gebhart/patrepeval huggingface dataset:
List Viterbi algorithms for wireless systems (2002)

The conventional list Viterbi algorithm (LVA) produces a list of the L best output sequences over a certain block length in decoding a terminated convolutional code. We show in this paper that the list Viterbi algorithm with a sufficiently long list is the optimum maximum likelihood decoder for the concatenated pair of a convolutional code and a cyclic redundancy check (CRC) block code with error detection. The CRC is used to select the output. New LVAs for continuous transmission are proposed and evaluated, where no termination bits are required for the convolutional code for every CRC block. For broadcasting high quality digital audio signals it is beneficial to use error concealment/error mitigation techniques to avoid the worst type of channel errors. We demonstrate how the LVA can significantly reduce the error mitigation flag rate compared to the regular VA for the same transmission parameters. A receiver optional LVA can reduce the flag rate by more than an order of magnitude.
HPMA Copolymer-Anticancer Drug-OV-TL16 Antibody Conjugates. 1. Influence of the Method of Synthesis on the Binding Affinity to OVCAR-3 Ovarian Carcinoma Cells in Vitro (1996)

The influence of different methods of binding the OV-TL16 antibody and its Fab' fragment to N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer--drug (adriamycin [ADR] or meso chlorin e6 mono(N-2-aminoethylamide) (Mce6)) conjugates on the affinity of conjugates to an ovarian carcinoma (OVCAR-3) cell associated antigen was investigated. The binding of the antibody to HPMA copolymer--drug (ADR or Mce6) conjugates via amino groups resulted in conjugates which were heterogeneous in their antigen binding. Coupling, the HPMA copolymer--Mce6 conjugate to the carbohydrate region of the antibody resulted in conjugates with a more homogeneous distribution of affinity constants than conjugates prepared by linking the antibody to the polymer via amino groups. However, both methods resulted in a decrease in the affinity constant compared to the native antibody. Conjugates prepared with the Fab' frgment of the OV-TL16 antibody demonstrated a more homogenous affinity than either conjugate prepared with the whole antibody. To verify the hypothesis that the changes in the binding affinity and homogeneity are a consequence of conformational changes in the antibody structure, a series of physiocochemical methods were employed to characterize the conjugates. The excitation energy transfer between OV-TL16 antibody and drugs (ADR and Mce6) and the spectral properties of Mce6 were used to monitor the interactions between the antibody and drugs. The quenching of the intrinsic fluorescence of the antibody was also employed to study its conformational changes. An attempt has been made to correlate the biorecognition at the cellular surface with the interactions of drug with the antibody molecule and with the changes in antibody conformation.
Immunoglobulin kappa light chain variable region gene complex organization and immunoglobulin genes encoding anti-DNA autoantibodies in lupus mice. (1988)

We have investigated the genetic origin of autoantibody production in several strains of mice that spontaneously develop a systemic lupus erythematosus-like disease. Restriction fragment length polymorphism analyses of gene loci encoding kappa light chain variable regions (Igk-V) demonstrated, as shown previously for the Ig heavy chain locus, that autoantibody production and disease occur in different Igk-V haplotypes. Moreover, autoimmune mice with known genetic derivation inherited their Igk-V loci essentially unaltered from their nonautoimmune ancestors. New Zealand black lupus mice, with unknown genetic derivation, had a possibly recombinant Igk-V haplotype, composed of V kappa loci that were primarily indistinguishable from those of nonautoimmune strains from either of the two potential donor haplotypes. The heavy and light chain gene segments (variable, diversity, joining) encoding anti-DNA antibodies were diverse and often closely related, or even identical, to those found in antibodies to foreign antigens in normal mice. Only 1 of 11 sequenced variable region genes could not be assigned to existing variable region gene families; however, corresponding germline genes were present in the genome of normal mice as well. These data argue against abnormalities in the genes and mechanisms generating antibody diversity in lupus mice and suggest a remarkable genetic and structural diversity in the generation of anti-DNA binding sites.
Identification and Characterization of an Activating TrkA Deletion Mutation in Acute Myeloid Leukemia (2000)

In this study, we utilized retroviral transfer of cDNA libraries in order to identify oncogenes that are expressed in acute myeloid leukemia (AML). From screens using two different cell types as targets for cellular transformation, a single cDNA encoding a variant of the TrkA protooncogene was isolated. The protein product of this protooncogene, TrkA, is a receptor tyrosine kinase for nerve growth factor. The isolated transforming cDNA encoded a TrkA protein that contains a 75-amino-acid deletion in the extracellular domain of the receptor and was named DeltaTrkA. DeltaTrkA readily transformed fibroblast and epithelial cell lines. The deletion resulted in activation of the tyrosine kinase domain leading to constitutive tyrosine phosphorylation of the protein. Expression of DeltaTrkA in cells led to the constitutive activation of intracellular signaling pathways that include Ras, extracellular signal-regulated kinase/mitogen-activated protein kinase, and Akt. Importantly, DeltaTrkA altered the apoptotic and growth properties of 32D myeloid progenitor cells, suggesting DeltaTrkA may have contributed to the development and/or maintenance of the myeloid leukemia from which it was isolated. Unlike Bcr-Abl, expression of DeltaTrkA did not activate Stat5 in these cells. We have detected expression of DeltaTrkA in the original AML sample by reverse transcriptase PCR and by Western blot analysis. While previous TrkA mutations identified from human tumors involved fusion to other proteins, this report is the initial demonstration that deletions within TrkA may play a role in human cancers. Finally, this report is the first to indicate mutations in TrkA may contribute to leukemogenesis.
Ligand-regulated site-specific recombination. (1995)

Site-specific recombination offers a potential way to alter a living genome by design in a precise and stable manner. This potential requires strategies which can be used to regulate the recombination event. We describe a strategy to regulate FLP recombinase activity which relies on expressing FLP as a fusion protein with steroid hormone receptor ligand binding domains (LBDs). In the absence of a ligand cognate to the LBD, the recombinase activity of the fusion protein is extremely low. Upon ligand administration, recombinase activity is rapidly induced. These results outline the basis for inducible expression or disruption strategies based on inducible recombination. Additionally, we have exploited the conditional nature of FLP-LBD fusion proteins to direct integration of a plasmid into a specific genomic site at frequencies approaching the frequency of random integration.
Pressure-induced mesomorphic transition of a liquid-crystalline polyester at high temperatures (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPressure-induced mesomorphic transition of a liquid-crystalline polyester at high temperaturesYoji Maeda and Junji WatanabeCite this: Macromolecules 1993, 26, 2, 401–403Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/ma00054a023https://doi.org/10.1021/ma00054a023research-articleACS PublicationsRequest reuse permissionsArticle Views81Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Vitamin D-3,5-cyclovitamin D rearrangement (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVitamin D-3,5-cyclovitamin D rearrangementMordechai Sheves and Yehuda MazurCite this: J. Am. Chem. Soc. 1975, 97, 21, 6249–6250Publication Date (Print):October 1, 1975Publication History Published online1 May 2002Published inissue 1 October 1975https://pubs.acs.org/doi/10.1021/ja00854a053https://doi.org/10.1021/ja00854a053research-articleACS PublicationsRequest reuse permissionsArticle Views171Altmetric-Citations35LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Targeted cellular ablation based on the morphology of malignant cells (2015)

Treatment of glioblastoma multiforme (GBM) is especially challenging due to a shortage of methods to preferentially target diffuse infiltrative cells, and therapy-resistant glioma stem cell populations. Here we report a physical treatment method based on electrical disruption of cells, whose action depends strongly on cellular morphology. Interestingly, numerical modeling suggests that while outer lipid bilayer disruption induced by long pulses (~100 μs) is enhanced for larger cells, short pulses (~1 μs) preferentially result in high fields within the cell interior, which scale in magnitude with nucleus size. Because enlarged nuclei represent a reliable indicator of malignancy, this suggested a means of preferentially targeting malignant cells. While we demonstrate killing of both normal and malignant cells using pulsed electric fields (PEFs) to treat spontaneous canine GBM, we proposed that properly tuned PEFs might provide targeted ablation based on nuclear size. Using 3D hydrogel models of normal and malignant brain tissues, which permit high-resolution interrogation during treatment testing, we confirmed that PEFs could be tuned to preferentially kill cancerous cells. Finally, we estimated the nuclear envelope electric potential disruption needed for cell death from PEFs. Our results may be useful in safely targeting the therapy-resistant cell niches that cause recurrence of GBM tumors.
Substrate isolation in 90nm RF-CMOS technology (2005)

Substrate coupling on advanced high-speed and RF integrated circuits can have a significant impact on circuit performances. This parasitic effect is studied in the present paper in a triple-well 90nm RF-CMOS technology. Various configurations are investigated, like distance between blocks, use of P or N type guard-rings and use of triple-well junction isolation. Electrical models are proposed for these structures. At 1GHz and for a distance between blocks of 20 /spl mu/m, a grounded P-ring improves the isolation by 15 dB compared to the case without guard ring. The most efficient protection to limit substrate coupling is a grounded P-ring around each block, placed at 20/spl mu/m. In this case, the maximum isolation level is achieved with 60dB at 1GHz.
Broadband network infrastructure of the future: roles of network design tools in technology deployment strategies (1998)

The rapid pace of technology introduction in the network infrastructure and services offered on this infrastructure are creating new challenges for telecommunication product and network planners. In particular, a multitude of choices, the unpredictability of future technologies and traffic, the need to operate heterogeneous networks, and the speed of change create a need for a set of tools which allow quantitative evaluation of alternatives quickly in early phases of decision making while allowing the same tools to migrate to more elaborate deployment help during the later stages. We have begun an effort to create such a set of tools under the umbrella of integrated network design tools (INDT). In this article, we describe key challenges and approaches used in INDT to meet these challenges. We also discuss the algorithmic and software architecture of INDT, and illustrate its use via examples from transport infrastructure evolution. Finally, we describe the migration path of INDT to move from early decision help to later deployment support tools. Specific topics discussed include: plesiosynchronous digital hierarchy, SONET/SDH systems, ATM, network topologies, traffic types and routing.
Accelerating two-dimensional page walks for virtualized systems (2008)

Nested paging is a hardware solution for alleviating the software memory management overhead imposed by system virtualization. Nested paging complements existing page walk hardware to form a two-dimensional (2D) page walk, which reduces the need for hypervisor intervention in guest page table management. However, the extra dimension also increases the maximum number of architecturally-required page table references.
ω-functionalized self-assembled monolayers chemisorbed on ultraflat Au(111) surfaces for biological scanning probe microscopy in aqueous buffers (1996)

Two immobilization procedures for ultimately carrying out scanning probe microscopy of native biological macromolecules in buffer solution are presented. They are based on the preparation of ultraflat template-stripped gold surfaces and subsequent chemisorption of bioreactive ω-functionalized self-assembled monolayers. Immobilization was achieved either via amide bond formation or diazo linkage. The first was carried out using a long-chain N-hydroxysuccinimide-ester functionalized disulfide, which binds amino-group-containing biomacromolecules under mild conditions. The latter was performed via chemisorption of a nitrobenzylalkylthiol, followed by in situ transformation to the active diazo intermediate. Typical targets were activated aromatic hydrogens, such as phenolic or imidazole groups. The preparation of these monolayers, their characterization by scanning tunneling microscopy and radiolabeling, and as an example the in situ atomic force microscopy study of clathrin cages under native conditions in appropriate buffers are presented.
Localization and photosensitization of murine tumors in vivo and in vitro by a chlorin-porphyrin ester. (1986)

Preparation of the tumor-localizing preparation called hematoporphyrin derivative involves a two-step reaction wherein hematoporphyrin is acetylated and the reaction product subjected to alkaline hydrolysis. We have proposed that the tumor-localizing fraction of this product is composed of hematoporphyrin units joined by ester linkages. Using an analogous synthetic procedure, we prepared some new sensitizers in which hematoporphyrin is esterified to chlorins (reduced porphyrins). Because of the differences in absorption spectra, the porphyrin-chlorin esters are 5-fold more potent photosensitizers than are the porphyrin-porphyrin esters, with light of wavelength greater than 600 nm.
IGF-1 Signaling Enhances Cell Survival in Periodontal Ligament Fibroblasts vs. Gingival Fibroblasts (2003)

The role of insulin-like growth factors (IGFs) in the regulation of apoptosis has been suggested, yet their impact on specific cells such as periodontal ligament fibroblasts (PDLF) and gingival fibroblasts (GF) remains unknown. The purpose of this study was to test the role of IGF-1 signaling in cell survival in PDLF compared with GF. In periodontal tissue sections, a significantly reduced apoptotic rate was first demonstrated in PDLF compared with GF. In vitro, IGF-1 substantially enhanced cell survival in PDLF compared with GF by the up-regulation of anti-apoptotic molecules and the down-regulation of pro-apoptotic molecules. Furthermore, the differential expression of insulin-like growth factor binding protein 5 (IGFBP-5) was observed in vitro, and its differential distribution was confirmed in vivo. Analysis of the present data suggests an enhanced cell survival in PDLF compared with GF by the up-regulation of IGF-1 signaling pathway.
Construction and analysis of simian virus 40 origins defective in tumor antigen binding and DNA replication. (1980)

We have inserted a 311-base pair DNA fragment containing the simian virus 40 (SV40) origin of DNA replication, the early promoter, and the tumor (T) antigen binding sites into a bacterial plasmid and cloned it. This recombinant plasmid, pSV01, binds to a purified T antigen in vitro and replicates in monkey cells when supplied with large T antigen. A series of deletion mutations was generated in the origin sequences of pSV01 DNA by mutagenesis in vitro. The replication of these mutant DNAs in monkey cells was compared with their ability to bind to purified D2 protein. Mutant DNAs deficient in binding to D2 protein also exhibit reduced levels of replication in monkey cells. These findings provide biochemical evidence that the initiation of SV40 DNA synthesis may involve a direct interaction of T antigen with sequences at the origin of replication.
Parathyroid Hormone Rapidly Stimulates Hyaluronan Synthesis by Periosteal Osteoblasts in the Tibial Diaphysis of the Growing Rat (2003)

Short term treatment (3-24 h) with parathyroid hormone (PTH) stimulated the synthesis and accumulation of hyaluronan (HyA) in explant cultures of tibial diaphyses from young rats. PTH increased the overall HyA content of periosteum 5-fold, with the basal cambium layer exhibiting the greatest enhancement ( approximately 8-fold). PTH increased the HyA content of cortical bone by 2-fold while not affecting the HyA content of bone marrow. PTH treatment greatly enhanced HyA staining throughout all layers of the periosteum, although its most dramatic effect occurred in the basal cambium layer. Here, unlike in the control tissue sections, nearly all cambium-lining osteoblasts stained intensely positive for HyA. PTH treatment enhanced the HyA staining of osteocytes in cortical bone tissue sections to the extent that the lacunocanalicular system became visualized. Three significant findings were revealed in this study. First, mature periosteal osteoblasts, under natural conditions, do not contain much HyA in their surrounding extracellular matrix but dramatically enhance their matrix HyA content when treated with PTH. Second, pre-osteocytes and osteocytes contain more HyA in their natural matrix than mature lining osteoblasts, and they appear to have functional PTH receptors because they responded to PTH treatment with an enhancement of HyA content. Finally, it was observed that the lining cells along the endosteal surface of the diaphysis did not stain strongly positive for HyA either naturally or when exposed to PTH treatment. This indicates that periosteal and endosteal osteoblastic cell populations exhibit metabolic differences in their extracellular matrix responses to PTH.
Management of refractory urinary urge incontinence following urogynecological surgery with sacral neuromodulation (2006)

Sacral neuromodulation appears to be an effective therapy in patients with refractory urge incontinence following urogynecological surgery. Larger prospective studies with longer follow-up are needed to assess the durability of this therapeutic modality.
Human Papillomavirus Testing for Cervical Cancer Screening: Results From a 6-Year Prospective Study in Rural China (2009)

Long-term follow-up evaluations of cervical screening approaches are limited in low-resource areas. This prospective study assessed the risk of future cervical intraepithelial neoplasia grade 2 or worse (CIN2+) associated with baseline human papillomavirus (HPV) and cytologic status. In rural China, 1,997 women were screened with 6 screening tests, including colposcopic evaluations, and underwent biopsies in 1999. In December 2005, 1,612 women with cervical intraepithelial neoplasia grade 1 or less at baseline were rescreened by visual inspection, liquid-based cytology, and HPV-DNA testing. All women underwent colposcopy at follow-up, with biopsies taken from women with visually apparent lesions or cytologic abnormalities. Twenty women developed incident CIN2+. The crude relative risk of CIN2+ for baseline HPV-positive women was 52 (95% confidence interval: 12.1, 222.5). The crude relative risk of CIN2+ was 167 (95% confidence interval: 21.9, 1,265) for baseline and follow-up repeatedly HPV-positive women compared with repeatedly HPV-negative women. Among 1,374 baseline HPV-negative women, 2 and no incident CIN2+ cases were detected in baseline cytologically normal and abnormal subgroups, respectively. Among 238 baseline HPV-positive women, 6 of 18 incident cases of CIN2+ developed in the cytologically normal group. This study demonstrates that a single oncogenic HPV-DNA test is more effective than cytology in predicting future CIN2+ status.
Pim Kinase Inhibitors Evaluated with a Single‐Molecule Engineered Nanopore Sensor (2015)

Abstract Protein kinases are critical therapeutic targets. Pim kinases are implicated in several leukaemias and cancers. Here, we exploit a protein nanopore sensor for Pim kinases that bears a pseudosubstrate peptide attached by an enhanced engineering approach. Analyte binding to the sensor peptide is measured through observation of the modulation of ionic current through a single nanopore. We observed synergistic binding of MgATP and kinase to the sensor, which was used to develop a superior method to evaluate Pim kinase inhibitors featuring label‐free determination of inhibition constants. The procedure circumvents many sources of bias or false‐positives inherent in current assays. For example, we identified a potent inhibitor missed by differential scanning fluorimetry. The approach is also amenable to implementation on high throughput chips.