gebhart/patrepeval huggingface dataset:
Antisense oligonucleotides for target validation in the CNS. (1999)

Although antisense oligonucleotides have been used in cell-based antisense experiments for nearly two decades, studies to investigate the function of CNS proteins in living animals were not successfully conducted until recently. Oligonucleotides are not transported across the blood-brain barrier to any appreciable extent. Consequently, these molecules need to be administered directly into the brain. Antisense approaches may be especially suited to investigation of CNS proteins. Due to their specificity, antisense sequences can more easily and selectively distinguish between closely related proteins, such as receptor subtypes, in contrast to the more traditional pharmacological agents such as small molecule ligands. This review discusses some unique technical aspects surrounding oligonucleotide delivery to the brain, and summarizes some of the more noteworthy applications of antisense tools to the study of CNS protein function during the past two years.
Androgens in the Etiology of Alzheimer's Disease in Aging Men and Possible Therapeutic Interventions (2007)

Animal experiments and cell biology studies have provided evidence that both estrogens and androgens can play a protective role against Alzheimer's disease (AD) related neurodegeneration. Males who become hypogonadal in later life often report problems with their memory. Lower than normal testosterone levels have also been detected in patients prior to the onset of AD, as well as in younger late-onset male AD patients, when compared to appropriate controls. The results of some small clinical trials suggest that testosterone can improve cognitive function in andropause. Although such improvement in cognitive function is subtle, patients on testosterone replacement therapy have reported memory improvements in both declarative and procedural domains. In contrast, there is no clinical evidence to date which suggest that the hormone dihydroepiandrosterone (DHEA) can improve cognitive function. Rises in the levels of the gonadotropins, follicle stimulating hormone (FSH) and luteinizing hormone (LH), have been associated with AD, but the clinical effects of reducing their levels remain to be determined. We hypothesize that androgens, gonadotropin modulators, or perhaps selective androgen receptor modulators may be useful components of therapy aimed at preventing the onset or delaying the progression of AD in male patients.
Biogenesis, Secretion, and Intercellular Interactions of Exosomes and Other Extracellular Vesicles (2014)

In the 1980s, exosomes were described as vesicles of endosomal origin secreted from reticulocytes. Interest increased around these extracellular vesicles, as they appeared to participate in several cellular processes. Exosomes bear proteins, lipids, and RNAs, mediating intercellular communication between different cell types in the body, and thus affecting normal and pathological conditions. Only recently, scientists acknowledged the difficulty of separating exosomes from other types of extracellular vesicles, which precludes a clear attribution of a particular function to the different types of secreted vesicles. To shed light into this complex but expanding field of science, this review focuses on the definition of exosomes and other secreted extracellular vesicles. Their biogenesis, their secretion, and their subsequent fate are discussed, as their functions rely on these important processes.
Signaling for Internet telephony (2002)

Internet telephony must offer the standard telephony services. However the transition to Internet-based telephony services also provides an opportunity to create new services more rapidly and with lower complexity than in the existing public switched telephone network (PSTN). The Session Initiation Protocol (SIP) is a signaling protocol that creates, modifies and terminates associations between Internet end systems, including conferences and point-to-point calls. SIP supports unicast, mesh and multicast conferences, as well as combinations of these modes. SIP implements services such as call forwarding and transfer placing calls on hold, camp-on and call queueing by a small set of call handling primitives. SIP implementations can re-use parts of other Internet service protocols such as HTTP and the Real-Time Stream Protocol (RTSP). We describe SIP, and show how its basic primitives can be used to construct a wide range of telephony services.
SONET bidirectional ring capacity analysis: a pragmatic view (2002)

This paper presents the results of a theoretical analysis of SONET bidirectional rings. It provides significant insight into ring planning by studying the impact of the number of nodes on a ring, realizable assignments, and ring interconnection. A new concept of realizable assignments is developed and studied. Realizable assignments provide a pragmatic method of determining the assignment capacity of the Bidirectional Line Switched Rings. The ring interconnection analysis studies the impact of inter-ring vs. intra-ring demand, drop and continue, and DS1 grooming at ring interconnect nodes on the economic prove-in of rings.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Surface Modification of an Organic Pigment by Grafting of Polymers (1996)

キナクリドン (5, 7, 12, 14-テトラヒドロキノ [2, 3-β] アクリジン-7, 14-ジオン) の表面を改質する目的で, キナクリドン表面へ導入したペルオキシエステル基で開始されるビニルモノマーの重合による, ポリマーの表面グラフト反応について検討した。キナクリドン表面へのペルオキシエステル基の導入は, アジポイルジクロリドとキナクリドン表面のアミノ基との反応で粒子表面へ導入したアシルクロリド基とtert-ブチルハイドロペルオキシドとの反応により行った。滴定法で求めた粒子表面へのペルオキシエステル基の導入量は, 0.09mmol/gであった。キナクリドン表面へ導入したtert-ブチルペルオキシエステル基により, メタクリル酸メチル (MMA), N-ビニル-2-ピロリドン (NVPD) などのビニルモノマーの重合が開始され, 対応するポリマーがキナクリドン表面ヘグラフトすることが分かった。ポリMMA, 及びポリNVPDのグラフト率は, それぞれ25.2%, 及び26.1%であった。グラフト効率は, 重合の初期においては約50%であったが, 重合の進行とともに急激に減少した。これは, 重合の後半においては, 非グラフトポリマーの生成が優勢になることを示唆している。ポリマーがグラフトしたキナクリドンは, グラフト鎖の良溶媒中へ安定に分散した。
Construction of insertion and deletion mxa mutants of Methylobacterium extorquens AM1 by electroporation (1998)

Methylobacterium extorquens AM1 is a pink-pigmented facultative methylotroph which is widely used for analyzing pathways of C1 metabolism with biochemical and molecular biological techniques. To facilitate this approach, we have applied a new method to construct insertion or disruption mutants with drug resistance genes by electroporation. By using this method, mutants were obtained in four genes present in the mxa methylotrophy gene cluster for which the functions were unknown, mxaR, mxaS, mxaC and mxaD. These mutants were unable to grow on methanol except the mutant of mxaD, which showed reduced growth on methanol.
Excited-State Hydrogen and Dihydrogen Bonding of a Dihydrogen-Bonded Phenol–Borane–Dimethylamine Complex (2011)

Abstract The excited-state hydrogen and dihydrogen bonding of a dihydrogen-bonded phenol–borane–dimethylamine (BDMA) complex was investigated theoretically by use of time-dependent density functional theory (TDDFT). The coexistence of an intermolecular dihydrogen bond (B–H···H–O) and hydrogen bond (N–H···O) was confirmed by the optimized geometric structure of the dihydrogen-bonded phenol–BDMA complex. The infrared spectra for both the ground and excited states of the dihydrogen-bonded phenol–BDMA complex were also calculated by use of density functional theory (DFT)/TDDFT. As a result, we demonstrated theoretically that the intermolecular dihydrogen bonds B–H···H–O can be significantly strengthened in the excited state. However, the intermolecular hydrogen bond N–H···O in the dihydrogen-bonded phenol–BDMA complex is weakened upon photoexcitation to the S1 state. The dynamic changes of the intermolecular dihydrogen and hydrogen bonding are consistent with the calculated bond lengths in different electronic states. The coexistent dihydrogen and hydrogen bonding in the electronic excited states of this dihydrogen-bonded complex was studied theoretically in this work. Furthermore, it was found that the N–H···O hydrogen bond in the cyclic structure of phenol–BDMA complex hindered the dehydrogenation reaction between dihydrogen bonded O–H and B–H1 groups, which has been reported for the phenol–borane–trimethylamine complex.
Therapeutic monoclonal antibodies for respiratory diseases: Current challenges and perspectives, March 31 – April 1, 2016, Tours, France (2016)

Monoclonal antibody (mAb) therapeutics have tremendous potential to benefit patients with lung diseases, for which there remains substantial unmet medical need. To capture the current state of mAb research and development in the area of respiratory diseases, the Research Center of Respiratory Diseases (CEPR-INSERM U1100), the Laboratory of Excellence "MAbImprove," the GDR 3260 "Antibodies and therapeutic targeting," and the Grant Research program ARD2020 "Biotherapeutics" invited speakers from industry, academic and government organizations to present their recent research results at the Therapeutic Monoclonal Antibodies for Respiratory Diseases: Current challenges and perspectives congress held March 31 - April 1, 2016 in Tours, France.
1,3-Diphenylguanidinium Trifluoroacetate (1998)

The two phenyl rings of the title compound, C13H14N3+.CF3CO2−, assume a syn conformation with respect to the unsubstituted N atom of the cation. Bond lengths and angles within the guanidinium moiety are close to those expected for a central Csp2 atom, accounting for some charge delocalization between the three C—N bonds. The structure is stabilized by a two-dimensional network of intermolecular hydrogen bonds, where the carboxylate O atoms of the anions are acceptors from the N—H groups of the diphenylguanidinium cations.
The Essential Distributed Objects Survival Guide (1995)

Client/Server with Objects CORBA: The Object Bus Distributed Object Services: ORB Meets Lego Components: Pluggable Parts OpenDoc Under the Hood OLE Under The Hood Client/Server With Parts.
Genetic analysis of growth inhibition by GAL4-L kappa B-alpha in Saccharomyces cerevisiae. (1995)

I kappa B proteins bind to and regulate Rel/NF- kappa B transcription factors. We showed previously that a fusion protein (GAL4-p40) containing the DNA-binding domain of GAL4 and sequences of chicken l kappa B-alpha (p40) inhibits growth in the yeast Saccharomyces cerevisiae. We now show that p40 must be bound to DNA to inhibit yeast growth, p40 proteins, bound to DNA either as GAL4 or LEXA fusion proteins, inhibit yeast growth. In contrast, p40 proteins that cannot bind to DNA, such as full-length p40, a GAL4-l kappa B fusion protein containing a mutant GAL4 DNA-binding domain, and a fusion protein (GAD-p40) containing the transcriptional activation domain of GAL4 fused to p40, each failed to inhibit cell growth. As with GAL4-VP16, GAL4-p40 needs a functional cellular ADA2 gene to exert its growth-inhibitory effect in S. cerevisiae. Using a high copy suppression strategy, we have isolated three S. cerevisiae genes that restore normal growth to yeast expressing GAL4-p40 or LEXA-p40. We have termed these rescuing genes collectively as SIK genes, for "Suppressors of 1 kappa B." Expression of the SIK genes specifically suppresses the growth-inhibitory activity of GAL4-p40 and LEXA-p40 because SIK gene expression cannot block GAL4-VP16-mediated growth inhibition in S. cerevisiae. SIK1 encodes a novel protein that contains a COOH-terminal repeat that has been found in many microtubule-binding proteins. SIK2 encodes NH2-terminal acetyltransferase, and SIK3 encodes the yeast ribosomal S4 protein. None of the SIK proteins binds directly to p40 sequences in vitro, suggesting that the SIK proteins are likely to act downstream of the direct point of growth inhibition by GAL4-p40. Our results may be useful for devising strategies for identifying vertebrate inhibitors of l kappa B proteins and of other proteins that inhibit growth in S. cerevisiae.
Sustained liver‐specific transgene expression from the albumin promoter in mice following hydrodynamic plasmid DNA delivery (2008)

Liver-specific sustained transgene expression can be obtained at very high levels from optimized pDNA vectors, without the use of integration systems. Such vectors will further facilitate biological studies of genes in vivo and may find application in gene therapy.
Characterization of Glycosaminoglycan-binding Domains Present in Insulin-like Growth Factor-binding Protein-3 (1996)

Matrix metalloproteinase 3 cleaves insulin-like growth factor-binding protein-3 (IGFBP-3) into six fragments, four of which bind heparin-Sepharose (Fowlkes, J. L., Enghild, J. J., Suzuki, K., and Nagase, H. (1994) J. Biol. Chem. 269, 25742-25746). Sequence analysis of IGFBP-3 heparin-binding fragments shows that all fragments contain at least one of two highly basic, putative heparin-binding consensus sequences present in IGFBP-3. Epitope-specific antibodies generated against synthetic peptides containing these domains recognized IGFBP-3, yet were significantly inhibited from binding in the presence of heparin, demonstrating that these regions of IGFBP-3 contain functional heparin-binding domains. IGFBP-3 peptides containing one of the two heparin-binding consensus sequences bound heparin in a solid phase binding assay in a dose-dependent and saturable manner. However, the IGFBP-3 peptide containing the heparin-binding consensus sequence 149KKGHA153 bound heparin with approximately 4-fold less affinity than the IGFBP-3 peptide containing the longer heparin-binding consensus sequence 219YKKKQCRP226. Examination of several well characterized glycosaminoglycans to inhibit the binding of heparin to both heparin-binding IGFBP-3 peptides revealed that the most potent inhibitors were heparin, heparan sulfate, and dermatan sulfate; chondroitin sulfate A and hyaluronic acid were intermediate in their inhibitory activities; and chondroitin sulfate C caused no inhibition. These studies identify and characterize the glycosaminoglycan-binding domains in IGFBP-3, providing a basis for the better understanding of IGFBP-3-glycosaminoglycan interactions at the cellular and extracellular interface.
Controlled Delivery of Crop Protection Agents (1990)

Part 1 Introduction: controlled delivery and foliar spraying - and soil application controlled release technology for pest management. Part 2 Controlled delivery by sprayable systems: development and uses of microencapsulated preparation of microencapsulated insecticides and their release mechanisms. Part 3 Granular systems and soil application: soil applied controlled release products and Suscon technology biodegradable polymer methods. Part 4 Release into the air: controlled release systems for the delivery of insect pheromones. Part 5 Aquatic applications: controlled release aquatic herbicides. Part 6 Controlled delivery of biopesticides: controlled release of biological control agents microbial pesticide controlled release formulations cellular delivery systems for insecticidal proteins - living and non-living mico-organisms. Part 7 Evaluation of controlled release systems: evaluation of controlled release - efficacy, environment and commercial aspects approaches to the evaluation of controlled release pesticides in the laboratory and field.
A new algorithm for real-time median filtering (1986)

An algorithm is presented to determine the median of a given set of samples W. The median is determined by making r comparisons of the elements of the "m-array," where r is the number of bits in the radix-2 representation of the largest element of W. The m-array has 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sup> elements, and m <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</inf> equals the number of samples of W greater than or equal to (k - 1). The method is suitable to determine the running median in median filtering since updating the m-array is a very simple task.
A New Type of Flavor Precursors inVitisviniferaL. cv. Sauvignon Blanc:S-Cysteine Conjugates (1998)

Three flavor-active volatile thiols (4-mercapto-4-methylpentan-2-one, 4-mercapto-4-methylpentan-2-ol and 3-mercaptohexan-1-ol) involved in Vitis vinifera L. var. Sauvignon blanc wine aroma can be generated in vitro from nonvolatile must extracts by the enzyme action of a cell-free extract obtained from the gastrointestinal bacterium Eubacterium limosum. The specificity of a cysteine conjugate β-lyase (EC 4.4.1.13) which is contained in the cell-free extract, strongly suggested the existence of precursor for these volatile thiols having a structure of S-cysteine conjugate. Gas-phase chromatography analysis coupled with mass spectrometry of must extract in the form of trimethylsilylated derivatives, verified this hypothesis. The release of flavor-active volatile thiols during alcoholic fermentation of the must is shown to be due to the degradation, by yeast, of the corresponding S-cysteine conjugates. This mechanism explains the amplification of the typical Sauvignon blanc grape aroma during alcoholic fermentation. Keywords: Cysteine conjugate β-lyase; Eubacterium limosum; flavor precursor; metal ion chelated column; Sauvignon blanc; S-cysteine conjugate; varietal aroma
A crucial role for HVEM and BTLA in preventing intestinal inflammation (2008)

The interaction between the tumor necrosis factor (TNF) family member LIGHT and the TNF family receptor herpes virus entry mediator (HVEM) co-stimulates T cells and promotes inflammation. However, HVEM also triggers inhibitory signals by acting as a ligand that binds to B and T lymphocyte attenuator (BTLA), an immunoglobulin super family member. The contribution of HVEM interacting with these two binding partners in inflammatory processes remains unknown. In this study, we investigated the role of HVEM in the development of colitis induced by the transfer of CD4(+)CD45RB(high) T cells into recombination activating gene (Rag)(-/-) mice. Although the absence of HVEM on the donor T cells led to a slight decrease in pathogenesis, surprisingly, the absence of HVEM in the Rag(-/-) recipients led to the opposite effect, a dramatic acceleration of intestinal inflammation. Furthermore, the critical role of HVEM in preventing colitis acceleration mainly involved HVEM expression by radioresistant cells in the Rag(-/-) recipients interacting with BTLA. Our experiments emphasize the antiinflammatory role of HVEM and the importance of HVEM expression by innate immune cells in preventing runaway inflammation in the intestine.
Detection of Frequency Resonance Energy Transfer Pair on Double-Labeled Microsphere and Bacillus anthracis Spores by Flow Cytometry (2003)

Development of an ultrasensitive biosensor for biological hazards in the environment is a major need for pollutant control and for the detection of biological warfare. Fluorescence methods combined with immunodiagnostic methods are the most common. To minimize background noise, arising from the unspecific adsorption effect, we have adapted the FRET (frequency resonance energy transfer) effect to the immunofluorescence method. FRET will increase the selectivity of the diagnosis process by introducing a requirement for two different reporter molecules that have to label the antigen surface at a distance that will enable FRET. Utilizing the multiparameter capability of flow cytometry analysis to analyze the double-labeling/FRET immunostaining will lead to a highly selective and sensitive diagnostic method. This work examined the FRET interaction of fluorescence-labeled avidin molecules on biotin-coated microspheres as a model system. As target system, we have used labeled polyclonal antibodies on Bacillus anthracis spores. The antibodies used were purified immunoglobulin G (IgG) molecules raised in rabbits against B. anthracis exosoporium components. The antibodies were fluorescence labeled by a donor-acceptor chromophore pair, alexa488 as a donor and alexa594 as an acceptor. On labeling the spores with alexa488-IgG as a donor and alexa594-IgG as an acceptor, excitation at 488 nm results in quenching of the alexa-488 fluorescence (E(q) = 35%) and appearance of the alexa594 fluorescence (E(s) = 22%), as detected by flow cytometry analysis. The FRET effect leads to a further isolated gate (FL1/FL3) for the target spores compared to competitive spores such as B. thuringiensis subsp. israelensis and B. subtilis. This new approach, combining FRET labeling and flow cytometry analysis, improved the selectivity of the B. anthracis spores by a factor of 10 with respect to B. thuringiensis subsp. israelensis and a factor of 100 with respect to B. subtilis as control spores.
Optimizing queries over multimedia repositories (1996)

Repositories of multimedia objects having multiple types of attributes (e.g., image, text) are becoming increasingly common. A selection on these attributes will typically produce not just a set of objects, as in the traditional relational query model (filtering), but also a grade of match associated with each object, indicating how well the object matches the selection condition (ranking). Also, multimedia repositories may allow access to the attributes of each object only through indexes. We investigate how to optimize the processing of queries over multimedia repositories. A key issue is the choice of the indexes used to search the repository. We define an execution space that is search-minimal, i.e., the set of indexes searched is minimal. Although the general problem of picking an optimal plan in the search-minimal execution space is NP-hard, we solve the problem efficiently when the predicates in the query are independent. We also show that the problem of optimizing queries that ask for a few top-ranked objects can be viewed, in many cases, as that of evaluating selection conditions. Thus, both problems can be viewed together as an extended filtering problem.
Nonlinear adaptive prediction of complex-valued signals by complex-valued PRNN (2005)

A complex-valued pipelined recurrent neural network (CPRNN) for nonlinear adaptive prediction of complex nonlinear and nonstationary signals is introduced. This architecture represents an extension of the recently proposed real-valued PRNN of Haykin and Li in 1995. To train the CPRNN, a complex-valued real time recurrent learning (CRTRL) algorithm is first derived for a single recurrent neural network (RNN). This algorithm is shown to be generic and applicable to general signals that have complex domain representations. The CRTRL is then extended to suit the modularity of the CPRNN architecture. Further, to cater to the possibly large dynamics of the input signals, a gradient adaptive amplitude of the nonlinearity within the neurons is introduced to give the adaptive amplitude CRTRL (AACRTRL). A comprehensive analysis of the architecture and associated learning algorithms is undertaken, including the role of the number of nested modules, number of neurons within the modules, and input memory of the CPRNN. Simulations on real-world and synthetic complex data support the proposed architecture and algorithms.
Water-Soluble Iron Oxide Nanocubes with High Values of Specific Absorption Rate for Cancer Cell Hyperthermia Treatment (2012)

Iron oxide nanocrystals (IONCs) are appealing heat mediator nanoprobes in magnetic-mediated hyperthermia for cancer treatment. Here, specific absorption rate (SAR) values are reported for cube-shaped water-soluble IONCs prepared by a one-pot synthesis approach in a size range between 13 and 40 nm. The SAR values were determined as a function of frequency and magnetic field applied, also spanning technical conditions which are considered biomedically safe for patients. Among the different sizes tested, IONCs with an average diameter of 19 ± 3 nm had significant SAR values in clinical conditions and reached SAR values up to 2452 W/g(Fe) at 520 kHz and 29 kAm(-1), which is one of the highest values so far reported for IONCs. In vitro trials carried out on KB cancer cells treated with IONCs of 19 nm have shown efficient hyperthermia performance, with cell mortality of about 50% recorded when an equilibrium temperature of 43 °C was reached after 1 h of treatment.