gebhart/patrepeval huggingface dataset:
Improving the signal intensity and sensitivity of MALDI mass spectrometry by using nanoliter spots deposited by induction-based fluidics (2008)

A new contact-free, small droplet deposition method using an induction-based fluidics (IBF) technique to dispense nanoliter drops is described and evaluated for sample preparation in matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The signal intensities available when using nanoliter spots are greater than those obtained with normal, microliter spots when the same amount of analyte is used. When using an ionic-liquid matrix, the improvement in sensitivity is equal to the concentration enhancement that was achieved by using smaller quantities of matrix. When using a conventional solid matrix, however, the increase in signal intensity shows a more complicated relationship to concentration. The approach of nanoliter deposition also supports multiple spotting to increase sample concentration and, thus, sample signal intensity. Nanoliter spotting not only improves the signal intensity and sensitivity achieved by MALDI-MS but also allows a major fraction of trace samples to be saved for other experiments, thus expanding the application of MALDI-MS to biological studies where sample quantity is limited.
Identification of MicroRNA for Intermuscular Bone Development in Blunt Snout Bream (Megalobrama amblycephala) (2015)

Intermuscular bone (IB), which occurs only in the myosepta of the lower teleosts, is attracting more attention of researchers due to its particular development and lack of genetic information. MicroRNAs (miRNAs) are emerging as important regulators for biological processes. In the present study, miRNAs from IBs and connective tissue (CT; encircled IBs) from six-month-old Megalobrama amblycephala were characterized and compared. The results revealed the sequences and expression levels of 218 known miRNA genes (belonging to 97 families). Of these miRNAs, 44 known microRNA sequences exhibited significant expression differences between the two libraries, with 24 and 20 differentially-expressed miRNAs exhibiting higher expression in the CT and IBs libraries, respectively. The expressions of 11 miRNAs were selected to validate in nine tissues. Among the high-ranked predicted gene targets, differentiation, cell cycle, metabolism, signal transduction and transcriptional regulation were implicated. The pathway analysis of differentially-expressed miRNAs indicated that they were abundantly involved in regulating the development and differentiation of IBs and CT. This study characterized the miRNA for IBs of teleosts for the first time, which provides an opportunity for further understanding of miRNA function in the regulation of IB development.
Pluripotent stem cells developed into regenerated tooth by organ germ method in combination with tooth germ-derived epithelium (2007)

The regenerative therapy ultimately aims to develop bioengineered organs that can replace lost or damaged organs following disease, injury or aging. Recently, we showed that the artificial organ germ, which generates a structurally correct tooth, could be reconstituted by in vitro cell manipulation (Nature Methods 4, 227-230, 2007). In this study, we revealed that neural crest-like cells, which were differentiated from pluripotent stem cells such as embryonal carcinoma (EC) cells, could develop the regenerated tooth by organ germ method with tooth germ epithelium. EC cells were stimulated with dimethyl sulfoxide (DMSO) and differentiated cells were isolated by cell sorting as DMSO-EC cells. We found that the expressions of pluripotent stem cell marker genes (Oct3/4 and Nanog) could not be detected in DMSO-EC cells. In contrast, the expressions of neural crest-marker genes (Pax3 and Slug) and of dental mesenchyme-marker genes (Msxl, Pax9 and Lhx7) increased in DMSO-EC cells, compared with those in EC cells. Furthermore, the structurally correct tooth can be generated by combining DMSO-EC cells and tooth germ epithelium, both in vitro and in vivo. Our current results indicated the possibility that pluripotent stem cells are applicable as a candidate of cell sources to develop of a bioengineered organ germ for the organ replacement in the future regenerative therapy.
Role of Primate Superior Colliculus in Preparation and Execution of Anti-Saccades and Pro-Saccades (1999)

We investigated how the brain switches between the preparation of a movement where a stimulus is the target of the movement, and a movement where a stimulus serves as a landmark for an instructed movement elsewhere. Monkeys were trained on a pro-/anti-saccade paradigm in which they either had to generate a pro-saccade toward a visual stimulus or an anti-saccade away from the stimulus to its mirror position, depending on the color of an initial fixation point. Neural activity was recorded in the superior colliculus (SC), a structure that is known to be involved in the generation of fast saccades, to determine whether it was also involved in the generation of anti-saccades. On anti-saccade trials, fixation during the instruction period was associated with an increased activity of collicular fixation-related neurons and a decreased activity of saccade-related neurons. Stimulus-related and saccade-related activity was reduced on anti-saccade trials. Our results demonstrate that the anti-saccade task involves (and may require) the attenuation of preparatory and stimulus-related activity in the SC to avoid unwanted pro-saccades. Because the attenuated pre-saccade activity that we found in the SC may be insufficient by itself to elicit correct anti-saccades, additional movement signals from other brain areas are presumably required.
A Comparison of Local Analysis, Global Analysis and Ontology-based Query Expansion Strategies for Bio-medical Literature Search (2006)

In this paper we present the design and evaluation of our biomedical literature searching approaches using the TREC 2004 ad hoc retrieval task in the genomics track. The main approach taken in our system is to expand queries by exploiting the three widely used strategies -local analysis, global analysis, and ontology-based term re-weighting across various search engines. The experimental results show that (1) ontology-based term re-weighting provides the best results among the three query expansion strategies, (2) expanding the initial query with more precise ontology-based term enhances LSI based local analysis substantially, and (3) including context to term re-weighting and LSI further improves the precision. Experimental results also show that the ontology-based term re-weighting with LUCENE or LEMUR search engines increases the average precision by up to 20.3% or 12.1%, respectively, compared to that of the baseline runs. In addition, the LSI-based local analysis increases the average precision by 9.2% with LEMUR search engine. We believe the approaches of the term re-weighting and LSI-based local analysis may be exploited in other bio-medical domains.
7-Deaza-2′-deoxyinosine: A Stable Nucleoside with the Ambiguous Base Pairing Properties of 2′-Deoxyinosine (1999)

Abstract The base pairing ambiguity of 7-deaza-2′-deoxyinosine (c7Id, 2) was studied and was found to be the same as that of 2′-deoxyinosine. The duplex stability decreases in the order [d(c7I-C) > d(c7I-A) > d(c7I-T) > d(c7I-G)]. Modified nucleosides were used to probe the various base pair motifs which were the same for dl and c7Id. The 7-deazapurine nucleoside (2) is extremely stable against acid or base. As oligonucleotides can be prepared using phosphoramidite chemistry and DNA is accessible by enzymic polymerisation of the triphosphate of 2, the latter can be used as an universal nucleoside for the sequencing of DNA by chemical degradation and is otherwise a facile substitute of 2′-deoxyinosine when stability in acidic or alkaline solution is required.
Theoretical analysis of energy harvesting performance for unimorph piezoelectric benders with interdigitated electrodes (2009)

A great amount of research has been done to develop piezoelectric material-based energy harvesting devices as power generators for a variety of portable and low power consuming devices. Among the possibilities for energy harvesters, the 31 type cantilever piezoelectric benders have generally been used. In this work a unimorph piezoelectric cantilever beam with an interdigitated electrode pattern was examined. The focus of this paper is to develop a model and propose design parameters to improve the energy generating performance of the interdigitated piezoelectric energy harvester.
Protocol to avoid noise in power line networks (2005)

This paper reviews established methods of communication using in-building power conductors with particular attention to the 100 kHz to 450 kHz frequency range. Measurements have shown that noise bursts on powerline conductors occur at regular times during the 60 Hz cycle and it was observed that transmission bit errors coincide with these noise bursts. The paper describes an adaptive transmission protocol whereby transmission is suspended during periods of high interference and then continues during quiet intervals. In an experimental implementation in a commercial office environment, throughput was measured at about 80% of the nominal modem rate.
Secure E-Commerce Scheme (2022)

E-commerce security has recently been an emerging topic due to the escalation in credit card fraud and stolen user accounts. In general, the security bridge and privacy leakage occur on the side of e-commerce companies due to various factors such as flaws in the design of their storage systems. The stored information of users increases the risk on privacy bridge and to remedy such risks e-commerce companies are forced to make costly investments. The security threats also enforce the development of robust security protocols and methods in digital commerce systems. The current protocols and methods generally bring extra communication and computation costs to all parties involving in the e-commerce system and the security risk on the side of e-commerce companies still remains. In this paper, we propose a Secure E-commerce Scheme (SES) which alleviates the security threats on the side of e-commerce companies and reduces communication costs for all parties. The proposed secure e-commerce protocol, SES, is implemented, analyzed and compared to two well-known schemes; Secure Electronic Transaction (SET) and 3D Secure.
Lung strips from guinea pigs as test system for lipoxygenase inhibitors. Inhibition of arachidonic acid-induced contractions by 3-t-butyl-4-hydroxyanisole and nordihydroguaiaretic acid. (1983)

Lung strips and tracheal spirals from guinea pigs and rats were compared as test systems for lipoxygenase inhibitors. The contraction of the smooth muscle was induced by addition of arachidonic acid. Lung strips of guinea pigs proved to be the most suitable in vitro model. Under basal conditions half-maximal contraction was produced by 13 microM arachidonic acid (AA) which was strongly inhibited by 50 microM nordihydroguaiaretic acid (NDGA) or 100 microM 3-t-butyl-4-hydroxyanisole (BHA). NDGA and BHA caused a shift of response towards higher concentrations of AA. BHA also produced pronounced dilatations of both basal tonus and carbachol-induced contractions of the preparations from the respiratory tract. It is concluded that the actions of NDGA and BHA on the airway preparations are due to inhibition of the lipoxygenase reaction and, therefore, of leukotriene synthesis. The assumption of the lipoxygenase inhibition is supported by their action on purified lipoxygenase from rabbit reticulocytes which was inhibited by 50% by 0.5 microM NDGA and 160 microM BHA. In contrast, the antioxidant 2,6-di-t-butyl-4-hydroxytoluene (BHT) did not inhibit at all at 1 mM. To the knowledge of the authors this is the first evidence so far reported for the bronchodilating action of BHA.
Interleukin-24 overcomes temozolomide resistance and enhances cell death by down-regulation of<i>O</i>6-methylguanine-DNA methyltransferase in human melanoma cells (2008)

Melanoma is the most malignant of skin cancers, highly resistant to chemotherapy and radiotherapy. Temozolomide, a promising new derivative of dacarbazine, is currently being tested for treatment of metastatic melanoma. Resistance to alkylating agents such as temozolomide correlates with increased expression of DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT). Interleukin-24 (IL-24; mda-7) is a tumor suppressor cytokine that selectively inhibits tumor cell growth by inducing apoptosis and cell cycle arrest in melanoma cell lines and solid tumors. This tumor-selective activity has been observed in multiple preclinical animal models and in clinical trials. In this study, we analyzed the ability of Ad-IL-24 and its protein product, IL-24, to overcome temozolomide resistance in human melanoma cells. We have shown that Ad-IL-24 via exogenous IL-24 protein induces combinatorial synergy of temozolomide-induced cell killing in temozolomide-resistant melanoma cells by inhibition of MGMT. Neutralizing antibodies against IL-24 or its receptors significantly blocked the apoptotic activity of IL-24 + MGMT treatment. We show that accumulation of functional p53 is essential for IL-24-induced down-regulation of MGMT. Using either MGMT small interfering RNA, p53 small interfering RNA, or a p53 dominant-negative mutant to block MGMT protein expression resulted in increased sensitization to temozolomide. However, MGMT blockade in combination with IL-24 + temozolomide resulted in loss of combinatorial synergy, indicating that MGMT expression is required for the reversal of temozolomide resistance in melanoma cells. This study shows that IL-24 can play a significant role in overcoming temozolomide resistance and that the clinical efficacy of temozolomide may be improved by using a biochemotherapy combination with IL-24.
Cassette dosing pharmacokinetics of a library of 2,6,9-trisubstituted purine cyclin-dependent kinase 2 inhibitors prepared by parallel synthesis (2004)

Determination of pharmacokinetic properties in the intact animal remains a major bottleneck in drug discovery. Cassette dosing involves administration of a cocktail of drugs to individual animals. Here we describe the cassette dosing properties of a 107-membered library of 2,6,9-trisubstituted purine cyclin-dependent kinase 2 (CDK2) inhibitors. A three-step parallel synthesis approach produced compounds with purity ranging from 63% to 100%. Cassette dosing was validated by comparing the pharmacokinetic parameters obtained following i.v. administration of a mixture of olomoucine, R-roscovitine (CYC202), and bohemine, each at 16.6 mg/kg, with results for administration of single agents at 50 mg/kg. No significant difference was observed between the pharmacokinetic parameters of agents when dosed in combination compared with those of individual compounds. CYC202 showed the highest area under the curve (AUC) and the longest elimination half-life (t(1/2)). Further cassettes evaluated the library of trisubstituted purines with CYC202 and purvalanol A included as pharmacokinetic standards in a validated limited sampling strategy. The ratios of pharmacokinetic parameters to that of CYC202 [AUC, maximum concentration (C(max)), and t(1/2)] remained similar when compounds were tested in two different cassettes or as individual compounds. Following dosing of the same cassette on three different days, there was less than 20% variation in pharmacokinetic parameters between days. The structure-pharmacokinetics relationship showed that the favored purine substituents are benzylamine and veratrylamine at position 6, amino-2 propanol at position 2, and methylpropyl or hydroxyethyl at position 9. Without cassette dosing, this study would have used 3 times as many animals and would have taken 4 times longer, illustrating the power of this method in lead optimization.
A single-chip MPEG-2 MP@ML audio/video encoder/decoder with a programmable video interface unit (2002)

We present a single-chip, MPEG-2 main profile at main level, audio and video encoder and decoder. It combines a RISC core, a 24-bit DSP, video and audio interface units, and several dedicated processing units. A programmable video interface unit supports multiple modes of pre- and post-processing and on-screen display (OSD). The codec has been implemented using a standard-cell library in 0.18 /spl mu/m CMOS technology.
The preparation of immobilized lactase and its use in the enzymatic hydrolysis of acid whey (1974)

Abstract The enzyme β‐galactosidase (lactose) obtained from several microbial sources was immobilized on zirconia‐coated porous glass particles. The immobilized enzymes were characterized by determining pH profiles, kinetic constants, thermal profiles, and operationalhalf‐lives in lactose and whey ultrafiltrate solutions. Studies were carried out on continuous reactor performance, and enzyme requirements for scale‐up were estimated. Lactose or whey hydrolyzed by this technique could find use commercially as a sweetener in a number of dairy products.
Nonlinear gain effects in quantum well, quantum well wire, and quantum well box lasers (1991)

The nonlinear gain effects due to the spectral hole burning in quantum well (QW), quantum well wire (QWW), and quantum well box (QWB) lasers are discussed. It is found that the gain nonlinearity is enhanced by the quantum confinement of carriers, and is further enhanced in the QWW and QWB lasers. These nonlinear gain effects significantly affect the modulation dynamics of the semiconductor lasers under high photon density conditions. It is emphasized that both the damping rate and the resonant relaxation frequency are degraded through reduction of the differential gain. The effects of nonlinear gain on the spectral dynamics are discussed. The result indicates that the gain nonlinearity causes enhancement of the linewidth enhancement factor with the increase of the photon density, which leads to the spectral rebroadening under high photon density conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Bidirectional WDM/TDM-PON Using DPSK Downstream Signals and a Narrowband AWG (2007)

We present an innovative architecture to realize a single feeder bidirectional amplified wavelength-division-multiplexing/time-division-multiplexing passive optical network based on modified nonreturn-to-zero differential phase-shift keying (DPSK) downstream signals at 20 Gb/s and a narrowband arrayed waveguide grating (AWG). The AWG plays at the same time the role of channel distributor, simultaneous demodulator for all DPSK channels, and eliminates the need for chromatic dispersion compensation. A saturated semiconductor optical amplifier (SOA) provides bidirectional amplification to compensate the splitter losses. The remodulated upstream signals are obtained at 1 Gb/s by means of a reflective SOA. Experimental results show error-free operation on both downstream and upstream signal.
Pythium elicitors in biological control of Botrytis cinerea. (2009)

Botrytis cinerea is a well-known necrotic pathogen, causing grey mould disease in grapevine and other crop plants, such as tomato and bean. The members of the genus Pythium are mostly saprophytes, present in the soil, sometimes acting as parasites, sometimes as effective mycoparasites. There are reports that they secrete proteins like oligandrin (P. oligandrum) that plays a vital role in the enhancement of systemic resistance in the plants. In this paper, we present the active involvement of substances secreted by P. hypogynum and P. canariense in providing control against B. cinerea to tomato and bean plants. Filtrates from Pythium spp., when applied either on the leaves or on the roots, prior to exposure to B. cinerea, reduced conidial germination on leaves, reduced disease severity and conferred disease resistance in tomato.
Sulfated glycoglycerolipid from archaebacterium inhibits eukaryotic DNA polymerase α, β and retroviral reverse transcriptase and affects methyl methanesulfonate cytotoxicity (1998)

A sulfated glycoglycerolipid, 1-O-(6'-sulfo-alpha-D-glucopyranosyl)-2,3-di-O-phytanyl- sn-glycerol (KN-208), a derivative of the polar lipid isolated from an archaebacterium, strongly inhibited DNA polymerase (pol) alpha and pol beta in vitro among 5 eukaryotic DNA polymerases (alpha, beta, gamma, delta, and epsilon). It also inhibited Escherichia coli DNA polymerase I Klenow fragment (E. coli pol I) and human immunodeficiency virus reverse transcriptase (HIV RT). The mode of inhibition of these polymerases was competitive with the DNA template primer and was non-competitive with the substrate dTTP. KN-208 inhibited pol beta most strongly, with a Ki value of 0.05 microM, 10-fold lower than that for pol alpha (0.5 microM) and 60- or 140-fold lower than that for HIV RT (3 microM) or for E. coli pol I (7 microM), respectively. The loss of sulfate on the 6'-position of glucopyranoside of this compound completely abrogated inhibition. However, the hydrophilic part of KN-208, glucose 6-sulfate alone, showed no inhibition. Other sulfated compounds containing different hydrophobic structures, such as dodecyl sulfate and cholesterol sulfate, exhibited a much weaker inhibition. Our results suggest that the whole molecular structure of KN-208 is required for inhibition. KN-208 was shown to be modestly cytotoxic for the human leukemic cell line K562. Interestingly, a subcytotoxic dose of KN-208 increased the sensitivity of the human leukemic cells to an alkylating agent, methyl methanesulfonate, while it did not potentiate the effects of ultraviolet light or of cisplatin.
TGF- <i>β</i> Promotes the Growth of Bovine Chondrocytes in Monolayer Culture and the Formation of Cartilage Tissue on Three-Dimensional Scaffolds (1995)

We have investigated the ability of transforming growth factor beta (TGF-beta) to promote the growth and differentiation of chondrocytes in monolayer and on three-dimensional scaffolds. Treatment of chondrocytes with TGF-beta and ascorbate individually stimulated the proliferation of bovine articular chondrocytes about 2-fold when cells were grown in monolayer culture: the combination of TGF-beta and ascorbate resulted in a 3-fold increase in cell number over a 72-h period. Peak stimulation with TGF-beta occurred at about 1.0 ng/ml: bFGF was slightly inhibitory in these assays. TGF-beta led to an increase in glycosaminoglycan synthesis as detected by Western blotting using anti-chondroitin sulfate antibodies. No significant change in collagen type II mRNA or protein was observed. When cells were grown on grown on three-dimensional scaffolds composed of polyglyocolic acid, TGF-beta treatment led to an increase in the size of the cartilage-like constructs produced. This was accompanied by increases in collagen and glycosaminoglycan deposition; immunohistochemical staining showed that the predominant collagen was type II. These results indicate that TGF-beta is capable of increasing the proliferation rate of chondrocytes in monolayer as well as increasing cartilage production on three-dimensional scaffolds and may find utility in the in vitro engineering of cartilage tissue.
Unusual Nondispersive Ambipolar Carrier Transport and High Electron Mobility in Amorphous Ter(9,9-diarylfluorene)s (2003)

Nondispersive ambipolar carrier transport with comparably high electron and hole mobilities for amorphous molecular solids that are composed of only a single type of chromophores was observed for the first time in amorphous ter(9,9-diarylfluorene)s. High hole and electron mobilities over 10-3 cm2/(V.s) can be achieved with these terfluorenes. In particular, the electron mobility observed represents the highest ever reported for amorphous molecular solids.