gebhart/patrepeval huggingface dataset:
Genome-wide analysis implicates microRNAs and their target genes in the development of bipolar disorder (2015)

Bipolar disorder (BD) is a severe and highly heritable neuropsychiatric disorder with a lifetime prevalence of 1%. Molecular genetic studies have identified the first BD susceptibility genes. However, the disease pathways remain largely unknown. Accumulating evidence suggests that microRNAs, a class of small noncoding RNAs, contribute to basic mechanisms underlying brain development and plasticity, suggesting their possible involvement in the pathogenesis of several psychiatric disorders, including BD. In the present study, gene-based analyses were performed for all known autosomal microRNAs using the largest genome-wide association data set of BD to date (9747 patients and 14 278 controls). Associated and brain-expressed microRNAs were then investigated in target gene and pathway analyses. Functional analyses of miR-499 and miR-708 were performed in rat hippocampal neurons. Ninety-eight of the six hundred nine investigated microRNAs showed nominally significant P-values, suggesting that BD-associated microRNAs might be enriched within known microRNA loci. After correction for multiple testing, nine microRNAs showed a significant association with BD. The most promising were miR-499, miR-708 and miR-1908. Target gene and pathway analyses revealed 18 significant canonical pathways, including brain development and neuron projection. For miR-499, four Bonferroni-corrected significant target genes were identified, including the genome-wide risk gene for psychiatric disorder CACNB2. First results of functional analyses in rat hippocampal neurons neither revealed nor excluded a major contribution of miR-499 or miR-708 to dendritic spine morphogenesis. The present results suggest that research is warranted to elucidate the precise involvement of microRNAs and their downstream pathways in BD.
Concentration Jump Experiments for the Precise Determination of Rate Constants of Reverse Reactions in the Millisecond Time Range (2001)

Low dissociation or reverse rate constants of single-step or multistep complex formation equilibria are usually obtained with reduced precision from standard stopped-flow binding experiments by determination of the intercept of the concentration dependence of k(obs). Large and fast concentration jumps, based on two different step-motor-driven mixing setups, are performed with 60-300-fold dilutions that allow the precise, convenient, and independent determination of dissociation rate constants in the range of approximately 0.1-100 s(-1) in a single stopped-flow dissociation experiment. A theoretical basis is developed for the design and for the evaluation of such dilution experiments by considering the rebinding occurring during dissociation. The kinetics of three chemical systems are investigated, the binding of Mg2+ to 8-hydroxyquinoline as well as of Ca2+ and K+ to the cryptand [2.2.2], by carrying out standard stopped-flow binding as well as dissociation experiments employing various dilution factors. The advantage of the dilution method for investigating chemical and biological systems is emphasized.
Molecular cloning and heterologous expression of the C-13 phenylpropanoid side chain-CoA acyltransferase that functions in Taxol biosynthesis (2002)

The structural pharmacophore of Taxol, responsible for binding the N terminus of the beta-subunit of tubulin to arrest cell proliferation, comprises, in part, the 13-O-(N-benzoyl-3-phenylisoserinoyl) side chain. To identify the side chain transferase of Taxol biosynthesis, a set of transacylases obtained from an enriched cDNA library (constructed from mRNA isolated from Taxus cuspidata cells induced with methyl jasmonate for Taxol production) was screened. A cDNA clone (designated TAX7) encoding a taxoid C-13 O-phenylpropanoyltransferase was isolated which yielded a recombinant enzyme that catalyzes the selective 13-O-acylation of baccatin III with beta-phenylalanoyl CoA as the acyl donor to form N-debenzoyl-2'-deoxytaxol. This enzymatic product was converted to 2'-deoxytaxol by chemical N-benzoylation, and the identity of this derivative was confirmed by spectrometric analyses. The full-length cDNA has an ORF of 1,335 bases and encodes a 445-aa protein with a calculated molecular weight of 50,546. Evaluation of kinetic parameters revealed K(m) values of 2.4 +/- 0.5 microM and 4.9 +/- 0.3 microM for baccatin III and beta-phenylalanoyl-CoA, respectively. The pH optimum for the recombinant O-(3-amino-3-phenylpropanoyl)transferase is at 6.8. Identification of this clone completes acquisition of the five aroyl/acyltransferases involved in the biosynthesis of Taxol. Application of these transacylase genes in suitable host cells can improve the production yields of Taxol and could enable the preparation of second-generation Taxol analogs possessing greater bioactivity and improved water solubility.
John Caulfield at POC: from holographic components to small system integration (2013)

With his exceptional scientific expertise, Professor John Caulfield was involved at Physical Optics Corporation (POC) from its inception (1985) to the present. This paper reviews his recent involvement at POC, which includes both optical and less well known nonoptical scientific and engineering areas.
Protein Nitration in Parkinsonʼs Disease (1998)

Oxidative stress has been proposed as a pathogenetic mechanism in Parkinson's disease (PD). One mechanism of oxidative cellular injury is the nitration of protein tyrosine residues, mediated by peroxynitrite, a reaction product of nitric oxide and superoxide radicals. We demonstrate here the presence of nitrotyrosine immunoreactivity in Lewy bodies within melanized neurons and in amorphous deposits associated with intact and degenerating neurons. The core of the Lewy body was frequently intensely immunolabeled, while the rim was lightly labeled or unlabeled. This likely reflects the fact that tyrosine residues of neurofilament proteins are primarily localized to Lewy body cores, and suggests that nitrotyrosine is present in neurofilament protein itself. Although these observations are as yet unable to provide a definitive link between oxidative stress and neuronal dysfunction, they demonstrate that oxidative stress has occurred within the vulnerable neurons of PD, leaving a permanent marker of oxidative modification of neuronal proteins within the target cells of neurodegeneration. In addition, these observations provide a potential link between excitotoxicity and oxidative stress within the vulnerable neurons of PD and represent a pathogenetic mechanism in common with the 2 other major age-related neurodegenerative diseases, Alzheimer disease and amyotrophic lateral sclerosis.
A 3-Dimensional Simplex Modulation Format with Improved OSNR Performance Compared to DP-BPSK (2020)

The novel 3-dimensional modulation format 3D-Simplex offers potentially 1.2 dB higher OSNR tolerance than DP-DPSK while exhibiting the same spectral occupancy, modulating two bits per symbol. We verify this benefit experimen-tally and evaluate the transmission performance in a non-linear environment. All experimental results are confirmed by simulations. The benefit of 3D-Simplex is not maintained in the highly non-linear regime, but the performance is still comparable to that of DP-DPSK.
Polarographic Analysis of the Hydrolysis of 2-Carboxy-4-aminodiphenyl Sulphide and 2-Carboxy-4-aminodiphenyl Sulphone in Aqueous Solution (1996)

Department of Chemistry, lnstitute of Science, Bombay-400 032 <em>Manuscript received 7 March 1994. revised 22 February 1995, accepted 22 May 1995</em> Polarographic Analysis of the Hydrolysis of 2-Carboxy-4-aminodiphenyl Sulphide and 2-Carboxy-4-aminodiphenyl Sulphone in Aqueous Solution.
Treponema (2015)

Abstract Trep.o.ne'ma. Gr. v. trepô to turn; Gr. neut. n. nema a thread; N.L. neut. n. treponema a turning thread. Host‐associated, helical cells 0.1–0.7 μm in diameter and 1–20 μm in length . Cells have tight regular or irregular spirals and one or more periplasmic flagella (axial fibrils or axial filaments) inserted at each end of the protoplasmic cylinder. Cytoplasmic filaments are seen in the protoplasmic cylinder just under the cytoplasmic membrane and running parallel with the periplasmic flagella. Under unfavorable cultural or environmental conditions, spherical cells are formed. These can also be seen in old cultures. Gram‐stain‐negative. Cells stain well with silver impregnation methods. Most species stain poorly, if at all, with Gram or Giemsa stain. Best observed with darkfield or phase‐contrast microscopy. Motile. Cells have rotational movement in liquid media, and translational motion in media with high viscosity [ e.g ., those containing 1 % ( w / v) methyl cellulose ]. In a semisolid or solid medium, cells exhibit a serpentine type movement, sometimes referred to as creeping motility. Strictly anaerobic or microaerophilic . Frank pathogens ( Treponema pallidum subspecies, Treponema carateum , and the rabbit pathogen Treponema paraluiscuniculi ) represent a closely related subset within this genus and are considered microaerophiles. Limited multiplication of Treponema pallidum subsp. pallidum strains has been obtained in a tissue culture system, but none of the pathogenic Treponema have been cultivated continuously in artificial media or in tissue culture. Chemo‐organotrophs , using a variety of carbohydrates or amino acids for carbon and energy sources . Cultivated anaerobic species are catalase‐ and oxidase‐negative. Some require long‐chain fatty acids found in serum for growth, while other cultivated species require short‐chain volatile fatty acids for growth. Host‐associated. Pathogenic Treponema pallidum subspecies cause skin lesions, and Treponema pallidum (particularly subspecies pallidum ) can cause systemic infections that, if untreated, can last for years to decades. Other species are found in the oral cavity, intestinal tract, and genital areas of humans or other mammals, and in the gut contents of wood‐feeding insects . DNA G + C content ( mol %): 37–54. Type species : Treponema pallidum subsp. pallidum (Schaudinn and Hoffman 1905) Schaudinn 1905, 1728 AL . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Treponema is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Spirochaetota / Spirochaetia / Spirochaetales / Treponemataceae / Treponema The genus Treponema can also be recovered in the Genome Taxonomy Database (GTDB) as g__Treponema (version v220) ** . GTDB classification: d__Bacteria / p__Spirochaetota / c__Spirochaetia / o__Treponematales / f__Treponemataceae / g__Treponema * <jats:mixed-citation public
Practical Compact Spatially-Coherent, Phase-Matched Extreme UV Source at 50 kHz (2009)

We report the first efficient source of spatially-coherent extreme-UV light at the high repetition rates (&gt;50kHz) needed for metrology and imaging applications. This practical compact tabletop EUV source uses IR pulse energy of only 25μJ.
Generation of CW Millimeter Wave Signals in a Lithium Niobate Nonlinear Optical Waveguide Using Modulated Optical Input (2000)

The generation of CW millimeter wave signals is observed in a LiNbO 3 nonlinear optical waveguide. Optical light that has two frequency components is introduced into an optical waveguide, and the millimeter waves which are generated are obtained from the terminal connected to the metallic traveling waveguide. This configuration is made with a LiNbO 3 commercial phase modulator. Millimeter waves are generated at frequencies up to 40 GHz. This is the first report of CW millimeter wave generation in a nonlinear ferroelectric waveguide, to our knowledge. A comparison of the measured signal levels with theoretically estimated ones is discussed.
Intracellular localization of the Epstein‐Barr virus BFRF1 gene product in lymphoid cell lines and oral hairy leukoplakia lesions (2003)

A novel protein encoded by the BFRF1 gene of the Epstein-Barr virus was identified recently [Farina et al. (2000) J Virol 74:3235-3244], which is antigenic "in vivo" and expressed early in the viral replicative cycle. In the present study, its subcellular localization was examined in greater detail comparing Epstein-Barr virus (EBV) induced producing and nonproducing cell lines by immunofluorescence: in 12-0-tetradecanoyl phorbol-13-acetate (TPA)-induced Raji and B95-8 cells, as well as in anti-IgG-stimulated Akata cells, the protein appeared to be localized over the cell nuclear membrane. A similar nuclear membrane localization was observed in epithelial cells of oral hairy leukoplakia, a pathological manifestation of permissive EBV infection. In contrast, upon transfection of BFRF1 in the EBV-negative Burkitt's lymphoma cell line DG75, the protein was localized predominantly over the plasma membrane. The membrane localization was abolished when DG75 cells were transfected with a C-terminal deletion mutant of BFRF1 lacking the transmembrane domain. Because induced Raji cells do not produce virus, the above observations indicate that the nuclear membrane localization is not associated with viral production, but requires the expression of EBV genes, and suggest that additional proteins, expressed early during viral lytic infection, might be necessary to target the protein to the nuclear membrane. Immunogold electron microscopy on ultrathin cryosections of induced B95-8 cells showed that BFRF1 on the nuclear membranes was concentrated over multilayered domains representing areas of active viral replication or at the sites of viral budding, suggesting that BFRF1 is involved in the process of viral assembly.
Mobile Communications Beyond 52.6 GHz: Waveforms, Numerology, and Phase Noise Challenge (2020)

In this article, the 5G New Radio (NR) physical layer evolution to support beyond 52.6 GHz communications is addressed. The performance of both OFDM based and DFT-s-OFDM based networks are evaluated with special emphasis on the phase noise (PN) induced distortion. It is shown that DFT-s-OFDM is more robust against PN under 5G NR Release 15 assumptions, specifically regarding the supported phase tracking reference signal (PTRS) designs. To further improve the PN compensation capabilities, the PTRS design for DFT-s-OFDM is revised, while for the OFDM waveform a novel block PTRS structure is introduced, providing similar link performance as DFT-s-OFDM with enhanced PTRS design. We demonstrate that the existing 5G NR Release 15 solutions can be extended to support deployments at 60 GHz bands with the enhanced PTRS structures. In addition, DFT-s-OFDM based downlink for user data could be considered for beyond 52.6 GHz communications to further improve system power efficiency and performance with higher order modulation and coding schemes. Finally, network link budget and cell size considerations are provided, showing that at certain bands with specific transmit power regulation, the cell size can eventually be downlink limited.
Oxidized LDL receptors: a recent update (2023)

Receptor-mediated oxLDL uptake results in cellular dysfunction of various cell types involved in atherogenesis and plaque development. The current advancements clearly demonstrate that targeting oxLDL-LOX-1 axis may lead to development of future therapeutics for the treatment of atherosclerotic cardiovascular and cerebrovascular diseases.
Supplementary Figure S8 from Rapid Expansion of Highly Functional Antigen-Specific T Cells from Patients with Melanoma by Nanoscale Artificial Antigen-Presenting Cells (2023)

&lt;p&gt;TCR repertoire analysis of MART-1 Tet+ CD8+ T-cells.&lt;/p&gt;
SCALIP - a scalable IP solution for pipelined arrays with limited feedback (2002)

Current IP methodologies are only useful within a limited design space low power, high performance or low area. A single IP methodology is needed that can span all of these design spaces with one specification. SCALIP is a methodology that can quickly and easily create multiple design points that span a much greater design space thin any current IP methodology utilizing only behavioral or RTL synthesis. One limitation of this methodology is that it is only useful for pipelined arrays with limited feedback.
Design and synthesis of new hybrid latency reversal agents for HIV treatment (2020)

Background: HIV latency reservoir remains one of the main barriers to eliminate the virus. The &ldquo;kick-and-kill&rdquo; strategy aims to reactivate the HIV latency reservoir in the first step &ldquo;kick&rdquo; and the elimination of these reactivated virus in the second step, &ldquo;kill&rdquo;. Latency-reversing agents such as histone deacetylase (HDAC) and bromodomain (BRD-4) inhibitors have been described in &ldquo;kick-and-kill&rdquo; strategy to reactivate HIV reservoirs. Here, we described the design, preparation and evaluation of hybrid compounds designed to target both BRD-4 and HDAC 1-3 simultaneously. Methods: In silico studies were performed using the molecular modelling Maestro by Schr&ouml;dinger environment, using BRD-4 (pdb code: 4WIV) and HDAC-2 (pdb code: 4LY1). All compounds were prepared through divergent synthesis. First, it was performed a Suzuki coupling reaction between the methyl 4-iodobenzoate and boronic acid derivatives. The ester function was hydrolysed and the compound was coupled with o-phenylenediamine using EDC. The ability of the compounds (at 10 mM) to inhibit both HDAC 1-3 and BRD-4 were evaluated. Results: Docking simulation suggests that all compounds are able to interact with BRD-4 and HDAC-2. Five compounds were synthesized at global yields ranging from 11-20%. All structures were characterized by analytical methods. The most promising compound was able to inhibit HDAC 1-3 and BRD4 at values of 75 %, 72 %, 57 % and 21 %, respectively. Conclusions: Hybrid compounds were designed, synthesized and evaluated against the enzymes HDAC and BRD. These dual compounds were able to inhibit BRD-4 and HDAC 1-3 suggesting its potential use as latency-reversing agents.
Autonomous Replication in Human Cells of Multimers of Specific Human and Bacterial DNA Sequences (1993)

Using modules of a specific 2,712-bp human DNA sequence and a specific 2,557-bp Escherichia coli DNA sequence, we created plasmids containing between 1 and 12 modules of single or chimeric sequence composition and tested them in human cells for their autonomous replication ability. We found that replication efficiency per generation increased with successive addition of human modules, to essentially 100% by six copies. Although a single copy of the bacterial module had negligible replication ability, the replication efficiency per generation of 12 bacterial modules was 66%. Chimeras composed of human and bacterial modules displayed intermediate replication levels. We also used two-dimensional gel electrophoresis to physically map where replication initiated on a half human-half E. coli plasmid. Our results suggest that autonomous replication in human cells is stimulated by simple sequence features which occur frequently in human DNA but are more rare in bacterial DNA.
Compensation of distant phase-distorting layers II Extended-field-of-view adaptive receiver system (2004)

We analyze the anisoplanatic adaptive receiver system field of view (FOV) and the possibility of controlling the system FOV by using an adaptive optics system with multiple wave-front sensors that sense wave-front phase aberrations of reference waves with different arrival angles. The conventional decoupled stochastic parallel gradient descent (D-SPGD) technique is generalized to include output signals from multiple wave-front sensors. The multiple-reference D-SPGD control algorithm introduced here is applied to obtain an anisotropic FOV in adaptive receiver systems by using two and three reference waves.
Structure-activity studies of β-carbolines. 4. Crystal and molecular structures of t-butyl β-carboline-3-carboxylate and 2-(methoxycarbonyl)canthine-6-one (1988)

The crystal and molecular structures of two ligands for the benzodiazepine (BZ) receptor, t-butyl β-carboline-3-carboxylate, I (C 16 H 16 N 2 O 2 ), and 2-(methoxycarbonyl)canthin-6-one, II (C 16 H 10 N 2 O 3 ), are reported. The t-butyl β-carboline compound has high affinity for the receptor and is an antagonist; in contrast, the canthin-6-one has a 10-fold lower affinity for the receptor and no determinable in vivo activity. The space group for I is P2 1 /c with a = 11.756(1), b = 11.2324(8), c = 11.964(1) Å, and β = 105.99(1)°. For II, the space group is also P2 1 /c with a = 9.317(1), b = 7.964(1), c = 17.180(3) Å, and β = 104.173(7)°. The orientation of the alkyl-carboxylate side chain is different in the two molecules and may be related to the difference in affinity and in vivo activity of the ligands. In addition, the packing arrangements in the two structures are dominated by π-stacking interactions; and, in the case of the t-butyl compound, by hydrogen bonding.
Expressing accessory proteins in cellulolytic Yarrowia lipolytica to improve the conversion yield of recalcitrant cellulose (2017)

This study has provided a potent cellulose-degrading <i>Y. lipolytica</i> strain that co-expresses a core set of cellulolytic enzymes and some accessory proteins. Results reveal that the tuning of cellulase production and the production of accessory proteins leads to optimized performance. Accordingly, the beneficial effect of accessory proteins for cellulase-mediated degradation of cellulose is underlined, especially when crystalline cellulose and complex biomass are used as substrates. Findings specifically underline the benefits and specific properties of swollenin. Although in our study swollenin clearly promoted cellulase action, its use requires process redesign to accommodate its specific mode of action.
Nonuniform linear antenna arrays minimising Cramér–Rao bounds for joint estimation of single source range and direction of arrival (2005)

Different antenna placements in nonuniform linear arrays for the joint estimation of the range and direction-of-arrival (DOA) of one source are considered. It is shown that the Cramér–Rao bound (CRB) for the range and DOA estimates can be expressed as a function of the angles at which the source sees the antennas. This new formulation of the CRB easily reveals the geometrical properties that the array should have in order to minimise the CRB. Based on the new representation of the CRB, a result found in the literature (which was concerned with the special case of a number of antennas that is divisible by four) is generalised to include the case of an arbitrary number of antennas. Furthermore, it is shown that symmetric arrays are close to uniformly optimal for different DOAs when the range is much larger than the aperture of the arrays.
Active Immunization Study of Colon Cancer Derived 1-8D Peptide in HHD Mice (2005)

1-8D gene is a member of human 1-8 interferon inducible gene family and was shown to be overexpressed in fresh colon cancer tissues. Three peptides 1-6, 3-5 and 3-7 derived from human 1-8D gene were shown to have immunogenicity against colon cancer. Methods: To study tumor immunotherapy, of three peptides we established an active immunization model using HHD mice. D b-/- ×β2 microglobulin (β2m) null mice transgenic for a chimeric HLA-A2.1/D b- 2m single chain (HHD mice) were challenged with B16/HHD/1-8D tumor cells and were immunized with irradiated peptide-loaded RMA- S/HHD/B7.1 transfectants. In therapy model tumor growth was retarded in HHD mice that were injected with 3-5 peptide-loaded RMA-S/HHD/B7.1. In survival test vaccination with 1-8D-derived peptide protects HHD mice from tumor progression after tumor challenge. Results: These studies show that peptide 3-5 derived from 1-8D gene can be the most effective candidate for the vaccine of immunotherapy against colon cancer and highlight 1-8D gene as putative colon carcinoma associated antigens. Conclusion: We demonstrated that RMA-S/HHD/ B7.1 loaded with 1-8D peptides, especially 3-5, immunization generates potent antitumor immunity against tumor cells in HHD mice and designed active immunization as proper immunotherapeutic protocols.