gebhart/patrepeval huggingface dataset:
Evaluation of Natural Products as Inhibitors of Human Immunodeficiency Virus Type 1 (HIV-1) Reverse Transcriptase (1991)

Inhibition of human immunodeficiency virus reverse transcriptase is currently considered a useful approach in the prophylaxis and intervention of acquired immunodeficiency syndrome (AIDS), and natural products have not been extensively explored as inhibitors of this enzyme. We currently report that the reverse transcriptase assay developed for the detection of the enzyme in virions involving polyadenylic acid.oligodeoxythymidylic acid (poly rA.oligo dT) and radiolabeled thymidine 5'-triphosphate (TTP), can be applied as a simple method for screening the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) inhibitory potential of natural products. As reported herein, 156 pure natural products have been examined in this system. Benzophenanthridine alkaloids such as faragaronine chloride [1] and nitidine chloride, which are known inhibitors of avian myeloblastosis virus reverse transcriptase, demonstrated potent activity in the HIV-1 RT system, and 1 (IC50 10 micrograms/ml) was adopted as a positive-control substance. Additional inhibitors found were columbamine iodide [2] and other protoberberine alkaloids, the isoquinoline alkaloid O-methylpsychotrine sulfate [3], and the iridoid fulvoplumierin [4]. A number of indolizidine, pyrrolizidine, quinolizidine, indole, and other alkaloids, as well as compounds of many other structural classes, were tested and found to be inactive. A total of 100 plant extracts have also been evaluated, and 15 of these extracts showed significant inhibitory activity. Because tannins and other polyphenolic compounds are potent reverse transcriptase inhibitors, methods were evaluated for the removal of these from plant extracts prior to testing. Polyphenolic compounds were found to be responsible for the activity demonstrated by the majority of plant extracts. After appropriate tannin removal procedures were established, the bioassay system was shown to be generally applicable to both pure natural products and plant extracts. The method also proved useful in directing an isolation procedure with Plumeria rubra to yield fulvoplumierin [4] as an active compound (IC50 45 micrograms/ml).
Identification of chaperones as essential components of the tumor rejection moieties of cancers. (2012)

During my graduate work (1979–81) at the Center for Cellular and Molecular Biology in Hyderabad, India, and far away from the epicenter of cancer immunology, I had identified a tumor-derived protein of 100,000 daltons (d) that could elicit tumor resistance in rats immunized with it (1). I had moved on to postdoctoral work in developmental biology at Yale University. Since my graduate work was done pretty much by myself in an environment where there was not much knowledge of immunology, I was unsure if my excitement about it was justified. To put some context to it, I sent the then-unpublished manuscript to Lloyd Old, whose name I knew only from the literature. I had read with intense delight many of his papers (mainly with Albert DeLeo) attempting to define the unique antigens of mouse sarcomas [see (2) for review], and I reasoned that he would be an ideal person to comment on my fledgling work. I did not hear from Old for about two months, and my repeated calls to his office were rebuffed by his secretary whom I would later come to know and love as Charlotte Daub. Frustrated by my inability to reach Old, I contacted the New York Telephone Operator and acquired his home telephone number.
CellProfiler™: Free, Versatile Software for Automated Biological Image Analysis (2007)

Careful visual examination of biological samples is quite powerful, but many visual analysis tasks done in the laboratory are repetitive, tedious, and subjective. Here we describe the use of the open-source software, CellProfiler, to automatically identify and measure a variety of biological objects in images. The applications demonstrated here include yeast colony counting and classifying, cell microarray annotation, yeast patch assays, mouse tumor quantification, wound healing assays, and tissue topology measurement. The software automatically identifies objects in digital images, counts them, and records a full spectrum of measurements for each object, including location within the image, size, shape, color intensity, degree of correlation between colors, texture (smoothness), and number of neighbors. Small numbers of images can be processed automatically on a personal computer and hundreds of thousands can be analyzed using a computing cluster. This free, easy-to-use software enables biologists to comprehensively and quantitatively address many questions that previously would have required custom programming, thereby facilitating discovery in a variety of biological fields of study.
Interactive collision detection (1993)

Collision detection and response can make a virtual-reality application seem more believable. Unfortunately, existing collision-detection algorithms are too slow for interactive use. The authors present a new algorithm that is not only fast but also interruptible, allowing an application to trade quality for more speed. The algorithm uses simple four-dimensional geometry to approximate motion, and sets of spheres to approximate three-dimensional surfaces. The algorithm allows a sample application to run five to seven times faster than it runs with existing algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Exploring Cellular Interactions of Liposomes Using Protein Corona Fingerprints and Physicochemical Properties (2016)

To control liposomes fate and transport upon contact with biofluids, it is essential to consider several parameters affecting the synthetic and biological identity of liposomes, as well as liposome–protein corona (PC) aspects. As a powerful tool in this data mining adventure, quantitative structure–activity relationship (QSAR) approach is used to correlate physicochemical properties of liposomes and their PC fingerprints to multiple quantified biological responses. In the present study, the relationship between cellular interactions of a set of structurally diverse liposomal formulations and their physicochemical and PC properties has been investigated via linear and nonlinear QSAR models. Significant parameters affecting cellular uptake and cell viability of liposomes in two important cancer cell lines (PC3 and HeLa) have been identified. The developed QSARs have the capacity to be implemented in advanced targeted delivery of liposomal drugs.
Shape Evolution and Single Particle Luminescence of Organometal Halide Perovskite Nanocrystals (2015)

Organometallic halide perovskites CH3NH3PbX3 (X = I, Br, Cl) have quickly become one of the most promising semiconductors for solar cells, with photovoltaics made of these materials reaching power conversion efficiencies of near 20%. Improving our ability to harness the full potential of organometal halide perovskites will require more controllable syntheses that permit a detailed understanding of their fundamental chemistry and photophysics. In this manuscript, we systematically synthesize CH3NH3PbX3 (X = I, Br) nanocrystals with different morphologies (dots, rods, plates or sheets) by using different solvents and capping ligands. CH3NH3PbX3 nanowires and nanorods capped with octylammonium halides show relatively higher photoluminescence (PL) quantum yields and long PL lifetimes. CH3NH3PbI3 nanowires monitored at the single particle level show shape-correlated PL emission across whole particles, with little photobleaching observed and very few off periods. This work highlights the potential of low-dimensional organometal halide perovskite semiconductors in constructing new porous and nanostructured solar cell architectures, as well as in applying these materials to other fields such as light-emitting devices and single particle imaging and tracking.
Utility of Genome‐Wide Association Study findings: prostate cancer as a translational research paradigm (2012)

Genome-wide association studies have identified thousands of consistently replicated associations between genetic markers and complex disease risk, including cancers. Alone, these markers have limited utility in risk prediction; however, when several of these markers are used in combination, the predictive performance appears to be similar to that of many currently available clinical predictors. Despite this, there are divergent views regarding the clinical validity and utility of these genetic markers in risk prediction. There are valid concerns, thus providing a direction for new lines of research. Herein, we outline the debate and use the example of prostate cancer to highlight emerging evidence from studies that aim to address potential concerns. We also describe a translational framework that could be used to guide the development of a new generation of comprehensive research studies aimed at capitalizing on these exciting new discoveries.
Physical Dependence Produced by Dihydroetorphine in Mice. (1994)

Using various administration schedules, the physical dependence produced by dihydroetorphine (DHE) was compared with that of morphine in mice. Physical dependence, evaluated by naloxone-precipitated withdrawal signs, did not develop following daily treatment with DHE (10, 20, 100 and 1000 micrograms/kg, i.p. or 30, 100 and 1000 ng/mouse, i.c.v.) for 6 d. However, 5 repeated injections of DHE (10 micrograms/kg, i.p.) at 1 or 2 h intervals did produce physical dependence and the dependent state disappeared after 2 h. Accordingly, it was demonstrated that a sufficient degree of antinociceptive activity needed to be maintained, longer than several hours, for the development of physical dependence on DHE and that the duration of the dependent state was very short. In the single dose suppression test, a single dose of DHE completely suppressed the natural withdrawal signs that appeared following abstinence in morphine-dependent animals without reappearance of significant withdrawal signs, indicating the suitability of DHE as a substitute for morphine. The characteristic properties of DHE, the extremely potent antinociceptive effect and minimal dependence, indicate the separation of the antinociceptive effect from dependence, and suggest that it may be possible to develop a novel drug which may be safely used in clinical situations.
Persistent RNNs: stashing recurrent weights on-chip (2016)

This paper introduces a new technique for mapping Deep Recurrent Neural Networks (RNN) efficiently onto GPUs. We show how it is possible to achieve substantially higher computational throughput at low mini-batch sizes than direct implementations of RNNs based on matrix multiplications. The key to our approach is the use of persistent computational kernels that exploit the GPU's inverted memory hierarchy to reuse network weights over multiple timesteps. Our initial implementation sustains 2.8 TFLOP/s at a mini-batch size of 4 on an NVIDIA TitanX GPU. This provides a 16× reduction in activation memory footprint, enables model training with 12× more parameters on the same hardware, allows us to strongly scale RNN training to 128 GPUs, and allows us to efficiently explore end-to-end speech recognition models with over 100 layers.
Increasing the antineoplastic potential of natural killer cells with a chimeric receptor activated by NKG2D ligands (2013)

The antineoplastic activity of natural killer (NK) cells is regulated by stimulatory and inhibitory receptors. We have recently constructed a chimeric receptor sharing the specificity of NKG2D that significantly increases the cytotoxicity of NK cells against hematopoietic and solid cancer cells, but not against their normal counterparts. This receptor is expected to improve the clinical potential of NK cell-based anticancer immunotherapies.
RNA-binding properties of influenza A virus matrix protein M1 (1989)

The matrix protein (M1) of influenza A virus, which has a critical role in viral assembly and can inhibit the viral transcriptase complex, has the ability to bind RNA. The RNA-binding property of M1 is specific for single-stranded RNA, like that of influenza nucleoprotein (NP) and shows similar sensitivity to pH and to salt concentration. M1:RNA complexes are stable, once formed, to competition from excess single-stranded RNA. The possible location of the RNA-binding regions in the M1 protein is discussed.
Low-threshold terahertz quantum-cascade lasers (2002)

A quantum-cascade laser operating at λ=66 μm is demonstrated. It consists of a three-quantum-well chirped-superlattice active region embedded in a waveguide based on a single interface plasmon and a buried contact. A threshold current density of 210 A/cm2 at T=12 K, a maximum peak optical power of 4 mW, and operation up to T=44 K are achieved in a 2.7 mm long device with a high reflectivity backfacet coating.
Peter Paul Rubens (1990)

Kaufvertrag über ein Haus „genaemt de Wapper“ und ein angrenzendes Grundstück, das als „bleyckhof“ oder „ramhof“ bezeichnet wird. Der Kaufpreis betrug 10000 Gulden, die in verschiedenen Raten bezahlt werden mußten. Zusätzlich verpflichtet sich Rubens „... tot een recognitie ende gedachtenisse van dese coope den voors. Hans Thysz sal toegeven en leveren een stuck schilderije by syn eijgen handt gemaeckt, soo groot en cleyn als hem Rubbens goetduncken sal, daer hy eere van sal begeren, en noch bovendien een soon van den voorsz.
Bandwidth improvement for a microstrip-fed seriesarray of dielectric resonator antennas (1996)

The impedance and pattern bandwidth of an array of dielectric resonator antennas series fed by a microstrip line, was significantly improved by replacing individual DRAs with paired DRAs. The DRAs in each pair are spaced slightly &lt;λg/4 apart so that their input reflections cancel. An array of eight DRA pairs was designed and fabricated, and its performance was compared to an array of eight single elements. The 10 dB return loss bandwidth improved from 2 to 18% and the 3 dB gain pattern bandwidth improved from 12 to 17%.
Synthesis and organization of nanoscale II–VI semiconductor materials using evolved peptide specificity and viral capsid assembly (2003)

Biological selection using the M13 bacteriophage was used to isolate peptide–phage fusions capable of specific recognition and nucleation of zinc sulfide (ZnS) and cadmium sulfide (CdS) nanocrystals. Advanced analytical electron microscopy data revealed that the phage constructs were found to control both crystal size and structure of semiconductor nanocrystals synthesized in aqueous solution at room temperature. Most significantly, different engineered peptide–phage constructs were found that directed the specific nucleation of either the zinc-blende or wurtzite structure for both ZnS and CdS nanocrystals. The ZnS specific peptides were found to function the same in either of two different fusion constructs, a pIII and pVIII fusion. As such, this method provides a new route to the synthesis of nanocrystals with specified physical characteristics such as size and crystal phase and has the potential to assemble biological II–VI hybrid materials into spatially complex functional mesoscopic electronic and photonic structures.
Characterization ofMdMADS2, a Member of theSQUAMOSASubfamily of Genes, in Apple1 (1999)

A MADS-box gene, MdMADS2, was isolated from the apple (Malus x domestica Borkh.) var Fuji and its developmental expression pattern was studied during flower development. MdMADS2 shares a high degree of amino acid sequence identity with the SQUAMOSA subfamily of genes. RNA blot analysis showed that MdMADS2 is transcribed through all stages of flower development, and its transcription was seen in the four floral organs. RNA in situ hybridization revealed that the MdMADS2 mRNA is expressed both in the inflorescence meristem and in the floral meristem. The MdMADS2 transcript was detected at all stages of flower development. Protein localization analysis showed that MdMADS2 protein was excluded from the stamen and carpel primordia, in which a considerable MdMADS2 mRNA signal was detected. This indicates that posttanscriptional regulation may be involved in the MdMADS2-mediated control of flower development. Transgenic tobacco expressing the MdMADS2 gene from the cauliflower mosaic virus 35S promoter showed early flowering and shorter bolts, but did not show any homeotic changes in the floral organs. These results suggest that MdMADS2 plays an important role during early stages of flower development.
EVOLUTION AND MEASUREMENT OF SPECIES DIVERSITY (1972)

Summary Given a resource gradient (e.g. light intensity, prey size) in a community, species evolve to use different parts of this gradient; competition between them is thereby reduced. Species relationships in the community may be conceived in terms of a multidimensional coordinate system, the axes of which are the various resource gradients (and other aspects of species relationships to space, time, and one another in the community). This coordinate system defines a hyperspace, and the range of the space that a given species occupies is its niche hypervolume, as an abstract characterization of its intra‐community position, or niche. Species evolve toward difference in niche, and consequently toward difference in location of their hypervolumes in the niche hyperspace. Through evolutionary time additional species can fit into the community in niche hypervolumes different from those of other species, and the niche hyperspace can become increasingly complex. Its complexity relates to the community's richness in species, its alpha diversity. Species differ in the proportions of the niche hyperspace they are able to occupy and the share of the community's resources they utilize. The share of resources utilized is expressed in species' productivities, and when species are ranked by relative productivity (or some other measurement) from most to least important, importance‐value or dominance‐diversity curves are formed. Three types of curves may represent manners in which resources are divided among species: (a) niche pre‐emption with strong dominance, expressed in a geometric series, (b) random boundaries between niches, expressed in the MacArthur distribution, and (c) determination of relative importance by many factors, so that species form a frequency distribution on a logarithmic base of importance values, a lognormal distribution. The forms of importance‐value curves do not permit strong inference about resource division, but are of interest for their expression of species relationships and bearing on measurement of diversity.
Investigation of Storage Options for Scientific Computing on Grid and Cloud Facilities (2012)

In recent years, several new storage technologies, such as Lustre, Hadoop, OrangeFS, and BlueArc, have emerged. While several groups have run benchmarks to characterize them under a variety of configurations, more work is needed to evaluate these technologies for the use cases of scientific computing on Grid clusters and Cloud facilities. This paper discusses our evaluation of the technologies as deployed on a test bed at FermiCloud, one of the Fermilab infrastructure-as-a-service Cloud facilities. The test bed consists of 4 server-class nodes with 40 TB of disk space and up to 50 virtual machine clients, some running on the storage server nodes themselves. With this configuration, the evaluation compares the performance of some of these technologies when deployed on virtual machines and on bare metal nodes. In addition to running standard benchmarks such as IOZone to check the sanity of our installation, we have run I/O intensive tests using physics-analysis applications. This paper presents how the storage solutions perform in a variety of realistic use cases of scientific computing. One interesting difference among the storage systems tested is found in a decrease in total read throughput with increasing number of client processes, which occurs in some implementations but not others.
Calcitonin (1981)

THE calcium-lowering and phosphate-lowering hormone calcitonin was discovered by Copp et al. in 1962,1 and it was soon viewed as a major calcium-regulating factor, along with parathyroid hormone (PTH) and vitamin D.2 However, the lack of clearly definable syndromes of calcitonin excess or deficiency led to suggestions that calcitonin is a vestigial hormone in human beings. Some even called it a "hormone in search of a function," and despite nearly 20 years of active investigation the exact role of calcitonin in human physiology remains controversial. The hormone has nonetheless acquired a secure place in the treatment of Paget's disease of . . .
Triptans to Calcitonin Gene‐Related Peptide Modulators – Small Molecules to Antibodies – the Evolution of a New Migraine Drug Class (2017)

Small-molecule CGRP receptor antagonists have shown efficacy, acutely and prophylactically, in randomized placebo clinical trials, giving pharmacological support for the important role of CGRP in migraine pain, and supporting CGRP modulation as a new therapeutic option. A CGRP receptor PET ligand (11C-MK-4262) was used to demonstrate that the mode of action of small molecule CGRP receptor antagonists was peripheral in origin, as there was no brain CGRP receptor target engagement at clinically effective anti-migraine doses. The knowledge that occupancy of peripheral sites could deliver clinical efficacy gave impetus to the development of long-acting biologic approaches to CGRP modulation for the prevention of migraine, through neutralizing antibody approaches to the CGRP peptide itself or to antibody blockade of the CGRP receptor. These biologic approaches are currently the subject of intensive clinical investigations, and are showing efficacy consistently in frequent episodic and chronic migraine multi-center clinical trials.
Tantalum as a diffusion barrier between copper and silicon: Failure mechanism and effect of nitrogen additions (1992)

The interaction of Cu with Si separated by thin (50 nm) layers of tantalum, Ta2N, and a nitrogen alloy of Ta has been investigated to determine the factors that affect the success of these materials as diffusion barriers to copper. Intermixing in these films was followed as a function of annealing temperature by in situ resistance measurements, Rutherford backscattering spectra, scanning electron microscopy, and cross-section transmission electron microscopy. Ta prevents Cu-silicon interaction up to 550 °C for 30 min in flowing purified He. At higher temperatures, copper penetration results in the formation of η″-Cu3Si precipitates at the Ta-Si interface. Local defect sites appear on the surface of the sample in the early stages of this reaction. The Ta subsequently reacts with the substrate at 650 °C to form a planar hexagonal-TaSi2 layer. Ta silicide formation, which does not occur until 700 °C in a Ta-Si binary reaction couple, is accelerated by the presence of Cu. Nitrogen-alloyed Ta is a very similar diffusion barrier to Ta. It was found that Ta2N is a more effective barrier to copper penetration, preventing Cu reaction with the substrate for temperatures up to at least 650 °C for 30 min. In this case, local Cu-Si reaction occurs along with the formation of a uniform Ta5Si3 layer at the Ta2N-Si interface.
Self-reported vs. actual use of medications in chronic pain patients (1982)

Inappropriate or excessive medication use is a commonly observed problem among patients with chronic pain. Comparing patients' self-reported drug use with actual observed drug use, this study examines the incidence, nature and magnitude of drug utilization in a selected population of pain patients and evaluates the reliability of patient estimates of their own drug use. The data support the clinical observation that patients with chronic pain tend to underestimate their medication use. This tendency is greater for narcotic analgesics than for a variety of other medications taken for pain and is greater for women than men.