gebhart/patrepeval huggingface dataset:
Synthesis of Two Distamycin Analogs and Their Binding Mode to d(CGCAAATTTGCG)2 in the 2:1 Solution Complexes as Determined by Two-Dimensional 1H-NMR (1995)

In the course of a study aimed at the synthesis of pyrrole amidine carboxamide DNA-binding agents as novel pharmacological agents, a series of carbamoyl analogues of distamycin, containing an increasing number of pyrrole units, have been obtained by total synthesis. The interaction of the tetrapyrrole carbamoyl 4 with the dodecamer d(CGCAAATTTGCG)2 in comparison with that of the corresponding formylamino analogue 3 has been examined by high-resolution 1H-NMR and molecular modeling. Either ligand binds to DNA in one-drug and symmetric two-drug modes at low drug:DNA ratios, while at high ratios only the two-drug complex was observed. In this article, the structure of 2:1 drugs DNA complexes has been studied by NMR and molecular modeling, which indicate that the two analogues bind the DNA in a similar fashion, in the minor groove of the 5'-AATTT region. In both complexes the two drugs are symmetrically placed along the complementary strands of DNA with the pyrrole ring of one molecule in close contact with those of the other one. Although another region of five consecutive A-T base pairs is available, no evidence of sliding of drug molecules between different binding sites, as in the case of the 2:1 complex of distamycin with the same dodecamer, is observed, thus indicating that increasing the number of N-methylpyrrolecarboxamide units from three to four cases a lengthening of the recognition sequence.
Techniques for measuring aberrations in lenses used in photolithography with printed patterns (1999)

In optical lithography, it is a serious problem that aberrations in projection lenses reduce the imaging quality. Therefore techniques to measure the aberrations are required that will predict the adverse effects of aberrations on lithographic imagery and reduce them. We present a measurement method that uses a fine grating and its imaging condition to quantify coma, astigmatism, and spherical aberration. With this method, these aberrations can be described with simple expressions from the measured results. Application of this method revealed the coma of Zernike polynomials for our krypton fluoride (KrF) excimer-laser scanner.
ENZYME PATTERNS IN HUMAN TISSUES. I. METHODS FOR THE DETERMINATION OF GLYCOLYTIC ENZYMES. (1964)

Summary The prospective aim of these studies is the development of consonant procedures for the determination of comparative enzyme patterns in human malignant and nonmalignant tissues. Based on the well established principle of using nicotinamide adenine dinucleotides to follow reaction rates, improved methods and a unified program for the determination of all the glycolytic and some related enzymes in crude tissue homogenates have been described. With rat tissues used as models, the precision of the measurements and the stability of the enzymes to storage in the intact tissues at -20°C. have been established. The consonant methodology permits direct comparison of the activities of all the enzymes. Although such enzyme patterns cannot yield information on the actual rates of metabolic processes in vivo, they do give information on the potential rates of metabolite flow, the steps in an enzymic reaction chain that are likely to be rate limiting, and the potential for alternate metabolic pathways.
Chairman's Letter (2000)

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Inotuzumab Ozogamicin versus Standard Therapy for Acute Lymphoblastic Leukemia (2016)

The rate of complete remission was higher with inotuzumab ozogamicin than with standard therapy, and a higher percentage of patients in the inotuzumab ozogamicin group had results below the threshold for minimal residual disease. Both progression-free and overall survival were longer with inotuzumab ozogamicin. Veno-occlusive liver disease was a major adverse event associated with inotuzumab ozogamicin. (Funded by Pfizer; INO-VATE ALL ClinicalTrials.gov number, NCT01564784.).
Identification of sequences important in the nucleolar localization of human immunodeficiency virus Rev: relevance of nucleolar localization to function (1990)

The human immunodeficiency virus rev gene product regulates the expression of viral structural genes. It was recently shown that Rev regulates the export of viral structural mRNAs from the nucleus to the cytoplasm. Analysis of Rev subcellular localization reveals marked accumulation in the nucleolus, suggesting a role for the nucleolus in this export process. We report here the identification of amino acid residues critical to the nucleolar localization of Rev. Consistent with this finding, a Rev/beta-galactosidase fusion protein, harboring this region of Rev, localized entirely within the nucleolus. Of most significance, mutations that eliminated nucleolar localization markedly diminished Rev function, even though accumulation in the nucleoplasm was retained. These findings support a model whereby Rev-induced export of human immunodeficiency virus structural mRNAs from the nucleus to the cytoplasm is likely to involve nucleolar events.
Roadmap on silicon photonics (2016)

Silicon photonics research can be dated back to the 1980s. However, the previous decade has witnessed an explosive growth in the field. Silicon photonics is a disruptive technology that is poised to revolutionize a number of application areas, for example, data centers, high-performance computing and sensing. The key driving force behind silicon photonics is the ability to use CMOS-like fabrication resulting in high-volume production at low cost. This is a key enabling factor for bringing photonics to a range of technology areas where the costs of implementation using traditional photonic elements such as those used for the telecommunications industry would be prohibitive. Silicon does however have a number of shortcomings as a photonic material. In its basic form it is not an ideal material in which to produce light sources, optical modulators or photodetectors for example. A wealth of research effort from both academia and industry in recent years has fueled the demonstration of multiple solutions to these and other problems, and as time progresses new approaches are increasingly being conceived. It is clear that silicon photonics has a bright future. However, with a growing number of approaches available, what will the silicon photonic integrated circuit of the future look like? This roadmap on silicon photonics delves into the different technology and application areas of the field giving an insight into the state-of-the-art as well as current and future challenges faced by researchers worldwide. Contributions authored by experts from both industry and academia provide an overview and outlook for the silicon waveguide platform, optical sources, optical modulators, photodetectors, integration approaches, packaging, applications of silicon photonics and approaches required to satisfy applications at mid-infrared wavelengths. Advances in science and technology required to meet challenges faced by the field in each of these areas are also addressed together with predictions of where the field is destined to reach.
Functionality for object migration among distributed, heterogeneous, autonomous DBS (2002)

In current enterprises, data are distributed over a multitude of heterogeneous, autonomous database systems. These systems are often isolated and an exchange of data among them is not easy. On the other hand, decreasing time-to-market periods and raising techniques like concurrent engineering require good support in dynamic change of data location in various granularities. Data will not reside in one database system all the time but need to be moved or duplicated concurrently to others. To fulfil this industrial requirement, we develop functionality enabling different granularities of data (object) migration among multiple database systems. The underlying architecture and concepts are being derived from a requirement analysis and extend a federated DBS approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analysis and design of active inductor as DC-link reactor for lightweight adjustable speed drive systems (2014)

Size and weight considerations are very important in certain specialized industries as offshore oil drilling and marine/subsea systems that employ adjustable speed drives (ASD). Typical ASD topology consists of a three phase diode rectifier front-end. It is also common to specify a dc-link inductor and/or ac line reactors to reduce utility line current harmonics to acceptable levels. However, the required dc-link inductor/ac line reactors contribute to additional weight and volume. In this paper an active inductor approach is explored to emulate a large size dc-link inductor. Analysis and design of an active inductor for a 1 MW ASD is proposed and analyzed. The required inductance value is commanded and current control regulates the active inductor current to match inductor behavior. It is shown that the proposed active inductor topology is similar in weight/volume as the smaller inductor while emulating a higher per unit inductance. The proposed active inductor meets the required compact and lightweight specifications of ASDs in retrofit and special applications. Furthermore, the active inductor is tunable to achieve high performance operation during faults. Experimental results from a scaled down prototype are presented. A size, weight and loss analysis is detailed and a soft switching method to reduce losses is also explained.
Do CARs Need a Driver's License? Adoptive Cell Therapy with Chimeric Antigen Receptor-Redirected T Cells Has Caused Serious Adverse Events (2010)

Adoptive transfer of genetically retargeted T cells provides promise in the therapy of malignant diseases; two severe adverse events, however, due to "on-targeted" activation of modified T cells occurred in recent trials. We here discuss the challenge to balance targeted anti-tumor responses whilst avoiding destruction of healthy tissues and the need of continued and carefully designed pre-clinical and clinical evaluations.
Tumor Necrosis Factor Receptor-associated Factor (TRAF) 5 and TRAF2 Are Involved in CD30-mediated NFκB Activation (1997)

Signals emanated from CD30 can activate the nuclear factor kappaB (NFkappaB). The two conserved subdomains, D1 and D2, in the C-terminal cytoplasmic region of CD30 were tested for interaction with two tumor necrosis factor receptor-associated factor (TRAF) proteins with NFkappaB activating capacity, TRAF2 and TRAF5. TRAF5 is the newest member of the TRAF family that binds to lymphotoxin beta receptor and CD40. TRAF5, as well as TRAF2, interacted with the D2 subdomain of CD30 in vitro and in vivo. Deletion analysis by the yeast two-hybrid system revealed that the C-terminal 22 and 30 amino acid residues are dispensable for interaction of TRAF5 and TRAF2 with CD30, respectively. Substitution of alanine for threonine at 463 abolished the interaction with TRAF2. Overexpression of the TRAF domain of TRAF2 or TRAF5 showed a dominant negative effect on CD30-mediated NFkappaB activation. Simultaneous expression of these TRAF domains further suppressed the NFkappaB activation, suggesting an interplay of these TRAF proteins. Expression of TRAF2 and TRAF5 mRNA was demonstrated in T- and B-cell lines that express CD30. Taken together, our results indicate that TRAF2 and TRAF5 directly interact with CD30 and are involved in NFkappaB activation by CD30 signaling.
Adaptive modulation for coded cooperative systems (2005)

Throughput plays a key role in data communications over a wireless link. In this paper, we use adaptive modulation for a cooperative relaying system with the goal of maximizing the data throughput. We compare the throughput performance of three different schemes with adaptive modulation: direct transmission, multihop and coded cooperation. We find that cooperation with adaptive modulation provides large throughput improvement over multihop and direct transmissions. We also observe that to maximize the data throughput in direct transmission and multihop, the modulation mode for each hop only depends on the channel quality from the transmitter to the receiver. However, in coded cooperation a system wide optimization is necessary.
Strength-duration and probability of success curves for defibrillation with biphasic waveforms. (1990)

Certain biphasic waveforms require less energy to defibrillate than do monophasic pulses of equal duration, although the mechanisms of this increased effectiveness remain unclear. This study used strength-duration and percent success curves for defibrillation with monophasic and biphasic truncated exponential waveforms to explore these mechanisms. In part 1, defibrillation thresholds were determined for both high- and low-tilt waveforms. The monophasic pulses tested ranged in duration from 1.0 to 20.0 msec, and the biphasic waveforms had first phases of either 3.5 or 7.0 msec and second phases ranging from 1.0 to 20.0 msec. In part 2, defibrillation percent success curves were constructed for 6.0 msec/6.0 msec biphasic waveforms with a constant phase-one amplitude and with phase-two amplitudes of approximately 21%, 62%, 94%, and 141% of phase one. This study shows that if the first phase of a biphasic waveform is held constant and the second phase is increased in either duration or amplitude, defibrillation efficacy first improves, then declines, and then again improves. For pulse durations of at least 14 msec, the second-phase defibrillation threshold voltage of a high-tilt biphasic waveform is higher than that of a monophasic pulse equal in duration to the biphasic second phase (p less than 0.05), indicating that the previously proposed hypothesis of stimulation by the second phase is not the sole mechanism of biphasic defibrillation. These facts indicate the importance of the degree of tilt for the defibrillation efficacy of biphasic waveforms and suggest at least two mechanisms exist for defibrillation with these waveforms, one that is more effective for smaller second phases and another that becomes more effective as the second phase is increased.
Apicidin, a histone deacetylase inhibitor, inhibits proliferation of tumor cells via induction of p21WAF1/Cip1 and gelsolin. (2000)

Apicidin [cyclo(N-O-methyl-L-tryptophanyl-L-isoleucinyl-D-pipecolinyl -L-2-amino-8-oxodecanoyl)] is a fungal metabolite shown to exhibit antiparasitic activity by the inhibition of histone deacetylase (HDAC). In this study, we evaluated apicidin as a potential antiproliferative agent. Apicidin showed a broad spectrum of antiproliferative activity against various cancer cell lines, although with differential sensitivity. The antiproliferative activity of apicidin on HeLa cells was accompanied by morphological changes, cell cycle arrest at G1 phase, and accumulation of hyperacetylated histone H4 in vivo as well as inhibition of partially purified HDAC in vitro. In addition, apicidin induced selective changes in the expression of p21WAF1/Cip1 and gelsolin, which control the cell cycle and cell morphology, respectively. Consistent with increased induction of p21WAF1/Cip1, phosphorylation of Rb protein was markedly decreased, indicating the inhibition of cyclin-dependent kinases, which became bound to p21WAF1/Cip1. The effects of apicidin on cell morphology, expression of gelsolin, and HDAC1 activity in vivo and in vitro appeared to be irreversible, because withdrawal of apicidin did not reverse those effects, whereas the induction of p21WAF1/Cip1 by apicidin was reversible. Taken together, the results suggest that induction of histone hyperacetylation by apicidin is responsible for the antiproliferative activity through selective induction of genes that play important roles in the cell cycle and cell morphology.
Molecular Cloning and Expression of the cDNAs Encoding Human and Yeast Mevalonate Pyrophosphate Decarboxylase (1996)

The importance of lowering serum cholesterol levels for the prevention of cardiovascular disease has been well documented. Because mevalonate pyrophosphate decarboxylase is a unique enzyme in the cholesterol biosynthetic pathway it is a potential therapeutic target for the treatment of hypercholesterolemia and other diseases. For this reason we cloned and expressed the cDNA for the human enzyme. We also cloned and expressed the yeast homolog using the human enzyme's similarity to a previously unidentified and incomplete genomic sequence. Northern blot analysis revealed a transcript of approximately 2 kilobases in a variety of human tissues. The recombinant human enzyme is a homodimer of 43-kDa subunits with a specific activity of 2.4 units/mg. Computer searches for similarity with known sequences showed that mevalonate pyrophosphate decarboxylase has little similarity to other proteins.
XBP-1 Regulates a Subset of Endoplasmic Reticulum Resident Chaperone Genes in the Unfolded Protein Response (2003)

The mammalian unfolded protein response (UPR) protects the cell against the stress of misfolded proteins in the endoplasmic reticulum (ER). We have investigated here the contribution of the UPR transcription factors XBP-1, ATF6alpha, and ATF6beta to UPR target gene expression. Gene profiling of cell lines lacking these factors yielded several XBP-1-dependent UPR target genes, all of which appear to act in the ER. These included the DnaJ/Hsp40-like genes, p58(IPK), ERdj4, and HEDJ, as well as EDEM, protein disulfide isomerase-P5, and ribosome-associated membrane protein 4 (RAMP4), whereas expression of BiP was only modestly dependent on XBP-1. Surprisingly, given previous reports that enforced expression of ATF6alpha induced a subset of UPR target genes, cells deficient in ATF6alpha, ATF6beta, or both had minimal defects in upregulating UPR target genes by gene profiling analysis, suggesting the presence of compensatory mechanism(s) for ATF6 in the UPR. Since cells lacking both XBP-1 and ATF6alpha had significantly impaired induction of select UPR target genes and ERSE reporter activation, XBP-1 and ATF6alpha may serve partially redundant functions. No UPR target genes that required ATF6beta were identified, nor, in contrast to XBP-1 and ATF6alpha, did the activity of the UPRE or ERSE promoters require ATF6beta, suggesting a minor role for it during the UPR. Collectively, these results suggest that the IRE1/XBP-1 pathway is required for efficient protein folding, maturation, and degradation in the ER and imply the existence of subsets of UPR target genes as defined by their dependence on XBP-1. Further, our observations suggest the existence of additional, as-yet-unknown, key regulators of the UPR.
Ancient DNA: recovery and analysis of genetic material from paleontological, archaeological, museum, medical, and forensic specimens (1994)

Ancient DNA refers to DNA which can be recovered and analyzed from clinical, museum, archaeological and paleontological specimens. Ancient DNA ranges in age from less than 100 years to tens of millions of years. The study of ancient DNA is a young field, but it has been revolutionized by the application of polymerase chain reaction technology, and interest is growing very rapidly. Fields as diverse as evolution, anthropology, medicine, agriculture, and even law enforcement have quickly found applications in the recovery of ancient DNA. This book contains contributions from many of the first generation researchers who pioneered the development and application of ancient DNA methods. their chapters present the protocols and precautions which have resulted in the remarkable results obtained in recent years. The range of subjects reflects the wide diversity of applications that are emerging in research on ancient DNA, including the study of DNA to analyze kinship, recovery of DNA from organisms trapped in amber, ancient DNA from human remains preserved in a variety of locations and conditions, DNA recovered from herbarium and museum specimens, and DNA isolated from ancient plant seeds or compression fossils. Ancient DNA will serve as a valuable source of information, ideas, and protocols for anyone interested in this extraordinary field.
Low-Density Lipoprotein Nanoparticles as Magnetic Resonance Imaging Contrast Agents (2006)

Low-density lipoproteins (LDLs) are a naturally occurring endogenous nanoplatform in mammalian systems. These nanoparticles (22 nm) specifically transport cholesterol to cells expressing the LDL receptor (LDLR). Several tumors overexpress LDLRs presumably to provide cholesterol to sustain a high rate of membrane synthesis. Amphiphilic gadolinium (Gd)-diethylenetriaminepentaacetic acid chelates have been incorporated into the LDL to produce a novel LDLR-targeted magnetic resonance imaging (MRI) contrast agent. The number of Gd chelates per LDL particle ranged between 150 and 496 Gd(III). In vitro studies demonstrated that Gd-labeled LDL retained a similar diameter and surface charge as the native LDL particle. In addition, Gd-labeled LDL retained selective cellular binding and uptake through LDLR-mediated endocytosis. Finally, Gd-labeled LDLs exhibited significant contrast enhancement 24 hours after administration in nude mice with human hepatoblastoma G2 xenografts. Thus, Gd-labeled LDL demonstrates potential use as a targeted MRI contrast agent for in vivo tumor detection.
Microbicidal Properties of a Silver-Containing Hydrofiber® Dressing Against a Variety of Burn Wound Pathogens (2004)

Partial-thickness burns are often characterized by microbial contamination and copious exudate produced during the early postburn period. Consequently, topical wound management often relies on the use of antimicrobial agents and absorbent dressings, and an AQUACEL Hydrofiber Dressing containing ionic silver has been designed to meet such needs. To assess the antimicrobial properties of the AQUACEL Hydrofiber dressing, samples were challenged with a wide variety of recognized burn wound pathogens in a simulated wound fluid model. Dressing samples were inoculated with the challenge organisms at time zero and then reinoculated on days 4 and 9 to mimic the worst-case clinical scenario. The dressing was shown to be microbicidal against aerobic and anaerobic bacteria (including antibiotic-resistant strains), yeasts, and filamentous fungi during a 14-day test period. Based on our results, the silver-containing dressing is likely to provide a barrier to infection, in addition to providing proven fluid-handling benefits of the AQUACEL Hydrofiber dressing, in the management of partial-thickness burns.