gebhart/patrepeval huggingface dataset:
The Genome Sequence of Avian PathogenicEscherichia coliStrain O1:K1:H7 Shares Strong Similarities with Human Extraintestinal PathogenicE. coliGenomes (2007)

Escherichia coli strains that cause disease outside the intestine are known as extraintestinal pathogenic E. coli (ExPEC) and include human uropathogenic E. coli (UPEC) and avian pathogenic E. coli (APEC). Regardless of host of origin, ExPEC strains share many traits. It has been suggested that these commonalities may enable APEC to cause disease in humans. Here, we begin to test the hypothesis that certain APEC strains possess potential to cause human urinary tract infection through virulence genotyping of 1,000 APEC and UPEC strains, generation of the first complete genomic sequence of an APEC (APEC O1:K1:H7) strain, and comparison of this genome to all available human ExPEC genomic sequences. The genomes of APEC O1 and three human UPEC strains were found to be remarkably similar, with only 4.5% of APEC O1's genome not found in other sequenced ExPEC genomes. Also, use of multilocus sequence typing showed that some of the sequenced human ExPEC strains were more like APEC O1 than other human ExPEC strains. This work provides evidence that at least some human and avian ExPEC strains are highly similar to one another, and it supports the possibility that a food-borne link between some APEC and UPEC strains exists. Future studies are necessary to assess the ability of APEC to overcome the hurdles necessary for such a food-borne transmission, and epidemiological studies are required to confirm that such a phenomenon actually occurs.
Thermodynamics of Small Electron-Bound Water Clusters (2003)

The relative stabilities of weak binding clusters are sensitive to temperature due to the entropy effect. Thus, here we report significant changes in relative stabilities between two low-energy electron-water trimer structures and those between three low-energy electron-water pentamer structures, as the temperature increases. The trimer and pentamer show structural changes around 200 K.
Spectrally enhanced imaging of occlusal surfaces and artificial shallow enamel erosions with a scanning fiber endoscope (2012)

An ultrathin scanning fiber endoscope, originally developed for cancer diagnosis, was used to image dental occlusal surfaces as well as shallow artificially induced enamel erosions from human extracted teeth (n=40). Enhanced image resolution of occlusal surfaces was obtained using a short-wavelength 405-nm illumination laser. In addition, artificial erosions of varying depths were also imaged with 405-, 404-, 532-, and 635-nm illumination lasers. Laser-induced autofluorescence images of the teeth using 405-nm illumination were also obtained. Contrast between sound and eroded enamel was quantitatively computed for each imaging modality. For shallow erosions, the image contrast with respect to sound enamel was greatest for the 405-nm reflected image. It was also determined that the increased contrast was in large part due to volume scattering with a smaller component from surface scattering. Furthermore, images obtained with a shallow penetration depth illumination laser (405 nm) provided the greatest detail of surface enamel topography since the reflected light does not contain contributions from light reflected from greater depths within the enamel tissue. Multilayered Monte Carlo simulations were also performed to confirm the experimental results.
Significance of the progesterone receptor and epidermal growth factor receptor, but not the estrogen receptor, in chemically induced lung carcinogenesis in female A/J mice (2014)

In the present study, the expression levels of female hormone receptors, estrogen receptor (ER) and progesterone receptor (PR) and the epidermal growth factor receptor, (EGFR), as well as proliferating cell nuclear antigen (PCNA) were examined in lung tumors that were induced by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in female A/J mice. Each seven-week-old mouse was administered with 2 mg NNK via intraperitoneal injection and the mice were subsequently euthanized at week 52. Lung tumors, including adenomas, carcinomas in adenomas and adenocarcinomas, were obtained and analyzed by immunohistochemistry for the expression levels of the receptors, ER, PR and EGFR, and PCNA. The results were as follows: i) In mouse lung adenomas, a significant correlation was identified between the size of the tumor and PCNA expression, although not with the expression of the receptors (ER, PR and EGFR); ii) in the carcinoma components of the carcinomas in adenomas, the size of the tumor and PCNA expression were correlated, while EGFR expression demonstrated a significant correlation with PR expression; iii) in adenocarcinomas, the tumor size significantly correlated with PCNA, EGFR and PR expression; and iv) EGFR and PR expression was identified to be significantly correlated in adenocarcinomas, and to a certain extent in the carcinoma components of the carcinomas in adenomas, although not in the adenomas. Notably, ER expression was not associated with tumor growth or the other factors, particularly EGFR expression, and no significant differences were identified between the three types of lesion. These results indicate that PR, like EGFR, may be significant in lung carcinogenesis.
Selective Silicon Epitaxy Using Reduced Pressure Technique (1982)

Silicon selective epitaxial growth using the SiH 2 Cl 2 –HCl–H 2 system was successfully accomplished on a window surrounded by fine patterned insulator films as a mask. Surface planarity was obtained at less than 80 Torr reduced pressure. Good selectivity was realized by suitable HCl injection during epitaxial growth. Moreover, it was found that the induced defect density on the epi-layer was less at lower growth temperature.
A Facile Lentiviral Vector System for Expression of Doxycycline-Inducible shRNAs: Knockdown of the Pre-miRNA Processing Enzyme Drosha (2007)

RNA interference (RNAi) is a powerful genetic tool for loss-of-function studies in mammalian cells and is also considered a potentially powerful therapeutic modality for the treatment of a variety of human diseases. During the past 3 years a number of systems for conditional RNAi have been developed that allow controlled expression of short hairpin RNA (shRNA) triggers of RNAi. The simplest strategy relies on tet-operable polymerase III-promoted shRNAs and co-expression of the tetracycline regulatory protein, TetR. In this study we have combined these features into a single lentiviral vector that upon delivery to target cells allows robust induction of shRNAs, even with low levels of doxycycline; importantly, we show minimal leakiness in the absence of inducer. We have exploited the regulatory properties of our system by targeting an essential cellular gene, the nuclear RNaseIII endonuclease Drosha. Drosha is the core catalytic component of the "microprocessor complex" and cleaves the primary microRNA (miRNA) transcripts into their pre-miRNA hairpin intermediates. We anticipate that our vector will facilitate functional studies of miRNA biogenesis.
Effects of Tissue Handling on RNA Integrity and Microarray Measurements From Resected Breast Cancers (2011)

Sample preservation in RNAlater improves RNA yield and quality, whereas cold ischemia increases RNA fragmentation as measured by the 3'/5' expression ratio of control genes. However, expression levels of single genes and multigene signatures that are of diagnostic relevance in breast cancer were mostly unaffected by sample preservation method or prolonged cold ischemic duration.
Differentiation antigens in fetal human pancreas. Reexpression in cancer (1986)

An antiserum was raised against pancreatic extracts obtained from human fetuses under 5 months of gestational age. After absorption with adult tissues, this antiserum specifically recognized antigens located in the cytoplasm of fetal pancreatic acini. All of the examined pancreatic tissues, ranging from 3 to 5 months of gestational age, showed a strong positive reaction of most of the acinar cells. The number of stained acini and the staining intensity gradually decreased from 5 months onwards and by the 7th-8th month only a few cells remained positive. Adult pancreas was completely negative as were a variety of normal adult and fetal tissues. This antiserum also reacted with tumor structures in 18/18 pancreatic adenocarcinomas as well as with pancreatic acini in the vicinity of tumor. Primary carcinomas of the liver, large bowel, stomach, breast, urinary bladder, lung and other localizations did not react with this antiserum. In some cases of chronic pancreatitis (3/12) a reaction was observed in a few acinar cells. Immunoblot assay after polyacrylamide electrophoresis revealed, in both fetuses and tumors, two main antigens of approximately 60 kDa and 110 kDa relative molecular weight. Several minor components were also observed. These results suggest that our polyclonal antiserum defines a new group of oncodevelopmental antigens with high organ specificity.
Regulation of p53 expression by thymidylate synthase (1999)

Previous studies showed that thymidylate synthase (TS), as an RNA binding protein, regulates its own synthesis by impairing the translation of TS mRNA. In this report, we present evidence that p53 expression is affected in a similar manner by TS. For these studies, we used a TS-depleted human colon cancer HCT-C cell that had been transfected with either the human TS cDNA or the Escherichia coli TS gene. The level of p53 protein in transfected cells overexpressing human TS was significantly reduced when compared with its corresponding parent HCT-C cells. This suppression of p53 expression was the direct result of decreased translational efficiency of p53 mRNA. Similar results were obtained upon transfection of HCT-C cells with pcDNA 3.1 (+) containing the E. coli TS gene. These findings provide evidence that TS, from diverse species, specifically regulates p53 expression at the translational level. In addition, TS-overexpressing cells with suppressed levels of p53 are significantly impaired in their ability to arrest in G1 phase in response to exposure to a DNA-damaging agent such as gamma-irradiation. These studies provide support for the in vivo biological relevance of the interaction between TS and p53 mRNA and identify a molecular pathway for controlling p53 expression.
African-American males and prostate cancer: assessing knowledge levels in the community. (1997)

Although the available evidence indicates that African-American males are at risk for developing prostate cancer, little is known about the level of awareness among African Americans about prostate cancer or how receptive they are to screening. This study examined the level of knowledge African-American males have about prostate cancer and the factors affecting knowledge levels. Face-to-face interviews were conducted among a sample of African-American males older than 25 years. All respondents were asked if they knew what prostate cancer was (N = 897), and those older than age 40 (N = 556) answered a series of seven questions related to prostate cancer. An index was created that reflected respondents level of knowledge about prostate cancer. Slightly more than 19% of the sample scored relatively high on the index related to prostate cancer knowledge, but 30% answered three or fewer questions correctly. Income, marital status, education, and type of insurance were significantly related to a respondent's level of knowledge. Having a regular physician and discussing prostate screening with a physician were both positively related to a respondent's level of understanding. This study indicates that African-American men do not have adequate knowledge about prostate cancer. Although many African Americans may be getting the prostate cancer message, educational efforts need to be strengthened to reach the less affluent and the less educated. These findings also raise questions about why more African-American men are not being screened and why more primary care physicians are not discussing prostate cancer with their African-American patients.
The Effectiveness of Low Dose Slow Release Aspirin as an Antiplatelet Agent (1993)

An open, randomized, parallel group study of three different aspirin preparations was carried out. The objective of this study was to compare their ability to inhibit the production of thromboxane A2 (measured as thromboxane B2 [TXB2]) from platelets. Three aspirin preparations were studied: Acetard 300 mg, Acetard 100 mg and Platet 100 mg. The study was conducted in 45 healthy adult volunteers and treatment continued once daily for 7 days. The results of the TXB2 assay show that the administration of all three treatment preparations produced a rapid drop in TXB2 levels of all volunteers. The baseline TXB2 level was reduced by 95% for all groups by day 3. Analysis by day showed a significant difference (P < 0.05) between treatments at day 1, with Acetard 100 mg having higher TXB2 levels than the other two groups. Analysis of changes from baseline showed a significant reduction (P < 0.05) in TXB2 levels at Days 1 to 14 for all three groups. Platelet aggregation also showed a significant reduction, being reduced to 10% of control at 7 days. It then reverted back to baseline by 28 days for all treatment groups. In conclusion, low dose aspirin is very effective as an antiplatelet agent and in a slow release form loses none of its patency.
Advantages of normothermic perfusion over cold storage in liver preservation (2002)

Normothermic sanguineous oxygenated perfusion is a superior method of preservation compared with simple cold storage in UW solution. In addition, perfusion allows the possibility to assess viability of the graft before transplantation.
Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication (2009)

RNA interference (RNAi) provides a powerful new means to inhibit viral infection specifically. However, the selection of siRNA-resistant viruses is a major concern in the use of RNAi as antiviral therapeutics. In this study, we conducted a lentiviral vector with a H1-short hairpin RNA (shRNA) expression cassette to deliver small interfering RNAs (siRNAs) into mammalian cells. Using this vector that also expresses enhanced green fluorescence protein (EGFP) as surrogate marker, stable shRNA-expressing cell lines were successfully established and the inhibition efficiencies of rationally designed siRNAs targeting to conserved regions of influenza A virus genome were assessed. The results showed that a siRNA targeting influenza M2 gene (siM2) potently inhibited viral replication. The siM2 was not only effective for H1N1 virus but also for highly pathogenic avian influenza virus H5N1. In addition to its M2 inhibition, the siM2 also inhibited NP mRNA accumulation and protein expression. A long term inhibition effect of the siM2 was demonstrated and the emergence of siRNA-resistant mutants in influenza quasispecies was not observed. Taken together, our study suggested that M2 gene might be an optimal RNAi target for antiviral therapy. These findings provide useful information for the development of RNAi-based prophylaxis and therapy for human influenza virus infection.
"Les nationaux-républicains de gauche et la construction européenne" (2000)

info:eu-repo/semantics/published
Histochemistry and Lipid Profiling Combine for Insights into Aging and Age-Related Maculopathy (2009)

Aging is the major risk factor for age-related maculopathy (ARM), the biggest cause of vision loss among the elderly in industrialized societies, and a major change in the affected tissues is the age-related accumulation of neutral lipid in Bruch's membrane (BrM) of the eye throughout adulthood. Here we show that esterified cholesterol (EC) is the major neutral lipid species in this tissue, which has implications for potential sources of this material. The combination of filipin histochemistry and comprehensive lipid profiling made possible this insight on a complex tissue.
Prostate Cancer Cell ProliferationIn vitroIs Modulated by Antibodies against Glucose-Regulated Protein 78 Isolated from Patient Serum (2006)

Circulating autoantibodies against the glucose-regulated protein of 78 kDa (GRP78) are present at high levels in prostate cancer patients and are a biomarker of aggressive tumor behavior. We purified the anti-GRP78 IgGs and examined their effect on 1-LN, PC-3, DU145, and LnCap human prostate cancer cells. We also evaluated its effects on the breast cancer MDA-MB231 and melanoma DM413 cell lines. The anti-GRP78 antibody binds only to cells expressing GRP78 on the surface, to a site also recognized by its physiologic agonist, activated alpha(2)-macroglobulin (alpha(2)M*). This antibody is completely specific for a peptide, including the primary amino acid sequence CNVKSDKSC, which contains a tertiary structural motif mimicking an epitope in GRP78. Tertiary structural analysis suggested the linear GRP78 primary amino acid sequence LIGRTWNDPSVQQDIKFL (Leu(98)-Leu(115)) as the putative binding site, containing the tertiary structual arrangement described above, which was confirmed experimentally. The anti-GRP78 antibodies from prostate cancer patients recognize almost exclusively this epitope. We produced animal antibodies against both these peptides, and they are able to mimic the effects of the human antibody. Our experiments also suggest this epitope as highly immunogenic, thereby explaining the specificity of the immune response against this epitope in GRP78, observed in humans. Using 1-LN cells as a model, we show that anti-GRP78 IgG purified from the sera of these patients mimics the proproliferative effects induced by alpha(2)M* via the common receptor, GRP78. Furthermore, increasing concentrations of human anti-GRP78 IgG show a dose-dependent protective effect on apoptosis induced by tumor necrosis factor alpha.
A highly variable segment of human subterminal 16p reveals a history of population growth for modern humans outside Africa (2000)

We have sequenced a highly polymorphic subterminal noncoding region from human chromosome 16p13.3 flanking the 5' end of the hypervariable minisatellite MS205, in 100 chromosomes sampled from different African and Euroasiatic populations. Coalescence analysis indicates that the time to the most recent common ancestor (approximately 1 million years) predates the appearance of anatomically modern human forms. The root of the network describing this variability lies in Africa. African populations show a greater level of diversity and deeper branches. Most Euroasiatic variability seems to have been generated after a recent out-of-Africa range expansion. A history of population growth is the most likely scenario for the Euroasiatic populations. This pattern of nuclear variability can be reconciled with inferences based on mitochondrial DNA.
Composite Sketch Shape Recognition Based on Dagsvm and Decision Tree (2006)

Sketch recognition provides the basis for semantic processing in sketching understanding, and it consists of two sequential and cyclic phases: primitive shape recognition and composite shape recognition. In this paper, a composite shape recognition algorithm based on support vector machines (SVM) and decision tree is proposed. Directed acyclic graphs SVM (DAGSVM) is used for primitive shape recognition and composite shape recognition. The decision tree is introduced to pre-classify the composite shape and to reduce the computational cost of recognition. The algorithm integrates the advantages of feature-based and similarity-based recognition approaches, and can deal with sketching sequence properly. Experiment demonstrates that the model is feasible
Structure of the NGFI-A gene and detection of upstream sequences responsible for its transcriptional induction by nerve growth factor. (1989)

The NGFI-A gene encodes a "zinc-finger" protein that is rapidly induced by nerve growth factor (NGF) in PC12 rat pheochromocytoma cells. The complete exon/intron organization and nucleotide sequence of the rat NGFI-A gene have been determined. The gene spans 3789 nucleotides (nt) and is interrupted by a single intron at nt 588. All three zinc-finger DNA-binding domains are contiguously coded for within the 3' exon; this is in contrast to the structure described by others for the Xenopus laevis transcription factor TFIIIA gene. To analyze the transcription of this gene, we have determined the transcription start site and nucleotide sequence of the 5' flanking region. Transfection of PC12 cells with a fragment from the 5' flanking region linked to the chloramphenicol acetyltransferase (CAT) gene revealed that it contains an element which imparts an NGF-inducible phenotype to the normally silent CAT gene. Several regions with homologies to recognizable sequence elements are present in this fragment, including a TATA box at nt -27, serum response elements at nt -84, -106, -370, and -408, a cAMP-responsive element at nt -140, and a transcription factor Sp1-binding site at nt -286. These results establish the genomic structure of this mammalian multifinger protein and demonstrate that an NGF-responsive element lies upstream of the NGFI-A gene.
Full Coherent Frequency Conversion between Two Propagating Microwave Modes (2013)

We demonstrate full frequency conversion in the microwave domain using a Josephson three-wave mixing device pumped at the difference between the frequencies of its fundamental eigenmodes. By measuring the signal output as a function of the intensity and phase of the three input signal, idler, and pump tones, we show that the device functions as a controllable three-wave beam splitter or combiner for propagating microwave modes at the single-photon level, in accordance with theory. Losses at the full conversion point are found to be less than 10(-2). Potential applications of the device include quantum information transduction and realization of an ultrasensitive interferometer with controllable feedback.
Transcripts from a single full-length cDNA clone of hepatitis C virus are infectious when directly transfected into the liver of a chimpanzee (1997)

We have succeeded in constructing a stable full-length cDNA clone of strain H77 (genotype 1a) of hepatitis C virus (HCV). We devised a cassette vector with fixed 5' and 3' termini and constructed multiple full-length cDNA clones of H77 in a single step by cloning of the entire ORF, which was amplified by long reverse transcriptase-PCR, directly into this vector. The infectivity of two complete full-length cDNA clones was tested by the direct intrahepatic injection of a chimpanzee with RNA transcripts. However, we found no evidence for HCV replication. Sequence analysis of these and 16 additional full-length clones revealed that seven clones were defective for polyprotein synthesis, and the remaining nine clones had 6-28 amino acid mutations in the predicted polyprotein compared with the consensus sequence of H77. Next, we constructed a consensus chimera from four of the full-length cDNA clones with just two ligation steps. Injection of RNA transcripts from this consensus clone into the liver of a chimpanzee resulted in viral replication. The sequence of the virus recovered from the chimpanzee was identical to that of the injected RNA transcripts. This stable infectious molecular clone should be an important tool for developing a better understanding of the molecular biology and pathogenesis of HCV.