gebhart/patrepeval huggingface dataset:
A novel interference suppression scheme for global navigation satellite systems using antenna array (2005)

This paper considers interference suppression and multipath mitigation in Global Navigation Satellite Systems (GNSSs). In particular, a self-coherence anti-jamming scheme is introduced which relies on the unique structure of the coarse/acquisition (C/A) code of the satellite signals. Because of the repetition of the C/A-code within each navigation symbol, the satellite signals exhibit strong self-coherence between chip-rate samples separated by integer multiples of the spreading gain. The proposed scheme utilizes this inherent self-coherence property to excise interferers that have different temporal structures from that of the satellite signals. Using a multiantenna navigation receiver, the proposed approach obtains the optimal set of beamforming coefficients by maximizing the cross correlation between the output signal and a reference signal, which is generated from the received data. It is demonstrated that the proposed scheme can provide high gains toward all satellites in the field of view, while suppressing strong interferers. By imposing constraints on the beamformer, the proposed method is also capable of mitigating multipath that enters the receiver from or near the horizon. No knowledge of either the transmitted navigation symbols or the satellite positions is required.
Prospects and limitations of recombinant poxviruses for prostate cancer immunotherapy. (1999)

Prostate cancer is a disease that may be amenable to immunotherapy approaches, as evidenced by the ability to induce human cytotoxic immune responses against prostate cancer cells. Recent interest in recombinant poxvirus vaccines coupled with the need for new prostate cancer therapies has led to the development of several recombinant poxvirus agents designed for prostate cancer treatment. Whether these agents will be effective in treating prostate cancer is under investigation in several ongoing and upcoming clinical trials. In the meantime, data from preclinical tumor models have provided information that may aid in improving recombinant poxviruses for clinical use. While animal studies have shown the ability of recombinant poxvirus vaccination to induce an immune response that protects against lethal tumor, these antitumor effects are variable and depend on a number of factors. Co-expression of immunomodulating gene products, such as cytokines and costimulatory molecules, have been shown to influence antitumor immunity; in fact, cytokine delivery alone can be enough to protect against tumor-related death. Patterns and levels of recombinant antigen expression also affect the immune response to that antigen, as seen by studies of various poxvirus promoters and cell compartment-targeting sequences. In addition, vaccine strategies targeting self-antigens have shown that immunological tolerance can negatively impact the induction of antitumor and antigen-specific immunity. Although vaccinia virus has been most intensely studied thus far, other poxviruses, including fowlpox and canarypox, are also promising vaccine candidates. These alternative vectors may circumvent some of the disadvantages associated with vaccinia virus, such as pre-existing vaccinia immunity. A deeper understanding of these factors and others that impact the development of antitumor immunity will be necessary to guide the development of recombinant poxviruses for prostate cancer therapy.
Proliferation and differentiation of fetal rat intestinal epithelial cells in primary serum-free culture (1992)

It has been a subject of controversy whether fibroblastic cells are necessary for the proliferation of intestinal epithelial cells in primary culture. To answer this question, we have developed a serum-free primary culture system which allows reproducible and quantitative assays of proliferation and differentiation of fetal rat intestinal epithelial cells in the absence of fibroblastic cells. Pure intestinal epithelial tissues were obtained from 16.5-day fetal rats without contamination of mesenchymal cells, and were successfully cultured on a collagen gel in a medium consisting of Ham's F12, bovine serum albumin, epidermal growth factor (EGF), insulin, cholera toxin, transferrin and hydrocortisone. The epithelial nature of the cultured cells was confirmed by the presence of cytokeratin in the cells. Under optimal culture conditions, intestinal epithelial cells readily attached to the substratum in a day, and proliferated rapidly in vitro, increasing their number about 10 times in the first 5 days. EGF, insulin, cholera toxin, transferrin and hydrocortisone synergistically induced the epithelial proliferation, and lack of any one of them resulted in a significant reduction of the proliferation. In contrast, fetal bovine or horse serums, which have been widely used to supplement culture media, severely inhibited the epithelial proliferation. Histological examination showed that the epithelial cells formed simple cuboidal epithelia with basally-located nuclei when cultured on collagen gels. The intestinal epithelial nature of the cells was affirmed by the presence of villin on their luminal surface. Ultrastructurally, cells were connected by tight junctions and desmosomes at the subluminal region, and microvilli were projecting on the luminal surface, indicating that the cells in primary culture retained some characteristics of absorptive epithelial cells.(ABSTRACT TRUNCATED AT 250 WORDS)
BIC and miR‐155 are highly expressed in Hodgkin, primary mediastinal and diffuse large B cell lymphomas (2005)

In a previous study we demonstrated high expression of the non-coding BIC gene in the vast majority of Hodgkin's lymphomas (HLs). Evidence suggesting that BIC is a primary microRNA transcript containing the mature microRNA-155 (miR-155) as part of a RNA hairpin is now accumulating. We therefore analysed HL cell lines and tissue samples to determine whether miR-155 is also expressed in HL. High levels of miR-155 could be demonstrated, indicating that BIC is processed into a microRNA in HL. Most non-HL subtypes were negative for BIC as determined by RNA-ISH. However, in diffuse large B cell lymphoma (DLBCL) and primary mediastinal B cell lymphoma (PMBL), significant percentages of positive tumour cells were observed in 12/18 and 8/8 cases. A higher proportion of tumour cells were positive for BIC in DLBCL with activated B cell-like phenotype than in DLBCL with germinal centre B cell-like phenotype. Differential BIC expression was confirmed by qRT-PCR analysis. Northern blot analysis showed expression of miR-155 in all DLBCL and PMBL derived cell lines and tissue samples analysed. In summary, we demonstrate expression of primary microRNA BIC and its derivative miR-155 in HL, PMBL and DLBCL.
Circulating melanoma cells and survival in metastatic melanoma (2011)

A validated assay for the enumeration of circulating melanoma cells (CMCs) may facilitate the development of more effective therapies for metastatic melanoma patients. In this study CD146+ cells were immunomagnetically enriched from 7.5 ml of blood. Isolated cells were fluorescently stained with DAPI, anti-molecular weight melanoma-associated antigen (HMW-MAA), anti-CD45 and CD34 and Ki67. CMCs were identified as CD146+, HMW-MAA+, CD45-, CD34-, Ki67-/+ cells. Eighty-eight percent of spiked SK-MEL28 cells in 7.5 ml blood were recovered. In all 55 healthy donors ≤1 CMCs were detected in 7.5 ml of blood. A retrospective analysis was conducted comparing CMC counts and overall survival in 79 blood samples from 44 melanoma patients. CMCs ranged from 0 to 8,042 per 7.5 ml. Two or more CMCs were detected in 18 (23%) of the patients and 30-100% (mean 84%) of the CMCs expressed the proliferation marker Ki67. Patients with ≥2 CMCs per 7.5 ml of whole blood, as compared with the group with <2 CMCs, had a shorter overall survival (2.0 months vs. 12.1 months, P=0.001).
Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs (2010)

The N(1)-methyl-Adenosine (m(1)A58) modification at the conserved nucleotide 58 in the TPsiC loop is present in most eukaryotic tRNAs. In yeast, m(1)A58 modification is essential for viability because it is required for the stability of the initiator-tRNA(Met). However, m(1)A58 modification is not required for the stability of several other tRNAs in yeast. This differential m(1)A58 response for different tRNA species raises the question of whether some tRNAs are hypomodified at A58 in normal cells, and how hypomodification at A58 may affect the stability and function of tRNA. Here, we apply a genomic approach to determine the presence of m(1)A58 hypomodified tRNAs in human cell lines and show how A58 hypomodification affects stability and involvement of tRNAs in translation. Our microarray-based method detects the presence of m(1)A58 hypomodified tRNA species on the basis of their permissiveness in primer extension. Among five human cell lines examined, approximately one-quarter of all tRNA species are hypomodified in varying amounts, and the pattern of the hypomodified tRNAs is quite similar. In all cases, no hypomodified initiator-tRNA(Met) is detected, consistent with the requirement of this modification in stabilizing this tRNA in human cells. siRNA knockdown of either subunit of the m(1)A58-methyltransferase results in a slow-growth phenotype, and a marked increase in the amount of m(1)A58 hypomodified tRNAs. Most m(1)A58 hypomodified tRNAs can associate with polysomes in varying extents. Our results show a distinct pattern for m(1)A58 hypomodification in human tRNAs, and are consistent with the notion that this modification fine tunes tRNA functions in different contexts.
Clusterin Plays an Important Role in Clear Renal Cell Cancer Metastasis (2013)

&lt;b&gt;&lt;i&gt;Objective:&lt;/i&gt;&lt;/b&gt; Clusterin (CLU) is implicated in regulating clear renal cell carcinoma (CRCC) progression and metastasis, yet the mechanisms are not elucidated. In the present study, we explored the potential role of CLU in CRCC metastasis. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; Levels of CLU mRNA and CLU protein were measured by RT-PCR and immunohistochemistry analysis in 22 CRCC with metastasis and 22 without metastasis and 22 samples of normal kidney tissue. After CLU silencing and re-expression, the migration and invasion in vitro and in vivo of Caki-2 cells were determined by wound healing assay, transwell migration assay and pulmonary nodule assay, respectively. The expression of pERK1/2 and MMP-9 were detected by RT-PCR and Western blot assay. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; We found a significant increase of CLU and CLU mRNA expression in CRCC, and the expression of CLU is strongly correlated in patients with metastatic disease. We discovered that CLU-rich Caki-2 cells displayed higher invasive ability which prompted us to investigate if CLU silencing could reduce the migration and invasion in Caki-2 cells. Compared with the vector-transfected cells, CLU knocked-down (CLUi) cells showed reduced migration and invasion in vitro, as well as decreased metastatic potential in experimental metastasis. Re-expression of CLU in CLUi cells restored the invasive phenotypes. We found that MMP-9 was downregulated in CLUi cells. We also discovered that levels of activated ERK1/2 correlated with the rich expression of CLU and MMP-9. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; Our data suggest that CLU may regulate aggressive behavior of human CRCC cells through modulating ERK1/2 signaling and MMP-9 expression.
Induction of Potent Immune Responses by Cationic Microparticles with Adsorbed Human Immunodeficiency Virus DNA Vaccines (2001)

The effectiveness of cationic microparticles with adsorbed DNA at inducing immune responses was investigated in mice, guinea pigs, and rhesus macaques. Plasmid DNA vaccines encoding human immunodeficiency virus (HIV) Gag and Env adsorbed onto the surface of cationic poly(lactide-coglycolide) (PLG) microparticles were shown to be substantially more potent than corresponding naked DNA vaccines. In mice immunized with HIV gag DNA, adsorption onto PLG increased CD8(+) T-cell and antibody responses by approximately 100- and approximately 1,000-fold, respectively. In guinea pigs immunized with HIV env DNA adsorbed onto PLG, antibody responses showed a more rapid onset and achieved markedly higher enzyme-linked immunosorbent assay and neutralizing titers than in animals immunized with naked DNA. Further enhancement of antibody responses was observed in animals vaccinated with PLG/DNA microparticles formulated with aluminum phosphate. The magnitude of anti-Env antibody responses induced by PLG/DNA particles was equivalent to that induced by recombinant gp120 protein formulated with a strong adjuvant, MF-59. In guinea pigs immunized with a combination vaccine containing HIV env and HIV gag DNA plasmids on PLG microparticles, substantially superior antibody responses were induced against both components, as measured by onset, duration, and titer. Furthermore, PLG formulation overcame an apparent hyporesponsiveness of the env DNA component in the combination vaccine. Finally, preliminary data in rhesus macaques demonstrated a substantial enhancement of immune responses afforded by PLG/DNA. Therefore, formulation of DNA vaccines by adsorption onto PLG microparticles is a powerful means of increasing vaccine potency.
Input couplers for thin light-guides and light-emitting diodes (2008)

As the demand toward a thin liquid crystal display accelerates, a backlight system must become thinner. Compact and efficient coupling of an LED to a thin light-guide is one of the key technologies. First, we consider simple face-down and prism coupling, and carry out experiments using a chip-type LED with a 2.4-mm-diam emission area and a 3.0-mm-thick light-guide. Face-down coupling guides only 12% of the LED output into the light-guide. With a right-angle prism, the efficiency is improved to 23%. We try to improve the coupling efficiency by altering the propagation direction of the light with an optical film. However, our experiments and simulations with off-the-shelf prism sheets and diffuser films show that the coupling efficiency decreases. Next, we carry out ray-tracing simulations for various input coupler designs. A chip-type LED with a 0.42-mm-diam emission area and a 0.1-mm-thick light-guide are assumed. Calculated efficiency greater than 50% is obtained by a square prism mounted obliquely on the light-guide, while the footprint of the coupler is about 1.3 mm. An input coupler based on an oblique cylinder improves the calculated efficiency to 73.5% at the expense of its footprint of 4.82 mm.
A 90-ns one-million erase/program cycle 1-Mbit flash memory (1989)

Describes the design and performance of a 245-mil/sup 2/ 1-Mbit (128K*8) flash memory targeted for in-system reprogrammable applications. Developed from a 1.0- mu m EPROM-base technology, the 15.2- mu m/sup 2/ single-transistor EPROM tunnel oxide (ETOX) cell requires only 42 percent of the area required by the previous 1.5- mu m device. One of the most significant aspects of this 1-Mbit flash memory is the one-million erase/program cycle capability. The 1-Mbit memory exhibits 90-ns read access time while the reprogramming performance gives a 900-ms array erase time and a 10- mu s/byte programming rate. Ample erase and program margins through one-million erase/program cycles are guaranteed by the internal verify circuits. Column redundancy is implemented with the utilization of flash memory cells to store repaired addresses.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Exploiting tumor metabolism: challenges for clinical translation (2013)

The metabolism of cancer cells differs from most normal cells, but how to exploit this difference for patient benefit is incompletely understood. Cancer cells require altered metabolism to efficiently incorporate nutrients into biomass and support abnormal proliferation. In addition, the survival of tumor cells outside of a normal tissue context requires adaptation of metabolism to different microenvironments. Some existing chemotherapies target metabolic enzymes, and there is a resurgent interest in developing new cancer drugs that interfere with metabolism. Success with this approach depends on understanding why specific metabolic pathways are important for cancer cells, determining how best to select patients, and developing technologies for monitoring patient response to therapies that target metabolic enzymes. The articles in this Review series address these issues, with a focus on how altered metabolism might influence tumor progression and how this knowledge might inform the use of new therapies targeting cancer metabolism. Emerging biomarker strategies to guide drug development are also highlighted.
Establishment of pure neuronal cultures from fetal rat spinal cord and proliferation of the neuronal precursor cells in the presence of fibroblast growth factor (1991)

A primary culture system of nearly pure neuronal cells from 14-day-old fetal rat spinal cord has been developed by combining a preplating step, the use of a chemically defined serum-free medium, and borated polylysine-coated dishes that prevented the formation of cell aggregates. About 98% of the cells were found to be immunostained with neuron-specific enolase antibodies, confirming their neuronal nature. The cultures are composed essentially of a population of non-motoneurons and contain few motoneurons, characterized by their large size and multipolar aspect, the presence of acetylcholinesterase (AChE), and the intense immunoreaction for growth-associated protein GAP-43. Neuronal precursor cells are also present in these cultures and proliferate during the first 3 days. The addition of bovine brain basic fibroblast growth factor (bFGF) stimulates their proliferation over a period of 2 days, as determined by measurement of [125I]iododeoxyuridine incorporation and by immunocytochemical reaction after bromodeoxyuridine incorporation into nuclei. The proliferating cells were characterized as neurons by immunostaining against neuron-specific enolase. Recombinant human bFGF and bovine brain acidic FGF (aFGF) exerted similar effects. Other growth factors, including epidermal growth factor (EGF), transforming growth factor beta 1 (TGF-beta 1), and thrombin, were without effect on the proliferative activity of these neuronal cells. bFGF has no effect on the survival of motoneurons and on the fiber outgrowth of the whole neuronal population. However, bFGF affects the development of bipolar AChE-positive neurons, probably belonging to the non-motoneuron population. The data indicate that bFGF and aFGF are mitogens for neuroblasts from rat spinal cord in culture and that bFGF influences the development of a subpopulation of spinal neurons that are AChE-positive.
Ureaplasma urealyticum in the immunocompromised host (1986)

The lack of antibody in hypogammaglobulinemic patients probably results in failure of mycoplasmas to be "neutralized" and accounts for the diminished ability of the patients to cope with these organisms escaping hematogenously from the respiratory and urogenital tracts. Furthermore Ureaplasma urealyticum and other mycoplasmas are ingested by neutrophils in the absence of opsonins, indicated by the fact that they are able to trigger the release of chemiluminescence from these cells; ureaplasmas are not killed during this process and it is possible that carriage occurs within phagocytes to various sites. Several mycoplasmal species have localized in joints and U. urealyticum organisms are no exception. They have been isolated from the purulent synovial fluids of at least three hypogammaglobulinemic patients in Canada, England and the United States, respectively, the arthritides responding to appropriate antibiotic therapy. In one male patient, however, repeated and prolonged episodes of arthritis over several years, associated with antibiotic-resistant ureaplasmas, responded only to the administration of specific hyperimmune serum. Apart from joint involvement subcutaneous abscesses have been seen, and in the latter patient persistent urethritis was caused by ureaplasmas, these being the only organisms recovered from the urethra. Chronic urethrocystitis/cystitis in hypogammaglobulinemic patients has been associated also with ureaplasmal infection. In addition polyarthritis with recovery of both ureaplasmas and Mycoplasma hominis from the joints has been seen in a kidney allograft patient on an immunosuppressive regimen. However, further evidence that ureaplasmas cause a problem in immunosuppressed patients or in those with the acquired immunodeficiency syndrome is lacking.
Structural analysis of the human inter‐ş‐trypsin inhibitor light‐chain gene (1990)

The human inter-alpha-trypsin inhibitor (ITI) light-chain gene, which codes for the two proteins alpha 1-microglobulin (protein HC) and ITI-derived human inhibitor of 30 kDa (HI-30), was isolated from a human genomic library. This gene, present as a single copy in the human genome, is composed of 10 exons and 9 introns distributed over 20 kbp. A single transcriptional initiation site was identified in the 5'-flanking region which contained promoter elements, but no typical TATA box. However a sequence equivalent to the TATA box is present on both sense and anti-sense strands in the 5'-flanking region of the first exon coding for HI-30. The exon-intron organization suggests that the regions coding for protein HC and other members of the lipocalin superfamily evolved from a common ancestral gene that is probably different from that coding for HI-30. These data suggest that two distinct ancestral genes could have existed and fused during evolution. Several direct and one inverted repeats are also found within this gene, as well as potential glucocorticoid-receptor binding sites.
Translation of the leader region of the Escherichia coli tryptophan operon (1978)

When the trp operon of Escherichia coli contains either of two deletions that fuse the initial portion of the leader region to the distal segments of the trpE gene, novel fusion polypeptides are produced. The new polypeptides are synthesized efficiently both in vivo and in vitro, and their synthesis is subject to repression by trp repressor. Fingerprint analyses of tryptic and chymotryptic digests of the new polypeptides show that both contain trpE polypeptide sequences and, despite their different sizes, share the same N-terminal sequence. Our results suggest that synthesis of the new polypeptides is initiated at the AUG-centered ribosome-binding site in the leader region and proceeds in phase to the region coding for the C-terminal end of the trpE polypeptide.
Cloning and restriction mapping of the alkaline phosphatase structural gene (phoA) of Escherichia coli and generation of deletion mutants in vitro (1981)

The structural gene for alkaline phosphatase (phoA) of Escherichia coli was cloned into the PstI site of pBR322, from a transducing bacteriophage, lambda p(phoA-proC). The restriction map of the plasmid was established. Based upon this information, several phoA deletion plasmids as well as a smaller phoA+ plasmid were constructed. The genetic map and restriction map were correlated by recombination analysis. Cells carrying one of the phoA+ plasmids overproduce alkaline phosphatase 10-fold upon phosphate limitation. However, both regulation and processing of the enzyme were found to be normal.