gebhart/patrepeval huggingface dataset:
G19.4(alpha CD3) x B43(alpha CD19) monoclonal antibody heteroconjugate triggers CD19 antigen-specific lysis of t(4;11) acute lymphoblastic leukemia cells by activated CD3 antigen-positive cytotoxic T cells (1992)

A highly purified, 300-Kd bispecific monoclonal antibody (MoAb) heteroconjugate was prepared by covalently linking the anti-CD3 MoAb, G19.4, to the anti-CD19 MoAb, B43. Dual-color staining techniques and multiparameter flow cytometry confirmed that this alpha CD3 x alpha CD19 heteroconjugate was able to bind to both CD3+ T cells and CD19+ t(4;11) acute lymphoblastic leukemia (ALL) cells. T-cell-mediated lysis of freshly isolated primary bone marrow blasts from nine newly diagnosed ALL patients with a t(4;11)(q21;q23) chromosomal translocation were studied with 51Cr-release assays. Picomolar concentrations of alpha CD3 x alpha CD19 MoAb heteroconjugate effectively triggered lysis of CD19+ t(4;11) ALL cells by interleukin-2- activated CD3+ peripheral blood T-cell (PBTC) effectors but did not augment the cytolytic activity of the same effectors against CD19- T- ALL cells. In contrast to the alpha CD3 x alpha CD19 heteroconjugate, neither the alpha CD3 x alpha CD3 homoconjugate control nor the alpha CD19 x alpha CD72 heteroconjugate control facilitated the cytolysis of t(4;11) ALL blasts. Occupation of the target CD19 binding sites on t(4;11) ALL blasts by preincubation with excess unconjugated alpha CD19 MoAb abrogated the potentiating effects of the alpha CD3 x alpha CD19 heteroconjugate on PBTC-mediated cytolysis. Thus, the cell type- specific cytolysis of t(4;11) ALL blasts by PBTC effectors is dependent on both the alpha CD19 and alpha CD3 moieties of the alpha CD3 x alpha CD19 heteroconjugate. To our knowledge, this is the first description of an effective bispecific antibody that facilitates the T-cell- mediated lysis of t(4;11) ALL blasts.
Classification using discriminative restricted Boltzmann machines (2008)

Recently, many applications for Restricted Boltzmann Machines (RBMs) have been developed for a large variety of learning problems.However, RBMs are usually used as feature extractors for another learning algorithm or to provide a good initialization for deep feed-forward neural network classifiers, and are not considered as a standalone solution to classification problems.In this paper, we argue that RBMs provide a self-contained framework for deriving competitive non-linear classifiers.We present an evaluation of different learning algorithms for RBMs which aim at introducing a discriminative component to RBM training and improve their performance as classifiers.This approach is simple in that RBMs are used directly to build a classifier, rather than as a stepping stone.Finally, we demonstrate how discriminative RBMs can also be successfully employed in a semi-supervised setting.
A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters (2012)

We provide an efficient and low-cost method for small RNA sequencing library preparation, which takes two days to complete and costs around $20 per library. This protocol has been tested in several plant species for small RNA sequencing including sweet potato, pepper, watermelon, and cowpea, and could be readily applied to any RNA samples.
The impact of low-grade toxicity in older people with cancer undergoing chemotherapy (2014)

Many older patients did not complete treatment as planned. Treatment was modified/discontinued even for one or two low-grade toxicities. Further work is required to clarify whether low-grade toxicity has a greater clinical impact in older people, or whether clinicians have a lower threshold for modifying/discontinuing treatment in older people.
A robust speech detection algorithm in a microphone array teleconferencing system (2002)

This paper describes a robust speech detection algorithm that can operate reliably in a microphone array teleconferencing system. High performance in a nonstationary noisy environment is achieved by combining the following techniques: (1) noise suppression by spectral subtraction, (2) silence detection by adaptive noise threshold and (3) non-stationary noise detection based on the availability of pitch signal. This algorithm can prevent the microphone-array-based speaker tracking system from being misguided by noises commonly present in a conference room. Real world experiments show that this algorithm performs very well and has the potential for practical applications.
Monolithically Integrated Multi-Stage All-Optical 10Gbps Push-Pull Wavelength Converter (2007)

This paper reports on the novel design and operation of a monolithically integrated multi-stage push-pull wavelength converter. Results show 4 dB improvement in extinction ratio and error-free performance for 10Gbps push-pull operation.
Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P (1995)

Folding of the ribozyme from Bacillus subtilis ribonuclease P (denoted P RNA) has been examined by Fe(II)-EDTA protection and bimolecular association. Fe(II)-EDTA results show that, in the presence of Mg2+, P RNA is folded into a core structure which includes most of the phylogenetically conserved nucleotides. Folding is cooperative and is complete at 5-6 mM Mg2+ with the [Mg2+]1/2 at 2-3 mM. The Hill constant indicates that this folding transition requires binding of at least three additional Mg2+ ions. Two RNA molecules consisting of nucleotides 62-239 [p(62-239)] and 240-401 + 1-61 [p(240-61)] of the B. subtilis P RNA have been constructed. These RNAs can in principle form the catalytically active structure primarily, if not solely, through tertiary interactions. Although either molecule by itself is inactive, the bimolecular complex is as active as the circularly permuted P RNAs from which it is derived. The binding constant of the complex can be as low as 0.1 microM and is strongly dependent on Mg2+ and K+ concentrations. Association of these molecules also induces a Mg2+ dependent cleavage at nucleotide 103 in p(62-239). p(62-239) gives a Fe(II)-EDTA protection pattern very similar to the wild-type P RNA at identical Mg2+ concentrations. However, Fe(II)-EDTA protection in p(240-61) is completely lost, even though it contains many nucleotides that are conserved among all P RNAs. These results suggest that, like other RNAs, P RNA contains domains that can fold in the absence of the rest of the molecule. The implications of these results are discussed in the context of the P RNA structure and catalysis.
ROS-activated Anticancer Prodrugs: a New Strategy for tumor-specific Damage (2012)

Targeting tumor cells is an important strategy to improve the selectivity of cancer therapies. With the advanced studies in cancer biology, we know that cancer cells are usually under increased oxidative stress. The high level of reactive oxygen species in cancer cells has been exploited for developing novel therapeutic strategies to preferentially kill cancer cells. Our group, amongst others, have used boronic acids/esters as triggers for developing ROS-activated anticancer prodrugs that target cancer cells. The selectivity was achieved by combining a specific reaction between boronates and H2O2, with the efficient masking of drug toxicity in the prodrug via boronates. Prodrugs activated via ferrocene-mediated oxidation have also been developed to improve the selectivity of anticancer drugs. We describe how the strategies of ROS-activation can be used for further development of new ROS-targeting prodrugs, eventually leading to novel approaches and/or combined technology for more efficient and selective treatment of cancers.
Growth Retardation, Early Death, and DNA Repair Defects in Mice Deficient for the Nucleotide Excision Repair Enzyme XPF (2004)

Xeroderma pigmentosum (XP) is a human genetic disease which is caused by defects in nucleotide excision repair. Since this repair pathway is responsible for removing UV irradiation-induced damage to DNA, XP patients are hypersensitive to sunlight and are prone to develop skin cancer. Based on the underlying genetic defect, the disease can be divided into the seven complementation groups XPA through XPG. XPF, in association with ERCC1, constitutes a structure-specific endonuclease that makes an incision 5' to the photodamage. XPF-ERCC1 has also been implicated in both removal of interstrand DNA cross-links and homology-mediated recombination and in immunoglobulin class switch recombination (CSR). To study the function of XPF in vivo, we inactivated the XPF gene in mice. XPF-deficient mice showed a severe postnatal growth defect and died approximately 3 weeks after birth. Histological examination revealed that the liver of mutant animals contained abnormal cells with enlarged nuclei. Furthermore, embryonic fibroblasts defective in XPF are hypersensitive to UV irradiation and mitomycin C treatment. No defect in CSR was detected, suggesting that the nuclease is dispensable for this recombination process. These phenotypes are identical to those exhibited by the ERCC1-deficient mice, consistent with the functional association of the two proteins. The complex phenotype suggests that XPF-ERCC1 is involved in multiple DNA repair processes.
Present status and future of functional oligosaccharide development in Japan (2002)

Abstract Several oligosaccharides such as glycosylsucrose, fructo-oligosaccharides, malto-oligosaccharides, isomalto-oligosaccharides (branched-oligosaccharides), galacto-oligosaccharides, xylo-oligosaccharides, isomaltulose (palatinose), and lactosucrose have been produced on an industrial scale. Recent developments in industrial enzymology have made possible a series of new starch oligosaccharides such as β-1,6 linked gentio-oligosaccharides, α,α-1,1 linked trehalose, α-1,3 linked nigero-oligosaccharides, and branched-cyclodextrins. Some new sweeteners, including trehalose and nigero-oligosaccharides, are being developed as food ingredients with physiologically unique functions such as superoxide dismutase-like activity and immunological activity. Also, soybean oligosaccharides containing raffinose, stachyose, and other oligosaccharides mentioned above are now used in beverages, confectionery, bakery products, yogurts, daily products, and infant milk. In 1991, the Japanese government legislated for Foods for Specified Health Use (FOSHU). FOSHU increased the total to 223 items of which more than 50 % incorporate oligosaccharides as the functional components. Furthermore, the Ministry of Health, Labor, and Welfare published the proposal for a new system named Foods with Health Claims (FHC), which was carried out in April 2002.
A statistical analysis of the Bloch–SiegertB1mapping technique (2013)

A number of B1 mapping methods have been introduced. A model to facilitate choice among these methods is valuable, as the performance of each technique is affected by a variety of factors, including acquisition signal-to-noise ratio (SNR). The Bloch-Siegert shift B1 mapping method has recently garnered significant interest. In this paper, we present a statistical model suitable for analysis of the Bloch-Siegert shift method. Unlike previously presented models, the analysis is valid in both low SNR and high SNR regimes. We present a detailed analysis of the performance of the Bloch-Siegert shift B1 mapping method across a broad range of acquisition scenarios, and compare it to two other B1 mapping techniques (the dual angle method and the phase sensitive method). Further validation of the model is presented through both Monte Carlo simulations and experimental results. The simulations and experimental results match the model well, lending confidence to its accuracy. Each technique is found to perform well with high acquisition SNR. However, our results suggest that the dual angle method is not reliable in low SNR environments. Furthermore, the phase sensitive method appears to outperform the Bloch-Siegert shift method in these low-SNR cases, although variations of the Bloch-Siegert method may be possible that improve its performance at low SNR.
Complement Components, but Not Complement Inhibitors, Are Upregulated in Atherosclerotic Plaques (2001)

Complement activation occurs in atherosclerotic plaques. The capacity of arterial tissue to inhibit this activation through generation of the complement regulators C1 inhibitor, decay accelerating factor, membrane cofactor protein (CD46), C4 binding protein (C4BP), and protectin (CD59) was evaluated in pairs of aortic atherosclerotic plaques and nearby normal artery from 11 human postmortem specimens. All 22 samples produced mRNAs for each of these proteins. The ratios of plaque versus normal artery pairs was not significantly different from unity for any of these inhibitors. However, in plaques, the mRNAs for C1r and C1s, the substrates for the C1 inhibitor, were increased 2.35- and 4.96-fold, respectively, compared with normal artery; mRNA for C4, the target for C4BP, was elevated l.34-fold; and mRNAs for C7 and C8, the targets for CD59, were elevated 2.61- and 3.25-fold, respectively. By Western blotting and immunohistochemistry, fraction Bb of factor B, a marker of alternative pathway activation, was barely detectable in plaque and normal arterial tissue. These data indicate that it is primarily the classical, not the alternative pathway, that is activated in plaques and that key inhibitors are not upregulated to defend against this activation.
Ac electrokinetics: a review of forces in microelectrode structures (1998)

Ac electrokinetics is concerned with the study of the movement and behaviour of particles in suspension when they are subjected to ac electrical fields. The development of new microfabricated electrode structures has meant that particles down to the size of macromolecules have been manipulated, but on this scale forces other than electrokinetic affect particles behaviour. The high electrical fields, which are required to produce sufficient force to move a particle, result in heat dissipation in the medium. This in turn produces thermal gradients, which may give rise to fluid motion through buoyancy, and electrothermal forces. In this paper, the frequency dependency and magnitude of electrothermally induced fluid flow are discussed. A new type of fluid flow is identified for low frequencies (up to 500 kHz). Our preliminary observations indicate that it has its origin in the action of a tangential electrical field on the diffuse double layer of the microfabricated electrodes. The effects of Brownian motion, diffusion and the buoyancy force are discussed in the context of the controlled manipulation of sub-micrometre particles. The orders of magnitude of the various forces experienced by a sub-micrometre latex particle in a model electrode structure are calculated. The results are compared with experiment and the relative influence of each type of force on the overall behaviour of particles is described.
Osmotic Response Element Is Required for the Induction of Aldose Reductase by Tumor Necrosis Factor-α (1999)

Induction of aldose reductase (AR) was observed in human cells treated with tumor necrosis factor-alpha (TNF-alpha). AR protein expression increased severalfold in human liver cells after 1 day of exposure to 100 units/ml TNF-alpha. An increase in AR transcripts was also observed in human liver cells after 3 h of TNF-alpha treatment, reaching a maximum level of 11-fold at 48 h. Among the three inflammatory cytokines: TNF-alpha, interleukin-1, and interferon-gamma, TNF-alpha (100 units/ml) gave the most induction of AR. Differences in the pattern of AR induction were observed in human liver, lens, and retinal pigment epithelial cells with increasing concentrations of TNF-alpha. A similar pattern of AR promoter response was observed between TNF-alpha and osmotically stressed human liver cells. The deletion of the osmotic response element (ORE) abolished the induction by TNF-alpha and osmotic stress. A point mutation that converts ORE to a nuclear factor-kappaB (NF-kappaB) sequence abolished the osmotic response but maintained the TNF-alpha response. Electrophoretic gel mobility shift assays showed two NF-kappaB proteins, p50 and p52, capable of binding ORE sequence, and gel shift Western assay detected NF-kappaB proteins p50 and p65 in the ORE complex. Inhibitors of NF-kappaB signaling, lactacystin, and MG132 abolished the AR promoter response to TNF-alpha.
The Extracellular Domain of the Human Interferon Gamma Receptor Interacts with a Species-Specific Signal Transducer (1991)

At least two species-specific gene products are required for signal transduction by interferon gamma (IFN-gamma). The first is the IFN-gamma receptor, which binds ligand with high affinity in a species-specific manner. The second is an undetermined species-specific signal transducer(s). To determine whether the human IFN-gamma receptor (hIFN-gamma R) interacts directly with this signal transducer(s) and, if so, with what functional domain(s), we constructed expression vectors for the hIFN-gamma R and three hybrid human-murine IFN-gamma receptors. The hybrid receptors contained the extracellular, human IFN-gamma (hIFN-gamma) binding domain of the hIFN-gamma R, either the human or murine transmembrane domain, and either the human or murine intracellular domain. The vectors encoding these receptors were stably transfected into two mouse cell lines, one of which (SCC-16-5) contains a single copy of human chromosome 21. The resulting cell lines were treated with hIFN-gamma, and murine major histocompatibility complex class I antigen expression was analyzed by immunofluorescence flow cytometry. All transfected cell lines lacking human chromosome 21 remained insensitive to hIFN-gamma. However, all four of the IFN-gamma receptors were able to signal when expressed in the cell line containing human chromosome 21. We conclude that the extracellular domain of the IFN-gamma receptor is involved not only in the species specificity of IFN-gamma binding but also in signalling through interaction with an as yet unidentified species-specific factor(s) encoded by a gene(s) on human chromosome 21.
In vitro retinoid binding and release from a collagen sponge material in a simulated intravaginal environment (1982)

Four in vitro preparations were constructed to simulate the intravaginal release of two retinoids, all-trans-retinoic acid (t-RA) and 13-cis-retinoic acid (c-RA), from a 0.7% collagen sponge diaphragm insert. Four t-RA concentrations, 0.019, 0.05, 0.1, and 0.15% in methanol were added to the sponge. The release into an artificial vaginal fluid was monitored serially over 72 h by serial analysis for t-RA and c-RA using high-pressure liquid chromatography. In each preparation, retinoid release was immediate and noncontinuous. At 37 degrees C, the retinoids were stable for at least 48 h. Trans-retinoic acid was the predominant retinoid recovered. Only trace amounts of the cis-isomer were released. Peak t-RA levels were 20 microM after 0.01%, 60-80 microM after 0.05%, 100-200 microM after 0.1%, and 320 microM after 0.15%. When the vaginal fluid bath was changed after 5 h, no further significant retinoid release occurred. There was significant loss of up to 70% of the applied t-RA into the collagen sponge. The retinoid binding was concentration dependent (higher binding with higher concentrations) and was maximal only after 24 h of co-incubation. The discontinuous release of t-RA and the high degree of binding to collagen would seem to preclude use of the diaphragm insert as a vaginal drug delivery system, at least for retinoids.
Expression of a cyanobacterial sucrose-phosphate synthase from Synechocystis sp. PCC 6803 in transgenic plants (2002)

Sucrose-phosphate synthase (SPS) from the cyanobacterium Synechocystis sp.PCC 6803 lacks all of the Ser residues known to be involved in the regulation of higher plant SPS by protein phosphorylation.The Synechocystis SPS is also not allosterically regulated by glucose 6-phosphate or orthophosphate.To investigate the effects of expressing a potentially unregulated SPS in plants, the Synechocystis sps gene was introduced into tobacco, rice and tomato under the control of constitutive promoters.The Synechocystis SPS protein was expressed at a high level in the plants, which should have been sufcient to increase overall SPS activity 28-fold in the leaves.However, SPS activities and carbon partitioning in leaves from transgenic and wild-type plants were not signicantly different.The maximal light-saturated rates of photosynthesis in leaves from tomato plants expressing the Synechocystis SPS were the same as those from wild-type plants.Tomato plants expressing the maize SPS showed 23-fold increases in SPS activity, increased partitioning of photoassimilate to sucrose and up to 58% higher maximal rates of photosynthesis.To investigate the apparent inactivity of the Synechocystis SPS the enzyme was puried from transgenic tobacco and rice plants.Surprisingly, the puried enzyme was found to have full catalytic activity.It is proposed that some other protein in plant cells binds to the Synechocystis SPS resulting in inhibition of the enzyme.
Formulation of Wave Propagation in Infinite Media by Normal Coordinates with an Application to Diffraction (1957)

In the theories of acoustical and electromagnetic vibrations of enclosures, as well as in field theory and electrodynamics, one quite commonly uses normal modes as generalized coordinates in Hilbert space. Here the method is extended to unlimited or partially limited mechanical media, essentially by first solving the problem for an enclosure and going to a limit while expanding all or some of the boundaries to infinity. This leads to a very useful technique, of somewhat more generality than analogous procedures used in field theory. Thus it is applicable to all non-dissipative mechanical continua, for any boundary conditions, irrespective of the order or number of differential operators describing the continua and regardless of whether the coordinate systems are separable or not. A general orthonormality condition valid in all such cases together with the necessary rules for dealing with divergent normalizing coefficients are easily obtained by limiting procedures. An equally general formulation for arbitrary sources is obtained from the principle of virtual work. The method is illustrated by simple examples, for the case of a point source representing the instantaneous injection of a unit volume, i.e., an idealized, infinitely rapid, explosion. It is shown that in the problem of diffraction by a rigid wedge or corner one is led very quickly to an explicit solution in closed form, involving elementary functions only. Some physical implications of this solution are mentioned briefly. The advantages of the normal coordinates method are discussed when thus used in propagation or diffraction problems in unlimited or partially limited mechanical continua. Obvious advantages are its generality, its flexibility in dealing with arbitrary sources, and the fact that it leads directly to the progressive transient solution.
Anesthesiology Journals, 1992 (1992)

Department of Anesthesiology, Yale University School of Medicine, New Haven, Connecticut Address correspondence to Dr. Greene, Department of Anesthesiology, Yale University School of Medicine, P.O. Box 3333, New Haven, CT 06510. Accepted for publication July 24, 1991.
An Audio Response Unit Based on Partial Autocorrelation (1972)

This paper describes an audio response unit used in data communication services. The speech segments necessary to respond are stored in a large capacity magnetic drum in terms of partial autocorrelation (PARCOR) coefficients and excitation source information. PARCOR coefficient is a new parameter to express accurately the spectrum envelope of speech signals. Multiple speech signals can be synthesized simultaneously by means of a timemultiplexed digital filter composed of a high-speed arithmetic unit. The unit is able to respond to more than 7000 speech segments of 1-s duration.