gebhart/patrepeval huggingface dataset:
A statistical modeling approach to location estimation (2002)

Some location estimation methods, such as the GPS satellite navigation system, require nonstandard features either in the mobile terminal or the network. Solutions based on generic technologies not intended for location estimation purposes, such as the cell-ID method in GSM/GPRS cellular networks, are usually problematic due to their inadequate location estimation accuracy. In order to enable accurate location estimation when only inaccurate measurements are available, we present an approach to location estimation that is different from the prevailing geometric one. We call our approach the statistical modeling approach. As an example application of the proposed statistical modeling framework, we present a location estimation method based on a statistical signal power model. We also present encouraging empirical results from simulated experiments supported by real-world field tests.
Molecular analysis of the FHIT gene at 3p14.2 in lung cancer cell lines. (1996)

Chromosome 3p is frequently deleted in various cancers including examples in the lung. A novel gene, termed FHIT, was recently isolated from the fragile site at 3p14.2, with aberrant transcripts being reported in lung cancer tumor specimens. To avoid overlooking tumor-specific altered transcripts due to contaminating normal cells in primary tumors, FHIT alterations were examined in 41 lung cancer cell lines in the present study. Lack of detectable expression or exclusive expression of aberrantly spliced transcripts, often accompanied by intragenic homozygous deletions, were observed in 7 of 24 non-small cell lung cancers (29%) but in 0 of 17 small cell lung cancers (0%). Extensive reverse transcription-PCR-single-strand conformation polymorphism analysis revealed polymorphisms and alternative splicing but failed to identify point mutations. These results suggest distinct mechanisms for FHIT alterations in lung tumorigenesis and that further studies of this interesting gene are warranted.
Biology of Hepatitis B Virus (1981)

Immunochemical investigations of the viral antigens and molecular characterization of the viral DNA have elucidated the nature of the hepatitis B virus infection underlying acute, chronic, and oncogenic disorders of the liver in man. Cloning and sequencing of viral DNA have made possible studies on the structure of the genome and on certain aspects of the biology of the virus, hitherto constrained for a lack of tissue culture systems and laboratory animal models useful in its propagation.
JNK2-dependent regulation of SIRT1 protein stability (2008)

Mammalian SIRT1 is an NAD-dependent deacetylase with critical roles in the maintenance of homeostasis and cell survival. Elevated levels of SIRT1 protein are evident in cancer in which SIRT1 can function as a cancer-specific survival factor. Here we demonstrate that elevated SIRT1 protein in human cells is not attributable to increased SIRT1 mRNA levels but, instead, reflects SIRT1 protein stability. RNAi-mediated depletion of JNK2 reduced the half-life of SIRT1 protein from >9 h to <2 h and this correlated with lack of SIRT1 protein phosphorylation at serine 27. In contrast, depletion of JNK1 had no effect upon SIRT1 protein stability and SIRT1 phosphorylation at serine 47 showed no correlation with SIRT1 protein stability. Thus we show that JNK2 is linked, directly or indirectly, with SIRT1 protein stability and that this function is coupled with SIRT1 phosphorylation at serine 27. Our observations identify a route for therapeutic modulation of SIRT1 protein levels in SIRT1-linked diseases including cancer, neurodegeneration and diabetes.
Cooperative Formation of Inorganic-Organic Interfaces in the Synthesis of Silicate Mesostructures (1993)

A model is presented to explain the formation and morphologies of surfactant-silicate mesostructures. Three processes are identified: multidentate binding of silicate oligomers to the cationic surfactant, preferential silicate polymerization in the interface region, and charge density matching between the surfactant and the silicate. The model explains present experimental data, including the transformation between lamellar and hexagonal mesophases, and provides a guide for predicting conditions that favor the formation of lamellar, hexagonal, or cubic mesostructures. Model Q(230) proposed by Mariani and his co-workers satisfactorily fits the x-ray data collected on the cubic mesostructure material. This model suggests that the silicate polymer forms a unique infinite silicate sheet sitting on the gyroid minimal surface and separating the surfactant molecules into two disconnected volumes.
Requirement for Capsule in Colonization by Streptococcus pneumoniae (2001)

Nasopharyngeal colonization is a necessary first step in the pathogenesis of Streptococcus pneumoniae. Using isolates containing defined mutations in the S. pneumoniae capsule locus, we found that expression of the capsular polysaccharide is essential for colonization by the type 2 strain D39 and the type 3 strains A66 and WU2. Nonencapsulated derivatives of each of these strains were unable to colonize BALB/cByJ mice. Similarly, type 3 mutants that produced < 6% of the parental amounts of capsule could not colonize. Capsule production equivalent to that of the parent strain was not required for efficient colonization, however, as type 3 mutants producing approximately 20% of the parental amounts of capsule colonized as effectively as the parent. This 80% reduction in capsule level had only a minimal effect on intraperitoneal virulence but caused a significant reduction in virulence via the intravenous route. In the X-linked immunodeficient CBA/N mouse, the type 3 mutant producing ~20% of the parental amount of capsule (AM188) was diminished in its ability to cause invasive disease and death following intranasal inoculation. Following intravenous or intraperitoneal challenge, however, only extended survival times were observed. Our results demonstrate an additional role for capsule in the pathogenesis of S. pneumoniae and show that isolates producing reduced levels of capsule can remain highly virulent.
A mutation that alters the nucleotide specificity of elongation factor Tu, a GTP regulatory protein. (1987)

A single amino acid substitution (Asp to Asn) at position 138 of Escherichia coli elongation factor Tu (EF-Tu) was introduced in the tufA gene clone by oligonucleotide site-directed mutagenesis. The mutated tufA gene was then expressed in maxicells. The properties of [35S]methionine-labeled mutant and wild type EF-Tu were compared by in vitro assays. The Asn-138 mutation greatly reduced the protein's affinity for GDP; however, this mutation dramatically increased the protein's affinity for xanthosine 5'-diphosphate. The mutant protein forms a stable complex with Phe-tRNA and xanthosine 5'-triphosphate, which binds to ribosomes, whereas it does not form a complex with Phe-tRNA and GTP (10 microM). These results suggest that in EF-Tu.nucleoside diphosphate complexes, amino acid residue 138 must interact with the substituent on C-2 of the purine ring. Thus, in wild type EF-Tu, Asp-138 would hydrogen bond to the 2-amino group of GDP, and in the mutant EF-Tu, Asn-138 would form an equivalent hydrogen bond with the 2-carbonyl group of xanthosine 5'-diphosphate. Aspartic acid 138 is conserved in the homologous sequences of all GTP regulatory proteins. This mutation would allow one to specifically alter the nucleotide specificity of other GTP regulatory proteins.
Palladium-Catalyzed Allylic C–H Fluorination (2013)

The first catalytic allylic C-H fluorination reaction using a nucleophilic fluoride source is reported. Under the influence of a Pd/Cr cocatalyst system, simple olefin substrates undergo fluorination with Et3N·3HF in good yields with high branched:linear regioselectivity. The mild conditions and broad scope make this reaction a powerful alternative to established methods for the preparation of allylic fluorides from prefunctionalized substrates.
CpG motifs of bacterial DNA exacerbate colitis of dextran sulfate sodium-treated mice (2002)

Inflammatory bowel disease (IBD) is characterized by a dysregulated intestinal immune response with elevated levels of the Th1 cytokines TNF, IL-12 and IFN-gamma. The luminal flora has been implicated as a major factor contributing to the initiation and perpetuation of chronic intestinal inflammation by as yet unknown mechanisms. Bacterial DNA contains unmethylated cytosine-guanosine dinucleotides (CpG) which strongly activate Th1-mediated immune responses. To test whether these CpG-motifs contribute to intestinal inflammation we treated mice with dextran-sulfate-sodium (DSS)-induced acute or chronic colitis for 5 days with CpG-containing oligodeoxynucleotides (CpG-ODN). Colonic inflammation was assessed by histological scoring. Colonic cytokine RNA was quantified by reverse transcription-PCR and cytokine secretion from mesenterial lymph node cells by ELISA. In chronic colitis, CpG-ODN treatment severely aggravated inflammation by 50%. Colonic expression of IFN-gamma and TNF was elevated (200- and 150-fold, respectively) and IFN-gamma and IL-12 secretion from lymph node cells was increased 5,000- and 8-fold, respectively, compared to GpG-ODN-treated controls. Similar effects were obtained in acute colitis. In conclusion, CpG-motifs of bacterial DNA have proinflammatory activity by strengthening the Th1 arm of immunity in DSS-induced colitis, and might therefore play a significant role in the initiation and perpetuation of inflammation in IBD.
Patterns of loss of heterozygosity at loci from chromosome arm 13q suggest a possible involvement of BRCA2 in sporadic breast tumors (1995)

Loss of heterozygosity (LOH) at loci from chromosome 13 is frequently observed in breast cancer. Chromosome 13 contains at least two cancer genes, the well-characterized RB1 gene located at 13q14 and the breast cancer-susceptibility gene, BRCA2, recently localized to 13q12. To investigate the possible involvement of BRCA2 in sporadic breast tumors, we looked at LOH at eight microsatellite (CA)n markers distributed along chromosome 13 in a panel of 59 primary breast carcinomas. We show that some LOH does not include the RB1 locus and is associated with the BRCA2 gene region.
Fondaparinux Compared with Enoxaparin for the Prevention of Venous Thromboembolism after Elective Major Knee Surgery (2001)

In patients undergoing elective major knee surgery, postoperative treatment with 2.5 mg of fondaparinux once daily was significantly more effective in preventing deep-vein thrombosis than 30 mg of enoxaparin twice daily.
TCP Servers: Offloading TCP Processing in Internet Servers. Design, Implementation, and Performance (2002)

TCP Server is a system architecture aiming to offload network processing from the host(s) running an Internet server. The basic idea is to execute the TCP/IP processing on a dedicated processor, node, or device (the TCP server) using low-overhead, non-intrusive communication between it and the host(s) running the server application. In this paper, we propose, implement, and evaluate three TCP Server architectures: (1) a dedicated network processor on a symmetric multiprocessor (SMP) server, (2) a dedicated node on a cluster-based server built around a memory-mapped communication interconnect such as VIA, and (3) an intelligent network interface in a cluster of intelligent devices with a switch-based I/O interconnect such as Infiniband. Based on our experience and results, we can draw a few important conclusions: (i) an SMP-based approach to TCP servers is more efficient than a cluster-based one, given the lower overheads and the slightly more even division of labor between application and network processors of the former approach, (ii) the benefits of SMP and cluster-based TCP servers reach 18% and 30% respectively, in the scenarios we studied, (iii) the simulation results show greater gains of up to 45% for a cluster of intelligent devices, and (iv) it is clear that greater gains are possible only if we perform dynamic load balancing between hosts and the TCP servers.
Effects of Fibrillar C–Terminal Fragment of Cleaved α1–Antitrypsin on Cholesterol Homeostasis in Hepg2 Cells (1999)

Amyloid fibrils of diverse origin are known to disturb vital cellular functions and induce cell death. In this study, the effects of amyloid fibrils from the C-terminal fragment (C-36) of cleaved alpha1-antitrypsin (AAT) on low-density lipoprotein (LDL) metabolism were investigated in HepG2 cells. Treatment of the cells with C-36 fibrils (10 micromol/L) enhanced 125I-LDL binding and uptake 10 to 15 times, and highly up-regulated levels of LDL receptor mRNA, as compared with control cells. Competition experiments using excess of unlabeled LDL and blockage experiments with a monoclonal LDL receptor antibody diminished or completely abolished the stimulatory effects of fibrils on LDL binding and LDL receptor mRNA levels, suggesting that fibrils act via the LDL receptor pathway. However, C-36 fibrils had no significant effect on [2-14C]acetate incorporation into cholesterol biosynthesis and cholesterol ester formation, but inhibited 125I-LDL degradation by 20% and reduced bile acid biosynthesis up to 48% in a dose-dependent manner. Preincubation of the cells with fibrils before the addition of LDL totally abolished the LDL inhibitory effect on unesterified cholesterol synthesis, further confirming the LDL receptors to be the target for C-36 fibrils. Moreover, the expression of sterol regulatory element binding protein-1 (SREBP-1) was found to increase twofold and more after 24 hours of incubation of the cells with several concentrations of C-36 fibrils. Our study suggests that the cytotoxicity of C-36 fibrils on HepG2 cells is associated with perturbed intracellular cholesterol homeostasis, induced through fibril-stimulated expression of the LDL receptors via the sterol-responsive element.
Theoretical design and implementation of a transcutaneous, multichannel stimulator for neural prosthesis applications (1981)

The development of a transcutaneous, implantable, multichannel neural stimulator is described. This was originally dedicated to the stimulation of the auditory nerve in profoundly deaf persons, but is sufficiently flexible in design and operation to be applicable to other areas of neural prosthetics. Control of both the amplitude and time of stimulation for up to fifteen independent channels is possible with a maximum stimulation rate of 1 kHz. Particular attention is given to the design of the transcutaneous link stage which allows both power and data to be transferred to the implanted device using a compact coupling inductor configuration. All circuit timing is derived from a single clock in the external transmitter unit, resulting in stable operation with predictable stimulus output characteristics. The implantable device, realised using thick film hybrid techniques, employs CMOS logic extensively to reduce power consumption. One such device has been implanted in a profoundly deaf volunteer for a period exceeding two years and has continued to operate reliably in conjunction with the complete prosthesis system.
A Comparison of Fast Blocking Methods for Record Linkage (2003)

Record linkage of millions of individual health records for ethically-approved research purposes is a computationally expensive task. Blocking methods are used in record linkage systems to reduce the number of candidate record comparison pairs to a feasible number whilst still maintaining linkage accuracy. New blocking methods have been implemented recently using high-dimensional indexing or clustering algorithms. We compare two new blocking methods, bigram indexing and canopy clustering with TFIDF (Term Frequency/Inverse Document Frequency), with two older methods of standard traditional blocking and sorted neighbourhood blocking. The results show that recently blocking methods such as bigram indexing and canopy clustering provide scalable blocking methods while maintaining or improving upon record linkage accuracy. There is a potential for large performance speed-ups and better accuracy to be achieved by these new blocking methods.
Alkali-Induced Optical Rotation Changes in Heparins and Heparan Sulfates, and Their Relation to Iduronic Acid-Containing Sequences (1993)

Abstract Under specific basic conditions, the glucosaminoglycans heparin and heparan sulfate, containing α-L-iduronic acid 2-O-sulfate, undergo selective epoxidation between C-2 and C-3 of this residue, with formation of a residue of 2,3-anhydro-α-L-guluronic acid. The epoxidation reaction was studied by means of 13C NMR and optical rotation measurements. The optical rotation values correlate well with the composition of the reaction products as determined by 13C NMR, thus indicating that the heparin- or heparan-like character of both natural and semisynthetic polysaccharides can be easily determined also through optical rotation measurements.
TNF receptor signal transduction. Ligand-dependent stimulation of a serine protein kinase activity associated with (CD120a) TNFR60. (1994)

TNF is a pluripotent cytokine that mediates activities through two distinct receptors of 55 to 60 kDa (CD120a, known as TNFR60) and 75 to 80 kDa (CD120b, known as TNFR80). These receptors share homology in the extracellular ligand binding region; however, the cytoplasmic domains are distinct and lack any inherent enzymatic activity, which suggests that ligand binding and subsequent receptor clustering leads to the association of active signaling molecules with TNFRs. To test this hypothesis, we isolated TNFRs by immunoprecipitation and examined the immune complexes for the presence of associated phosphoproteins and protein kinase activity. In the U-937 monocytic cell line, prelabeled with 32PO4, TNF induces the association of several phosphoproteins with TNFR60, but not TNFR80. The TNFR60 immune complexes also contain a TNF-dependent serine protein kinase activity, which was detected by an in vitro kinase assay, that phosphorylates proteins of 125, 97, 85, and 60 kDa, which are of apparent molecular masses that are similar to those of TNF-induced phosphoproteins that coprecipitate with TNFR60. Association of serine protein kinase activity with TNFR60 is rapid and dependent on the concentration of TNF. Proteins of molecular mass similar to the 125- and 97-kDa protein kinase substrates seem to be associated with TNFR60 immune complexes only after exposure of U-937 cells to TNF. The TNFR60-associated protein kinase activity is inhibited by staurosporine, but not by the protein kinase A and C inhibitors, HA-1004 and H7. Staurosporine greatly enhanced the sensitivity of U-937 cells to the cytotoxic effect of TNF. These results suggest a serine protein kinase(s), and, possibly, other TNF-dependent TNFR60-associated proteins may be involved in mediating signals through TNFR60 in response to ligand binding.
Comparative Activities of Daptomycin, Linezolid, and Tigecycline against Catheter-Related Methicillin-Resistant Staphylococcus Bacteremic Isolates Embedded in Biofilm (2007)

In the setting of catheter-related bloodstream infections, intraluminal antibiotic lock therapy could be useful for the salvage of vascular catheters. In this in vitro study, we investigated the efficacies of the newer antibiotics daptomycin, linezolid, and tigecycline, in comparison with those of vancomycin, minocycline, and rifampin, against methicillin-resistant Staphylococcus aureus (MRSA) embedded in biofilm. We also assessed the emergence of MRSA strains resistant to these antibiotics, alone or in combination with rifampin, after 4-hour daily use for catheter lock therapy. Minocycline, daptomycin, and tigecycline were more efficacious in inhibiting MRSA in biofilm than linezolid, vancomycin, and the negative control (P < 0.001) after the first day of exposure to these antibiotics, with minocycline being the most active, followed by daptomycin and then tigecycline, and with vancomycin and linezolid lacking activity, similar to the negative control. After 3 days of 4-hour daily exposures, daptomycin was the fastest in eradicating MRSA from biofilm, followed by minocycline and tigecycline, which were faster than linezolid, rifampin, and vancomycin (P < 0.001). When rifampin was used alone, it was the least effective in eradicating MRSA from biofilm after 5 days of 4-hour daily exposures, as it was associated with the emergence of rifampin-resistant MRSA. However, when rifampin was used in combination with other antibiotics, the combination was significantly effective in eliminating MRSA colonization in biofilm more rapidly than each of the antibiotics alone. In summary, daptomycin, minocycline, and tigecycline should be considered further for antibiotic lock therapy, and rifampin should be considered for enhanced antistaphylococcal activity but not as a single agent.
Platelet-Derived Growth Factor Enhances Deoxyribonucleic Acid and Collagen Synthesis in Osteoblast-Enriched Cultures from Fetal Rat Parietal Bone* (1989)

Platelet-derived growth factor (PDGF) or closely related proteins are found in bone matrix and are produced by cultured osteosarcoma cells. In serum-deprived osteoblast-enriched (ob) cultures from fetal rat bone, recombinant human PDGF (composed of a B chain homodimer) at 0.1-3 nM enhanced the rate of DNA synthesis by 2- to 8-fold within 24 h of treatment, and 0.3-3 nM PDGF increased cell number by 1.3- to 1.6-fold. Unlike results with rat kidney fibroblast cultures, the mitogenic effect of PDGF in ob cultures was not synergistic with that of insulin-like growth factor I. PDGF at 0.3-10 nM also enhanced the rates of collagen and noncollagen protein synthesis in ob cultures by 1.5- to 4.0-fold, and these increases were blocked when DNA synthesis was prevented. The stimulatory effects of PDGF did not appear specific to ob cultures from fetal rat bone, since similar increases were found in bone cell cultures containing fibroblasts and osteoblast precursors. PDGF binding at 4 C to ob cultures indicated a single class of receptors with a Kd of 0.16 nM and approximately 60,000 sites/cell. Polyacrylamide gel of 125I-PDGF bound and cross-linked to ob cultures revealed a single radioactive band at approximately 180,000-190,000 mol wt. The present studies, therefore, indicate that PDGF can directly increase replication and matrix protein synthesis by both differentiated and undifferentiated bone cells, and that bone- or platelet-derived PDGF may have an important anabolic role in bone remodeling or fracture repair.
Studies on pyrimidine derivatives. XV. Homolytic acylation and amidation of simply substituted pyrimidines. (1980)

The reaction of 2, 6-disubstituted pyrimidines with acyl radicals generated either from pyruvic acid-AgNO3-(NH4)2S2O8 (method A) or from aldehyde-FeSO4-t-BuOOH (method B) in aq. H2SO4, gave the corresponding 2, 6-disubstituted 4-acylpyrimidines. However, 4, 6-disubstituted pyrimidines gave 2-acetyl-and 2, 5-diacetyl-4, 6-disubstituted pyrimidines under the same conditions (methods A and B). Similarly, homolytic amidation of pyrimidines in which the 2- or 4-positions are free yielded pyrimidine-2- or -4-carboxamides.