gebhart/patrepeval huggingface dataset:
Load balancing routing with bandwidth-delay guarantees (2004)

The current generation of network carriers competes intensely to satisfy the diverse wide-area connectivity requirements of customers. At the same time, the carriers inherently wish to maximize the usage efficiency of their network infrastructure. Much of the research in network resource management has been devoted to providing bandwidth guarantees and preventing network congestion. However, the rapid growth in number and diversity of real-time network applications has made it imperative to consider the impact of end-to-end delay of traffic requirements on network resource provisioning. We present an efficient network resource provisioning algorithm, called link criticality based routing (LCBR), which relies on the guiding theme that load balancing leads to higher resource utilization efficiency. LCBR applies a simple but very effective notion of link criticality to achieve networkwide load balance while simultaneously meeting the QoS requirements of bandwidth and end-to-end delay. In addition, LCBR can simultaneously provision both primary and backup routes to support fast recovery from node or link failures. This article reviews the state of the art in network resource provisioning with QoS guarantees, introduces the LCBR algorithm, and identifies future research challenges.
Biocompatible Wound Dressings Based on Chemically Degradable Triblock Copolymer Hydrogels (2008)

The synthesis of a series of thermo-responsive ABA triblock copolymers in which the outer A blocks comprise poly(2-hydroxypropyl methacrylate) and the central B block is poly(2-(methacryloyloxy)ethyl phosphorylcholine) is achieved using atom transfer radical polymerization. These novel triblock copolymers form thermo-reversible physical gels with critical gelation temperatures and mechanical properties that are highly dependent on the copolymer composition and concentration. TEM studies on dried dilute copolymer solutions indicate the presence of colloidal aggregates, which is consistent with micellar gel structures. This hypothesis is consistent with the observation that incorporating a central disulfide bond within the B block leads to thermo-responsive gels that can be efficiently degraded using mild reductants such as dithiothreitol (DTT) over time scales of minutes at 37 degrees C. Moreover, the rate of gel dissolution increases at higher DTT/disulfide molar ratios. Finally, these copolymer gels are shown to be highly biocompatible. Only a modest reduction in proliferation was observed for monolayers of primary human dermal fibroblasts, with no evidence for cytotoxicity. Moreover, when placed directly on 3D tissue-engineered skin, these gels had no significant effect on cell viability. Thus, we suggest that these thermo-responsive biodegradable copolymer gels may have potential applications as wound dressings.
A research perspective on computer-assisted office work (1979)

A study of the evolution of office work in this research laboratory provides valuable insight into requirements for an office of the future that is comfortable for its occupants.
Development of Reflective Optical Systems for XUV Projection Lithography* (1991)

We discuss the performance requirements for reflective imaging systems which will be needed to obtain ~0.1-μn resolution via projection lithography in the extreme-ultraviolet (XUV) wavelength region ≤100 nm. Designs are considered that use centered, non-tilted, annular optical elements. The inter-relationships between the illumination system, degree of spatial coherence, and the reduction system are evaluated, and the tradeoffs in performance for the total system between using an optimized annular illumination system and full illumination are analyzed. It will be shown that for our designs, annular illumination with XUV wavelengths does not significantly improve system performance. This result simplifies the illumination system design.
Primary Surgical Management of Ovarian Cancer (2003)

In the United States, ovarian cancer is the fifth most common cause of female cancer death behind lung, breast, colorectal, and pancreatic cancers. It is estimated that 14,500 women in the United States will die of ovarian cancer in 1999 (1). Epithelial ovarian carcinoma accounts for 90% of all ovarian cancers and an even greater percentage of ovarian cancer mortality (2). In this chapter, we will review the role of primary surgery in the management of epithelial ovarian carcinoma. A brief discussion of interval cytoreduction is also included.
Recent Advances in the Development of Methods for Detecting Single-base Substitutions Associated with Human Genetic Diseases (1986)

The ability to detect single-base mutations in human genomic DNA is of fundamental importance in the diagnosis of genetic diseases. This was first accomplished by using restriction endonucleases and the Southern blotting technique to detect the loss or gain of restriction enzyme recognition sites (Flavell et al. 1978; Geever et al. 1981). Unfortunately, this approach is limited by the fact that most single-base substitutions do not alter restriction endonuclease cleavage sites. In fact, sickle cell anemia is the only genetic disease that has been directly diagnosed by this method in the clinic on a routine basis (Chang and Kan 1982; Orkin et al. 1982). However, many genetic diseases can be diagnosed by this method by virtue of their linkage to restriction site polymorphisms (see, e.g., Kan and Dozy 1978; Gusella et al. 1982; Orkin et al. 1982). Base substitutions that do not alter restriction enzyme cleavage sites can be detected...
A new method for random mutagenesis of complete genes: enzymatic generation of mutant libraries in vitro (1988)

A new efficient in vitro mutagenesis method for the generation of complete random mutant libraries, containing all possible single base substitution mutations in a cloned gene is described. The method is based on controlled use of polymerases. Four populations of DNA molecules are first generated by primer elongation so that they terminate randomly, but always just before a known type of base (before A, C, G or T respectively). Each of the four populations is then mutagenized in a separate misincorporation reaction, where the correct base can now be omitted. The regeneration of wild-type sequences can thus be efficiently avoided. Also, the misincorporating nucleotide concentrations can be optimized to give the three possible single mutations in close to equal ratio. The mutagenesis can be precisely localized within a predetermined target region of any size, and vector sequences remain intact. We have mutagenized the DNA coding for the alpha-fragment of Escherichia coli beta-galactosidase, and identified 176 different base substitution mutations by sequencing. The present method gives mutant yields of 40-60%, when the mutants contain about one amino acid change per protein molecule. All types of base substitution mutations can be generated and deletions are rare. The efficiency of this method permits the use of relatively elaborate screening systems to isolate mutants of either structural genes or regulatory regions.
Recent advances in systemic therapy for breast cancer (1998)

During the past year there have been a number of important advances in the area of systemic therapy for breast cancer. Combined chemoendocrine therapy has been shown to be more effective than tamoxifen alone in the adjuvant therapy of node-negative estrogen receptor-positive breast cancer. Preliminary results of a randomized trial suggest that the addition of paclitaxel to adjuvant AC (Adriamycin and Cytoxan) improves survival in patients with operable node-positive disease. In the treatment of metastatic disease, preliminary results of a randomized trial have shown docetaxel to be superior to doxorubicin in response rate. In hormonal therapy, third generation aromatase inhibitors have replaced megestrol acetate as second-line hormonal therapy in receptor-positive disease. There are promising recent data about anti-HER-2 antibody therapy and other new approaches. This article reviews these and other recent advances in the systemic therapy of breast cancer.
Effects of activated macrophages on Mycobacterium leprae (1991)

Five alternative methods were used to explore in vitro the effects of normal and activated murine macrophages on the metabolic well-being of intracellular Mycobacterium leprae: fluorescein diacetate-ethidium bromide staining, ATP content, synthesis of phenolic glycolipid 1, and two techniques to quantitate oxidation of palmitic acid. In relatively short-term experiments (7 to 10 days), each of these procedures provided strong evidence that activated macrophages exerted a deleterious effect on the leprosy bacillus. These findings appear to confirm the contention that activated macrophages underlie host resistance to clinical leprosy and limitation of M. leprae growth in paucibacillary leprosy.
Synthesis and characterization of the first discrete potassium thiolates displaying three different coordination spheres at potassium in one molecule (1996)

Potassium hydride reacts with HSC6H2Pri3-2,4,6 (HSR) in THF or thf–tmen (tmen =N,N,N′,N′-tetramethylethylenediamine) to afford the first discrete, hexameric potassium thiolates [{K(SR)}2{K(thf)(SR)}2{K(thf)2(SR)}2] 3 and [{K(SR)}2{K(thf)(SR)}2{K(tmen)(SR)}2], 4·thf, exhibiting an unusual box-shaped structure with three different coordination spheres for the three independent potassium atoms.
The cHS4 Insulator Increases the Probability of Retroviral Expression at Random Chromosomal Integration Sites (2000)

Retroviruses are highly susceptible to transcriptional silencing and position effects imparted by chromosomal sequences at their integration site. These phenomena hamper the use of recombinant retroviruses as stable gene delivery vectors. As insulators are able to block promoter-enhancer interactions and reduce position effects in some transgenic animals, we examined the effect of an insulator on the expression and structure of randomly integrated recombinant retroviruses. We used the cHS4 element, an insulator from the chicken beta-like globin gene cluster, which has been shown to reduce position effects in transgenic Drosophila. A large panel of mouse erythroleukemia cells that bear a single copy of integrated recombinant retroviruses was generated without using drug selection. We show that the cHS4 increases the probability that integrated proviruses will express and dramatically decreases the level of de novo methylation of the 5' long terminal repeat. These findings support a primary role of methylation in the silencing of retroviruses and suggest that cHS4 could be useful in gene therapy applications to overcome silencing of retroviral vectors.
Sub-ppt detection limits for copper ions with Gly-Gly-His modified electrodes (2001)

An electrochemical metal ion sensor has been developed with a detection limit of less than 0.2 ppt by the covalent attachment of the tripeptide Gly-Gly-His as a recognition element to a 3-mercaptopropionic acid modified gold electrode.
Loss of ERβ expression as a common step in estrogen-dependent tumor progression (2004)

The characterization of estrogen receptor beta (ERbeta) brought new insight into the mechanisms underlying estrogen signaling. Estrogen induction of cell proliferation is a crucial step in carcinogenesis of gynecologic target tissues, and the mitogenic effects of estrogen in these tissues (such as breast, endometrium and ovary) are well documented both in vitro and in vivo. There is also an emerging body of evidence that colon and prostate cancer growth is influenced by estrogens. In all of these tissues, most studies have shown decreased ERbeta expression in cancer as compared with benign tumors or normal tissues, whereas ERalpha expression persists. The loss of ERbeta expression in cancer cells could reflect tumor cell dedifferentiation but may also represent a critical stage in estrogen-dependent tumor progression. Modulation of the expression of ERalpha target genes by ERbeta or ERbeta-specific gene induction could explain that ERbeta has a differential effect on proliferation as compared with ERalpha. ERbeta may exert a protective effect and thus constitute a new target for hormone therapy, such as ligand specific activation. The potential distinct roles of ERalpha and ERbeta expression in carcinogenesis, as suggested by experimental and clinical data, are discussed in this review.
Suppressors of Cytokine Signaling 4 and 5 Regulate Epidermal Growth Factor Receptor Signaling (2004)

Suppressors of cytokine signaling (SOCS) are Src homology-2-containing proteins originally identified as negative regulators of cytokine signaling. Accumulating evidence indicates a role for SOCS proteins in the regulation of additional signaling pathways including receptor tyrosine kinases. Notably, SOCS36E, the Drosophila ortholog of mammalian SOCS5, was recently implicated as a negative regulator of the Drosophila ortholog of EGFR. In this study, we aimed at characterizing the role of SOCS5 in the negative regulation of EGFR. Here we show that the expression of SOCS5 and its closest homolog SOCS4 is elevated in cells following treatment with EGF, similar to several negative feedback regulators of EGFR whose expression is up-regulated upon receptor activation. The expression of SOCS5 led to a marked reduction in EGFR expression levels by promoting EGFR degradation. The reduction in EGFR levels and EGF-induced signaling in SOCS5-expressing cells requires both the Src homology-2 and SOCS box domains of SOCS5. Interestingly, EGFR is degraded by SOCS5 prior to EGF treatment in a ligand- and c-Cbl-independent manner. SOCS5 can associate with EGFR and can also bind the ElonginBC protein complex via its SOCS box, which may recruit an E3 ubiquitin ligase to promote EGFR degradation. Thus, we have characterized a novel function for SOCS5 in regulating EGFR and discuss its potential role in controlling EGFR homeostasis.
Luminescent Platinum(II) Terpyridyl Complexes: Effect of Counter Ions on Solvent‐Induced Aggregation and Color Changes (2005)

A series of platinum(II) terpyridyl complexes [Pt(tpy)(C triple bond C-C triple bond CH)]X, 1-X (X=OTf-; PF6-; ClO4-; BF4-; BPh4-); [Pt(tpy)(C triple bond CC6H5)]X, 2-X (X=OTf-; PF6-; ClO4-; BF4-); [Pt(tpy)(C triple bond CC6H4OCH3-4)]OTf, 3-OTf, and [Pt(4'-CH3O-tpy)(C triple bond CC6H5)]OTf, 4-OTf (tpy=2,2':6',2''-terpyridine, OTf=trifluoromethanesulfonate) were synthesized and their photophysical properties determined. Electronic absorption and emission studies showed the formation of a new band upon increasing the diethyl ether content in an acetonitrile/diethyl ether mixture. This was ascribed to the formation of complex aggregates, the solution color of which is dependent on the nature of the anions. This indicates that counter ions play an important role in governing the degree of aggregation and the extent of interactions within these aggregates. Addition of various anions to solutions of 1-OTf and 1-PF6 produced anion-induced color changes upon solvent-induced aggregation, indicating that these complexes may serve as potential colorimetric anion probes.
Vascular and nonvascular expression of INCAM-110. A target for mononuclear leukocyte adhesion in normal and inflamed human tissues. (1991)

Inducible cell adhesion molecule 110 (INCAM-110), is a 110-kd adhesion receptor for lymphocytes and monocytes identified on cytokine-activated endothelium. Using immunoperoxidase techniques, little or no INCAM-110 was detected on endothelium in normal human tissues. In contrast, INCAM-110 was expressed in postcapillary venules in a variety of active inflammatory processes. In acute appendicitis, INCAM-110 was found coincident with strong expression of endothelial leukocyte adhesion molecule 1 (ELAM-1), a cytokine-inducible molecule that functions in neutrophil adhesion. However, in certain chronic inflammatory processes (eg, sarcoidosis), INCAM-110 was observed without simultaneous ELAM-1 expression. Anti-INCAM-110 antibody E1/6 also marked several extravascular cell types, including lymphoid dendritic cells, some tissue macrophages, synovial lining cells, and reactive mesothelial cells. These data suggest a role for endothelial INCAM-110 in the pathophysiology of both acute and chronic inflammatory reactions. Furthermore INCAM-110 may function as an adhesion molecule for mononuclear leukocytes in a variety of extravascular sites.
Establishment of transgenic herbicide‐resistant creeping bentgrass ( Agrostis stolonifera L.) in nonagronomic habitats (2006)

Concerns about genetically modified (GM) crops include transgene flow to compatible wild species and unintended ecological consequences of potential transgene introgression. However, there has been little empirical documentation of establishment and distribution of transgenic plants in wild populations. We present herein the first evidence for escape of transgenes into wild plant populations within the USA; glyphosate-resistant creeping bentgrass (Agrostis stolonifera L.) plants expressing CP4 EPSPS transgenes were found outside of cultivation area in central Oregon. Resident populations of three compatible Agrostis species were sampled in nonagronomic habitats outside the Oregon Department of Agriculture control area designated for test production of glyphosate-resistant creeping bentgrass. CP4 EPSPS protein and the corresponding transgene were found in nine A. stolonifera plants screened from 20,400 samples (0.04 +/- 0.01% SE). CP4 EPSPS-positive plants were located predominantly in mesic habitats downwind and up to 3.8 km beyond the control area perimeter; two plants were found within the USDA Crooked River National Grassland. Spatial distribution and parentage of transgenic plants (as confirmed by analyses of nuclear ITS and chloroplast matK gene trees) suggest that establishment resulted from both pollen-mediated intraspecific hybridizations and from crop seed dispersal. These results demonstrate that transgene flow from short-term production can result in establishment of transgenic plants at multi-kilometre distances from GM source fields or plants. Selective pressure from direct application or drift of glyphosate herbicide could enhance introgression of CP4 EPSPS transgenes and additional establishment. Obligatory outcrossing and vegetative spread could further contribute to persistence of CP4 EPSPS transgenes in wild Agrostis populations, both in the presence or absence of herbicide selection.
M1.3 – a small scaffold for DNA origami (2012)

The DNA origami method produces programmable nanoscale objects that form when one long scaffold strand hybridizes to numerous oligonucleotide staple strands. One scaffold strand is dominating the field: M13mp18, a bacteriophage-derived vector 7249 nucleotides in length. The full-length M13 is typically folded by using over 200 staple oligonucleotides. Here we report the convenient preparation of a 704 nt fragment dubbed "M1.3" as a linear or cyclic scaffold and the assembly of small origami structures with just 15-24 staple strands. A typical M1.3 origami is large enough to be visualized by TEM, but small enough to show a cooperativity in its assembly and thermal denaturation that is reminiscent of oligonucleotide duplexes. Due to its medium size, M1.3 origami with globally modified staples is affordable. As a proof of principle, two origami structures with globally 5'-capped staples were prepared and were shown to give higher UV-melting points than the corresponding assembly with unmodified DNA. M1.3 has the size of a gene, not a genome, and may function as a model for gene-based nanostructures. Small origami with M1.3 as a scaffold may serve as a workbench for chemical, physical, and biological experiments.
Requirements for the self-directed replication of flock house virus RNA 1 (1995)

The larger segment (RNA 1) of the bipartite, positive-sense RNA genome of the nodavirus flock house virus encodes the viral RNA-dependent RNA polymerase. Two nonstructural viral proteins are made during the self-directed replication of this RNA: protein A (110 kDa), the translation product of RNA 1 itself, and protein B (11 kDa), the translation product of a subgenomic RNA (RNA 3) that is produced from RNA 1 during replication. To examine the roles of these proteins in RNA replication, specialized T7 transcription plasmids that contained wild-type or mutant copies of flock house virus RNA 1 cDNA were constructed and used in cells infected with the vaccinia virus-T7 RNA polymerase recombinant to make full-length transcripts that directed their own replication. Sequences in the primary transcripts that extended beyond the ends of the authentic RNA 1 sequence inhibited self-directed RNA replication, but plasmids that were constructed to minimize these terminal extensions produced primary transcripts that replicated as abundantly as authentic RNA 1. Truncation or mutation of the open reading frame for protein A eliminated self-directed replication, although the mutant RNA 1 remained a competent template for replication by wild-type protein A supplied in trans. These results showed that protein A was essential for RNA replication and that the process was not inseparably coupled to complete translation of the template. In contrast, protein B could be eliminated without inhibiting replication by mutations that disrupted the second of the two overlapping open reading frames on RNA 3. Furthermore, a mutant of RNA 1 in which the first nucleotide of the RNA 3 region was changed from G to U replicated at levels as high as those of the wild type without making either RNA 3 or protein B. However, diminishing replication levels were observed during subsequent replicative passages of RNA from both the mutants that could not make protein B. Roles for this protein that could account for the subtle phenotype of these mutants are discussed.
Sensitive Detection of Prostatic Hematogenous Tumor Cell Dissemination Using Prostate Specific Antigen and Prostate Specific Membrane-Derived Primers in the Polymerase Chain Reaction (1995)

We developed a polymerase chain reaction based assay enabling sensitive detection of hematogenous tumor cell dissemination in patients with prostate cancer. We performed "nested polymerase chain reaction," amplifying messenger ribonucleic acid sequences unique to prostate specific antigen (PSA) and to the prostate specific membrane antigen, and compared the respective results. Prostatic tumor cells were detected in 2 of 30 patients (6.7%) by polymerase chain reaction with PSA derived primers, while prostate specific membrane primers detected tumor cells in 19 (63.3%). All 16 negative controls had negative PSA and prostate specific membrane polymerase chain reaction. Assays were repeated to confirm results, and polymerase chain reaction products were verified by deoxyribonucleic acid sequencing and Southern analysis. Patients harboring circulating prostatic tumor cells as detected by prostate specific membrane and not by PSA polymerase chain reaction included 7 of 13 previously treated by radical prostatectomy who had nonmeasurable serum PSA levels at the time of this assay. The significance of these findings with respect to future disease recurrence and progression will be investigated.