative data are provided to illustrate its successful application. This system was found to be capable of conducting multiple simultaneous isothermal and nonisothermal kinetic studies with user-defined temperature profiles, sampling periods, and data logging.
HTS Automation Study: Results from a 2001 Survey of the Current vs. Desired State of HTS Automation
Authors: Hamilton Steven D.
Published: October 2018

A survey of directors of screening organizations was conducted in 2001 to evaluate their perceptions of the current vs. desired state of high-throughput screening (HTS) automation. The survey encompassed attributes such as automation flexibility, throughput and operation. These and other automation attributes were ranked based on importance to the respondent and/or the limitations these attributes imposed on the screening organization.
Transferring Industrial Automation Technology to the Laboratory
Authors: Harding David , Bradford David , Brown Gavin
Published: October 2018

Over the past few years, there has been much discussion about transferring industrial technology to laboratories. While it is easy to look at the superficial similarities, it is more important to examine the different requirements of different industries. In this way, it is possible to identify the technologies and techniques that can be successfully transferred to the laboratory to improve performance.

This paper takes three very different industries — the bakery, High Throughput Screening (HTS) and mobile phone assembly and examines their different requirements. These industries have been selected from among the many sectors where the RTS Group operates — thus allowing real data from a number of situations to be used.

One of the most important areas in automation design is the relationship between flexibility and throughput. This paper focuses on this relationship and its influence over machine configuration when comparing the requirements of the different industries.
Automation and Control of an Imaging Internal Laser Desorption Fourier Transform Mass Spectrometer (I2LD-FTMS)
Authors: McJunkin Timothy R. , Tremblay Paul L. , Scott Jill R.
Published: October 2018

This paper describes the automation of an imaging internal source laser desorption Fourier transform mass spectrometer (I2LD-FTMS). The I2LD-FTMS consists of a laser-scanning device [Scott and Tremblay, Rev. Sci. Instrum.2002, 73, 1108–1116] that has been integrated with a laboratory-built FTMS using a commercial data acquisition system (ThermoFinnigan FT/MS, Bremen, Germany). A new user interface has been developed in National Instrument's (Austin, Texas) graphical programming language LabVIEW to control the motors of the laser positioning system and the commercial FTMS data acquisition system. A feature of the FTMS software that allows the user to write macros in a scripting language is used creatively to our advantage in creating a mechanism to control the FTMS from outside its graphical user interface. The new user interface also allows the user to configure target locations. Automation of the data analysis along with data display using commercial graphing software is also described.
Automated Purification of DNA from Large Samples: A Study of Effectiveness and Labor Efficiency
Authors: O'Brien Darin P. , Benedict Kristen A. , Morken Nathaniel W. , Heath Ellen M. , Bleecker Eugene R. , Howard Timothy D.
Published: October 2018

Investigations into the underlying genetic contributions to human disease are transitioning from small family-based traditional linkage analyses to large population-based studies designed to identify genetic factors in more complex and common diseases that have the greatest impact on human health. These types of studies have driven the need for larger numbers of samples for analysis and more efficient and effective methods for DNA purification, especially for large samples that provide sufficient quantities of DNA for extensive analysis. The Autopure LS™ Nucleic Acid Purification Instrument, by Gentra Systems, Inc., a platform capable of high-throughput sample purification from large samples, was developed to meet the demands of these large studies. This article presents data demonstrating the equivalency of DNA purified using the Autopure LS automated instrument and the manual method based on the same purification process. In addition, we present data demonstrating the in-lab time savings realized by automating the purification process.
Converting a Protease Assay to a Caliper® Format LabChip System
Authors: Johnson Michael , Li Chuck , Rasnow Brian , Grandsard Peter , Xing Hong , Fields Angelica
Published: October 2018

The push for higher throughput screening coupled with the desire to use smaller volumes of material has sparked the development of new technologies. Caliper Technologies, Corp. (Mountain View, CA) has designed a microfluidics chip with unique properties yet to be fully exploited. The translation from a traditional plate-based assay to a microfluidic chip format has provided insights into assay development, screening data requirements, and the technology itself. Running a screen with this new technology presented challenges in throughput, signal acquisition from slow-conversion enzymes, the provision for a negative control, the translation of a time series into a single data point per compound, reagent adhesion in the channels, and fluid property mismatches. Overcoming these obstacles has resulted in a simple, robust system with significant savings in reagent use. Measures to improve throughput and generalize the system will be discussed.
Cellular Telephone-Aided Real-Time Reporting System for Emergency Laboratory Test Results
Authors: Sugimachi Mitsuhiko , Kawasaki Seiji , Nagumo Fumio , Tadano Jutaro
Published: October 2018

The authors established a system for real-time reporting of clinical laboratory test results utilizing the mailing function of a cellular telephone service. The reporting system is composed of systems for sample transportation and automatic analysis, verification of test results, and reporting of test results. The introduction of the system has completely eliminated time delays at all stages of the laboratory testing process from start of testing to reporting of the test result. This has enabled doctors to receive test results in a timely manner wherever they are and to respond promptly to the patient condition.
Automated High Throughput Purification of BigDye™ Terminator Fluorescent DNA Sequencing Reactions Using Wizard™ MagneSil™ Paramagnetic Particles
Authors: Otto Paul , Larson Brad , Krueger Steve
Published: October 2018

We describe a reagent system and robotic methods for the purification of BigDye™ Terminator sequencing reactions prior to automated fluorescent sequence analysis. The methods use MagneSil™ paramagnetic particles to isolate sequencing extension products from unincorporated dye-labeled terminators and exchanges sequencer loading solution for reaction buffer. Processed samples give usable data that is greater than 98% accurate from primer plus 5–15 bases to over 700 bases. Typical Phred greater than 20 quality scores range from 600 to over 700 bases. This process has been adapted to a number of liquid handling robotic platforms in both 96- and 384-well formats. One method using a single POD Beckman Biomek® FX can process up to four plates in approximately 40 minutes.
The Automatic Metric Monitoring Program
Authors: Schultz Henry , Alexander John , Petersen Jim , Hartmann Thomas , Overland Doug , Gigante Bill , Grandsard Peter
Published: October 2018

Automation of large-scale compound storage, biological and chemical assays, and many other biopharmaceutical R&D processes have prompted the need for immediate and regular determination of equipment performance levels. The Automatic Metric Monitoring Program (AMMP) in Amgen Research is designed to fill this need. Standardized tests are performed at regular intervals with results instantaneously retrieved, analyzed, and stored in a database. Critical information is automatically tracked using control charts allowing immediate notification via e-mail alerts when problems or nonconforming performance is discovered. System usage and errors are automatically compiled with tabulated results provided at regular intervals and e-mail alarms issued for nonconforming operation. AMMP now provides researchers with needed real-time feedback on the performance of their automation systems.
A Demonstration of High-Throughput Electrophoresis
Authors: Wu Hui-Chung , Nguyen Ricky , Goldsborough Mindy , Margalit Ilana , Breed Cindy , Azarani Arezou
Published: October 2018

Automating electrophoresis significantly reduces the time required for loading a large number of samples, increases the speed of electrophoresis analysis, and maximizes the resolution power (clear separation of fragments) of this technique. In addition, automation increases the precision of electrophoresis analysis. Here we demonstrate an automated, high-throughput method of loading 96 samples simultaneously onto an electrophoresis gel, using the Apogent Discoveries Tango™ system and the Invitrogen™ E-Gel® 96 system.
Automated High-Throughput mRNA Selection from Eukaryotic Total RNA
Authors: Fang Xingwang , Willis Roy C. , Siano Michael A. , Quinto-Pozos Manuel , Conrad Richard C.
Published: October 2018

We describe a new technology (patent pending) for high-throughput selection of poly(A)+ RNA from total RNA. A novel binding solution is used to ensure the efficient and specific binding of mRNA to oligo(dT) magnetic beads with high stringency, virtually eliminating the non-specific binding of ribosomal RNA (rRNA) either to oligo(dT) beads or to the poly(A)+ RNA bound to the beads. As quantified by real-time RT-PCR, more than 99% of the rRNA is removed in a single round selection and mRNAs are fully recovered for both highly-expressed (GAPDH) and poorly-expressed (DDPK) genes from a few μg total RNA. The protocol is adaptable to any generic robotic workstation and takes ∼30 minutes to process 96 samples.
Design and Analysis of Microcantilevers for Biosensing Applications
Authors: Zhang Xuan , Yang Mo , Vafai Kambiz , Ozkan Cengiz S.
Published: October 2018

We have analyzed the detection of microcantilevers utilized in biosensing chips. First, the primary deflection due to the chemical reaction between the analyte molecules and the receptor coating, which produces surface stresses on the receptor side is analyzed. Oscillating flow conditions, which are the main source of turbulence in cantilever based biosensing chips, are found to produce substantial deflections in the microcantilever at relatively large frequency of turbulence. Then mechanical design and optimization of piezoresistive cantilevers for biosensing applications is studied. Models are described for predicting the static behavior of cantilevers with elastic and piezoresistive layers. Chemo-mechanical binding forces have been analyzed to understand issues of saturation over the cantilever surface.

Furthermore, the introduction of stress concentration regions during cantilever fabrication has been discussed which greatly enhances the detection sensitivity through increased surface stress, and novel microcantilever assemblies are presented for the first time that can increase the deflection due to chemical reaction. Finally an experiment was made to demonstrate the shift of resonant frequency of cantilever used as biosensor. The relation between resonant frequency shift and the surface stress was analyzed.
Automated Construction of an Open Reading Frame Library from Sinorhizobium meliloti
Authors: Edwards Todd C. , Marsh Amber , Sanders Christina , Albala Joanna S. , Prange Christa K. , Prange Christa K.
Published: October 2018

An automated, high-throughput, open reading frame (ORF) library construction process has been developed. ORFs from genomic DNA of the microbe Sinorhizobium meliloti were amplified by PCR and cloned into the library vector by homologous recombination instead of traditional ligation. From 960 targets, we successfully generated 723 (75.3%) ORFs from the initial PCR. After cloning the successful samples into the library vector, transforming into E. coli and PCR colony screening, 371 (38.6% overall) ORFs were placed into the new library and sequenced. Our prototype library contained 314 (32.7% overall) clones with sequence identity to the Sinorhizobium meliloti genome.
Development of an Automated High-Throughput Analytical Characterization System for Support of a Central Sample Collection Resource
Authors: Choi Bernard K. , Yates Nathan A. , Springer James P. , Schwartz Robert E. , Roberts Andrew
Published: October 2018

Ahigh-throughput analytical characterization system was developed for quality control support of a central sample collection resource. This system utilizes liquid chromatography mass spectrometry with in-house developed data automation applications. Continuous operation of analytical instrumentation is accomplished by fully automating sample submission and report processing functions. Comprehensive analytical information characteristic of quality, chemical, and physical properties (e.g. relative purity, detection sensitivity, LogD) are automatically transferred to an on-line database. The application of this database for detailed quality assessment of a small sample library (ca. 24,000 compounds) is demonstrated.
Two-Color Capillary Electrophoresis with On-Column Excitation and Wave-Guide Based Fluorescent Detection
Authors: Iyer Srinivas , Stark Peter , Olivares José ,   Support: USDOE OBER and the LANL LDRD
Published: October 2018

An optical wave-guide based two-color capillary electrophoresis laser induced fluorescence (CE-LIF) instrument is described. The wave-guide based approach allows for on column excitation and detection with two-color discrimination. The instrument is designed to allow either electrokinetic or hydrodynamic injections. In its present configuration, the attainable limit of detection (LOD, S/N = 3) was 50 × 10−21 moles of fluorescein with a 488-nm excitation source. This study was designed to test the instrument design for applications in protein analyses. Fluorescent dyes with two different wavelengths were simultaneously separated and detected as were complexes formed by labeled antibodies to NF'B p65 and cdc2p34. Quantification of both proteins in THP-1 cell lysates performed using this approach illustrates a rapid screening application of this instrument.