gebhart/patrepeval huggingface dataset:
Redistribution of phosphatidylethanolamine at the cleavage furrow of dividing cells during cytokinesis (1996)

Ro09-0198 is a tetracyclic polypeptide of 19 amino acids that recognizes strictly the structure of phosphatidylethanolamine (PE) and forms a tight equimolar complex with PE on biological membranes. Using the cyclic peptide coupled with fluorescence-labeled streptavidin, we have analyzed the cell surface localization of PE in dividing Chinese hamster ovary cells. We found that PE was exposed on the cell surface specifically at the cleavage furrow during the late telophase of cytokinesis. PE was exposed on the cell surface only during the late telophase and no alteration in the distribution of the plasma membrane-bound cyclic peptide was observed during the cytokinesis, suggesting that the surface exposure of PE reflects the enhanced scrambling of PE at the cleavage furrow. Furthermore, cell surface immobilization of PE induced by adding the cyclic peptide coupled with streptavidin to prometaphase cells effectively blocked the cytokinesis at late telophase. The peptide-streptavidin complex treatment had no effect on furrowing, rearrangement of microtubules, and nuclear reconstitution, but specifically inhibited both actin filament disassembly at the cleavage furrow and subsequent membrane fusion. These results suggest that the redistribution of the plasma membrane phospholipids is a crucial step for cytokinesis and the cell surface PE may play a pivotal role in mediating a coordinate movement between the contractile ring and plasma membrane to achieve successful cell division.
Incorporating Memory Management into User-Level Network Interfaces (1997)

User-level network interfaces allow applications direct access to the network without operating system inter-vention on every send and receive. Messages are transferred directly to and from user-space by the network interface while observing the traditional protection boundaries between processes. Current user-level network interfaces limit this message transfer to a per-process region of permanently-pinned physical memory to allow safe DMA. This approach is inflexible in that it requires data to be copied into and out of this memory region, and does not scale to a large number of processes. This paper presents an extension to the U-Net user-level network architecture (U-Net/MM) allowing messages to be transferred directly to and from any part of an applications address space. This is achieved by integrating a translation look-aside buffer into the network interface and coordinating its operation with the operating sys-tems virtual memory subsystem. This mechanism allows network buffer pages to be pinned and unpinned dynamically. Two implementations of U-Net/MM are described, demonstrating that existing commodity hard-ware and commercial operating systems can efficiently support the architecture.
Cytoplasmic expression system based on constitutive synthesis of bacteriophage T7 RNA polymerase in mammalian cells. (1990)

A mouse cell line that constitutively synthesizes the bacteriophage T7 RNA polymerase was constructed. Fluorescence microscopy indicated that the T7 RNA polymerase was present in the cytoplasmic compartment. The system provided, therefore, a unique opportunity to study structural elements of mRNA that affect stability and translation. The in vivo activity of the bacteriophage polymerase was demonstrated by transfection of a plasmid containing the chloramphenicol acetyltransferase (CAT) gene flanked by T7 promoter and termination signals. Synthesis of CAT was dependent on the presence of a cDNA copy of the untranslated region of encephalomyocarditis virus (ECMV) RNA downstream of the T7 promoter, consistent with the absence of RNA-capping activity in the cytoplasm. CAT expression from a plasmid, pT7EMCAT, containing the T7 and EMCV regulatory elements was detected within 4 hr after transfection and increased during the next 20 hr, exceeding that obtained by transfection of a plasmid with the CAT gene attached to a retrovirus promoter and enhancer. Nevertheless, the presumably cap-independent transient expression of CAT from pT7EMCAT was increased more than 500-fold when the transfected cells also were infected with wild-type vaccinia virus. A protocol for high-level expression involved the infection of the T7 RNA polymerase cell line with a single recombinant vaccinia virus containing the target gene regulated by a T7 promoter and EMCV untranslated region.
End-to-End Containment of Internet Worm Epidemics (2006)

This dissertation is not substantially the same as any I have submitted for a degree or diploma or any other qualification at any other university. Further, no part of the dissertation has already been or is being concurrently submitted for any such degree, diploma or other qualification. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collab-oration except where specifically indicated in the text. This dissertation contains less than 60,000 words, including tables, footnotes, appendices, bibliography, and diagrams. Worms — programs that self-replicate automatically over computer networks — are a serious threat to hosts connected to the Internet. They infect hosts by exploiting software vulnerabilities, and they can use their victims for many malicious activities. Past outbreaks show that worms can spread too fast for humans to respond, hence worm containment must be automatic. Recent work proposed network-level techniques to automate worm contain-
EphB2 as a Therapeutic Antibody Drug Target for the Treatment of Colorectal Cancer (2004)

Analysis of human colorectal cancer specimens revealed overexpression of the EphB2 receptor tyrosine kinase. Monoclonal antibodies (MAbs) to extracellular sequence of EphB2 were raised and tested for activity against colorectal cancer cells. One of the MAbs, 2H9, effectively blocked the interaction of ephB2 with ephrin ligands and inhibited the resulting autophosphorylation of the receptor. However, this antibody did not affect the proliferation of cancer cells expressing ephB2. Immunocytochemical analysis revealed rapid internalization of the MAb 2H9 on binding ephB2, suggesting that target-dependent cell killing could be achieved with an antibody-drug conjugate. When MAb 2H9 was conjugated to monomethylauristatin E through a cathepsin B-cleavable linker, it specifically killed ephB2-expressing cancer cells in vitro and in vivo. Our results suggest that ephB2 is an attractive target for immunoconjugate cancer therapy.
A cell culture assay for compounds which inhibit hepatitis B virus replication (1991)

Infection by hepatitis B virus (HBV) is a major worldwide health problem with over 200 million individuals chronically-infected with HBV (Beasley and Hwang, 1984). In addition to causing both acute and chronic liver disease, HBV infection is epidemiologically linked to the formation of primary hepatocellular carcinoma (HCC) (Beasley and Hwang, 1984; Popper, et al., 1987). Several types of treatment regimens have been reported for individuals with chronic HBV infection, including interferons and nucleoside analogs (see Tabor, 1987 and Thomas, 1987 for reviews). However, these treatments have moderate to serious side effects, are only transiently effective in suppressing HBV, or are effective for only a small percentage of the general population of HBV-infected individuals. A major obstacle in the development of new therapeutic agents for HBV is the lack of a suitable in vitro culture system which accurately models chronic HBV infection in man. Relevant animal models of HBV infection and disease, including HCC, have been developed (e.g. the woodchuck hepatitis virus (WHV) and its natural host, the Eastern woodchuck (Gerin, 1984; Popper et al., 1986)). Several potentially suitable HBV culture systems have been developed by transfection of human liver cell lines with cloned HBV DNA (Sureau et al., 1986; Sells et al., 1987; Tsurimoto et al., 1987). The various HBV genomic forms present in chronically infected cells represent well characterized stages of viral replication (Sum-
Designing a practical ATM LAN (1993)

The adaptor cards and driver software for workstations and local asynchronous transfer mode (ATM) switches and switch control software used in an ATM local area network (LAN) system are discussed. It is shown that the ATM hardware and software components together provide services that are essential for ATM to be considered a realistic alternative to current shared-media LANs. These services include: completely transparent support for the TCP/IP protocol suite, an application programming interface for full access to the underlying ATM capabilities, support for AAL5, AAL3/4, and the null AAL, both connection-oriented and connectionless service, dynamic connection establishment or switched virtual circuits, resource reservation of guaranteed bandwidth and quality of service, full-bandwidth multicast and broadcast, virtual path and channel routing among multiple switches, automatic configuration and failure recovery, dynamic address assignment and internetwork address resolution, and network management via the simple network management protocol (SNMP).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Adaptive Maximum-Likelihood Receiver for Carrier-Modulated Data-Transmission Systems (1974)

A new look is taken at maximum-likelihood sequence estimation in the presence of intersymbol interference. A uniform receiver structure for linear carrier-modulated data-transmission systems is derived which for decision making uses a modified version of the Viterbi algorithm. The algorithm operates directly on the output signal of a complex matched filter and, in contrast to the original algorithm, requires no squaring operations; only multiplications by discrete pulse-amplitude values are needed. Decoding of redundantly coded sequences is included in the consideration. The reason and limits for the superior error performance of the receiver over a conventional receiver employing zero-forcing equalization and symbol-by-symbol decision making are explained. An adjustment algorithm for jointly approximating the matched filter by a transversal filter, estimating intersymbol interference present at the transversal filter output, and controlling the demodulating carrier phase and the sample timing, is presented.
Does Blood of Healthy Subjects Contain Bacterial Ribosomal DNA? (2001)

ABSTRACT Real-time PCR methods with primers and a probe targeting conserved regions of the bacterial 16S ribosomal DNA (rDNA) revealed a larger amount of rDNA in blood specimens from healthy individuals than in matched reagent controls. However, the origins and identities of these blood-associated bacterial rDNA sequences remain obscure.
Long-term in vitro culture and characterisation of avian embryonic stem cells with multiple morphogenetic potentialities (1996)

Petitte, J.N., Clarck, M.E., Verrinder Gibbins, A. M. and R. J. Etches (1990; Development 108, 185-189) demonstrated that chicken early blastoderm contains cells able to contribute to both somatic and germinal tissue when injected into a recipient embryo. However, these cells were neither identified nor maintained in vitro. Here, we show that chicken early blastoderm contains cells characterised as putative avian embryonic stem (ES) cells that can be maintained in vitro for long-term culture. These cells exhibit features similar to those of murine ES cells such as typical morphology, strong reactivity toward specific antibodies, cytokine-dependent extended proliferation and high telomerase activity. These cells also present high capacities to differentiate in vitro into various cell types including cells from ectodermic, mesodermic and endodermic lineages. Production of chimeras after injection of the cultivated cells reinforced the view that our culture system maintains in vitro some avian putative ES cells.
POSH2 is a RING finger E3 ligase with Rac1 binding activity through a partial CRIB domain (2010)

The Plenty of SH3 domains protein (POSH) is an E3 ligase and a scaffold in the JNK mediated apoptosis, linking Rac1 to downstream components. We here describe POSH2 which was identified from a p21-activated kinase 2 (PAK2) interactor screen. POSH2 is highly homologous with other members of the POSH family; it contains four Src homology 3 (SH3) domains and a RING finger domain which confers E3 ligase activity to the protein. In addition POSH2 contains an N-terminal extension which is conserved among its mammalian counterparts. POSH2 interacts with GTP-loaded Rac1. We have mapped this interaction to a previously unrecognized partial Cdc42/Rac1-interactive binding domain.
Future of polio vaccines (2009)

Over the past half-century, global use of highly effective vaccines against poliomyelitis brought this disease to the brink of elimination. Mounting evidence supports the argument that a high level of population immunity must be maintained after wild poliovirus circulation is stopped to preserve a polio-free status worldwide. Shifting factors in the risk-benefit-cost equation favor the creation of new poliovirus vaccines for use in the foreseeable future. Genetically stable attenuated virus strains could be developed for an improved oral poliovirus vaccine, but proving their safety and efficacy would be impractical owing to the enormous size of the clinical trials required. Novel versions of inactivated poliovirus vaccine that could be used globally should be developed. An improved inactivated poliovirus vaccine must be efficacious, inexpensive, safe to manufacture and easy to administer. Combination products containing inactivated poliovirus vaccine and other protective antigens should become part of routine childhood immunizations around the world.
Conservative amino acid substitution in the myelin proteolipid protein of jimpymsd mice (1990)

The capacity for synthesizing and maintaining a compact myelin sheath is destroyed in a number of inborn errors of myelin metabolism. One class of hypomyelinating mutations, which displays an X-linked pattern of inheritance, is distinguished by marked disturbances in oligodendrocyte differentiation. We have defined the molecular defect in one such mutant that lacks mature oligodendrocytes, the X-linked jimpy myelin synthesis deficient (jpmsd) trait in mice. The structure of the gene encoding the most abundant myelin protein, proteolipid protein (PLP), was determined by mapping and partially sequencing genomic clones from jpmsd and wild-type mice. Jpmsd mice have a single base change in PLP, a C----T transition in exon 6 that would substitute a valine for alanine in both PLP and its alternatively spliced isoform, DM20. The mutation was confirmed by polymerase chain reaction- amplifying exon 6 from genomic DNA and then either sequencing the amplified DNA or directly probing exon 6 with oligonucleotides designed to detect a single base mismatch. The conservative amino acid replacement in PLP/DM20 of jpmsd mice results in a pleiotropic phenotype similar to that observed for the allelic mutation jimpy, in which a splicing defect has radically altered the PLP/DM20 protein. The accelerated turnover of oligodendrocytes in both mouse mutants suggests a function for PLP/DM20 in oligodendrocyte differentiation distinct from the role of these proteolipid proteins as structural components of the myelin sheath.
Answering the question you wish they had asked (2006)

State-of-the-art Question Answering (QA) systems are very sensitive to variations in the phrasing of an information need. Finding the preferred language for such a need is a valuable task. We investigate that claim by adopting a simple MT-based paraphrasing technique and evaluating QA system performance on paraphrased questions. We found a potential increase of 35% in MRR with respect to the original question.
Additive Effect of Dornase Alfa and Nacystelyn on Transportability and Viscoelasticity of Cystic Fibrosis Sputum (2002)

The combination of DA and NAL exhibits an additive effect for both the viscoelasticity and transportability of CF sputum samples. The two agents appear to act well together in breaking down the bonding due to extracellular DNA and mucins. Clinical studies should be undertaken to see whether the additive combination at lower concentration produces the anticipated benefits of improved airway clearance and fewer side effects.
On the Validity of Macroscopic Viscous Fingering Models for 2D and 3D-Flows (1994)

A new fingering function is introduced into the Fayers macroscopic model, in which its single parameter represents the gas concentration just inside the leading edge of the fingers. High resolution simulation (HRS) of viscous fingers is used to validate the new model, and comparisons are also made with the Todd and Longstaff empirical method. Both particle tracking and finite difference variants of HRS are deployed, which yield similar average behaviors, and some small systematic differences between 2D and 3D-results are identified. The macroscopic! empirical models are investigated for rectilinear flows with gravity in both stabilizing and destabilizing directions. The new Fayers fingering function is extended to include a heterogeneity parameter, and is found to have superior attributes for a problem with “mild” heterogeneities, including the above gravity interactions.
Fluorescently tagged polymer bioconjugates from protein derived macroinitiators (2006)

BSA and lysozyme have been transformed into macroinitiators for living radical polymerisation and used to produce well-defined bioconjugates which can be fluorescently labelled providing a versatile strategy for the preparation of bioconjugates which is complementary to traditional PEGylation.
A nanoliter rotary device for polymerase chain reaction (2002)

Polymerase chain reaction (PCR) has revolutionized a variety of assays in biotechnology. The ability to implement PCR in disposable and reliable microfluidic chips will facilitate its use in applications such as rapid medical diagnostics, food control testing, and biological weapons detection. We fabricated a microfluidic chip with integrated heaters and plumbing in which various forms of PCR have been successfully demonstrated. The device uses only 12 nL of sample, one of the smallest sample volumes demonstrated to date. Minimizing the sample volume allows low power consumption, reduced reagent costs, and ultimately more rapid thermal cycling.
Trigger factor: a soluble protein that folds pro-OmpA into a membrane-assembly-competent form. (1987)

Pro-OmpA that is synthesized in vitro can assemble into bacterial inner membrane vesicles in the presence of ATP and NADH. We have purified pro-OmpA to determine which additional soluble proteins are necessary for its membrane assembly. [35S]Pro-OmpA was bound to Sepharose-linked antibody to OmpA, then eluted with 8 M urea and chromatographed on an anion-exchange resin in 8 M urea. This pro-OmpA is purified 2000-fold and is radiochemically pure. After dialysis, it is soluble but incompetent for membrane assembly. Addition of an Escherichia coli cytoplasmic fraction (S100) to the assembly reaction does not allow translocation. However, when S100 is added to pro-OmpA prior to dialysis, full assembly competence is restored, suggesting that a soluble factor, termed "trigger factor," triggers the folding of pro-OmpA into an assembly-competent form as the urea is removed. We noted that, prior to the last purification step, the immunoaffinity-purified pro-OmpA was partially competent for membrane assembly without addition of trigger factor. To test whether trigger factor had bound to the antibody column by means of its association with pro-OmpA, the crude pro-OmpA was acid-denatured prior to immunoadsorption. In this experiment, the trigger factor did not bind to the anti-OmpA column, and S100 was required for renaturation of this [35S]pro-OmpA. As suggested by this experiment, the crude [35S]pro-OmpA was in a complex with other proteins. Sedimentation velocity studies showed that the trigger factor has an apparent molecular weight of approximately 60,000. We propose that it is required for translocation-competent folding of pro-OmpA and other precursor proteins.
Leveraging Student Misconceptions to Improve Teaching of Biochemistry & Cell Biology (2021)

Students come to science class with many ideas of how the natural world works, some of which do not match the consensus of the scientific community and can lead to misunderstandings. Because a growing body of educational research indicates that these misconceptions can serve as resources for learning, we developed a four-point plan to leverage knowledge of common misconceptions to improve classroom teaching by refining instructional focus, providing opportunities for reflective practice, applying evidence-based practices, and promoting exploration of learning theories. By sharing this plan with our teaching colleagues, we were able to foster a collaborative approach to our and others’ practice. To do this, we compiled a resource bank of common student misconceptions using data collected from the University of Toronto’s National Biology Competition, developed a guide for using this misconception resource bank to promote best teaching practices, then shared this plan with our teaching colleagues in order to foster a collaborative approach to our pedagogy. In this article, we present the resource bank and guide and provide teaching tips that can be applied to a wide array of scientific course types and educational levels.
The derived demand for imported cheese in Hong Kong (2002)

The objective of this paper was to provide the U.S. dairy industry with empirical estimates of Hong Kong’s derived demand for imported cheese differentiated by source country of production. These estimates were used to simulate the effects of European Union (EU) subsidy reductions on the U.S. share of Hong Kong cheese imports. Simulation results suggested that Oceania was the primary beneficiary from EU subsidy reductions. Hong Kong cheese imports from the U.S. were expected to increase by 12% if subsidy reductions continue at the same pace as the 1994 GATT agreement and 21% if reductions were twice the pace.
A collagen/gelatin-binding decapeptide derived from bovine propolypeptide of von Willebrand factor (1992)

Propolypeptide of von Willebrand factor (pp-vWF) binds to type I collagen, and we have reported that a binding domain exists in a 21.5/21-kDa fragment originated from the C-terminal portion [Takagi, J., Fujisawa, T., Sekiya, F., & Saito, Y. (1991) J. Biol. Chem. 266, 5575-5579]. The collagen-binding property of the 21.5/21-kDa fragment was compared with that of the intact pp-vWF. Although pp-v WF preferentially binds to native type I collagen fibrils, the isolated fragment no longer has this specificity and binds well to collagen of other types in the native and heat-denatured states. In order to determine the critical site that mediates this collagen/gelatin binding, several peptides were synthesized based on the primary structure of the 21.5/21-kDa fragment. Among these, a 25-residue peptide strongly inhibited the binding of the 125I-labeled 21.5/21-kDa fragment to collagen. Using this inhibitory effect as an index, the binding site was defined to the sequence as follows: WREPSFCALS. Furthermore, a decapeptide of this sequence bound to collagen and gelatin, indicating that this sequence is responsible for the binding of the 21.5/21-kDa fragment to collagen/gelatin.