gebhart/patrepeval huggingface dataset:
Studies on the progestational endometrium of the rabbit. II. Electron microscopy, day 0 to day 13 of gonadotrophininduced pseudopregnancy (1975)

The fine structure of the endometrial epithelium of the pseudo-pregnant rabbit from the day of induced ovulation (day 0) to the 13th day is here correlated with previously defined light microscopic phases. In Phase 1 (0-1 day), in which there is a presumed "priming" of the endometrium by ovarian steroidal hormones, no changes were observed. In Phase 2 (1-3 days), in addition to mitotic activity, the epithelium showed a disappearance of the mucification and lymphocytic migration typical of Phase 1 and also of the non-pregnant or "estrous" phase, and showed other nuclear and cytoplasmic changes which probably reflect endogenous growth and protein synthesis. In Phase 3 (4-6 days), two distinct populations of reacting cells were present: (1) surface and cryptal cells investing the now folded mucosal surface, and (2) glandular cells. The first group showed characteristic dome-like protrusions of the cytoplasm into the lumen, and also showed distinct cytoplasmic and nuclear changes which appear to be a prelude to the succeeding phase of fusion but are not necessarily secretory in type. The glandular cells, in contrast, showed cytoplasmic changes which appear to reflect active secretory activity (hypertrophy of the Golgi area, cytoplasmic vacuoles containing electron-opaque material, etc.). This phase coincides with the maximal secretion of uterine-specific proteins, and electron-opaque material is abundant within the endometrial lumen. In Phase 4 (6-8 days), the surface and cryptal epithelium undergoes a transformation into multinucleated cells, the result of a process of lysis of intervening plasma membranes, the precise mechanism of which (i.e., with or without initial membrane fusion) was not determined. Cell fusion proceeded earlier and more actively mesometrially than antimesometrially. The glandular cells showed evidence of reduced secretory activity, but did not at any stage undergo multinucleate-cell transformation. In Phase 5 (8-13 days) there was progressive fusion, and the number of nuclei per cytoplasmic sac appeared increased, presumably due to the continued action of progesterone which is maximal during this phase. Glandular cells showed further reduced secretory activity but remained columnar. Ciliation of the epithelium was sporadic in the pre-secretory phases and rare or absent in the secretory and fusion phases; it became widespread during the phase of decline after day 14, a period which will not be included in this study. The fine structure of the ciliated cells was the same at all stages; there was no evidence for their origin from a reserve population; it is possible that they arise by modification of the multinucleated cells. Cytoplasmic crystals and intramitochondrial densities or lamellae were observed during the secretory and fusion stages, the former only in the glands, the latter in the surface and cryptal epithelium. They appear to be associated with rising or maximal progesterone secretion.
Molecular Classification of Tamoxifen-Resistant Breast Carcinomas by Gene Expression Profiling (2005)

Our data show that gene expression profiling can be used to discriminate between breast cancer patients with progressive disease and objective response to tamoxifen. Additional studies are needed to confirm if the predictive signature might allow identification of individual patients who could benefit from other (adjuvant) endocrine therapies.
Low Plasma Adiponectin Levels and Risk of Colorectal Cancer in Men: A Prospective Study (2005)

In this prospective nested case-control study, men with low plasma adiponectin levels had a higher risk of colorectal cancer than men with higher levels. More prospective observational studies, particularly in women, and mechanistic studies are required to fully understand the relationship between adiponectin and carcinogenesis.
Structure of a cloned circular Moloney murine leukemia virus DNA molecule containing an inverted segment: implications for retrovirus integration. (1980)

Closed circular Moloney murine leukemia virus (M-MuLV) DNA was prepared from recently infected cells and cloned in a lambda vector. Four classes of cloned M-MuLV inserts were found: Class I, full length 8.8-kilobase (kb) inserts with two tandem long terminal repeats (LTRs) of 600 base pairs; class 2, 8.2-kb inserts with a single copy of a LTR; class 3, M-MuLV DNA inserts with various portions deleted; and class 4, an 8.8-kb insert with an internal sequence inversion. Determination of nucleotide sequence at the junction between the two LTRs from a class 1 insert suggested that circularization occurred by blunt-end ligation of an 8.8-kb linear DNA. The class 4 molecule had an inversion that was flanked by inverted LTRs, each of which had lost two terminal base pairs at the inversion end points. Also, four base pairs that were present only once in standard M-MuLV DNA were duplicated at either end of the inversion. This molecule was interpreted as resulting from an integrative inversion in which M-MuLV DNA has integrated into itself. Its analysis thus provided explicit information concerning the mechanism by which retrovirus DNA integrates into host cell DNA. Models of retrovirus integration based on bacterial DNA transposition mechanisms are proposed.
A protected biotin containing deoxycytidine building block for solid phase synthesis of biotinylated oligonucleotides (1990)

The synthesis of a modified 2'-deoxycytidine-3'-O-phosphoramidite carrying an N-t-butylbenzoyl protected biotin on a long polar spacer arm attached to the 4-N position is described. The presence of the bulky lipophilic t-butylbenzoyl protecting group enables the direct solid phase synthesis of biotinylated oligoribonucleotides and a variety of analogues in high yield without modification of the biotin moiety. Biotinylated antisense oligonucleotides incorporating this new derivative allow convenient isolation and purification of ribonucleic acid-protein complexes. The kinetics of biotin binding to streptavidin agarose is facilitated by the long polar spacer arm.
Specialized functional properties of the integrin alpha 4 cytoplasmic domain. (1995)

For functional studies of the integrin alpha 4 cytoplasmic domain, we have expressed the following in K562 and Chinese hamster ovary (CHO) cells: 1) wild-type alpha 4 (called X4C4), 2) two chimeric forms of alpha 4 (called X4C2 and X4C5) that contain the cytoplasmic domains of alpha 2 and alpha 5, respectively, and 3) alpha 4 with no cytoplasmic domain (X4C0). Cytoplasmic domain exchange had no effect on VLA-4-dependent static cell adhesion or tethering to VCAM-1 in conditions of shear flow. However, the presence of the alpha 2 or alpha 5 tails markedly enhanced VLA-4-dependent K562 cells spreading (X4C2 > X4C5 > X4C4 > X4C0), increased localization of VLA-4 into focal adhesion-like complexes in CHO cells (X4C2 > X4C5 > X4C4), and strengthened CHO and K562 cell resistance to detachment from VCAM-1 in conditions of shear flow (X4C2 > X4C5 > X4C4 > X4C0). Conversely, the alpha 4 tail supported greater VLA-4-dependent haptotactic and chemotactic cell migration. In the absence of any alpha tail (i.e., X4C0), robust focal adhesions were observed, even though cell spreading and adhesion strengthening were minimal. Thus, such focal adhesions may have relatively little functional importance, and should not be compared with focal adhesions formed when alpha tails are present. Together, these results indicate that all three alpha-chain tails exert defined positive effects (compared with no tail at all), but suggest that the alpha 4 cytoplasmic domain may be specialized to engage in weaker cytoskeletal interactions, leading to diminished focal adhesion formation, cell spreading, and adhesion strengthening, while augmenting cell migration and facilitating rolling under shear flow. These properties of the alpha 4 tail are consistent with the role of alpha 4 integrins on highly motile lymphocytes, monocytes, and eosinophils.
Differential human T cell-dependent B cell differentiation induced by staphylococcal superantigens (SAg). Regulatory role for SAg-dependent B cell cytolysis (1995)

Microbial superantigens (SAg), by virtue of their binding to TCR V beta elements and to class II MHC molecules on accessory cells, trigger T cell proliferation in a dose-dependent fashion. In contrast, SAg-induced T cell-dependent B cell differentiation occurs only at SAg concentrations that are orders of magnitude lower that those required for optimal mitogenesis (low-dose SAg). At optimal mitogenic doses (high-dose SAg), SAg-driven B cell differentiation does not ensue. In this report, we demonstrate that this dichotomy in SAg-driven B cell differentiation is due to the active inhibition of B cell differentiation by high-dose SAg. Such inhibition is not reversed by feeding cultures with fresh medium, with conditioned media, or with IL2 +/- IL4, and impaired B cell differentiation is observed in cultures containing purified T cells or CD4+ T cells + B cells, as well as in PBMC cultures. Although preincubation of either T cells or B cells with high-dose SAg impairs subsequent SAg-induced B cell differentiation, high-dose SAg is not toxic per se, since high-dose SAg does promote vigorous B cell differentiation in cultures of mitomycin C-treated T cells + B cells and does not inhibit T cell-independent B cell differentiation. No correlation exists between SAg-induced B cell surface expression of CTLA4 ligand and generation of Ig-secreting cells, but the dose of SAg does correlate with T cell-mediated SAg-dependent cytolysis of transformed B cell targets or autologous nontransformed activated B cell targets. B cell recovery from cultures stimulated with high-dose SAg is lower than that from cultures stimulated with low-dose SAg, whereas B cell apoptosis is greater in the former cultures than that in the latter cultures. T cells stimulated with high-dose SAg do not inhibit differentiation of activated B cells in the absence of physical contact between the T cells and the target B cells, supporting the notion of direct killing of activated B cells by T cells. The ability of low doses of SAg to promote B cell differentiation without generating biologically meaningful cytolytic activity and the ability of higher doses of SAg to modulate Ig production may have important pathogenetic and therapeutic ramifications for certain autoimmune disorders, such as systemic lupus erythematosus.
Antiviral dynamics and sex differences of zidovudine and lamivudine triphosphate concentrations in HIV-infected individuals (2003)

Zidovudine and lamivudine triphosphate concentration thresholds were independently associated with the antiviral activity of zidovudine, lamivudine, and indinavir. The significantly elevated triphosphate concentrations in women and individuals with low baseline CD4 cell counts, groups that historically experience high rates of serious NRTI toxicities, provide a hypothesis for the pathogenesis of these events.
Cholera Toxin Binding Affinity and Specificity for Gangliosides Determined by Surface Plasmon Resonance (1996)

The present study determines the affinity of cholera toxin for the ganglioside series GM1, GM2, GM3, GD1A, GD1B, GT1B, asialo GM1, globotriosyl ceramide, and lactosyl ceramide using real time biospecific interaction analysis (surface plasmon resonance, SPR). SPR shows that cholera toxin preferably binds to gangliosides in the following sequence: GM1 > GM2 > GD1A > GM3 > GT1B > GD1B > asialo-GM1. The measured binding affinity of cholera toxin for the ganglioside sequence ranges from 4.61 x 10-12 M for GM1 to 1.88 x 10-10 M for asialo GM1. The picomolar values obtained by surface plasmon resonance are similar to Kd values determined with whole-cell binding assays. Both whole-cell assays and SPR measurements on synthetic membranes are higher than free solution measurements by several orders of magnitude. This difference may be caused by the effects of avidity and charged lipid head-groups, which may play a major role in the binding between cholera toxin, the receptor, and the membrane surface. The primary difference between free solution binding studies and surface plasmon resonance studies is that the latter technique is performed on surfaces resembling the cell membrane. Surface plasmon resonance has the further advantage of measuring apparent kinetic association and dissociation rates in real time, providing direct information about binding events at the membrane surface.
Plasmonic Purcell effect reveals obliquely ordered phosphorescent emitters in Organic LEDs (2017)

The non-isotropic alignment of molecules can increase the interaction efficiency with propagating light fields. This applies to both emissive and absorptive systems and can be exploited for achieving unprecedented efficiencies of organic opto-electronic devices such as organic light-emitting diodes. Optical analysis has revealed certain phosphorescent emitters to align spontaneously in an advantageous orientation. Unfortunately, established approaches only determine an average orientation because emission patterns solely depend on the second moments of the transition dipole vector distribution. In order to resolve further details of such a distribution, additional differences in the emission characteristics of parallel and perpendicularly oriented emitters need to be introduced. A thin metal layer near the emitters introduces plasmon mediated losses mostly for perpendicular emitters. Then, analyzing the emission at different polarizations allows one to measure emission lifetimes of mostly parallel or mostly perpendicular oriented emitters. This should alter the transient emission when observing the temporal phosphorescence decay under different directions and/or polarizations. The angular width of the orientation distribution can be derived from the degree of such lifetime splitting. Our results suggest a narrow but obliquely oriented molecular ensemble of Ir(MDQ)<sub>2</sub>(acac) doped into the α-NPD host inside an Organic LED stack.
Crystallization and preliminary X-ray crystallographic studies on a Fab fragment of the mouse anti-human Fas monoclonal antibody HFE7A (2001)

The Fas-Fas ligand system is involved in apoptosis. The mouse anti-human Fas monoclonal antibody HFE7A (m-HFE7A) has a potential use in human therapy against autoimmune diseases such as rheumatoid arthritis. Information on the three-dimensional structure is essential for antibody humanization. Crystals of an antigen-binding fragment (Fab) of m-HFE7A were obtained by the hanging-drop vapour-diffusion method using sodium citrate as a precipitant and 2-methyl-2,4-pentanediol as an additive. Fast optimization to produce single crystals suitable for X-ray analysis was achieved by the streak-seeding technique. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 43.4, b = 74.0, c = 133.8 A. The crystals diffract at least to 2.5 A resolution.
Quinoline Derivatives as Promising Inhibitors of Antibiotic Efflux Pump in Multidrug Resistant Enterobacter Aerogenes Isolates (2006)

Efflux pumps protect the bacterial cell by expelling toxic compounds before they reach intracellular targets. Because this mechanism actively contributes to the resistance of a given bacterium to more than one class of antibiotics, molecules that are able to block the relevant efflux pump are of potential significance to combat drug resistance caused by efflux pumps. Different quinoline derivatives including alkoxy, alkylamino, thioalkoxy and chloroquinolines have been previously reported to make Enterobacter aerogenes resistant isolates that over express the mechanism of efflux, noticeably more susceptible to structurally unrelated antibiotics. In addition, various quinoline derivatives significantly increase the intracellular concentration of chloramphenicol as reported with other inhibitors, thereby suggesting the inhibition of the drug transport by AcrAB-TolC pump, which is fully active in the clinicaly resistant isolates investigated. Here, we discuss the respective properties of this molecular family, taking into account the recent insights into the structural data of AcrB pump.
Identification of the gonococcal glmU gene encoding the enzyme N-acetylglucosamine 1-phosphate uridyltransferase involved in the synthesis of UDP-GlcNAc (1995)

In searching for the gonococcal sialyltransferase gene(s), we cloned a 3.8-kb DNA fragment from gonococcus strain MS11 that hybridized with the oligonucleotide JU07, which was derived from the conserved C terminus of the sialyl motif present in mammalian sialyltransferases. Sequencing of the fragment revealed four putative open reading frames (ORFs), one of which (ORF-1) contained a partial sialyl motif including the amino acid sequence VGSKT, which is highly conserved among sialyltransferases. The gene was flanked by two inverted repeats containing the neisserial DNA uptake sequence and was preceded by a putative sigma 54 promoter. Database searches, however, revealed a high degree of homology between ORF-1 and the N-acetylglucosamine 1-phosphate uridyltransferase (GlmU) of Escherichia coli and Bacillus subtilis and not with any known sialyltransferase. This homology was further established by the successful complementation of an orf-1 mutation by the E. coli glmU gene. Enzyme assays demonstrated that ORF-1 did not possess sialyltransferase activity but mimicked GlmU function catalyzing the conversion of N-acetylglucosamine 1-phosphate into UDP-N-acetylglucosamine, which is a key metabolite in the syntheses of lipopolysaccharide, peptidoglycan, and sialic acids.
Oxidation studies of SiGe (1989)

We have studied the kinetics and mechanism of oxidation of SiGe alloys deposited epitaxially onto Si substrates by low-temperature chemical vapor deposition. Ge is shown to enhance oxidation rates by a factor of about 3 in the linear regime, and to be completely rejected from the oxide so that it piles up at the SiO2/SiGe interface. We demonstrate that Ge plays a purely catalytic role, i.e., it enhances the reaction rate while remaining unchanged itself. Electrical properties of the oxides formed under these conditions are presented, as well as microstructures of the oxide/substrate, Ge-enriched/SiGe substrate, and SiGe/Si substrate interfaces, and x-ray photoemission studies of the early stages of oxidation. Possible mechanisms are discussed and compared with oxidation of pure silicon.
Aquaporin expression in human lymphocytes and dendritic cells (2004)

Aquaporins (AQPs) are molecular water channels, and 10 related AQPs have been identified in mammals. So far, the study of mammalian AQP expression has been limited mainly to mice and rat lung, kidney, brain, and gastrointestinal tract. Although AQP3 and AQP7 have been shown to be involved in volume-regulating mechanisms in dendritic cells, the exact patterns of AQP expression in the human immune system are not well understood. Using reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of peripheral blood from healthy donors, we demonstrated the expression of AQP1, AQP3, and AQP5 in activated B and T lymphocytes and the expression of AQP3 and AQP5 in immature dendritic cells. None of the tested AQPs was expressed in inactivated B or T lymphocytes. In situ hybridization studies using human tonsils showed that AQP1, AQP3, and AQP5 were expressed almost exclusively in the germinal centers. Further in situ hybridization showed that expression of AQP1, AQP3, and AQP5 were detected in tumor-infiltrating lymphocytes surrounding bronchogenic carcinoma of the lung and that expression of AQP3 and AQP5 was detected in dendritic cells. These findings provide new insights into the expression patterns of AQPs in the human immune system. While the exact role of AQPs in the human immune system remains to be determined, we propose that AQP expression patterns may be used as a marker to study lymphocyte activation and proliferation.
Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production (2012)

Wax ester synthases (WSs) can synthesize wax esters from alcohols and fatty acyl coenzyme A thioesters. The knowledge of the preferred substrates for each WS allows the use of yeast cells for the production of wax esters that are high-value materials and can be used in a variety of industrial applications. The products of WSs include fatty acid ethyl esters, which can be directly used as biodiesel. Here, heterologous WSs derived from five different organisms were successfully expressed and evaluated for their substrate preference in Saccharomyces cerevisiae. We investigated the potential of the different WSs for biodiesel (that is, fatty acid ethyl esters) production in S. cerevisiae. All investigated WSs, from Acinetobacter baylyi ADP1, Marinobacter hydrocarbonoclasticus DSM 8798, Rhodococcus opacus PD630, Mus musculus C57BL/6 and Psychrobacter arcticus 273-4, have different substrate specificities, but they can all lead to the formation of biodiesel. The best biodiesel producing strain was found to be the one expressing WS from M. hydrocarbonoclasticus DSM 8798 that resulted in a biodiesel titer of 6.3 mg/L. To further enhance biodiesel production, acetyl coenzyme A carboxylase was up-regulated, which resulted in a 30% increase in biodiesel production. Five WSs from different species were functionally expressed and their substrate preference characterized in S. cerevisiae, thus constructing cell factories for the production of specific kinds of wax ester. WS from M. hydrocarbonoclasticus showed the highest preference for ethanol compared to the other WSs, and could permit the engineered S. cerevisiae to produce biodiesel.
Theory and experiment agree: Single-walled carbon nanotube caps grow catalyst-free with chirality preference on a SiC surface (2006)

High-temperature quantum chemical molecular dynamics simulations have been performed on model systems of thin SiC crystal surfaces with two graphene sheets placed on top of either C or Si face. In agreement with experiment, we find that (a) the C-face-attached graphene layer warps readily to form small diameter, stable nanocaps, suitable for further perpendicular growth of nanotubes, (b) the Si-face-attached graphene sheet does not readily wrap and forms more volatile Si-graphene bonds, and (c) C face nanocaps appear to anneal to dome-shape structures with zigzag chirality.
PARKINSON’S DISEASE, AUTOIMMUNITY, AND OLFACTION (2009)

Parkinson's disease (PD) is a common progressive neurodegenerative disorder, mainly classified as a movement disorder which manifests among others nonmotor symptoms such as olfactory dysfunction. The etiopathogenesis of this disease has yet to be elucidated, though it seems to be interconnected with a complex set of genetic, environmental, and immunological interactions. This review unfolds the immune alterations observed in PD patients by describing the increase in the innate immune components including complement and cytokines within their substantia nigra and cerebrospinal fluid (CSF). These alterations extended to the adaptive immune response with the elevation of T cells and autoantibodies (anti-α-synuclein and anti-GM1-ganglioside) in the peripheral blood and CSF of PD patients. Interestingly, another etiopathogenic triad has recently emerged linking PD to autoimmunity through olfactory dysfunction. Smell deficit is one of the earliest signs of PD and a unique observation suggesting olfactory declines to be a consequence of autoimmune mechanisms. Therefore, we considered several undisputed autoimmune diseases known for their olfactory consequences as template examples that may shed more light on the relationship between autoimmunity and PD. We hope that understanding the nature of this disease may lay the ground for successes in the quest to halt the progressive neurodegenerative process.