gebhart/patrepeval huggingface dataset:
A 1536-Well Quantitative High-Throughput Screen to Identify Compounds Targeting Cancer Stem Cells (2012)

Tumor cell subpopulations called cancer stem cells (CSCs) or tumor-initiating cells (TICs) have self-renewal potential and are thought to drive metastasis and tumor formation. Data suggest that these cells are resistant to current chemotherapy and radiation therapy treatments, leading to cancer recurrence. Therefore, finding new drugs and/or drug combinations that cause death of both the differentiated tumor cells as well as CSC populations is a critical unmet medical need. Here, we describe how cancer-derived CSCs are generated from cancer cell lines using stem cell growth media and nonadherent conditions in quantities that enable high-throughput screening (HTS). A cell growth assay in a 1536-well microplate format was developed with these CSCs and used to screen a focused collection of oncology drugs and clinical candidates to find compounds that are cytotoxic against these highly aggressive cells. A hit selection process that included potency and efficacy measurements during the primary screen allowed us to efficiently identify compounds with potent cytotoxic effects against spheroid-derived CSCs. Overall, this research demonstrates one of the first miniaturized HTS assays using CSCs. The procedures described here should enable further testing of the effect of compounds on CSCs and help determine which pathways need to be targeted to kill them.
Histone H1 Phosphorylation by Cdk2 Selectively Modulates Mouse Mammary Tumor Virus Transcription through Chromatin Remodeling (2001)

Transcriptional activation of the mouse mammary tumor virus (MMTV) promoter by ligand-bound glucocorticoid receptor (GR) is transient. Previously, we demonstrated that prolonged hormone exposure results in displacement of the transcription factor nuclear factor 1 (NF1) and the basal transcription complex from the promoter, the dephosphorylation of histone H1, and the establishment of a repressive chromatin structure. We have explored the mechanistic link between histone H1 dephosphorylation and silencing of the MMTV promoter by describing the putative kinase responsible for H1 phosphorylation. Both in vitro kinase assays and in vivo protein expression studies suggest that in hormone-treated cells the ability of cdk2 to phosphorylate histone H1 is decreased and the cdk2 inhibitory p21 protein level is increased. To address the role of cdk2 and histone H1 dephosphorylation in the silencing of the MMTV promoter, we used potent cdk2 inhibitors, Roscovitine and CVT-313, to generate an MMTV promoter which is associated predominantly with the dephosphorylated form of histone H1. Both Roscovitine and CVT-313 block phosphorylation of histone H1 and, under these conditions, the GR is unable to remodel chromatin, recruit transcription factors to the promoter, or stimulate MMTV mRNA accumulation. These results suggest a model where cdk2-directed histone H1 phosphorylation is a necessary condition to permit GR-mediated chromatin remodeling and activation of the MMTV promoter in vivo.
Antigenicity of Alum and Aqueous Adenovirus Hexon Antigen Vaccines in Man (1971)

Abstract The availability of similarly prepared hexon antigen vaccines of three different serotypes of adenovirus (types 1, 2 and 5) provided the opportunity to systematically examine the responses in man to several variables of subunit vaccine and vaccination. Each of the vaccines exhibited differing antigenicity for guinea pigs and was available as an aqueous and an adjuvant preparation. In addition to examining the effect of these variables of the vaccine, the effect of one and two injections and route of inoculation were also examined. Recent studies with diphtheria toxoid in aqueous and adjuvant form have suggested that the physical state of antigen is of paramount importance for development of 11S IgA secretory antibody (1). In those studies, the aqueous diphtheria toxoid preparation stimulated secretory antibody following topical as well as parenteral administration. However, when adjuvant vaccine was given parenterally, volunteers developed high serum antibody titers but no 11S IgA secretory antibody and when given topically this vaccine was apparently non-antigenic. In view of these findings and those in recent studies which suggest that 11S IgA secretory antibody is of primary importance for prevention of infection with several respiratory viruses (2–4), we examined the antibody response to the type 5 antigen preparations given topically and parenterally.
Current and future antimicrobial treatment of gonorrhoea – the rapidly evolving Neisseria gonorrhoeae continues to challenge (2015)

Neisseria gonorrhoeae has developed antimicrobial resistance (AMR) to all drugs previously and currently recommended for empirical monotherapy of gonorrhoea. In vitro resistance, including high-level, to the last option ceftriaxone and sporadic failures to treat pharyngeal gonorrhoea with ceftriaxone have emerged. In response, empirical dual antimicrobial therapy (ceftriaxone 250-1000 mg plus azithromycin 1-2 g) has been introduced in several particularly high-income regions or countries. These treatment regimens appear currently effective and should be considered in all settings where local quality assured AMR data do not support other therapeutic options. However, the dual antimicrobial regimens, implemented in limited geographic regions, will not entirely prevent resistance emergence and, unfortunately, most likely it is only a matter of when, and not if, treatment failures with also these dual antimicrobial regimens will emerge. Accordingly, novel affordable antimicrobials for monotherapy or at least inclusion in new dual treatment regimens, which might need to be considered for all newly developed antimicrobials, are essential. Several of the recently developed antimicrobials deserve increased attention for potential future treatment of gonorrhoea. In vitro activity studies examining collections of geographically, temporally and genetically diverse gonococcal isolates, including multidrug-resistant strains particularly with resistance to ceftriaxone and azithromycin, are important. Furthermore, understanding of effects and biological fitness of current and emerging (in vitro induced/selected and in vivo emerged) genetic resistance mechanisms for these antimicrobials, prediction of resistance emergence, time-kill curve analysis to evaluate antibacterial activity, appropriate mice experiments, and correlates between genetic and phenotypic laboratory parameters, and clinical treatment outcomes, would also be valuable. Subsequently, appropriately designed, randomized controlled clinical trials evaluating efficacy, ideal dose, toxicity, adverse effects, cost, and pharmacokinetic/pharmacodynamics data for anogenital and, importantly, also pharyngeal gonorrhoea, i.e. because treatment failures initially emerge at this anatomical site. Finally, in the future treatment at first health care visit will ideally be individually-tailored, i.e. by novel rapid phenotypic AMR tests and/or genetic point of care AMR tests, including detection of gonococci, which will improve the management and public health control of gonorrhoea and AMR. Nevertheless, now is certainly the right time to readdress the challenges of developing a gonococcal vaccine.
The Gator Tech Smart House (2009)

In this paper, we describe the Gator Tech Smart House (GTSH), an assistive environment for independence and wellbeing, with focus on the elderly population. We give a quick overview of the GTSH and its services before presenting our experience and some of the lessons we learnt in this real world deployment project. We present the Atlas architecture -- a key enabling technology for the automatic integration of devices and sensors and show how can Atlas be used to develop smart environments without requiring a team of engineers or system integrators. Finally, we discuss ongoing related Atlas developments.
Inhibition of leukocyte locomotion by hyaluronic acid (1981)

The effect of hyaluronate on neutrophil motility in vitro was studied by the micropore filter technique and by direct visual analysis of the locomotion of neutrophils on glass. Both directed and random locomotion of neutrophils was inhibited by physiological concentrations (0.5-6.0 mg ml(-1)) of hyaluronate in a dose- and molecular weight-dependent manner. Inhibition of cell movement was more pronounced for high molecular weight chemoattractants such as casein than for small chemotactic peptides such as f-Met-Leu-Phe. Chemotactic factor gradient formation in filter chambers was profoundly retarded by hyaluronate, which may partly explain the inhibitory effects of hyaluronate on directed neutrophil locomotion. In addition, hyaluronate inhibited the binding of chemotactic factor to the neutrophil surface. This effect, together with a reduction in cell-to-substratum adhesion, may provide an additional explanation for hyaluronate-induced inhibition of random neutrophil locomotion. Inhibition of locomotion by hyaluronate was easily reversed by washing the cells free of hyaluronate; thus competition by hyaluronate for cell-surface binding sites is unlikely, and physical effects such as steric exclusion or molecular sieving by the large hyaluronate polymer provide the most probable explanations of its inhibitory effect on cell locomotion. Since hyaluronate is a major constituent of tissue matrices, these results draw attention to the importance of the extracellular environment in regulating inflammatory cell movement in vivo.
A One-Step, Solvothermal Reduction Method for Producing Reduced Graphene Oxide Dispersions in Organic Solvents (2010)

Refluxing graphene oxide (GO) in N-methyl-2-pyrrolidinone (NMP) results in deoxygenation and reduction to yield a stable colloidal dispersion. The solvothermal reduction is accompanied by a color change from light brown to black. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) images of the product confirm the presence of single sheets of the solvothermally reduced graphene oxide (SRGO). X-ray photoelectron spectroscopy (XPS) of SRGO indicates a significant increase in intensity of the C=C bond character, while the oxygen content decreases markedly after the reduction is complete. X-ray diffraction analysis of SRGO shows a single broad peak at 26.24 degrees 2theta (3.4 A), confirming the presence of graphitic stacking of reduced sheets. SRGO sheets are redispersible in a variety of organic solvents, which may hold promise as an acceptor material for bulk heterojunction photovoltaic cells, or electromagnetic interference shielding applications.
A 11-15 GHz CMOS +2 frequency divider for broad-band I/Q generation (2005)

This paper presents a 0.13 /spl mu/m CMOS frequency divider for I/Q generation. To achieve a wide locking range, a novel topology based on two stages injection-locking ring oscillator is adopted. This architecture can reach a larger input frequency range and better phase accuracy with respect to injection-locking LC oscillators, because of the smoother slope of its phase-frequency plot. Post layout simulations show that the circuit is able to divide an input signal spanning from 6 to 24 GHz, although the available tuning range of the signal source (integrated VCO) limited the experimental verification to the interval 11-15 GHz, with a consequent measured 31% locking range. A single divider dissipates 3 mA from 1.2 V power supply.
Comparison of Two-Dimensional Power and Phase Spectra Generated from Sample Modulation Step-Scan FT-IR Experiments (1994)

In the past fifteen years, sample modulation infrared spectroscopy has been introduced for the analysis of dynamic processes. Sample modulation measurements were initially restricted to a few custom-built dispersive instruments, but the recent introduction of commercial step-scan Fourier transform infrared (FT-IR) spectrometers has made dynamic infrared spectrometry widely practical.
Blacks and the Draft (1971)

Since 1917, nearly two million blacks have been drafted into the Armed Forces of the United States. Due to the restrictions placed on black enlistments prior to 1948, these draftees comprise the great majority of black servicemen in this century. Numerous studies have examined what happened to blacks once they entered the Armed Forces, but no one has yet seriously looked at the process by which Afro-Americans were selected for military service. The operation of the draft has involved both the Selective Service System and the various branches of the armed forces, particularly the Army. None of these institutions has ever been free of racism, and blacks have never received equal treatment in the draft. The selection of black draftees can be viewed as an example of institutional racism. However, the pattern of racism changed from World War I to World War II and has changed again during the Vietnam War. By tracing the history of institutional racism in the draft, it is possible to observe both the racist manner in which America chooses men for military duty and the ambivalent attitude of white Americans toward black soldiers.
Photochemical Generation and the Reactivity of<i>o</i>-Naphthoquinone Methides in Aqueous Solutions (2009)

Irradiation of 3-hydroxy-2-naphthalenemethanol (3a) and 2-hydroxy-1-naphthalenemethanol (4a) results in efficient (Phi(254) = 0.17 and 0.20) dehydration and the formation of isomeric naphthoquinone methides, 2,3-naphthoquinone-3-methide (1) and 1,2-naphthoquinone-1-methide (2), respectively. In aqueous solution, naphthoquinone methides 1 and 2 undergo rapid hydration to regenerate starting materials (tau(H2O) (1) = 7.4 ms and tau(H2O) (2) = 4.5 ms at 25 degrees C). The hydration reaction is strongly catalyzed by the hydroxide ion but shows acid catalysis only at pH < 1. Reactive intermediates 1 and 2 can be intercepted by other nucleophiles, such as the azide ion (k(N3)(1) = 2.0 x 10(4) M(-1) s(-1) and k(N3)(2) = 3.0 x 10(4) M(-1) s(-1)) or thiol (k(SH)(1) = 2.2 x 10(5) M(-1) s(-1) and k(SH)(2) = 3.3 x 10(5) M(-1) s(-1)). Ethyl vinyl ether readily reacts with 1 and 2 (k(DA)(1) = 4.1 x 10(4) M(-1) s(-1) and k(DA)(2) = 6.0 x 10(4) M(-1) s(-1)) to produce Diels-Alder adducts in excellent yield. o-Naphthoquinone methides 1 and 2 were also generated by photolysis of 3-ethoxymethyl- (3b) and 1-(ethoxymethyl)-2-naphthols (4b), as well as from (2-hydroxy-3-naphthyl)methyl- (3c) and [(2-hydroxy-1-naphthyl)methyl] trimethylammonium iodides (4c). Laser flash photolysis of 3a,b and 4a,b allows the detection of short-lived (tau(25 degrees C) approximately 12 micros) precursors of naphthoquinone methides 1 and 2. On the basis of the precursor reactivity and the results of DFT calculations, 2H-naphthoxete structure was assigned to these species.
Efficient suffix trees on secondary storage (1996)

We present a new representation for suffix trees, a data structure used in full text searching, that uses little more storage than the log n bits per index point required to store the list of index points. We also show algorithms for maintaining the structure on secondary storage in such a way that we minimize the number of disk accesses while searching and we can efficiently handle changes to the text. Using this new representation, suffix trees are competitive in terms of space with, and actually offer significantly better performance than, existing methods for full text searching. While we present new algorithms and data structures in this paper, the emphasis is on practical searching methods that have been empirically verified against real data.
Growth Of Diamond Films By Hot Filament Chemical Vapor Deposition (1989)

Results of research on diamond films grown by the hot filament chemical vapor deposition process are discussed. The parameters for film deposition have been surveyed and the conditions for routine and reproducible film formation established for our deposition system. These were: 800°C substrate temperature, 52-78 sccm flow rate, 5x103 Pa deposition pressure and 99.5% H2, 0.5% CH4 gas composition. Characterization of the deposited films has been accomplished with scanning electron microscopy (SEM), x-ray diffraction (XRD), Auger electron spectroscopy (AES), electron energy loss spectroscopy (EELS) and Raman spectroscopy; and the presence of the diamond phase was verified. Initial depositions on Si and Al203 substrates resulted in individual diamond particles showing the distinct diamond morphology. These particles, when examined by Raman microprobe spectroscopy, displayed the diamond spectra. Subsequently, continuous diamond films were formed after pretreating the substrates by rubbing with 1 pm diamond abrasive before deposition. Films, all shown to be diamond, grown on fused silica, polycrystalline SiC and different orientations of single crystal Si (all pretreated), exhibit very similar surface topography and x-ray diffraction patterns. Additionally, x-ray diffraction shows no preferred orientation in the films. Mechanical surface measurements on a 5 pm thick film grown on Si show that the films possess an average surface roughness of 0.4 μm and a peak-to-valley roughness of 2.5 μm. Films deposited on optically clear fused silica substrates could be seen to be water white, suggesting no significant optical absorption. Considerable optical scatter, however, is present due to the roughness of the film surface. Deposition rates were of the order of 0.1 μm/hr, with the fastest apparent growth occurring on pretreated polycrystalline SiC substrates.
Multiphoton plasmon-resonance microscopy (2003)

A novel method for detection of noble-metal nanoparticles by their nonlinear optical properties is presented and applied for specific labeling of cellular organelles. When illuminated by laser light in resonance with their plasmon frequency these nanoparticles generate an enhanced multiphoton signal. This enhanced signal is measured to obtain a depth-resolved image in a laser scanning microscope setup. Plasmon-resonance images of both live and fixed cells, showing specific labeling of cellular organelles and membranes, either by two-photon autofluorescence or by third-harmonic generation, are presented.
Adsorption of <i>Clostridium thermocellum</i> cellulases onto pretreated mixed hardwood, avicel, and lignin (1993)

Adsorption of Avicel-hydrolyzing activity was examined with respect to: mixed hardwood flour pretreated with 1% sulfuric acid for 9 s at 220 degrees C (PTW220), lignin prepared from PTW220 by either acid or enzymatic hydrolysis, and Avicel. Experiments were conducted at 60 degrees C for all materials, and also at 25 degrees C for PTW220. Based on transient adsorption results and reaction rates, times were selected at which to characterize adsorption at 60 degrees C as follows: PTW220, 1 min; lignin, 30 min; and Avicel, 45 min. Similar results were obtained for adsorption of cellulase activity to PTW220 at 25 and 60 degrees C, and for lignin prepared by enzymatic and acid hydrolysis. For all materials, adsorption was described well by a Langmuir equation, although the reversibility of adsorption was not investigated. Langmuir affinity constants (L/g) were: PTW220, 109; lignin, 17.9; Avicel, 4.3; cellulose from PTW220, > or =187. Langmuir capacity constants were 760 for PTW220 and 42 for Avicel; the cellulase binding capacity of lignin appeared to be very high under the conditions examined, and could not be determined. At low and moderate cellulase loadings at least, the majority of cellulase activity adsorbed to PTW220 is bound to the cellulosic component. The results indicate that PTW220, and its cellulose component in particular, differ radically from Avicel with respect to adsorption. Avicel-hydrolyzing activity and CMC-hydrolyzing activities were found to bind to Avicel with a constant ratio of essentially one, consistent with adsorption of a multi-activity complex.
Boron diffusion within TaSi2 /poly-Si gates (1989)

The redistribution of boron implanted into TaSi2 /poly-Si gates after high temperature anneals has been investigated as a function of the implantation dose and energy as well as the implantation scheme, i.e., boron implantation either into the silicide or into the poly-Si prior to TaSi2 deposition. Implantation and diffusion profiles were obtained by means of secondary ion mass spectrometry whereas the electrical characterization of the resulting structures was performed using high-frequency capacitance–voltage measurements. The results indicate that boron can easily diffuse from TaSi2 into poly-Si and vice versa at 900 °C. Independent of the implantation scheme, the boron concentration within poly-Si was found to saturate at ∼1×1019 at/cm3 for boron doses &gt;5×1014 at/cm2. The excess of boron always accumulates within the silicide. The solubility limit of boron within TaSi2 was estimated to be &gt;3.5×1020 at/cm3. Boron concentrations of ∼1×1019 at/cm3 within poly-Si were found to be sufficient to realize p+ -polycide gates with stable and reproducible threshold voltages similar to p+ -poly-Si gates. The observed boron redistribution behavior within the polycide is discussed in terms of combined lattice and grain boundary diffusion as well as grain boundary segregation.
Recurrent Temporal Sparse Autoencoder for attention-based action recognition (2016)

Visual context is fundamental to understand human actions in videos. However, to efficiently employ temporal context information presents an enormous challenge to this area. Two main problems are long-standing: (1) video frames are redundant while discriminative information is sparse; (2) large amount of interference information is mixed in frame sequences. These factors results in redundant computation and recognition failures. In this paper, we propose a learnable temporal attention mechanism to automatically select important time points from action sequences. We design an unsupervised Recurrent Temporal Sparse Autoencoder (RTSAE) network, which learns to extract sparse key-frames to sharpen discriminative yet to retain descriptive capability, as well to shield interfere information. By applying this technique to a recent proposed action recognition model Adaptive Recurrent-convolutional Hybrid network (ARCH), we significantly improve its performance in both speed and accuracy. Experiments demonstrate that, with the help of the RTSAE, ARCH outperforms most state-of-the-art methods on UCF101 and HMDB51 datasets.
Expression of Randomly Integrated Single Complete Copy Transgenes Does not Vary in Arabidopsis thaliana (2005)

The high variability of transgene expression is frequently observed in independent transgenic lines. Variability of transgene expression has been attributed to several factors, including differences in chromosome position, repeat sequences and copy number. The eukaryotic genome, with a heterogeneous chromatin structure, is not homogeneous for transcriptional activity. Chromatin structure at the site of integration can affect transgene expression; this phenomenon is called the position effect. In this study, we investigated whether position effects confer variability of transgene expression in Arabidopsis thaliana. We analyzed the expression of randomly integrated single 'complete' (intact, non-truncated, non-rearranged) copy transgenes in A. thaliana. Ten independent lines containing single complete copies of the transgene located at different chromosome positions showed very similar levels of transgene expression, and variability of transgene expression was not observed. This result indicates that position effects may not generally be a major cause of variability of transgene expression in A. thaliana.