Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes

Human rhinoviruses, the most important etiologic agents of the common cold, are messenger-active single-stranded monocistronic RNA viruses that have evolved a highly complex cascade of proteolytic processing events to control viral gene expression and replication. Most maturation cleavages within the precursor polyprotein are mediated by rhinovirus 3C protease (or its immediate precursor, 3CD), a cysteine protease with a trypsin-like polypeptide fold. High-resolution crystal structures of the enzyme from three viral serotypes have been used for the design and elaboration of 3C protease inhibitors representing different structural and chemical classes. Inhibitors having α,β-unsaturated carbonyl groups combined with peptidyl-binding elements specific for 3C protease undergo a Michael reaction mediated by nucleophilic addition of the enzyme’s catalytic Cys-147, resulting in covalent-bond formation and irreversible inactivation of the viral protease. Direct inhibition of 3C proteolytic activity in virally infected cells treated with these compounds can be inferred from dose-dependent accumulations of viral precursor polyproteins as determined by SDS/PAGE analysis of radiolabeled proteins. Cocrystal-structure-assisted optimization of 3C-protease-directed Michael acceptors has yielded molecules having extremely rapid in vitro inactivation of the viral protease, potent antiviral activity against multiple rhinovirus serotypes and low cellular toxicity. Recently, one compound in this series, AG7088, has entered clinical trials.

Direct Evidence for Rapid Degradation of Bacillus thuringiensis Toxin mRNA as a Cause of Poor Expression in Plants1

It is well established that the expression of Bacillus thuringiensis (B.t.) toxin genes in higher plants is severely limited at the mRNA level, but the cause remains controversial. Elucidating whether mRNA accumulation is limited transcriptionally or posttranscriptionally could contribute to effective gene design as well as provide insights about endogenous plant gene-expression mechanisms. To resolve this controversy, we compared the expression of an A/U-rich wild-type cryIA(c) gene and a G/C-rich synthetic cryIA(c) B.t.-toxin gene under the control of identical 5′ and 3′ flanking sequences. Transcriptional activities of the genes were equal as determined by nuclear run-on transcription assays. In contrast, mRNA half-life measurements demonstrated directly that the wild-type transcript was markedly less stable than that encoded by the synthetic gene. Sequences that limit mRNA accumulation were located at more than one site within the coding region, and some appeared to be recognized in Arabidopsis but not in tobacco (Nicotiana tabacum). These results support previous observations that some A/U-rich sequences can contribute to mRNA instability in plants. Our studies further indicate that some of these sequences may be differentially recognized in tobacco cells and Arabidopsis.

Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE.

We report a general mass spectrometric approach for the rapid identification and characterization of proteins isolated by preparative two-dimensional polyacrylamide gel electrophoresis. This method possesses the inherent power to detect and structurally characterize covalent modifications. Absolute sensitivities of matrix-assisted laser desorption ionization and high-energy collision-induced dissociation tandem mass spectrometry are exploited to determine the mass and sequence of subpicomole sample quantities of tryptic peptides. These data permit mass matching and sequence homology searching of computerized peptide mass and protein sequence data bases for known proteins and design of oligonucleotide probes for cloning unknown proteins. We have identified 11 proteins in lysates of human A375 melanoma cells, including: alpha-enolase, cytokeratin, stathmin, protein disulfide isomerase, tropomyosin, Cu/Zn superoxide dismutase, nucleoside diphosphate kinase A, galaptin, and triosephosphate isomerase. We have characterized several posttranslational modifications and chemical modifications that may result from electrophoresis or subsequent sample processing steps. Detection of comigrating and covalently modified proteins illustrates the necessity of peptide sequencing and the advantages of tandem mass spectrometry to reliably and unambiguously establish the identity of each protein. This technology paves the way for studies of cell-type dependent gene expression and studies of large suites of cellular proteins with unprecedented speed and rigor to provide information complementary to the ongoing Human Genome Project.

Investigating and Understanding Student Learning Outcomes in an Online and Face-to-Face Graduate Level Legal Administration Course: An Embedded Mixed Methods Design

Online education is a new teaching and learning medium with few current guidelines for faculty, administrators or students. Its rapid growth over the last decade has challenged academic institutions to keep up with the demand, while also providing a quality education. Our understanding of the factors that determine quality and effective online learning experiences that lead to student learning outcomes is still evolving. There is a lack of consensus on the effectiveness of online versus face-to-face education in the current research. The U.S. Department of Education conducted a meta-analysis in 2009 and concluded that student-learning outcomes in online courses were equal to and, often times, better than face-to-face traditional courses. Subsequent research has found contradictory findings, and further inquiry is necessary. The purpose of this embedded mixed methods design research study is to further our understanding of the factors that create quality and successful educational outcomes in an online course. To achieve this, the first phase of this study measured and compared learning outcomes in an online and in class graduate-level legal administration course. The second phase of the study entailed interviews with those students in both the online and face-to-face sections to understand their perspectives on the factors contributing to learning outcomes. Six themes emerged from the qualitative findings: convenience, higher order thinking, discussions, professor engagement, professor and student interaction, and face-to-face interaction. Findings from this study indicate the factors students perceive as contributing to learning outcomes in an online course are consistent among all students and are supported in the existing literature. Higher order thinking, however, emerged as a stronger theme than indicated in the current research, and the face-to-face nature of the traditional classroom may be more an issue of familiarity than a factor contributing to learning outcomes. As education continues to reach new heights and developments in technology advance, the factors found to contribute to student learning outcomes will be refined and enhanced. These developments will continue to transform the ways in which we deliver and receive knowledge in both traditional and online classrooms. While there is a growing body of research on online education, the field’s evolution has unsettled earlier findings and posed new areas to investigate.

3D-based reconstruction using growing neural gas landmark: application to rapid prototyping in shoe last manufacturing

Customizing shoe manufacturing is one of the great challenges in the footwear industry. It is a production model change where design adopts not only the main role, but also the main bottleneck. It is therefore necessary to accelerate this process by improving the accuracy of current methods. Rapid prototyping techniques are based on the reuse of manufactured footwear lasts so that they can be modified with CAD systems leading rapidly to new shoe models. In this work, we present a shoe last fast reconstruction method that fits current design and manufacturing processes. The method is based on the scanning of shoe last obtaining sections and establishing a fixed number of landmarks onto those sections to reconstruct the shoe last 3D surface. Automated landmark extraction is accomplished through the use of the self-organizing network, the growing neural gas (GNG), which is able to topographically map the low dimensionality of the network to the high dimensionality of the contour manifold without requiring a priori knowledge of the input space structure. Moreover, our GNG landmark method is tolerant to noise and eliminates outliers. Our method accelerates up to 12 times the surface reconstruction and filtering processes used by the current shoe last design software. The proposed method offers higher accuracy compared with methods with similar efficiency as voxel grid.

Report to the Los Angeles Metropolitan Transit Authority on a monorail rapid transit line for Los Angeles, January 15, 1954.

Part of the illustrative material is fold., part col.

Design Expressions and Dynamic Evaluation of CFST Bridges Subjected to Seismic Hazards

Thesis (Ph.D.)--University of Washington, 2016-06

The mental health country profile: Background, design and use of a systematic method of appraisal

This article describes the construction and use of a systematic structured method of mental health country situation appraisal, in order to help meet the need for conceptual tools to assist planners and policy makers develop and audit policy and implementation strategies. The tool encompasses the key domains of context, needs, resources, provisions and outcomes, and provides a framework for synthesizing key qualitative and quantitative information, flagging up gaps in knowledge, and for reviewing existing policies. It serves as an enabling tool to alert and inform policy makers, professionals and other key stakeholders about important issues which need to be considered in mental health policy development. It provides detailed country specific information in a systematic format, to facilitate global sharing of experiences of mental health reform and strategies between policy makers and other stakeholders. Lastly, it is designed to be a capacity building tool for local stakeholders to enhance situation appraisal, and multisectorial policy development and implementation.

Participatory approach for the identification of dairy industry needs in the design of research, development and extension actions: Australian and Brazilian case studies

In both Australia and Brazil there are rapid changes occurring in the macroenvironment of the dairy industry. These changes are sometimes not noticed in the microenvironment of the farm, due to the labour-intensive nature of family farms, and the traditionally weak links between production and marketing. Trends in the external environment need to be discussed in a cooperative framework, to plan integrated actions for the dairy community as a whole and to demand actions from research, development and extension (R, D & E). This paper reviews the evolution of R, D & E in terms of paradigms and approaches, the present strategies used to identify dairy industry needs in Australia and Brazil, and presents a participatory strategy to design R, D & E actions for both countries. The strategy incorporates an integration of the opinions of key industry actors ( defined as members of the dairy and associated communities), especially farm suppliers ( input market), farmers, R, D & E people, milk processors and credit providers. The strategy also uses case studies with farm stays, purposive sampling, snowball interviewing techniques, semi-structured interviews, content analysis, focus group meetings, and feedback analysis, to refine the priorities for R, D & E actions in the region.

A rapid dietary assessment tool to determine intake of folate was developed and validated

Background and Objective: Estimates of dietary folate intake are currently of considerable interest, but no rapid tools are available to assess dietary intake of folate that are well suited to everyday health promotion activities, We developed and tested the reliability and validity of two prototypes of a rapid dietary assessment tool (a folate intake tool, FIT) to determine dietary intake of folate. Study Design and Setting: Five hundred and sixty eight men and women aged 33-93 years from Perth, Western Australia. Completed one of the two prototypes of the tool and gave a fasting blood sample for measurement of serum folate. A subset (n - 277) of participants completed the same tool on a second occasion 3-6 weeks later. Results: The Pearson correlations (r) between folate score from the tool and serum folate were moderately high for both prototypes (FIT-A r = 0.54-, FIT-B r = 0.49). The folate scores for the two prototypes were similar on repeat testing and correlated strongly (FIT-A r = 0.75; FIT-B r = 0.68). Conclusions: The rapid dietary assessment tool described here, FIT, provides a valid and reliable measurement of dietary intake of folate for both men and women. (c) 2005 Elsevier Inc. All rights reserved.

Recommendations and guidelines for the performance of accurate heat transfer measurements in rapid forming processes

The published requirements for accurate measurement of heat transfer at the interface between two bodies have been reviewed. A strategy for reliable measurement has been established, based on the depth of the temperature sensors in the medium, on the inverse method parameters and on the time response of the sensors. Sources of both deterministic and stochastic errors have been investigated and a method to evaluate them has been proposed, with the help of a normalisation technique. The key normalisation variables are the duration of the heat input and the maximum heat flux density. An example of application of this technique in the field of high pressure die casting is demonstrated. The normalisation study, coupled with previous determination of the heat input duration, makes it possible to determine the optimum location for the sensors, along with an acceptable sampling rate and the thermocouples critical response-time (as well as eventual filter characteristics). Results from the gauge are used to assess the suitability of the initial design choices. In particular the unavoidable response time of the thermocouples is estimated by comparison with the normalised simulation. (c) 2006 Elsevier Ltd. All rights reserved.

Analysis of stroke patients' and carers' reading ability and the content and design of written materials: Recommendations for improving written stroke information

Objective: This study (a) evaluated the reading ability of patients following stroke and their carers and the reading level and content and design characteristics of the written information provided to them, (b) explored the influence of sociodemographic and clinical characteristics on patients' reading ability, and (c) described an education package that provides well-designed information tailored to patients' and carers' informational needs. Methods: Fifty-seven patients and 12 carers were interviewed about their informational needs in an acute stroke unit. Their reading ability was assessed using the Rapid Estimate of Adult Literacy in Medicine (REALM). The written information provided to them in the acute stroke unit was analysed using the SMOG readability formula and the Suitability Assessment of Materials (SAM). Results: Thirteen (22.8%) patients and 5 (41.7%) carers had received written stroke information. The mean reading level of materials analysed was 11th grade while patients read at a mean of 7-8th grade. Most materials (89%) scored as only adequate in content and design. Patients with combined aphasia read significantly lower (4-6th grade) than other patients (p = 0.001). Conclusion: Only a small proportion of patients and carers received written materials about stroke and the readability level and content and design characteristics of most materials required improvement. Practice implications: When developing and distributing written materials about stroke, health professionals should consider the reading ability and informational needs of the recipients, and the reading level and content and design characteristics of the written materials. A computer system can be used to generate written materials tailored to the informational needs and literacy skills of patients and carers. (c) 2005 Elsevier Ireland Ltd. All rights reserved.

Rapid Atrophy of the Lumbar Multifidus Follows Experimental Disc or Nerve Root Injury.

Study Design. Experimental study of muscle changes after lumbar spinal injury. Objectives. To investigate effects of intervertebral disc and nerve root lesions on cross-sectional area, histology and chemistry of porcine lumbar multifidus. Summary of Background Data. The multifidus cross-sectional area is reduced in acute and chronic low back pain. Although chronic changes are widespread, acute changes at 1 segment are identified within days of injury. It is uncertain whether changes precede or follow injury, or what is the mechanism. Methods. The multifidus cross-sectional area was measured in 21 pigs from L1 to S1 with ultrasound before and 3 or 6 days after lesions: incision into L3 - L4 disc, medial branch transection of the L3 dorsal ramus, and a sham procedure. Samples from L3 to L5 were studied histologically and chemically. Results. The multifidus cross-sectional area was reduced at L4 ipsilateral to disc lesion but at L4 - L6 after nerve lesion. There was no change after sham or on the opposite side. Water and lactate were reduced bilaterally after disc lesion and ipsilateral to nerve lesion. Histology revealed enlargement of adipocytes and clustering of myofibers at multiple levels after disc and nerve lesions. Conclusions. These data resolve the controversy that the multifidus cross-sectional area reduces rapidly after lumbar injury. Changes after disc lesion affect 1 level with a different distribution to denervation. Such changes may be due to disuse following reflex inhibitory mechanisms.

The rapid screen of concussion: An evaluation of the non-word repetition test for use in mTBI research

Primary objectives: (1) To investigate the Nonword Repetition test (NWR) as an index of sub-vocal rehearsal deficits after mild traumatic brain injury (mTBI); (2) to assess the reliability, validity and sensitivity of the NWR; and (3) to compare the NWR to more sensitive tests of verbal memory. Research design: An independent groups design. Methods and procedures: Study 1 administered the NWR to 46 mTBI and 61 uninjured controls with the Rapid Screen of Concussion (RSC). Study 2 compared mTBI, orthopaedic and uninjured participants on the NWR and the Hopkins Verbal Learning Test (HVLT-R). Main outcomes and results: The NWR did not improve the diagnostic accuracy of the RSC. However, it is reliable and indexes sub-vocal rehearsal speed. These findings provide evidence that although the current form of the NWR lacks sensitivity to the impact of mTBI, the development of a more sensitive test of sub-vocal rehearsal deficits following mTBI is warranted.

Design and characterisation of novel blends of poly(lactic acid)

This thesis is concerned with the effect of polymer structure on miscibility of the three component blends based on poly(lactic acid) (PLA) with using blending techniques. The examination of novel PLA homologues (pre-synthesised poly(a-esters)), including a range of aliphatic and aromatic poly(a-esters) is an important aspect of the work. Because of their structural simplicity and similarity to PLA, they provide an ideal system to study the effect of polyester structures on the miscibility of PLA polymer blends. The miscibility behaviour of the PLA homologues is compared with other aliphatic polyesters (e.g. poly(e-caprolactone) (PCL), poly(hydroxybutyrate hydroxyvalerate) (P(HB-HV)), together with a series of cellulose-based polymers (e.g. cellulose acetate butyrate (CAB)). The work started with the exploration the technique used for preliminary observation of the miscibility of blends referred to as “a rapid screening method” and then the miscibility of binary blends was observed and characterised by percent transmittance together with the Coleman and Painter miscibility approach. However, it was observed that symmetrical structures (e.g. a1(dimethyl), a2(diethyl)) promote the well-packing which restrict their chains from intermingling into poly(L-lactide) (PLLA) chains and leads the blends to be immiscible, whereas, asymmetrical structures (e.g. a4(cyclohexyl)) behave to the contrary. a6(chloromethyl-methyl) should interact well with PLLA because of the polar group of chloride to form interactions, but it does not. It is difficult to disrupt the helical structure of PLLA. PLA were immiscible with PCL, P(HB-HV), or compatibiliser (e.g. G40, LLA-co-PCL), but miscible with CAB which is a hydrogen-bonded polymer. However, these binary blends provided a useful indication for the exploration the novel three component blends. In summary, the miscibility of the three-component blends are miscible even if only two polymers are miscible. This is the benefit for doing the three components blend in this thesis, which is not an attempt to produce a theoretical explanation for the miscibility of three components blend system.