gebhart/patrepeval huggingface dataset:
Current Trends in Microbial Diagnostics Based on Mass Spectrometry (2012)

Recently, a major increase in mass spectrometer installations has occurred in routine clinical microbiology laboratories worldwide. At present, there are hundreds of various instruments sold and the market is still far from being saturated. Although the clinical community still declares it has discovered a “new technology”, the first mass spectrometry investigation of whole microorganism analysis was published in 1970, and the first commercial protein mass-fingerprinting package was introduced in 2000. This critical review covers the microbiology literature related to mass spectrometry published primarily in the 2011−2012 period. It also reports on mass spectrometry vendor sales,pending patent applications and company plans for the near future
Establishment of embryonic stem cell lines from cynomolgus monkey blastocysts produced by IVF or ICSI (2001)

Human embryonic stem (ES) cells are predicted to be a valuable source for producing ES-derived therapeutic spare tissues to treat diseases by controlling their growth and differentiation. To understand the regulative mechanisms of their differentiation in vivo and in vitro, ES cells derived from nonhuman primates could be a powerful tool. We established four ES cell lines from cynomolgus monkey (Macaca fascicularis) blastocysts produced by in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI). The ES cells were characterized by the expression of specific markers such as alkaline phosphatase and stage-specific embryonic antigen-4. They were successfully maintained in an undifferentiated state and with a normal karyotype even after more than 6 months of culture. Pluripotential competence was confirmed by the formation of teratomas containing ectoderm-, mesoderm-, and endoderm- derivatives after subcutaneous injection into SCID mice. Differentiation to a variety of tissues was identified by immunohistochemical analyses using tissue-specific antibodies. Therefore, we established pluripotent ES cell lines derived from monkeys that are widely used as experimental animals. These lines could be a useful resource for preclinical stem cell research, including allogenic transplantation into monkey models of disease.
Enumeration and phenotypic characterization of synovial fluid multipotential mesenchymal progenitor cells in inflammatory and degenerative arthritis (2004)

Our findings prove the presence of rare tripotential MPCs, at the single-cell level, in the SF of patients with arthritis. SF MPCs are clonogenic and multipotential fibroblasts that, despite the pathologic environment within a diseased joint, have a phenotype similar to that of uncultured BM MPCs. The higher prevalence of MPCs in OA SF suggests their likely origin from disrupted joint structures. These findings could determine the role of MPCs in the pathogenesis of inflammatory arthritis, together with their role in attempted joint regeneration in degenerative arthritis, which has yet to be established.
Catechol Quinones of Estrogens in the Initiation of Breast, Prostate, and Other Human Cancers (2006)

Estrogens can be converted to electrophilic metabolites, particularly the catechol estrogen-3,4-quinones, estrone(estradiol)-3,4-quinone [E(1)(E(2))-3,4-Q], which react with DNA to form depurinating adducts. These adducts are released from DNA to generate apurinic sites. Error-prone repair of this damage leads to the mutations that initiate breast, prostate, and other types of cancer. The reaction of E(1)(E(2))-3,4-Q with DNA forms the depurinating adducts 4-hydroxyE(1)(E(2))-1-N3adenine [4-OHE(1)(E(2))-1-N3Ade] and 4-OHE(1)(E(2))-1-N7guanine(Gua). These two adducts constitute >99% of the total DNA adducts formed. The E(1)(E(2))-2,3-Q forms small amounts of the depurinating 2-OHE(1)(E(2))-6-N3Ade adducts. Reaction of the quinones with DNA occurs more abundantly when estrogen metabolism is unbalanced. Such an imbalance is the result of overexpression of estrogen-activating enzymes and/or deficient expression of deactivating (protective) enzymes. Excessive formation of E(1)(E(2))-3,4-Q is the result of this imbalance. Oxidation of catechols to semiquinones and quinones is a mechanism of tumor initiation not only for endogenous estrogens, but also for synthetic estrogens such as hexestrol and diethylstilbestrol, a human carcinogen. This mechanism is also involved in the initiation of leukemia by benzene, rat olfactory tumors by naphthalene, and neurodegenerative diseases such as Parkinson's disease by dopamine. In fact, dopamine quinone reacts with DNA similarly to the E(1)(E(2))-3,4-Q, forming analogous depurinating N3Ade and N7Gua adducts. The depurinating adducts that migrate from cells and can be found in body fluids can also serve as biomarkers of cancer risk. In fact, a higher level of estrogen-DNA adducts has been found in the urine of men with prostate cancer and in women with breast cancer compared to healthy controls. This unifying mechanism of the origin of cancer and other diseases suggests preventive strategies based on the level of depurinating DNA adducts that generate the first critical step in the initiation of diseases.
Genetics, evolution, and expression of the 68,000-mol-wt neurofilament protein: isolation of a cloned cDNA probe. (1985)

A 1.2-kilobase (kb) cDNA clone (NF68) encoding the mouse 68,000-mol-wt neurofilament protein is described. The clone was isolated from a mouse brain cDNA library by low-stringency cross-hybridization with a cDNA probe encoding mouse glial fibrillary acidic protein (Lewis et al., 1984, Proc. Natl. Acad. Sci. USA., 81:2743-2746). The identity of NF68 was established by hybrid selection using mouse brain polyA+ mRNA, and cell-free translation of the selected mRNA species. The cell-free translation product co-migrated with authentic 68,000-mol-wt neurofilament protein on an SDS/polyacrylamide gel, and was immunoprecipitable with a monospecific rabbit anti-bovine neurofilament antiserum. In addition, DNA sequence analysis of NF68 showed 90% homology at the amino acid level compared with the sequence of the porcine 68,000-mol-wt neurofilament protein. At high stringency, NF68 detects a single genomic sequence encoding the mouse 68,000-mol-wt neurofilament protein. Two mRNA species of 2.5 kb and 4.0 kb are transcribed from the single gene in mouse brain. The level of expression of these mRNAs remains almost constant in postnatal mouse brains of all ages and, indeed, in the adult. At reduced stringency, NF68 detects a number of mRNAs that are expressed in mouse brain, one of which encodes the 150,000-mol-wt neurofilament protein. The NF68 probe cross-hybridizes at high stringency with genomic sequences in species as diverse as human, chicken, and (weakly) frog, but not with DNA from Drosophila or sea urchin.
Single-molecule fluorescence detection: autocorrelation criterion and experimental realization with phycoerythrin. (1989)

A theory for single-molecule fluorescence detection is developed and then used to analyze data from subpicomolar solutions of B-phycoerythrin (PE). The distribution of detected counts is the convolution of a Poissonian continuous background with bursts arising from the passage of individual fluorophores through the focused laser beam. The autocorrelation function reveals single-molecule events and provides a criterion for optimizing experimental parameters. The transit time of fluorescent molecules through the 120-fl imaged volume was 800 microseconds. The optimal laser power (32 mW at 514.5 nm) gave an incident intensity of 1.8 x 10(23) photons.cm-2.s-1, corresponding to a mean time of 1.1 ns between absorptions. The mean incremental count rate was 1.5 per 100 microseconds for PE monomers and 3.0 for PE dimers above a background count rate of 1.0. The distribution of counts and the autocorrelation function for 200 fM monomer and 100 fM dimer demonstrate that single-molecule detection was achieved. At this concentration, the mean occupancy was 0.014 monomer molecules in the probed volume. A hard-wired version of this detection system was used to measure the concentration of PE down to 1 fM. This single-molecule counter is 3 orders of magnitude more sensitive than conventional fluorescence detection systems.
Synthesis and Antitumor Activity of Quinonoid Derivatives of Cannabinoids (2004)

Three cannabis constituents, cannabidiol (1), Delta(8)-tetrahydrocannabinol (3), and cannabinol (5), were oxidized to their respective para-quinones 2, 4, and 6. In the 1960s, the oxidized product 4 had been assigned a para-quinone structure, which was later modified to an ortho-quinone. To distinguish between the two possible quinone structures, a detailed NMR investigation was undertaken. The original para-quinone structure was confirmed. X-ray crystallography elucidated the structures of the crystalline 2 and 6. All three compounds displayed antiproliferative activity in several human cancer cell lines in vitro, and quinone 2 significantly reduced cancer growth of HT-29 cancer in nude mice.
Location of a Constriction in the Lumen of a Transmembrane Pore by Targeted Covalent Attachment of Polymer Molecules (2001)

Few methods exist for obtaining the internal dimensions of transmembrane pores for which 3-D structures are lacking or for showing that structures determined by crystallography reflect the internal dimensions of pores in lipid bilayers. Several approaches, involving polymer penetration and transport, have revealed limiting diameters for various pores. But, in general, these approaches do not indicate the locations of constrictions in the channel lumen. Here, we combine cysteine mutagenesis and chemical modification with sulfhydryl-reactive polymers to locate the constriction in the lumen of the staphylococcal alpha-hemolysin pore, a model protein of known structure. The rates of reaction of each of four polymeric reagents (MePEG-OPSS) of different masses towards individual single cysteine mutants, comprising a set with cysteines distributed over the length of the lumen of the pore, were determined by macroscopic current recording. The rates for the three larger polymers (1.8, 2.5, and 5.0 kD) were normalized with respect to the rates of reaction with a 1.0-kD polymer for each of the seven positions in the lumen. The rate of reaction of the 5.0-kD polymer dropped dramatically at the centrally located Cys-111 residue and positions distal to Cys-111, whether the reagent was applied from the trans or the cis side of the bilayer. This semi-quantitative analysis sufficed to demonstrate that a constriction is located at the midpoint of the pore lumen, as predicted by the crystal structure, and although the constriction allows a 2.5-kD polymer to pass, transport of a 5.0-kD molecule is greatly restricted. In addition, PEG chains gave greater reductions in pore conductance when covalently attached to the narrower regions of the lumen, permitting further definition of the interior of the pore. The procedures described here should be applicable to other pores and to related structures such as the vestibules of ion channels.
Characterization of conceptus-produced goat interferon τ and analysis of its temporal and cellular distribution during early pregnancy (1998)

Two proteins (17 and 22-24 kDa) produced by day 17 goat conceptuses were purified from in vitro culture media. Analysis of their N-terminal amino acid sequences and of their antiviral activity confirmed that both proteins belonged to the interferon tau family characteristic of ruminant conceptuses. The two molecules were glycosylated (22-24 kDa) or nonglycosylated (17 kDa) isoforms of the same protein. The time course of secretion was plotted and immunoblotting of the protein contents of uterine flushings from day 13 to day 21 of pregnancy was performed. The nonglycosylated isoform (17 kDa) was first detected on day 16; both isoforms were present at day 17 and, thereafter during pregnancy, the two proteins were not present in uterine flushings. Immunohistochemistry was used to show that the goat interferon tau was present in the trophoblastic cells as early as day 14 and until day 17. However, immunostaining was not uniform along the conceptus; labelling was greater at the abembryonic pole than at the embryonic pole. By day 18, as implantation proceeded, goat interferon tau was no longer detected. These results confirmed that the goat conceptus secretes interferon tau during the period of maternal recognition of pregnancy but its rapid decrease suggests that other factors need to be present by day 18 to take over its role in the maintenance of luteal function.
239 BACTERIAL ENDOTOXIN MODULATION OF CACO-2 INTESTINAL EPITHELIAL TIGHT JUNCTION PERMEABILITY. (2004)

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Gene Silencing of CD47 and Antibody Ligation of Thrombospondin-1 Enhance Ischemic Tissue Survival in a Porcine Model (2008)

Antibody ligation of TSP1 or antisense morpholino knock down of CD47 greatly increased tissue survival to ischemia. Given the similarity between porcine and human soft tissues these results suggest significant therapeutic potential for people.
Superconducting Properties in a Bi-Sr-Ca-Cu-O System (1988)

Superconducting properties in a Bi-Sr-Ca-Cu-O system have been studied. Two types of superconductors were observed: one has a transition temperature of 80 K, and the other has two transitions at 80 K and 110 K. XRD measurements suggest that the latter superconductor has at least two phases. The phase which seemed to be responsible for the superconductivity above 80 K was investigated by means of XRD, SEM and XMA.
Noninvasive measurements of bone mass, structure, and strength: current methods and experimental techniques. (1991)

Current methods for assessing osteoporotic fracture risk involve measuring the content and/or density of bone at a number of skeletal sites and relating the measurement to that in either age-matched or young control subjects measured at the same site with the same technique. These densitometric methods have been used to predict several types of fractures; however, engineering principles verify that the bone structure and loading conditions also affect skeletal strength. Many densitometric measurements inherently contain information about skeletal structure and bone distribution, yet this information is not clinically used. In this paper, the currently available techniques for assessing bone content and density, namely, single-photon absorptiometry, dual-photon absorptiometry, dual-energy X-ray absorptiometry, and quantitative CT, and their usefulness in assessing fracture risk and distinguishing between patients with and without osteoporosis are reviewed. Extensions of conventional densitometry that have been developed by several researchers to include information in addition to bone mass also are presented. Results from recent studies using new applications of ultrasound techniques and MR imaging are reviewed. Preliminary studies show the value of these new techniques in noninvasive measurement of bone structure in order to estimate bone strength and assess fracture risk more accurately. However, to become clinically useful, many of these methods require further investigation to increase their ease of use and decrease their cost.
Cell-Specific Delivery of a Chemotherapeutic to Lung Cancer Cells (2004)

We report that lung cancer-targeting peptides isolated from a peptide library can be used to deliver an active chemotherapeutic in a cell-specific fashion. The peptides were removed from the context of the phage and placed on a pegylated tetrameric scaffold. The tetrameric peptides were shown to block uptake of their cognate phage. The tetrameric peptides were coupled to doxorubicin, and their cytotoxicity against a panel of different cell lines was tested. Our data demonstrate that these targeting peptides can deliver an active anticancer agent in a cell-specific fashion, resulting in an increase of the therapeutic index of the targeted drug compared to systemic delivery. The efficacy of the peptide conjugate correlates to the affinity of the targeting peptide for a particular cell line. As such, we have demonstrated that cell-specific targeted drugs can be synthesized, even when the cell surface target is unknown.
Generalized Discriminant Analysis Using a Kernel Approach (2000)

We present a new method that we call generalized discriminant analysis (GDA) to deal with nonlinear discriminant analysis using kernel function operator. The underlying theory is close to the support vector machines (SVM) insofar as the GDA method provides a mapping of the input vectors into high-dimensional feature space. In the transformed space, linear properties make it easy to extend and generalize the classical linear discriminant analysis (LDA) to nonlinear discriminant analysis. The formulation is expressed as an eigenvalue problem resolution. Using a different kernel, one can cover a wide class of nonlinearities. For both simulated data and alternate kernels, we give classification results, as well as the shape of the decision function. The results are confirmed using real data to perform seed classification.
A Dynamic Channel Assignment Scheme for Distributed Antenna Networks (2012)

In this paper, we propose a dynamic channel assignment (DCA) scheme for distributed antenna networks (DANs). DANs, in which many antennas are distributed in each cell, significantly reduce the transmit power compared to conventional cellular networks (CNs). In DAN, a different group of channels should be assigned for each distributed antenna to avoid the interference. Since DAN can also reduce the interference power due to its low transmit power property, the same channel groups can be reused even within the same cell. Proposed DCA scheme dynamically assigns the channels based on the co-channel interference measurement. Computer simulation results demonstrate that the DAN using proposed DCA achieves higher spectrum efficiency than the conventional CN.
A review of the phenotypic variation due to the Denys-Drash syndrome-associated germlineWT1 mutation R362X (2002)

The gene WT1 is required for the normal development and function of the urogenital tract. Constitutional mutations are associated with familial Wilms tumor and syndromes such as Denys-Drash syndrome (DDS) characterized by nephropathy, genital anomalies and often a predisposition to Wilms tumor. We report a case of constitutional WT1 mutation in an XX female with multifocal Wilms tumor but no genital anomalies or renal dysfunction and, for the first time, review patients previously reported with this germline mutation. The mutation (1084C>T) changes the amino acid arginine at position 362 to the translation stop codon TGA (R362X) resulting in a predicted truncated protein lacking three of the four zinc finger domains necessary for correct functioning of the gene. This constitutional mutation has been reported to cause a variety of phenotypes in eleven different patients, including the classical Denys-Drash phenotype of diffuse mesangial sclerosis which leads to early renal failure, genital anomalies in XY individuals and Wilms tumors. The absence of mesangial sclerosis and renal failure in our patient excludes DDS. Our case differs from those previously described as the normal kidney tissue shows some small subcapsular glomeruli indicating that the WT1 mutation has impaired nephron development. This patient extends the range and variation of phenotypes that may arise from a specific germline mutation in WT1.
The Effects of Megestrol Acetate Suspension for Elderly Patients with Reduced Appetite After Hospitalization: A Phase II Randomized Clinical Trial (2005)

Megestrol acetate at doses of 400 mg and 800 mg increases prealbumin in recently hospitalized older persons. Cortisol suppression is common at higher doses and may be persistent. In this small study, the drug did not confer benefit on other nutritional or clinical outcomes.
Mammalian Sperm-Egg Fusion: The Development of Rat Oolemma Fusibility during Oogenesis Involves the Appearance of Binding Sites for Sperm Protein “DE”1 (1996)

Rat epididymal protein DE mediates gamete fusion through complementary sites localized on the egg surface. To investigate whether these egg components are involved in the development of rat oolemma fusibility, both the presence of DE-binding components and the ability of the oolemma to fuse with sperm during oogenesis were examined. Localization of DE-complementary sites by indirect immunofluorescence revealed the absence of fluorescent labeling on growing oocytes with a diameter < 50 microns, and the presence of a uniform staining over the entire surface of germinal vesicle oocytes with a diameter > 50 microns. This localization of oolemma components changed progressively to a patchy distribution during maturation. Whereas sperm incorporation was observed only in maturing oocytes, the development of the Hoechst transfer technique to evaluate membrane fusion revealed that germinal vesicle oocytes with a diameter > 50 microns were already competent to fuse with sperm. The involvement of the DE-complementary sites in the oolemma fusibility of these oocytes was confirmed by the fact that the presence of DE during gamete coincubation significantly (p < 0.001) reduced the percentage of oocytes with fused sperm. Together, these observations indicate that the acquisition of fusibility by the rat oolemma occurs during the growth period and involves the appearance of DE-binding components on the oocyte surface. This study provides novel information on the molecular mechanism by which the mammalian egg plasma membrane becomes competent to fuse with sperm during oogenesis.
In vivo molecular-genetic imaging: multi-modality nuclear and optical combinations (2003)

Multi-modality, noninvasive in vivo imaging is increasingly being used in molecular-genetic studies and will soon become the standard approach for reporter gene imaging studies in small animals. The coupling of nuclear and optical reporter genes, as described here, represents only the beginning of a far wider application of this technology in the future. Optical imaging and optical reporter systems are cost-effective and time-efficient; they require less resources and space than PET or MRI, and are particularly well suited for imaging small animals, such as mice. Optical reporter systems are also very useful for the quantification and selection of transduced cells using FACS, and for performing in vitro assays to validate the function and sensitivity of constitutive and specific-inducible reporter systems. However, optical imaging techniques are limited by depth of light penetration and do not yet provide optimal quantitative or tomographic information. These issues are not limiting for PET- or MRI-based reporter systems, and PET- and MRI-based animal studies are more easily generalized to human applications. Many of the shortcomings of each modality alone can be overcome by the use of dual- or triple-modality reporter constructs that incorporate the opportunity for PET, fluorescence and bioluminescence imaging.