gebhart/patrepeval huggingface dataset:
TCP Performance Implications of Network Path Asymmetry (2002)

This document describes TCP performance problems that arise because of asymmetric effects. These problems arise in several access networks, including bandwidth-asymmetric networks and packet radio subnetworks, for different underlying reasons. However, the end result on TCP performance is the same in both cases: performance often degrades significantly because of imperfection and variability in the ACK feedback from the receiver to the sender.
Kinetic Studies of FR-1, a Growth Factor-Inducible Aldo-Keto Reductase (1998)

Murine fibroblasts cultured in the presence of fibroblast growth factor-1 express relatively high levels of FR-1, a approximately 36 kDa protein related to the aldo-keto reductase superfamily [Donohue, P. J., Alberts, G. F., Hampton, B. S., Winkles, J. A. (1994) J. Biol. Chem. 269, 8604-8609]. While the crystal structure of FR-1 shows striking homology with human aldose reductase [Wilson, D. K., Nakano, T., Petrash, J. M., Quiocho, F. A. (1995) Biochemistry 34, 14323-14330], an enzyme linked to the pathogenesis of diabetic complications, the physiological role of FR-1 is not known. We show that FR-1 is capable of reducing a broad range of aromatic and aliphatic aldehydes, including the abundant and highly reactive lipid-derived aldehyde 4-hydroxy-2-nonenal (HNE; Km approximately 9 microM). However, in the absence of coenzyme, HNE caused a time-dependent inactivation of FR-1. Results from electrospray ionization-mass spectrometry and Edman-degradation of peptides derived from HNE-modified FR-1 were consistent with formation of a Michael adduct at Cys298. This was confirmed with a C298S mutant, which was resistant to HNE-induced inactivation. Since steady-state Km values determined with alkanals, alpha,beta-unsaturated alkenals, alkadienals, and 4-hydroxyalkenals fall within their physiological concentrations, lipid-derived aldehydes appear to be potential in vivo substrates for FR-1.
Survey of Pedestrian Detection for Advanced Driver Assistance Systems (2009)

Advanced driver assistance systems (ADASs), and particularly pedestrian protection systems (PPSs), have become an active research area aimed at improving traffic safety. The major challenge of PPSs is the development of reliable on-board pedestrian detection systems. Due to the varying appearance of pedestrians (e.g., different clothes, changing size, aspect ratio, and dynamic shape) and the unstructured environment, it is very difficult to cope with the demanded robustness of this kind of system. Two problems arising in this research area are the lack of public benchmarks and the difficulty in reproducing many of the proposed methods, which makes it difficult to compare the approaches. As a result, surveying the literature by enumerating the proposals one--after-another is not the most useful way to provide a comparative point of view. Accordingly, we present a more convenient strategy to survey the different approaches. We divide the problem of detecting pedestrians from images into different processing steps, each with attached responsibilities. Then, the different proposed methods are analyzed and classified with respect to each processing stage, favoring a comparative viewpoint. Finally, discussion of the important topics is presented, putting special emphasis on the future needs and challenges.
Gadolinium-DTPA Liposomes as a Potential MRI Contrast Agent (1988)

To evaluate the use of liposomes containing Gadolinium-DTPA (Gd-DTPA) as potential intravascular contrast agents, we synthesized and tested Gd-DTPA liposomes. A freeze-thaw extrusion process was used to synthesize neutral unilamellar vesicles. Using this technique, we prepared 0.4 micron vesicles with encapsulation efficiency as high as 39% for Gd-DTPA. In vitro dialysis showed that essentially 100% of the Gd-DTPA was retained with the liposomes after 72 hours of dialysis. MR imaging of in vitro samples showed concentration-dependent increase in signal intensity with Gd-DTPA liposomes. Imaging of rats after intravenous injection of Gd-DTPA liposomes showed sustained intravascular contrast enhancement of vascular structures and liver greater than free Gd-DTPA. There was no evidence of acute toxicity in rats during the imaging experiments or on follow-up of two months. Paramagnetic liposomes may be useful to enhance the vasculature, liver, and spleen.
Low defect densities in molecular beam epitaxial GaAs achieved by isoelectronic In doping (1986)

We have studied the effects of adding small amounts of In (0.2–1.2%) to GaAs grown by molecular beam epitaxy. The density of four electron traps decreases in concentration by an order of magnitude, and the peak intensities of prominent emissions in the excitonic spectra are reduced with increase in In content. Based on the higher surface migration rate of In, compared to Ga, at the growth temperatures it is apparent that the traps and the excitonic transitions are related to point defects. This agrees with earlier observations by F. Briones and D. M. Collins [J. Electron. Mater. 11, 847 (1982)] and B. J. Skromme, S. S. Bose, B. Lee, T. S. Low, T. R. Lepkowski, R-Y. DeJule, G. E. Stillman, and J. C. M. Hwang [J. Appl. Phys. 58, 4702 (1985)].
Anterior segment development relevant to glaucoma (2004)

Development of the ocular anterior segment involves a series of inductive interactions between neural ectoderm, surface ectoderm and periocular mesenchyme. The timing of these events is well established but less is known about the molecular mechanisms involved. Various genes that participate in these processes have been identified. As the roles of more genes are determined, developmental pathways and networks will emerge. Here, we focus on recent advances made using mouse models. We summarize key morphological events in formation of anterior chamber structures, including the aqueous humor drainage structures that are involved in intraocular pressure (IOP) regulation and glaucoma. We discuss the developmental roles of genes that associate with abnormal anterior segment development and elevated IOP or glaucoma (including Bmp4, Cyp1b1, Foxc1, Foxc2, Pitx2, Lmx1b and Tyr ) and how some of these genes may fit into developmental networks.
Peptide vaccines incorporating a ‘promiscuous’ T‐cell epitope bypass certain haplotype restricted immune responses and provide broad spectrum immunogenicity (1993)

An ideal peptide vaccine should contain both B- and T-cell epitopes. Recognition of antigen by B cells is highly dependent on the three-dimensional conformation of the antigen whereas T cells recognize antigen only after it has been processed to release a peptide fragment which is bound to the major histocompatibility complex (MHC) class II molecule. However, T cells provide 'help' to B cells displaying the same processed, MHC-restricted form of the antigen, demonstrating that the T-cell response to a protein antigen is under genetic control. Thus, strategies for co-inclusion of T cell 'helper' epitopes with the B-cell determinant elicit immune responses that are in most cases genetically restricted to only one or a few alleles of the MHC with limited activity across divergent MHC class II haplotypes. This genetically restricted T cell stimulatory activity of peptides is a serious obstacle and consequently such constructs would be of limited practical value as a vaccine targeted to a majority of an outbred population. In the study described here, we have engineered two peptides to encompass the sequences from the universally immunogenic tetanus toxoid (TT) epitope and the contraceptive vaccine candidate lactate dehydrogenase C4 (LDH-C4). We demonstrate the feasibility of using 'promiscuous' T-cell epitopes colinearly constructed with a defined B-cell epitope to induce high titer antipeptide IgG antibodies specific for native protein antigen LDH-C4 in several inbred strains of mice, outbred mice and rabbits. There appears to be a strong correlation between the capacity for the hybrid peptides to be stimulatory for the corresponding T cells in C57BL/6 (H-2b) and C3H/HeJ (H-2k) mice and their ability to be immunogenic. This correlation, however, appears to break down in H-2d strains of mice since no antibodies were detected in BALB/c and barely detectable levels of antibodies in B10.D2 although activated T cells were detectable. Conversely, high titers of antipeptide antibodies are elicited in some strains (B10.BR (H-2k); C57BL/10 (H-2b) without detectable IL-2 responses. Finally, we show that a determinant which was previously restricted to H-2k can be rendered immunogenic in H-2b with the 'promiscuous' TT epitope. Thus, certain haplotype-restricted immune responses can be bypassed, setting forth the ground work for the design of a universal vaccine by broadening the effective response in a larger number of individuals typical of the genetically diverse outbred human population.
Securely implementing remote access within health information management. (1998)

As technology changes, our definition of the workplace expands, and we no longer are limited to working at our desk in an office. The authors describe technologies that enable us to work from home or on the road and examine security regulations and precautions.
Inhibition of Allergic Inflammation in the Airways Using Aerosolized Antisense to Syk Kinase (2002)

Activation of the protein tyrosine kinase Syk is an early event that follows cross-linking of Fc gamma R and Fc epsilon R, leading to the release of biologically active molecules in inflammation. We reported previously that aerosolized Syk antisense oligodeoxynucleotides (ASO) depresses Syk expression in inflammatory cells, the release of mediators from alveolar macrophages, and pulmonary inflammation. To study the effect of Syk ASO in allergic inflammation and airway hyperresponsiveness, we used the Brown Norway rat model of OVA-induced allergic asthma. Syk ASO, delivered in a liposome, carrier/lipid complex by aerosol to rats, significantly inhibited the Ag-induced inflammatory cell infiltrate in the bronchoalveolar space, decreasing both neutrophilia and eosinophilia. The number of eosinophils in the lung parenchyma was also diminished. Syk ASO also depressed up-regulation of the expression of beta(2) integrins, alpha(4) integrin, and ICAM-1 in bronchoalveolar lavage leukocytes and reversed the Ag-induced decrease in CD62L expression on neutrophils. Furthermore, the increase in TNF levels in bronchoalveolar lavage following Ag challenge was significantly inhibited. Syk ASO also suppressed Ag-mediated contraction of the trachea in a complementary model. Thus, aerosolized Syk ASO suppresses many of the central components of allergic asthma and inflammation and may provide a new therapeutic approach.
Mona/Gads SH3C Binding to Hematopoietic Progenitor Kinase 1 (HPK1) Combines an Atypical SH3 Binding Motif, R/KXXK, with a Classical PXXP Motif Embedded in a Polyproline Type II (PPII) Helix (2004)

Hematopoietic progenitor kinase 1 (HPK1) is implicated in signaling downstream of the T cell receptor. Its non-catalytic, C-terminal half contains several prolinerich motifs, which have been shown to interact with different SH3 domain-containing adaptor proteins in vitro. One of these, Mona/Gads, was also shown to bind HPK1 in mouse T cells in vivo. The region of HPK1 that binds to the Mona/Gads C-terminal SH3 domain has been mapped and shows only very limited similarity to a recently identified high affinity binding motif in SLP-76, another T-cell adaptor. Using isothermal titration calorimetry and x-ray crystallography, the binding of the HPK1 motif to Mona/Gads SH3C has now been characterized in molecular detail. The results indicate that although charge interactions through an RXXK motif are essential for complex formation, a PXXP motif in HPK1 strongly complements binding. This unexpected binding mode therefore differs considerably from the previously described interaction of Mona/Gads SH3C with SLP-76. The crystal structure of the complex highlights the great versatility of SH3 domains, which allows interactions with very different proteins. This currently limits our ability to categorize SH3 binding properties by simple rules.
Plasma Concentration of the Neurofilament Light Protein (NFL) is a Biomarker of CNS Injury in HIV Infection: A Cross-Sectional Study (2015)

These results show that plasma NFL may prove a valuable tool to evaluate ongoing CNS injury in HIV infection that may be applied in the clinic and in research settings to assess the presence if active CNS injury. Because CSF NFL is also elevated in a variety of other CNS disorders, sensitive measures of plasma NFL may similarly prove useful in other settings.
siRNAs and shRNAs: skeleton keys to the human genome. (2003)

The use of RNA interference (RNAi) to evoke gene silencing in mammalian cell systems is rapidly becoming a standard laboratory technique. Recent experiments have also proven the utility of RNAi in animals. The next few years will bear witness to the first RNAi-based genome-wide screens in mammals, breaking the barrier to the use of mammalian cells as a genetic system. In this review, some of the key features of RNAi in mammalian systems are discussed.
Synthesis of Stable Multifunctional Perfluorocarbon Nanoemulsions for Cancer Therapy and Imaging (2016)

Nanotechnology provides a promising platform for drug-delivery in medicine. Nanostructured materials can be designed with desired superparamagnetic or fluorescent properties in conjunction with biochemically functionalized moieties (i.e., antibodies, peptides, and small molecules) to actively bind to target sites. These multifunctional properties make them suitable agents for multimodal imaging, diagnosis, and therapy. Perfluorohexane nanoemulsions (PFH-NEs) are novel drug-delivery vehicles and contrast agents for ultrasound and photoacoustic imaging of cancer in vivo, offering higher spatial resolution and deeper penetration of tissue when compared to conventional optical techniques. Compared to other theranostic agents, our PFH-NEs are one of the smallest of their kind (<100 nm), exhibit minimal aggregation, long-term stability at physiological conditions, and provide a noninvasive cancer imaging and therapy alternative for patients. Here, we show, using high-resolution imaging and correlative techniques, that our PFH-NEs, when in tandem with silica-coated gold nanoparticles (scAuNPs), can be used as a drug-loaded therapeutic via endocytosis and as a multimodal imaging agent for photoacoustic, ultrasound, and fluorescence imaging of tumor growth.
Inhibition of TRAIL-Induced Apoptosis and Forced Internalization of TRAIL Receptor 1 by Adenovirus Proteins (2001)

Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) induces apoptosis through two receptors, TRAIL-R1 (also known as death receptor 4) and TRAIL-R2 (also known as death receptor 5), that are members of the TNF receptor superfamily of death domain-containing receptors. We show that human adenovirus type 5 encodes three proteins, named RID (previously named E3-10.4K/14.5K), E3-14.7K, and E1B-19K, that independently inhibit TRAIL-induced apoptosis of infected human cells. This conclusion was derived from studies using wild-type adenovirus, adenovirus replication-competent mutants that lack one or more of the RID, E3-14.7K, and E1B-19K genes, and adenovirus E1-minus replication-defective vectors that express all E3 genes, RID plus E3-14.7K only, RID only, or E3-14.7K only. RID inhibits TRAIL-induced apoptosis when cells are sensitized to TRAIL either by adenovirus infection or treatment with cycloheximide. RID induces the internalization of TRAIL-R1 from the cell surface, as shown by flow cytometry and indirect immunofluorescence for TRAIL-R1. TRAIL-R1 was internalized in distinct vesicles which are very likely to be endosomes and lysosomes. TRAIL-R1 is degraded, as indicated by the disappearance of the TRAIL-R1 immunofluorescence signal. Degradation was inhibited by bafilomycin A1, a drug that prevents acidification of vesicles and the sorting of receptors from late endosomes to lysosomes, implying that degradation occurs in lysosomes. RID was also shown previously to internalize and degrade another death domain receptor, Fas, and to prevent apoptosis through Fas and the TNF receptor. RID was shown previously to force the internalization and degradation of the epidermal growth factor receptor. E1B-19K was shown previously to block apoptosis through Fas, and both E1B-19K and E3-14.7K were found to prevent apoptosis through the TNF receptor. These findings suggest that the receptors for TRAIL, Fas ligand, and TNF play a role in limiting virus infections. The ability of adenovirus to inhibit killing through these receptors may prolong acute and persistent infections.
Incidence of BRAF Oncogene Mutation and Clinical Relevance for Primary Cutaneous Melanomas (2004)

The study suggests that BRAF mutation may be acquired during development of metastasis but is not a significant factor for primary tumor development and disease outcome.
Involvement of Glycoprotein VI in Platelet Thrombus Formation on Both Collagen and von Willebrand Factor Surfaces Under Flow Conditions (2002)

GP VI plays crucial roles in platelet thrombus formation on the surface of collagen under flow conditions in humans and is also involved in the process of firm platelet adhesion on the surface of vWF.
An update on promising agents for the treatment of cancer cachexia (2009)

A number of promising new agents are currently being developed but are not as yet regarded as standard of care. They include: selective COX-2 inhibitors, ghrelin mimetics, oxandrolone, selective androgen receptor modulators (ostarine), olanzapine, anti-IL-6 antibody and an innovative approach of multitargeted combined treatment. The data reported seem to suggest that the most effective treatment for cancer cachexia may be a combination regimen rather than single-agent treatments. This is in keeping with the general consensus that cancer cachexia is a multifactorial process and, hence, a potentially effective approach should be multimodal.
Mouse Col18a1 is expressed in a tissue-specific manner as three alternative variants and is localized in basement membrane zones. (1995)

We have isolated overlapping cDNAs encoding the N-terminal non-triple-helical region of mouse alpha 1(XVIII) collagen and shown that three different variants of alpha 1(XVIII) collagen exist. Each of the three variants shows characteristic tissue-specific expression patterns. Immunohistochemical studies show positive staining for alpha 1(XVIII) collagen along the basement membrane zones of vessels in the intestinal villi, the choroid plexus, skin, liver, and kidney. Thus, we conclude that alpha 1(XVIII) collagen may interact (directly or indirectly) with components in basement membrane zones or on the basal surface of endothelial/epithelial cells.
Feeling in Crisis: Vicissitudes of Response in Experiments with Global Justice Education (2011)

This paper considers the nexus of affective engagement, a critical analysis of systemic discrimination, and reflexive self-implication in education committed to social change. I ask how our inherited models and theories of learning and teaching for social change can curb our vigilance vis-à-vis the ways libidinal dynamics organize our curriculum as affective wish and our pedagogy as affective defense. I focus specifically on the qualities of global justice education—the ethical and political stakes of this project, the theories of learning, pedagogical strategies and discourses of moral development it inherits—that render learning, teaching, and learning to teach (none of which are discrete) affectively and ethically fraught. The paper examines student writing samples from a mandatory pre-service course on social and global justice education, one designed to engage future teachers in considering the inequitable global distribution of precarity and recognizability (Butler) within contemporary contexts of neoliberal globalization and war. In the writing samples, students reflect on the challenges they faced making sense of representations of the ravages of militarized capitalist globalization, in particular the challenges of creating and facilitating curriculum within which their peers might encounter such difficult knowledge. I ask, firstly, what students’ narrations of teaching social justice tell us about what is difficult in studying/teaching the devastation of the contemporary militarized, imperial global capitalist order in which we are profoundly implicated as citizens in the global North. Secondly, what can student narrations of teaching social justice tell me about what is difficult in global justice teacher education, specifically the wishes, the anxieties and discursive foreclosures underpinning my own conduct of it in this course?
Regeneration of skeletal muscle from transplanted immortalised myoblasts is oligoclonal (2004)

Myoblasts transplanted into muscles of recipient mice mostly die, only a minor stem cell-like subpopulation surviving and participating in muscle regeneration. To investigate this phenomenon further, we used a retrovirus expressing beta-galactosidase to provide a unique marker for satellite-cell-derived muscle precursor cells, before transplanting them into myopathic mdx nu/nu mouse muscle. We employed inverse polymerase chain reaction to identify viral integrations, to follow the fate of clones present within the injected cells. Mass-infected cultures contained many marked clones, some of which contributed disproportionately to muscle regeneration. Although no particular clones showed overall predominance, some were present in more than one injected muscle, an eventuality unlikely to arise by chance. Conversely, in grafts of muscle precursor cells that had either been labelled as sparse satellite-cell derived cultures, or had been cloned, all clones were shown to be able to survive and form muscle in vivo. Moreover, all clones contributed to further generations of new-formed muscle fibres following a series of injuries administered to injected muscles, demonstrating that some cells of each clone had been retained as stem-cell-like muscle precursors. Furthermore, retrovirally marked satellite-cell-derived clones were derived from muscles that had been injected with marked muscle precursor cells. These cells formed muscle following their transplantation into a new host mouse, confirming their stem cell properties.