Iterative optimization of high-affinity proteases inhibitors using phage display. 1. Plasmin

We generated a series of libraries having variants of the first Kunitz domain of human lipoprotein-associated coagulation inhibitor (LACI-D1, also known as tissue-factor pathway inhibitor-I) displayed on bacteriophage M13 as pIII-fusions. We varied LACI-DI iteratively in two regions: the P1 region (positions 10-21) and the "second loop", (positions 31-39), which together form one end of the domain. Display-phage library Lib#1 allows 31 200 amino-acid sequences in P1 region (residues 13, 16-19). Preliminary, we screened Lib#1 against human plasmin (PLA, EC 3.4.21.7) immobolized on agarose to enrich for phage displaying variants with PLA affinity. We introduced a 1600-fold increase in second-loop diversity (residues 31, 32, 34, 39) into the population of selectants from Lib#1, yielding Lib#2. Lib#2 (allowing approximately 50 million amino-acid sequences) was screened against PLA-agarose to isolate highest affinity binders. Protein EPI-P211, derived from the best isolate of Lib#2, inhibits PLA with Ki = 2 nM (at least 500-fold better than LACI-D1) and with high specificity. We used amino-acid sequences of PLA-binding selectants to design a PLA-biased library (Lib#3) which we screened against PLA. The protein EPI-P302 (derived from the best binder obtained from Lib#3) has Ki for PLA inhibition of 87 pM, which is 25-fold better than the first-round best binder and > or = 12 500-fold better than LACI-D1. EPI-P302 also shows very high specificity for PLA vs other human proteases and is resistant to inactivation by oxidants and extremes of temperature or pH. Thus, one can use selectants from one library to design target-tailored combinatorial libraries and obtain quite stable, highly specific, very high-affinity binding molecules while maintaining an essentially human framework.     

Mentor modeling: the internalization of modeled professional thinking in an epistemic game

Players of epistemic games – computer games that simulate professional practica – have been shown to develop epistemic frames: a profession's particular way of seeing and solving problems. This study examined the interactions between players and mentors in one epistemic game, Urban Science. Using a new method called epistemic network analysis, we explored how players develop epistemic frames through playing the game. Our results show that players imitate and internalize the professional way of thinking that the mentors model, suggesting that mentors can effectively model epistemic frames, and that epistemic network analysis is a useful way to chart the development of learning through mentoring relationships.     

Internet traffic measurement

The Internet's evolution over the past 30 years (1971-2001), has been accompanied by the development of various network applications. These applications range from early text-based utilities such as file transfer and remote login to the more recent advent of the Web, electronic commerce, and multimedia streaming. For most users, the Internet is simply a connection to these applications. They are shielded from the details of how the Internet works, through the-information-hiding principles of the Internet protocol stack, which dictates how user-level data is transformed into network packets for transport across the network and put back together for delivery at the receiving application. For many networking researchers however, the protocols themselves are of interest. Using specialized network measurement hardware or software, these researchers collect information about network packet transmissions. With detailed packet-level measurements and some knowledge of the IP stack, they can use reverse engineering to gather significant information about both the application structure and user behavior, which can be applied to a variety of tasks like network troubleshooting, protocol debugging, workload characterization, and performance evaluation and improvement. Traffic measurement technologies have scaled up to provide insight into fundamental behavior properties of the Internet, its protocols, and its users. The author introduces the tools and methods for measuring Internet traffic and offers highlights from research results     

Deriving engineering software from requirements

With the advent of intelligent computer aided design systems, companies such as Boeing are embarking on an era in which core competitive engineering knowledge and design rationale is being encoded in software systems. The promise of this technology is that this knowledge can be leveraged across many different designs, product families, and even different uses (e.g., generative process planning for manufacturing). The current state of the practice attempts to achieve this goal through the reuse of software components. A fundamental problem with this approach to knowledge sharing and reuse is that what we are trying to reuse is software—the end artifact in a long and complicated process that goes from requirement specifications, through a process of design, to implementations. Knowledge sharing and reuse can not easily and uniformly occur at the software level. So what can be done as an alternative? This paper describes a theory, methodology, language, and tool for the semi-automatic development and maintenance of engineering software from requirement specifications. In essence, this paradigm for software development and maintenance is one that explicitly captures requirement specifications, designs, implementations, and the refinement processes that lead from requirements all the way down to software. By recording this entire refinement history, we stand a better chance of leveraging knowledge for different uses.     

The course of geriatric depression with "reversible dementia": a controlled study

OBJECTIVE: The goals of this longitudinal investigation were 1) to study the rate of development of irreversible dementia in elderly depressed patients with a dementia syndrome that subsided after improvement of depression and 2) to compare it with that of depressed, never-demented patients. METHOD: The subjects were 57 elderly patients consecutively hospitalized for major depression. At entry into the study, 23 subjects also met criteria for "reversible dementia," while 34 were without dementia. After a systematic clinical evaluation, the subjects were followed up at approximately yearly intervals for an average of 33.8 months. RESULTS: Irreversible dementia developed significantly more frequently in the depressed group with reversible dementia (43%) than in the group with depression alone (12%). Survival analysis showed that the group with reversible dementia had a 4.69-times higher chance of having developed dementia at follow-up than the patients with depression alone. No clinical characteristics at entry into the study were found to discriminate the subjects who developed irreversible dementia during the follow-up period from those who remained nondemented. CONCLUSIONS: These findings suggest that geriatric depression with reversible dementia is a clinical entity that includes a group of patients with early-stage dementing disorders. Therefore, identification of a reversible dementia syndrome is an indication for a thorough diagnostic workup and frequent follow-ups in order to identify treatable neurological disorders.     

Just how insoluble are monoterpenes?

Prior generalizations about the ecological roles of monoterpenes may be misleading if based on the presumed insolubility of monoterpenes in water. We determined the aqueous solubility of 31 biologically active monoterpenes by gas chromatography. While hydrocarbons were of low solubility (< 35 ppm), oxygenated monoterpenes exhibited solubilities one or two orders of magnitude higher, with ranges of 155–6990 ppm for ketones and of 183–1360 ppm for alcohols. Many monoterpenes are phytotoxic in concentrations under 100 ppm, well below the saturated aqueous concentrations of oxygenated monoterpenes. Therefore, even dilute, unsaturated solutions of monoterpenes, occurring naturally in plant tissues and soil solutions, may act as potent biological inhibitors.     

Frequency multiplexed superconducting quantum interference device readout of large bolometer arrays for cosmic microwave background measurements

A technological milestone for experiments employing transition edge sensor bolometers operating at sub-Kelvin temperature is the deployment of detector arrays with 100s-1000s of bolometers. One key technology for such arrays is readout multiplexing: the ability to read out many sensors simultaneously on the same set of wires. This paper describes a frequency-domain multiplexed readout system which has been developed for and deployed on the APEX-SZ and South Pole Telescope millimeter wavelength receivers. In this system, the detector array is divided into modules of seven detectors, and each bolometer within the module is biased with a unique ～MHz sinusoidal carrier such that the individual bolometer signals are well separated in frequency space. The currents from all bolometers in a module are summed together and pre-amplified with superconducting quantum interference devices operating at 4 K. Room temperature electronics demodulate the carriers to recover the bolometer signals, which are digitized separately and stored to disk. This readout system contributes little noise relative to the detectors themselves, is remarkably insensitive to unwanted microphonic excitations, and provides a technology pathway to multiplexing larger numbers of sensors.     

Bias in bacteriophage morphological classification by transmission electron microscopy due to breakage or loss of tail structures

Virtually every study that has used transmission electron microscopy (TEM) to estimate viral diversity has acknowledged that loss of phage tails during sample preparation may have biased the results. However, the magnitude of this potential bias has yet to be constrained. To characterize biases in virus morphological diversity due to tail loss, six phage strains representing the order Caudovirales were inoculated into sterile sediments and soils. Phage particles were then extracted using standard methods. Morphologies of extracted phage particles were compared to those of unmanipulated control samples to determine the extent of tail breakage incurred by extraction procedures. Podoviruses exhibited the smallest frequency of tail loss during extraction (1.2-14%), myoviruses were moderately susceptible to tail breakage (15-40%), and siphoviruses were highly susceptible (32-76%). Thus, TEM assessments of viral diversity in soils or sediments by distribution of tail morphologies may be biased toward podoviruses and virions lacking tails, while simultaneously underestimating the abundance of siphoviruses. However, since the majority of viral capsids observed under TEM were intact, estimates of viral diversity based on the distribution of capsid diameters may provide a more reliable basis for morphological comparisons within and across ecosystems.     

The implications of cross-regional differences for the design of In-vehicle Information Systems: a comparison of Australian and Chinese drivers

The increasing global distribution of automobiles necessitates that the design of In-vehicle Information Systems (IVIS) is appropriate for the regions to which they are being exported. Differences between regions such as culture, environment and traffic context can influence the needs, usability and acceptance of IVIS. This paper describes two studies aimed at identifying regional differences in IVIS design needs and preferences across drivers from Australia and China to determine the impact of any differences on IVIS design. Using a questionnaire and interaction clinics, the influence of cultural values and driving patterns on drivers' preferences for, and comprehension of, surface- and interaction-level aspects of IVIS interfaces was explored. Similarities and differences were found between the two regional groups in terms of preferences for IVIS input control types and labels and in the comprehension of IVIS functions. Specifically, Chinese drivers preferred symbols and Chinese characters over English words and were less successful (compared to Australians) at comprehending English abbreviations, particularly for complex IVIS functions. Implications in terms of the current trend to introduce Western-styled interfaces into other regions with little or no adaptation are discussed.