gebhart/patrepeval huggingface dataset:
5-Substituted 2-Aminopyridine C-Nucleosides as Protonated Cytidine Equivalents:  Increasing Efficiency and Selectivity in DNA Triple-Helix Formation (1997)

The easily accessible C-nucleoside 2-amino-5-(2‘-deoxy-β-d-ribofuranosyl)pyridine (P) and its 3-methyl (MeP) and 2‘-O-methyl (POMe) derivatives were synthesized and incorporated as protonated cytidine equivalents in homopyrimidine oligodeoxynucleotides. Tm measurements indicate that oligonucleotides containing P or MeP have a higher affinity to double-stranded DNA over the pH range of 6−8 than 5-methylcytidine (MeC) containing oligonucleotides. This increase in stability is most pronounced above pH 7.0. The average increase in Tm/modification for the dissociation of oligonucleotide d(TTTTTMePTMePTMePTMePTMePT) from a 21-mer target duplex at pH 7.5 is 2.3 °C relative to oligonucleotide d(TTTTTMeCTMeCTMeCTMeCTMeCT). The pH dependence and sequence composition effects are much less pronounced for MeP (and also P) containing oligonucleotides than for MeC containing ones. While oligonucleotide d(TTTMeCMeCMeCMeCTTTTMeCTTT) shows no longer any affinity to the target duplex above pH 6.5, oligonucleotide d(TTTMePMePMePMePTTTTMePTTT) displays preserved binding with a Tm of 32.5 °C at pH 7.0 and even binds with a Tm of 23.3 °C at pH 8.0. Oligonucleotides containing POMe show distinctly less stable triple helices. The average decrease in Tm/modification for oligonucleotide d(TTTTTPOMeTPOMeTPOMeTPOMeTPOMeT) at pH 6.5 is 6.7 °C relative to the MeC containing oligonucleotide. DNase I footprint titration experiments indicate that d(TTTTTMePTMePTMePTMePTMePT) binds not only five times stronger to a 229 base pair DNA fragment than d(TTTTTMeCTMeCTMeCTMeCTMeCT) but also with higher selectivity. UV-melting experiments show that duplexes of d(TTTTTCTXTCTCTCT) (where X = P, MeP, or POMe) with their antiparallel Watson−Crick complement are dramatically less stable (ΔTm < −12 °C) at pH 8.0 than the corresponding natural duplex. Thus the new bases P and MeP show Hoogsteen specific pairing behavior.
Alleles of the Ly-17 alloantigen define polymorphisms of the murine IgG Fc receptor. (1985)

Antibodies specific for allelic determinants of the cell membrane alloantigen Ly-17 were found to react with genetically determined polymorphic sites on the murine IgG Fc receptor (Fc gamma R). Monoclonal antibodies specific for Ly-17.2 and the Fc gamma R detected identical populations of cells in thymus, spleen, lymph node, and bone marrow and had nearly identical reactivity with a large number of hematopoietic neoplasms. Antibodies to the Fc gamma R and either allele of Ly-17 blocked binding of rabbit IgG dimers to the Fc gamma R on spleen and bone marrow cells. Antibodies to the Fc gamma R also blocked binding of antibodies to either allele of Ly-17, whereas anti-Ly-17 antibodies only partially blocked the binding of antibodies to the Fc gamma R. Biochemical studies showed that antibodies to Ly-17 and the Fc gamma R precipitated proteins of Mr 55,000-60,000. The identity of the proteins recognized by these antibodies was confirmed by sequential immunoprecipitation.
Cyclodextrin-Derived Host Molecules as Reversal Agents for the Neuromuscular Blocker Rocuronium Bromide:  Synthesis and Structure−Activity Relationships (2002)

A series of mono- and per-6-substituted cyclodextrin derivatives were synthesized as synthetic receptors (or host molecules) of rocuronium bromide, the most widely used neuromuscular blocker in anaesthesia. By forming host-guest complexes with rocuronium, these cyclodextrin derivatives reverse the muscle relaxation induced by rocuronium in vitro and in vivo and therefore can be used as reversal agents of the neuromuscular blocker to assist rapid recovery of patients after surgery. Because this supramolecular mechanism of action does not involve direct interaction with the cholinergic system, the reversal by these compounds, e.g., compound 14 (Org 25969), is not accompanied by cardiovascular side effects usually attendant with acetylcholinesterase inhibitors such as neostigmine. The structure-activity relationships are consistent with this supramolecular mechanism of action and are discussed herein. These include the effects of binding cavity size and hydrophobic and electrostatic interaction on the reversal activities of these compounds.
Optimization of molecular distillation to concentrate ethyl esters of eicosapentaenoic (20:5 ω‐3) and docosahexaenoic acids (22:6 ω‐3) using simplified phenomenological modeling (2011)

The theoretical model and the optimization give decision criteria about the operative conditions for reaching the highest yield during molecular distillation of ω-3 fatty acid ethyl esters.
Antibody–cytotoxic agent conjugates for cancer therapy (2005)

Antibody-based delivery of cytotoxic agents, including toxins, to tumours can dramatically reduce systemic toxicity and increase therapeutic efficacy. The advantage of a monoclonal antibody (mAb) is superior selectivity towards antigens expressed on the surface of cancer cells. Recent advances in biotechnology accelerated progress in the pharmaceutical applications of mAbs. A cytotoxic warhead is attached to a mAb in an immunoconjugate via a linker, which is stable in circulation but efficiently cleaved in the tumour tissue. The warhead, mAb and linker play important roles in the successful design of potent and efficient immunoconjugates. To date, one mAb-cytotoxic agent conjugate has been approved by the FDA and several other candidates are in various stages of clinical trials. This review describes the recent progress in the design and development of mAb-based immunoconjugates of cytotoxic agents, and summarises the criteria for the critical choices of a suitable mAb, linker and cytotoxic agent to design an efficacious immunoconjugate.
Dynamic defect-limited yield prediction by criticality factor (2007)

In this paper, we present a new methodology for inline yield prediction based on defect inspection and design data. We derive a new metric called Criticality Factor (CF), which is essentially a fractional critical area for a defect of the reported size in a small layout window around the reported defect location. CF would be a good predictor of yield if geometrical considerations alone determined whether an electrical fail will result. Since other properties of the defect affect the electrical outcome (such as material properties), we employ a Training Set of wafers where the functional relation between CF and die yield is learned for each critical inspection step. From that point on these curves are used to predict the yield impact of in-line defects for new wafers. In addition, we show that highly-systematic defects (i.e. layout dependent) deviate from the CF functional curves, and hence add noise to the calculation. We suggest a technique to separate these defects from the random population, and calculate a corrected CF value for them.
The Histopathology of Treated Barrett's Esophagus (1998)

Columnar metaplasia of the lower esophageal epithelium (Barrett's esophagus) occurs in response to acid reflux, and its most important long-term complication is malignancy. In view of this, techniques are being explored for the eradication of Barrett's esophagus, and histopathologists will increasingly be required to assess response to these therapies in esophageal biopsy samples. The histopathologic features before and after treatment were studied in biopsy samples from 16 patients receiving omeprazole only, 10 treated by KTP laser photoablation, and five who underwent photodynamic therapy. All the treatment modalities resulted in histologic changes with at least partial squamous reepithelialization of the metaplastic columnar epithelium. The histologic findings suggest three main mechanisms for this: encroachment of adjacent squamous epithelium at the squamocolumnar junction, extension of epithelium from the submucosal gland duct to form squamous islands, and squamous metaplasia within the Barrett's columnar mucosa itself. The latter mechanism implies the existence of pluripotential stem cells within Barrett's mucosa. A relatively common finding was residual glandular mucosa, nonneoplastic and dysplastic, beneath squamous epithelium indicating the requirement for histologic confirmation of endoscopically suspected complete squamous reepithelialization with sufficiently deep biopsies.
The effect of betahistine, a histamine H1 receptor agonist/H3 antagonist, on olanzapine-induced weight gain in first-episode schizophrenia patients (2005)

Histamine antagonism has been implicated in antipsychotic drug-induced weight gain. Betahistine, a histamine enhancer with H1 agonistic/H3 antagonistic properties (48 mg t.i.d.), was coadministered with olanzapine (10 mg/day) in three first-episode schizophrenia patients for 6 weeks. Body weight was measured at baseline and weekly thereafter. Clinical rating scales were completed at baseline and at week 6. All participants gained weight (mean weight gain 3.1+/-0.9 kg) and a similar pattern of weight gain was observed: an increase during the first 2 weeks and no additional weight gain (two patients) or minor weight loss (one patient) from weeks 3 to 6. None gained 7% of baseline weight, which is the cut-off for clinically significant weight gain. Betahistine was safe and well tolerated and did not interfere with the antipsychotic effect of olanzapine. Our findings justify a placebo-controlled evaluation of the putative weight-attenuating effect of betahistine in olanzapine-induced weight gain.
Effect of Omega-3 Fatty Acid Ethyl Esters on the Oxylipin Composition of Lipoproteins in Hypertriglyceridemic, Statin-Treated Subjects (2014)

ClinicalTrials.gov NCT00959842.
Is (9Z)‐“meso”‐zeaxanthin optically active? (2001)

The question raised in the title was answered. (3R, 3'S)-meso-Zeaxanthin was submitted to iodine catalyzed photochemical stereoisomerisation. The enantiomeric (9Z) and (9'Z) geometrical isomers were isolated by semipreparative HPLC and separated as diastereomeric dicarbamates on a chiral column only. Cleavage of the carbamate could not be effected. CD-Spectra of (1"S, 1"S)- and (1"R, 1"R)-dicarbamates of geometrical isomers of (3R, 3'R)- and (3R, 3'S)-meso-zeaxanthin were systematically studied and the contribution from the carbamate moieties revealed. It was concluded that (9Z, 3R, 3'S)-"meso"-zeaxanthin, in spite of having no symmetry elements, is optically inactive. The result has been rationalised in line with the current hypothesis on the origin of carotenoid CD spectra.
Interactive television advertising: A research agenda (2005)

Digital television and digital video recorders (DVRs) open up new possibilities for interactive television (iTV) advertising. Little is known about whether iTV advertising will be more effective than traditional linear TV advertising and what iTV ad models are more effective than others. This paper summarises the few studies that have been published so far. However, the main contribution of this paper is the development of a conceptual framework for advancing research in this emerging area. The conceptual framework is based on the five elements in a basic model of how iTV ads are processed: (1) viewer characteristics, (2) iTV ad content factors, (3) situational influences on viewing, (4) the sequential steps by which iTV ads are processed, and (5) the communication effects or impacts that result from viewing iTV ads. From these five elements we derive five research questions, and the totality of these questions forms, we believe, a rich and varied research agenda that we hope will act as a launching pad and a guide for future research.
High-capacity wavelength demultiplexer with a large-diameter GRIN rod lens (1982)

A high capacity (twelve-channel) fiber optic wavelength demultiplexer incorporating a large diameter GRIN rod lens and grating was developed and fully characterized. The demultiplexer operates over the 740-930-nm wavelength range with an average channel spacing of 17 nm. The insertion loss, measured and averaged over all twelve channels, was approximately 3 dB, and the average adjacent channel optical cross talk was 32 dB.
Models for motion-based video indexing and retrieval (2000)

With the rapid proliferation of multimedia applications that require video data management, it is becoming more desirable to provide proper video data indexing techniques capable of representing the rich semantics in video data. In real-time applications, the need for efficient query processing is another reason for the use of such techniques. We present models that use the object motion information in order to characterize the events to allow subsequent retrieval. Algorithms for different spatiotemporal search cases in terms of spatial and temporal translation and scale invariance have been developed using various signal and image processing techniques. We have developed a prototype video search engine, PICTURESQUE (pictorial information and content transformation unified retrieval engine for spatiotemporal queries) to verify the proposed methods. Development of such technology will enable true multimedia search engines that will enable indexing and searching of the digital video data based on its true content.
Frequency-Wavenumber Domain Filtering for Improved Damage Visualization (2007)

This paper presents a technique for the analysis of full wavefield data in the wavenumber/frequency domain as an effective tool for damage detection, visualization and characterization. Full wavefield data contain a wealth of information regarding the space and time variation of propagating waves in damaged structural components. Such information can be used to evaluate the response spectrum in the frequency/wavenumber domain, which effectively separates incident waves from reflections caused by discontinuities encountered along the wave paths. This allows removing the injected wave from the overall response through simple filtering strategies, thus highlighting the presence of reflections associated to damage. The concept is first illustrated on analytical and numerically simulated data, and then tested on experimental results. In the experiments, full wavefield measurements are conveniently obtained using a Scanning Laser Doppler Vibrometer, which allows the detection of displacements and/or velocities over a user‐defined grid, and it is able to provide the required spatial and time information in a timely manner. Tests performed on a simple aluminum plate with artificially seeded slits simulating longitudinal cracks, and on a disbonded tongue and groove joint show the effectiveness of the technique and its potential for application to the inspection of a variety of structural components.
Multiple radio zone plans in mobile radio systems (1976)

Multiple zone structure in a land mobile system seems to offer a flexibility in radio zone planning by using different interference distances conforming to the different system requirements in a system, thus improving the frequency utilization. A multiple zone structure can be formed by a tessellation of basic zone groups with an identical shape in parallel translation on a plane. To assure the possibility of the tessellation, two types of basic zone groups are investigated. One has several hexagonally shaped zones covered by an omnidirectional antenna beam from the zone center, while another is constructed as a subdivision of hexagons covered by a directive antenna beam. The former is expected to facilitate reduced interference distance between adjacent frequencies. An estimate of the latter type has shown better frequency economy than that in a conventional zone structure.
Prognostic Importance of 6-Mercaptopurine Dose Intensity in Acute Lymphoblastic Leukemia (1999)

6-Mercaptopurine (6MP) and methotrexate are the backbone of continuation therapy for childhood acute lymphoblastic leukemia (ALL). In studies of oral 6MP and methotrexate, indices of chronic systemic exposure to active metabolites of these agents, namely, red blood cell (RBC) concentrations of methotrexate polyglutamates (MTXPGs) and thioguanine nucleotides (TGNs) have positively correlated with event-free survival (EFS). Our objective was to evaluate whether MTXPGs, TGNs, and the dose intensity of administered methotrexate and 6MP were prognostic in the setting of a treatment protocol in which all treatment was coordinated through a single center, and the weekly doses of methotrexate were given parenterally. On protocol Total XII, 182 children achieved remission and received weekly methotrexate 40 mg/m2 parenterally and daily oral 6MP, interrupted every 6 weeks during the first year by pulse chemotherapy. A total of 709 TGN, 418 MTX-PG, and 267 thiopurine methyltransferase (TPMT) measurements, along with complete dose intensity information (dose received divided by protocol dose per week) for 19,046 weeks of 6MP and methotrexate, were analyzed. In univariate analyses, only higher dose intensity of 6MP and of weekly methotrexate were significant predictors of overall EFS (P =.006 and. 039, respectively). The occurrence of neutropenia was associated with worse outcome (P =.040). In a multivariate analysis, only higher dose intensity of 6MP (P =.020) was a significant predictor of EFS, with lower TPMT activity (P =.096) tending to associate with better outcome. 6MP dose intensity was also associated (P =.007) with EFS among patients with homozygous wild-type TPMT phenotype. Lower 6MP dose intensity was primarily due to missed weeks of therapy and not to reductions in daily dose. We conclude that increased dose-intensity of oral 6MP is an important determinant of EFS in ALL, particularly among those children with a homozygous wild-type TPMT phenotype. However, increasing intensity of therapy such that neutropenia precludes chemotherapy administration may be counterproductive.
On lamellar organization in certain polyethylene spherulites (1978)

Abstract The lamellar structure of certain polyethylene spherulites grown very slowly at low supercoolings (regime I crystallization) has been exposed by using new techniques. A highly regular texture is found whose main element is ridged sheets of alternating {201} facets, ca. 1 pm wide, growing outwards with b as spherulitic radius. The first-formed sheets enclose columns of melt leading to the lateral segregation of slower crystallizing species and eventually to mimicry of a fibrous habit with a breadth and cross section controlled by the facet width. Although the morphology is similar to that expected according to the theory of Keith &amp; Padden (1963), the facet width is ca. 10~5 of their characteristic length Apparently additional factors need to be invoked to explain spherulitic crystallization under conditions of extremely slow growth. {201} facets agree with earlier predictions but it is considered that folds cannot lie exclusively in {200} planes. The sectored morphology with its regular geometry indicates that folds have a preferred shape and that fold surfaces are ordered to an extent. The degree of ordering decreases for lower crystallization temperatures and for longer molecules.
A Prospective Evaluation of Catheter Ablation of Ventricular Tachycardia as Adjuvant Therapy in Patients With Coronary Artery Disease and an Implantable Cardioverter-Defibrillator (1997)

Radiofrequency ablation of ventricular tachycardia as adjuvant therapy in patients with coronary artery disease and an ICD has a reasonable success rate, significantly reduces ICD therapies, and appears to be associated with an improved quality of life.
Thermal modification of connective tissues: basic science considerations and clinical implications. (2001)

Wound healing is a natural and well-orchestrated biologic event. Indeed, the ability of wounds to heal is the foundation on which the practice of surgery is predicated. The successful surgeon maintains a delicate alliance with nature, balancing the magnitude of the surgical insult against the capacity of the tissue for repair. Thermal injury is one of the most traumatic insults a tissue can sustain and the high degree of cell death and matrix alteration associated with thermal burns have been shown to result in a protracted healing time. Thus, the use of thermal energy as a stimulant for tissue shrinkage must be tempered with an appreciation of the biologic events that accompany this phenomenon. Furthermore, it must be realized that the initial degree of capsular shrinkage observed following the application of thermal energy may have little bearing on the long-term biologic and biomechanical status of the joint capsule. Therefore, the desire to see a redundant capsule shrink and become taut at surgery should be weighed very carefully against the level of damage imparted to the tissue to achieve this result. The simple initiation of the healing response may be sufficient to rehabilitate an incompetent structure via the creation of new cellular tissue. While the ultimate application(s) of thermal modification of connective tissues has yet to be completely defined, its ultimate role may be best suited to that of a low level stimulant for inducing a biologic repair response rather than a highly aggressive mechanism for primary tissue shrinkage.
Tracking, tuning, and terminating microbial physiology using synthetic riboregulators (2010)

The development of biomolecular devices that interface with biological systems to reveal new insights and produce novel functions is one of the defining goals of synthetic biology. Our lab previously described a synthetic, riboregulator system that affords for modular, tunable, and tight control of gene expression in vivo. Here we highlight several experimental advantages unique to this RNA-based system, including physiologically relevant protein production, component modularity, leakage minimization, rapid response time, tunable gene expression, and independent regulation of multiple genes. We demonstrate this utility in four sets of in vivo experiments with various microbial systems. Specifically, we show that the synthetic riboregulator is well suited for GFP fusion protein tracking in wild-type cells, tight regulation of toxic protein expression, and sensitive perturbation of stress response networks. We also show that the system can be used for logic-based computing of multiple, orthogonal inputs, resulting in the development of a programmable kill switch for bacteria. This work establishes a broad, easy-to-use synthetic biology platform for microbiology experiments and biotechnology applications.
Monte Carlo Simulations of a Coarse Grain Model for Block Copolymers and Nanocomposites (2008)

A coarse grain model and a Monte Carlo sampling formalism are proposed for simulations of self-assembly in block copolymer melts and nanoparticle−copolymer composites. Our approach relies on a particle-based representation of the system, it does not invoke a saddle point approximation, and it permits treatment of large three-dimensional systems. We provide a detailed description of the model and methods and discuss their relationship to results from self-consistent-field theory and single chain in mean field simulations. The validity of the proposed approach is addressed by applying it to study systems whose description within existing approaches would be demanding. In particular, we use it to examine the directed assembly of copolymer blends and nanoparticles on nanopatterned substrates. We show that results from simulations are in good agreement with experiment, and we use our theoretical findings to help explain the experimental observations.