gebhart/patrepeval huggingface dataset:
16S rRNA-Based Analysis of Microbiota from the Cecum of Broiler Chickens (2002)

The microbiota of the intestinal tract of chickens plays an important role in inhibiting the establishment of intestinal pathogens. Earlier culturing and microscopic examinations indicated that only a fraction of the bacteria in the cecum of chickens could be grown in the laboratory. Therefore, a survey of cecal bacteria was done by retrieval of 16S rRNA gene sequences from DNA isolated from the cecal content and the cecal mucosa. The ribosomal gene sequences were amplified with universal primers and cloned or subjected to temporal temperature gradient gel electrophoresis (TTGE). Partial 16S rRNA gene sequences were determined from the clones and from the major bands in TTGE gels. A total of 1,656 partial 16S rRNA gene sequences were obtained and compared to sequences in the GenBank. The comparison indicated that 243 different sequences were present in the samples. Overall, sequences representing 50 phylogenetic groups or subgroups of bacteria were found, but approximately 89% of the sequences represented just four phylogenetic groups (Clostridium leptum, Sporomusa sp., Clostridium coccoides, and enterics). Sequences of members of the Bacteroides group, the Bifidobacterium infantis subgroup, and of Pseudomonas sp. each accounted for less than 2% of the total. Sequences related to those from the Escherichia sp. subgroup and from Lactobacillus, Pseudomonas, and Bifidobacterium spp. were generally between 98 and 100% identical to sequences already deposited in the GenBank. Sequences most closely related to those of the other bacteria were generally 97% or less identical to those in the databases and therefore might be from currently unknown species. TTGE and random cloning indicated that certain phylogenetic subgroups were common to all birds analyzed, but sequence data from random cloning also provided evidence for qualitative and quantitative differences among the cecal microbiota of individual birds reared under very similar conditions.
Tumorigenicity of fibroblast lines expressing the adenovirus E1a, cellular p53, or normal c-myc genes. (1986)

Cellular and viral oncogenes have been linked to the transformation of established cell lines in vitro, to the induction of tumors in vivo, and to the partial transformation or immortalization of primary cells. Based on the ability to cooperate with mutated ras oncogenes in the transformation of primary cells, the adenovirus E1a and cellular p53 genes have been assigned an immortalizing activity. It is demonstrated in this paper that the adenovirus type 5 E1a gene and simian virus 40 promoter-linked p53 cDNA are able to transform previously immortalized cells to a tumorigenic phenotype without a significant change in cell morphology. It is also shown that, when linked to a constitutive promoter, the normal mouse and human c-myc genes have the same transforming activity. Cells transformed by each of these oncogenes have an increased capacity to grow in the absence of growth factors and a limited anchorage-independent growth capability.
[Analysis of 28 clinical cases and bone in stress around every tooth with pericementitis caused by occlusal trauma] (1994)

28 cases of pericementitis on occlusal trauma were observed,treated and followed up for 2 years;The bone in stress around every involved tooth was analysed according to the stress analysis by three demensinal photoelastic models loading excessive occlusal forces in various direction and coincided with the area of abnormality on the tooth radiograph.The result showed that the present methods of examination and treatment for tooth with traumatic pericementitis could diagnose exactly and cure effectively this disease;the rate of cure for 2 years was 86.7%,subtle occlusal adjustment by 3-4 appointments could maintain stable curative effect.It is suggested that clinicians should pay more attention to discover and treat both with traumatic pericementitis,the earliest clinical manifestation of both injury in occlusal trauma in order to protect them from severe injury in occlusal disharmony as well as periodontal trauma.
Treatment of Parainfluenza Virus Type 3 Bronchiolitis and Pneumonia in a Cotton Rat Model Using Topical Antibody and Glucocorticosteroid (1996)

Treatment of parainfluenza virus type 3 bronchiolitis and pneumonia in the cotton rat using topical IgG cleared infectious virus within 24 h but did not reduce pulmonary pathology. Treatment with topical triamcinolone acetonide dramatically reduced pathology but increased virus titers >10-fold. Combined therapy, however, demonstrated both favorable effects. Animals treated 3,4, and 5 days after infection showed a rebound of lung lesions to levels of untreated animals without reappearance of virus, but treatment through 8 days resulted in virus-free lungs without rebound of lesions. There was no difference in response to rechallenge 21 days after the original infection between treated and untreated animals. Combined antiviral and antiinflammatory therapy looks promising for viral bronchiolitis and pneumonia, but further questions relating to mechanism of action and to range of infections that can be treated in this fashion will need to be answered in animal models.
Photo‐fluorodecarboxylation of 2‐Aryloxy and 2‐Aryl Carboxylic Acids (2012)

Coming to light: The title reaction simply requires an aqueous alkaline solution of Selectfluor and light. The method is inexpensive and effective for a wide range of neutral and electron-poor 2-aryloxy and 2-aryl acetic acids to provide fluoromethyl ethers (see scheme) and benzyl fluorides, respectively. The mechanism most likely proceeds through an initial aryl excitation with a subsequent single-electron transfer.
Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics (2015)

Detection of bacteria in bloodstream infections and their antibiotic susceptibility patterns is critical to guide therapeutic decision-making for optimal patient care. Current culture-based assays are too slow (>48 h), leading to excessive up-front use of broad-spectrum antibiotics and/or incorrect antibiotic choices due to resistant bacteria, each with deleterious consequences for patient care and public health. To approach this problem, we describe a method to rapidly isolate bacteria from whole blood using inertial microfluidics and directly determine pathogen identity and antibiotic susceptibility with hybridization-based RNA detection. Using the principle of Dean flow fractionation, bacteria are separated from host blood cells in a label-free separation method with efficient recovery of even low abundance bacteria. Ribosomal RNA detection can then be applied for direct identification of low abundance pathogens (~100 per mL) from blood without culturing or enzymatic amplification. Messenger RNA detection of antibiotic-responsive transcripts after brief drug exposure permits rapid susceptibility determination from bacteria with minimal culturing (~10(5) per mL). This unique coupling of microfluidic cell separation with RNA-based molecular detection techniques represents significant progress towards faster diagnostics (~8 hours) to guide antibiotic therapy.
Grb2 and Shc Adapter Proteins Play Distinct Roles in Neu (ErbB-2)-Induced Mammary Tumorigenesis: Implications for Human Breast Cancer (2001)

Amplification of the Neu (ErbB-2 or HER-2) receptor tyrosine kinase occurs in 20 to 30% of human mammary carcinomas, correlating with a poor clinical prognosis. We have previously demonstrated that four (Y1144 Y1201, Y1227 and Y1253) of the five known Neu autophosphorylation sites can independently mediate transforming signals. The transforming potential of two of these mutants correlates with their capacity to recruit Grb2 directly to Y1144 (YB) or indirectly through Shc to Y1227 (YD). Here, we demonstrate that these transformation-competent neu mutants activate extracellular signal-regulated kinases and stimulate Ets-2-dependent transcription. Although the transforming potential of three of these mutants (YB, YD, and YE) was susceptible to inhibition by Rap1A, a genetic antagonist of Ras, the transforming potential of YC was resistant to inhibition by Rap1A. To further address the significance of these ErbB-2-coupled signaling molecules in induction of mammary cancers, transgenic mice expressing mutant Neu receptors lacking the known autophosphorylation sites (NYPD) or those coupled directly to either Grb2 (YB) or Shc (YD) adapter molecules were derived. In contrast to the NYPD strains, which developed focal mammary tumors after a long latency period with low penetrance, all female mice derived from YB and YD strains rapidly developed mammary tumors. Although female mice from several independent YB or YD lines developed mammary tumors, the YB strains developed lung metastases at substantially higher rates than the YD strains. These observations argue that Grb2 and Shc play important and distinct roles in ErbB-2/Neu-induced mammary tumorigenesis and metastasis.
Methylation profiling in acute myeloid leukemia (2001)

Aberrant methylation of multiple CpG islands has been described in acute myeloid leukemia (AML), but it is not known whether these are independent events or whether they reflect specific methylation defects in a subset of cases. To study this issue, the methylation status of 14 promoter-associated CpG islands was analyzed in 36 cases of AML previously characterized for estrogen-receptor methylation (ERM). Cases with methylation density of 10% or greater were considered positive. Seventeen cases (47%) were ERM(+) while 19 cases were ERM(-). Hypermethylation of any of the following, p15, p16, CACNA1G, MINT1, MINT2, MDR1, THBS1, and PTC1 (2 promoters), was relatively infrequent (6% to 31% of patients). For each of these CpG islands, the methylation density was positively correlated with ERM density (rank order correlation coefficients, 0.32-0.59; 2-tailed P < or = .058 for each gene). Hypermethylation of MYOD1, PITX2, GPR37, and SDC4 was frequently found in AML (47% to 64% of patients). For each of these genes as well, methylation density was positively correlated with ERM density (correlation coefficients 0.43 to 0.69, P < or = .0087 for each gene). MLH1 was unmethylated in all cases. Hypermethylation of p15, MDR1, and SDC4 correlated with reduced levels of expression. There was an inverse correlation between age and the number of genes methylated (P = .0030). It was concluded that CpG-island methylation in AML results from methylation defects in subsets of cases. These results have potential implications for the classification and prognosis of AML and for the identification of patients who may benefit from treatment with methylation inhibitors.
Applications, Environmental Impact and Microstructure of Light-Emitting Diodes* (2007)

The environmental challenges which our planet currently faces demand a reduction in greenhouse gas emissions and fossil fuel usage. Here, we discuss the environmental impact of popular current lighting solutions and describe the increasing use of lightemitting diodes based on gallium nitride and related semiconductors to reduce our energy consumption. It is unclear why these devices are largely unaffected by the high density of dislocations that they contain, although some microstructural feature of the InGaN quantum wells (the active layer of the LED) must hold the key. For a long time, this vital feature was thought to be a significant nm-scale inhomogeneity in composition. However, our studies suggest that these ‘gross indium-rich clusters’ are an artifact of electron beam damage. 3D atom probe analysis suggests that InGaN is in fact indistinguishable from a random alloy. An alternative microstructural feature, on a much broader scale, is suggested to be key, in at least some LEDs.
Everninomicin, a new oligosaccharide antibiotic: its antimicrobial activity, post-antibiotic effect and synergistic bactericidal activity. (1995)

Antimicrobial activity of everninomicin (SCH) 27899) in comparison with two glycopeptides (vancomycin, teicoplanin) and six beta-lactam agents was evaluated against recent clinical isolates of Gram-positive bacteria. Everninomicin showed the highest activity against the species tested and MICs90% of everninomicin against Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus faecalis, Enterococcus faecium and Clostridium difficile were 0.1, 0.1, 0.2, 0.39, 0.1 microgram/ml, respectively. MICs90% of everninomicin against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis (MRSE) were 0.78 microgram/ml. Laboratory induced resistance to everninomicin in strains of S. aureus and E. faecalis occurred in a stepwise manner and at a very slow rate. Post-antibiotic effect against strains of S. aureus and E. faecalis were 1.8 and 2.6 h, respectively, and a little longer than that of vancomycin. Adherence to glass surface of an MRSA strain was strongly repressed by the addition of sub MIC of everninomicin in combination with fosfomycin.
Serum Amyloid P and Cardiovascular Disease in Older Men and Women (2006)

Although both are pentraxins, SAP and CRP may represent different facets of inflammation. The association of SAP with CVD in these older adults further supports the role of innate immunity in atherosclerosis.
Requirement of Cysteines and Length of the Human Respiratory Syncytial Virus M2-1 Protein for Protein Function and Virus Viability (2001)

The M2-1 protein of human respiratory syncytial virus (hRSV) promotes processive RNA synthesis and readthrough at RSV gene junctions. It contains four highly conserved cysteines, three of which are located in the Cys(3)-His(1) motif at the N terminus of M2-1. Each of the four cysteines, at positions 7, 15, 21, and 96, in the M2-1 protein of hRSV A2 strain was individually replaced by glycines. When tested in an RSV minigenome replicon system using beta-galactosidase as a reporter gene, C7G, C15G, and C21G located in the Cys(3)-His(1) motif showed a significant reduction in processive RNA synthesis compared to wild-type (wt) M2-1. C96G, which lies outside the Cys(3)-His(1) motif, was fully functional in supporting processive RNA synthesis in vitro. Each of these cysteine substitutions was introduced into an infectious antigenomic cDNA clone derived from hRSV A2 strain. Except for C96G, which resulted in a viable virus, no viruses were recovered with mutations in the Cys(3)-His(1) motif. This indicates that the Cys(3)-His(1) motif is critical for M2-1 function and for RSV replication. The functional requirement of the C terminus of the M2-1 protein was examined by engineering premature stop codons that caused truncations of 17, 46, or 67 amino acids from the C terminus. A deletion of 46 or 67 amino acids abolished the synthesis of full-length beta-galactosidase mRNA and did not result in the recovery of viable viruses. However, a deletion of 17 amino acids from the C terminus of M2-1 reduced processive RNA synthesis in vitro and was well tolerated by RSV. Relocation of the M2-1 termination codon upstream of the M2-2 initiation codons did not significantly affect the expression of the M2-2 protein. Both rA2-Tr17 and rA2-C96G did not replicate as efficiently as wt rA2 in HEp-2 cells and was restricted in replication in the respiratory tracts of cotton rats.
Selenium dioxide oxidation of alkylcoumarins and related methyl‐substituted heteroaromatics (1988)

Abstract By the use of selenium dioxide as the specific oxidizing agent in the coumarin series, the 4‐ethyl, 4‐propyl and 4‐benzyl substituents of coumarin were converted into α‐alcohols 2 and/or ketones 3 , while 3‐methyl‐ and 3‐benzylcoumarins were converted into 3‐acyl derivatives 7 . The methyl substituent of the analogous thiocoumarin 5 , chromones 10 or thiochromone 11 was also oxidized into the formyl functionality. Facile oxidative desulfurization into the ketone functionality, prior to methyl oxidation, was observed for the thione derivatives of 1a, 5, 6 and 10.
Diaphragmatic motion in the sitting and supine positions: Healthy subject study using a vertically open magnetic resonance system (2004)

Diaphragmatic movement in the supine position is greater than that in the sitting position, especially in the posterior part of the diaphragm.
ErbB2 Potentiates Breast Tumor Proliferation through Modulation of p27 Kip1 -Cdk2 Complex Formation: Receptor Overexpression Does Not Determine Growth Dependency (2000)

Overexpression of the ErbB2 receptor, a major component of the ErbB receptor signaling network, contributes to the development of a number of human cancers. ErbB2 presents itself, therefore, as a target for antibody-mediated therapies. In this respect, anti-ErbB2 monoclonal antibody 4D5 specifically inhibits the growth of tumor cells overexpressing ErbB2. We have analyzed the effect of 4D5-mediated ErbB2 inhibition on the cell cycle of the breast tumor cell line BT474. 4D5 treatment of BT474 cells resulted in a G(1) arrest, preceded by rapid dephosphorylation of ErbB2, inhibition of cytoplasmic signal transduction pathways, accumulation of the cyclin-dependent kinase inhibitor p27(Kip1), and inactivation of cyclin-Cdk2 complexes. Time courses demonstrated that 4D5 treatment redirects p27(Kip1) onto Cdk2 complexes, an event preceding increased p27(Kip1) expression; this correlates with the downregulation of c-Myc and D-type cyclins (proteins involved in p27(Kip1) sequestration) and the loss of p27(Kip1) from Cdk4 complexes. Similar events were observed in ErbB2-overexpressing SKBR3 cells, which exhibited reduced proliferation in response to 4D5 treatment. Here, p27(Kip1) redistribution resulted in partial Cdk2 inactivation, consistent with a G1 accumulation. Moreover, p27(Kip1) protein levels remained constant. Antisense-mediated inhibition of p27(Kip1) expression in 4D5-treated BT474 cells further demonstrated that in the absence of p27(Kip1) accumulation, p27(Kip1) redirection onto Cdk2 complexes is sufficient to inactivate Cdk2 and establish the G(1) block. These data suggest that ErbB2 overexpression leads to potentiation of cyclin E-Cdk2 activity through regulation of p27(Kip1) sequestration proteins, thus deregulating the G(1)/S transition. Moreover, through comparison with an ErbB2-overexpressing cell line insensitive to 4D5 treatment, we demonstrate the specificity of these cell cycle events and show that ErbB2 overexpression alone is insufficient to determine the cellular response to receptor inhibition.
Attachment of Mycoplasma pneumoniae to respiratory epithelium (1976)

The attachment of radioisotope-labeled Mycoplasma pneumoniae to hamster tracheal rings in organ culture was examined by radioautography and liquid scintillation counting. Radioautographs of individual rings exposed for 8 h to (3H) thymidine-labeled virulent M. pneumoniae revealed a dense extracellular collection of emulsion grains along the luminal surface of epithelial cells. Similar exposure of rings to isotope-labeled avirulent M. pneumoniae resulted in no accumulation of emulsion grains. The numbers of attached virulent mycoplasmas, as measured by liquid scintillation counting of infected rings, were found to increase in a nearly linear fashion over an 8-h incubation period. Viability of the mycoplasmas and metabolic integrity of the tracheal rings were important for optimal attachment. Pretreatment of rings with neuraminidase or sodium periodate significantly impaired orgainism adherence. These data suggest a specificity of interation between virulent M. pneumoniae and tracheal epithelial cells that can be further examined through the use of isotopically labeled mycoplasmas.
Synthesis of silver nanowires by the photochemical method and their formation mechanism (2004)

Using seed-mediated and photochemical reduction approach in the presence of poly(vinyl pyrrolidone) (PVP), Ag nanowires with diameters of 50 similar to 120 nm and lengths up to similar to 50 mum and elegant silver dendrites were prepared at room temperature. It was found that experimental conditions including the molar ratio of PVP to AgNO3, the volume of silver seeds, and the reaction time all play influential roles in the formation of silver nanostructures. The mechanisms of formation of those silver nanostructures were discussed preliminarily.
Functional analysis of Arabidopsis thaliana rRNA gene and spacer promoters in vivo and by transient expression. (1993)

In eukaryotes, RNA polymerase I transcription is controlled by DNA elements located within the spacers that separate the tandemly arranged rRNA genes. Unlike rRNA coding sequences, the intergenic spacers evolve rapidly and have little sequence similarity even among closely related species. Nonetheless, the arrangement of functional elements, such as spacer promoters and enhancers, is thought to be highly conserved. Here, we identify spacer promoters in the plant Arabidopsis thaliana, thereby demonstrating their existence in both the plant and animal kingdoms. We also use an Arabidopsis transient expression system to perform transcriptional analysis of the ribosomal gene promoter. Spacer promoters share sequence similarity with the gene promoter from -91 to +22 relative to the transcription start site, +1. Deletion analysis shows that sequences required for RNA polymerase I transcription reside within these boundaries. Spacer sequences upstream of the gene promoter have only a small positive effect on transcription in transfected protoplasts but can increase transcription from a Xenopus ribosomal gene promoter in injected frog oocytes. This trans-kingdom enhancer effect further suggests that the functional elements within eukaryotic ribosomal genes are highly conserved.
A Data Warehouse Solution for Analyzing RFID-Based Baggage Tracking Data (2013)

Today, airport baggage handling is far from perfect. Baggage goes on the wrong flights, is left behind, or gets lost, which costs a lot of money for the airlines, as well as frustration for the passengers. To remedy the situation, we present a data warehouse (DW) solution for storing and analyzing spatio-temporal Radio Frequency Identification (RFID) baggage tracking data. Analysis of this data can yield interesting results on baggage flow, the causes of baggage mishandling, and the parties responsible for the mishandling(airline, airport, handler,...), which can ultimately lead to improved baggage handling quality. The paper presents a carefully designed data warehouse (DW), with a relational schema sitting underneath a multidimensional data cube, that can handle the many complexities in the data. The paper also discusses the Extract-Transform-Load (ETL) flow that loads the data warehouse with the appropriate tracking data from the data sources. The presented concepts are generalizable to other types of multi-site indoor tracking systems based on Bluetooth and RFID. The system has been tested with large amount of real-world RFID-based baggage tracking data from a major industry initiative. The developed solution is shown to both reveal interesting insights as well as being several orders of magnitude faster than computing the results directly on the data sources.