gebhart/patrepeval huggingface dataset:
Holographic Optical Elements (1975)

This article is a survey of the characteristics, technology and applications of Holographic Optical Elements (HOEs), considered as general elements in an optical system. HOEs function by diffraction of light from a generalized grating structure with nonuniform groove spacing. HOEs provide a system of thin film optics. They are capable of unique system functions and configurations, show a rapid variation of optical power and image characteristics with wavelength, have relatively large amounts of astigmatism and coma, and require special consideration of optical efficiency during system design. Comparison of the aberrations of specific, f/3.3 elements shows that the on-axis HOE and the conventional glass lens element have similar aberration levels, while the off-axis HOE has four times as much astigmatism and twice as much coma. We show that these grating aberrations, which appear for conjugate points that are different from the HOE construction points, are proportional to the average surface grating spatial frequency of an off-axis HOE. HOE technology is similar to conventional optics technology, but is less developed. The relative complexity of optical systems with HOEs, and the lack of a suitable aberration theory, produce a relince on computer-based raytracing for system design and development. We give the basic raytracing equations and discuss the special requirements for hologram recording appara-tus and materials. In applications, HOEs will usually provide unique capabilities rather than replace conventional elements, and will usually operate over narrow spectral bandwidths. The use of HOEs in several types of laser optical systems, and in visual displays, appears to be not only advantageous, but also technically and economically feasible.
Rapid Kinetics of tBid-induced Cytochrome c and Smac/DIABLO Release and Mitochondrial Depolarization (2002)

Cleavage of Bid has been shown to promote apoptosis by inducing mitochondrial membrane permeabilization with the resultant release of apoptosis-inducing proteins from the intermembrane space into the cytosol. However, direct visualization of the Bid-induced release of various proteins from the highly compartmentalized intermembrane space and the changes in the mitochondrial metabolic machinery remain elusive. Using green fluorescent protein fusion proteins and immunostaining in individual permeabilized HepG2 cells, first we demonstrated that truncated Bid (15.5-kDa C-terminal fragment, tBid) evoked a rapid and essentially complete release of cytochrome c and Smac/DIABLO from every mitochondrion. To establish at a resolution of seconds the kinetics of tBid-induced cytochrome c and Smac/DIABLO release and depolarization, we monitored the mitochondrial membrane potential (DeltaPsi(m)) fluorimetrically in permeabilized cells and applied a rapid filtration method to obtain cytosolic fractions for Western blotting. We found that subnanomolar doses of tBid were sufficient to evoke cytochrome c release and mitochondrial depolarization, whereas full-length Bid was 100-fold less effective. Bcl-x(L) prevented tBid-induced cytochrome c release and depolarization. In response to 2.5 nm tBid, cytochrome c release started after a 10 s delay, displayed rapid progression, and was complete at 50-70 s. Release of Smac/DIABLO was synchronized with cytochrome c release, whereas the loss of DeltaPsi(m) lagged slightly behind cytochrome c release. Furthermore, tBid-induced cytochrome c release was insensitive to changes in substrate composition, but tBid-induced depolarization did not occur in the presence of extramitochondrial ATP supply. Thus, tBid-induced permeabilization of the outer membrane permits rapid release of cytochrome c and Smac/DIABLO from all domains of the intermembrane space. The tBid-induced loss of DeltaPsi(m) occurs after cytochrome c release and reflects impairment of oxidative metabolism.
Pathogenesis of Pulmonary Aspergillosis. Granulocytopenia Versus Cyclosporine and Methylprednisolone-Induced Immunosuppression (1995)

Patients with chemotherapy-induced granulocytopenia for neoplastic diseases and those receiving cyclosporin A plus corticosteroids for prevention and treatment of organ transplant rejection are two immunologically distinct patient populations with high risks for development of invasive pulmonary aspergillosis. In order to compare the pathogenesis of aspergillosis in these two high-risk populations and to further characterize the role of cyclosporin A in development of pulmonary aspergillosis, we studied the patterns of infection and inflammation in two clinically applicable rabbit models of invasive pulmonary aspergillosis. There were striking differences in the patterns of infection and inflammation of invasive pulmonary aspergillosis according to the type of underlying immune defect. Among rabbits challenged with the same intratracheal inoculum, there was a 100% mortality for invasive pulmonary aspergillosis in profoundly granulocytopenic rabbits in comparison with a 100% mortality for invasive pulmonary aspergillosis in profoundly granulocytopenic rabbits in comparison with a 100% survival in rabbits immunosuppressed with cyclosporin A plus methylprednisolone (CsA+MP). Lesions of pulmonary aspergillosis in granulocytopenic rabbits consisted predominantly of coagulative necrosis, intraalveolar hemorrhage, and scant mononuclear inflammatory infiltrate. By comparison, pulmonary foci in rabbits immunosuppressed by CsA+MP consisted mainly of neutrophilic and monocytic infiltrates, inflammatory necrosis, and scant intraalveolar hemorrhage. There was extensive infiltration by hyphae with angioinvasion in granulocytopenic rabbits, whereas conidia in various stages of germination predominated in CsA+MP treated animals in which there was a paucity of hyphae or angioinvasion. Extrapulmonary disease predominated in granulocytopenic rabbits. Methylprednisolone was the major immunosuppressive drug in rabbits treated with CsA+MP. Cyclosporin A alone did not increase the progression of pulmonary aspergillosis and did so only when used chronically with methylprednisolone.
Rational Synthesis of Meso-Substituted Chlorin Building Blocks (2000)

Chlorins provide the basis for plant photosynthesis, but synthetic model systems have generally employed porphyrins as surrogates due to the unavailability of suitable chlorin building blocks. We have adapted a route pioneered by Battersby to gain access to chlorins that bear two meso substituents, a geminal dimethyl group to lock in the chlorin hydrogenation level, and no flanking meso and beta substituents. The synthesis involves convergent joining of an Eastern half and a Western half. A 3,3-dimethyl-2,3-dihydrodipyrrin (Western half) was synthesized in four steps from pyrrole-2-carboxaldehyde. A bromodipyrromethane carbinol (Eastern half) was prepared by sequential acylation and bromination of a 5-substituted dipyrromethane followed by reduction. Chlorin formation is achieved by a two-flask process of acid-catalyzed condensation followed by metal-mediated oxidative cyclization. The latter reaction has heretofore been performed with copper templates. Investigation of conditions for this multistep process led to copper-free conditions (zinc acetate, AgIO(3), and piperidine in toluene at 80 degrees C for 2 h). The zinc chlorin was obtained in yields of approximately 10% and could be easily demetalated to give the corresponding free base chlorin. The synthetic process is compatible with a range of meso substituents (p-tolyl, mesityl, pentafluorophenyl, 4-[2-(trimethylsilyl)ethynyl]phenyl, 4-iodophenyl). Altogether four free base and four zinc chlorins have been prepared. The chlorins exhibit typical absorption spectra, fluorescence spectra, and fluorescence quantum yields. The ease of synthetic access, presence of appropriate substituents, and characteristic spectral features make these types of chlorins well suited for incorporation in synthetic model systems.
Frequent aberrant DNA methylation of ABCB1, FOXC1, PPP2R2B and PTEN in ductal carcinoma in situ and early invasive breast cancer (2010)

Quantitative methylation analysis identified ABCB1, FOXC1, PPP2R2B and PTEN as novel genes to be methylated in DCIS. In particular, FOXC1 showed a significant increase in the methylation frequency in invasive tumours. Low FOXC1 gene expression in both methylated and unmethylated DCIS and IDCs indicates that the loss of its expression is an early event during breast cancer progression.
Induction of Exosome Release in Primary B Cells Stimulated via CD40 and the IL-4 Receptor (2008)

Exosomes are lipid-bound nanovesicles formed by inward budding of the endosomal membrane and released following fusion of the endosomal limiting membrane with the plasma membrane. We show here that primary leukocytes do not release exosomes unless subjected to potent activation signals, such as cytokine or mitogen stimulation. In particular, high levels of exosomes were released when murine splenic B cells were stimulated via CD40 and the IL-4 receptor. This property was shared by B cells from different anatomic locations, as newly formed marginal zone and follicular B cells were capable of secreting exosomes upon CD40/IL-4 triggering. B cell exosomes expressed high levels of MHC class I, MHC class II, and CD45RA (B220), as well as components of the BCR complex, namely, surface Ig, CD19, and the tetraspanins CD9 and CD81. Ig on the plasma membrane of primary B cells was targeted to the exosome pathway, demonstrating a link between the BCR and this exocytic pathway. IgD and IgM were the predominant Ig isotypes associated with CD40/IL-4 elicited exosomes, though other isotypes (IgA, IgG1, IgG2a/2b, and IgG3) were also detected. Together, these results suggest that exosome release is not constitutive activity of B cells, but may be induced following cell: cell signaling.
Structure-Function relationships for the EGF/TGF-α family of mitogens (1994)

Epidermal growth factor (EGF) and transforming growth factor alpha (TGF-alpha) are ligands for the EGF-receptor and act as mitogens for a variety of tissues. TGF-alpha, in particular, has been implicated as an autocrine growth factor for several cancer cell lines. Over the last 10 years many groups have examined the structure-function relationships in EGF/TGF-alpha in attempts to develop antagonists or agonists. In this review the results of these studies are summarised and related to the three-dimensional structure of EGF/TGF-alpha. The difficulties associated with the purification and characterisation of analogues of EGF/TGF-alpha and with the biological assays are discussed. It is clear that these difficulties have, in some cases, led to apparently contradicting results. The available binding data indicate that the receptor interaction surface for EGF/TGF-alpha might encompass one complete side of the molecule with a few strong binding determinants, in particular Arg41 and Leu47. The arginine at position 41 is the most critical residue and its full hydrogen-bonding capacity is needed for strong binding of EGF/TGF-alpha to the EGF-receptor. As this side of the molecule consists of residues from both the N- and C-terminal domain, it seems unlikely that agonists or antagonists can be developed on the basis of short peptides taken from the primary sequence. This concept is supported by the available binding and activity data.
Ineffectiveness of Neurokinin-1 Antagonist in Acute Migraine (1997)

Lanepitant is a high-affinity, selective neurokinin-1 receptor (NK-1) and is effective in the dural inflammation model of acute migraine. Lanepitant 30, 80, and 240 mg given orally was evaluated in a double-blind, placebo-controlled crossover study to determine its effect in reducing migraine pain and severity of associated symptoms. Outpatients treated four migraine headaches of moderate or severe pain intensity with study drug according to a randomization schedule. They recorded their pain intensity and severity of migraine-associated symptoms at 30, 60, 90, and 120 min. Although 53 patients were randomly allocated to a treatment sequence, only 40 patients completed all treatments. There was no statistically significant difference in improvement in migraine pain at any time for any of the treatments. Additionally, there was no change in severity of migraine-associated symptoms associated with lanepitant therapy. No adverse events could be attributed to lanepitant. Lanepitant was ineffective orally in treating acute migraine in this trial. This may be due to poor bioavailability during a migraine attack. Alternatively, the neurogenic inflammation hypothesis may not apply to migraine.
Geometric invariance in computer vision (1992)

Part 1 Foundations: algebraic invariants - invariant theory and enumerative combinatorics of young tableaux, Shreeram S. Abhyankar, geometric interpretation of joint conic invariants, Joseph L. Mundy, et al, an experimental evaluation of projective invariants, Christopher Coelho, et al the projection of two non-coplanar conics, Stephen J. Maybank the non-existence of general-case view-invariants, J. Brian Burns, et al invariants of non-algebraic curves - noise resistant invariants of curves, Isaac Weiss, semi-differential invariants, Luc J. Van Gool, et al, projective invariants for curves in two and three dimensions, Michael H. Brill, et al, numerical evaluation of differential and semi-differential invariants, Christopher Brown, recognizing general curved objects efficiently, Andrew Zisserman, et al fitting affine invariant conics to curves, Deepak Kapur and Joseph L. Mundy, projectively invariant decomposition of planar shapes, Stefan Carlsson invariants from multiple views - invariant linear methods in photogrammetry and model-matching, Eamon B. Barrett, et al semi-differential invariants for nonplanar curves, Luc J. Van Gool, et al disambiguating stereo matches with spatio-temporal surfaces, Olivier Faugeras and Theo Papadopoulo. Part 2 Applications: transformation invariant indexing, Haim J. Wolfson and Yehezkel Lamdan affine invariants for model-based recognition, John E. Hopcroft, et al object recognition based on moment (or algebraic) invariants, Gabriel Taubin and David B. Cooper fast recognition using algebraic invariants, Charles A. Rothwell, et al toward 3D curved object recognition from image contours, Jean Ponce and David J. Kriegman relative positioning with uncalibrated cameras, Roger Mohr, et al. Appendix: projective geometry for machine vision, Joseph L. Mundy and Andrew Zisserman.
Sites of interaction between rod G-protein alpha-subunit and cGMP-phosphodiesterase gamma-subunit. Implications for the phosphodiesterase activation mechanism. (1992)

In photoreceptor cells of vertebrates light activates a series of protein-protein interactions resulting in activation of a cGMP-phosphodiesterase (PDE). Interaction between the GTP-bound form of rod G-protein alpha-subunit (alpha t) and PDE inhibitory gamma-subunit (P gamma) is a key event for effector enzyme activation. This interaction has been studied using P gamma labeled with the fluorescent probe, lucifer yellow vinyl sulfone, at Cys-68 (P gamma LY) and sites of interaction on alpha t and P gamma have been investigated. Addition of alpha tGTP gamma S to P gamma LY produced a 3.2-fold increase in the fluorescence of P gamma LY. The Kd for alpha tGTP gamma S.P gamma LY interaction was 36 nM. Addition of 1 microM alpha tGDP had no effect, but in the presence of A1F4-, alpha tGDP increased P gamma LY fluorescence by 85%. When P gamma LY was reconstituted with P alpha beta to form fluorescent holo-PDE, alpha tGTP gamma S increased the fluorescence of holo-PDE with a K0.5 = 0.7 microM. Also, alpha tGTP gamma S stimulated the activity of this PDE over an identical range of concentrations with a similar K0.5 (0.6 microM). alpha tGTP gamma S enhanced the fluorescence of a COOH-terminal P gamma fragment, P gamma LY-46-87, as well (Kd = 1.5 microM). We demonstrate that an alpha t peptide, alpha t-293-314, which activated PDE (Rarick, H. M., Artemyev, N. O., and Hamm, H. E. (1992) Science 256, 1031-1033), mediates PDE activation by interacting with the P gamma-46-87 region. Peptide alpha t-293-314 bound to P gamma LY (K0.5 = 1.2 microM) as well as to the carboxyl-terminal P gamma fragment, P gamma LY-46-87 (K0.5 = 1.7 microM) as measured by fluorescence increase, while other alpha t peptides had no effect. A peptide from the P gamma central region, P gamma-24-46, blocked the interaction between alpha tGTP gamma S and P gamma LY. The Kd for alpha tGTP gamma S.P gamma-24-46 interaction was 0.7 microM. On the other hand, P gamma-24-46 had no effect on alpha t-293-314 interaction with P gamma LY. Our data suggest that there are at least two distinct sites of interaction between alpha tGTP gamma S and P gamma. The interaction between alpha t-293-314 and P gamma-46-87 is important for PDE activation.(ABSTRACT TRUNCATED AT 400 WORDS)
End-to-End Dense Video Captioning with Masked Transformer (2018)

Dense video captioning aims to generate text descriptions for all events in an untrimmed video. This involves both detecting and describing events. Therefore, all previous methods on dense video captioning tackle this problem by building two models, i.e. an event proposal and a captioning model, for these two sub-problems. The models are either trained separately or in alternation. This prevents direct influence of the language description to the event proposal, which is important for generating accurate descriptions. To address this problem, we propose an end-to-end transformer model for dense video captioning. The encoder encodes the video into appropriate representations. The proposal decoder decodes from the encoding with different anchors to form video event proposals. The captioning decoder employs a masking network to restrict its attention to the proposal event over the encoding feature. This masking network converts the event proposal to a differentiable mask, which ensures the consistency between the proposal and captioning during training. In addition, our model employs a self-attention mechanism, which enables the use of efficient non-recurrent structure during encoding and leads to performance improvements. We demonstrate the effectiveness of this end-to-end model on ActivityNet Captions and YouCookII datasets, where we achieved 10.12 and 6.58 METEOR score, respectively.
Redesigning nucleic acids (1998)

A research program has applied the tools of synthetic organic chemistry to systematically modify the structure of DNA and RNA oligonucleotides to learn more about the chemical principles underlying their ability to store and transmit genetic information. Oligonucleotides (as opposed to nucleosides) have long been overlooked by synthetic organic chemists as targets for structural modification. Synthetic chemistry has now yielded oligonucleotides with 12 replicatable letters, modified backbones, and new insight into why Nature chose the oligonucleotide structures that she did.
Herpes simplex virus type 1 ICP27 deletion mutants exhibit altered patterns of transcription and are DNA deficient (1989)

Infected cell polypeptide 27 (ICP27, alpha 27, IE63) is the 63-kilodalton product of an immediate-early gene of herpes simplex virus. Functional analysis of temperature-sensitive mutants in herpes simplex virus type 1 ICP27 demonstrated that this protein plays an essential role in virus replication (W. R. Sacks, C. C. Greene, D. P. Aschman, and P. A. Schaffer, J. Virol. 55:796-805, 1985). Because the temperature-sensitive forms of ICP27 induced by the mutants affected gene expression to differing degrees, these mutants were not suitable for establishing the ICP27 null phenotype. For this purpose we generated deletion mutants in ICP27--3dl1.2 and 5dl1.2--lacking the transcriptional start site as well as portions of the promoter and coding sequences of the gene. These mutants failed to specify ICP27-specific transcripts and proteins and were replication incompetent. The mutants induced the synthesis of greatly reduced levels of viral DNA (18% of wild-type levels) and were characterized by the overexpression of early proteins, reduced levels of gamma 1 proteins, and the absence of detectable gamma 2 proteins. The alterations in viral protein synthesis appeared to occur at the level of transcription. The phenotypic properties of the mutants were consistent with the results of transient expression assays demonstrating that ICP27 acts to down-regulate transcription of early genes and to further up-regulate transcription of late genes whose expression is induced by ICP0 and ICP4. Because ICP27 is not thought to be directly involved in viral DNA synthesis, it is likely that the reduced levels of viral DNA characteristic of deletion mutant-infected cells is a consequence of aberrant regulation of certain early genes whose products are involved in viral DNA synthesis and late genes whose products are required to stabilize viral DNA once synthesized. Taken together, these findings suggest an essential role for ICP27 in the modulation of early and late gene expression at the transcriptional level.
Linewidth reduction in DFB laser by detuning effect (1987)

The detuning effect on the spectral linewidth in the DFB laser has been investigated. When we set the lasing wavelength of the DFB laser at the shorter side of the gain peak by 10 nm, a reduction in spectral linewidth of 50% was obtained experimentally. This result agreed with the theoretical prediction.
The FIBROID Registry (2005)

Uterine embolization results in substantial symptom improvement for most patients, with hysterectomy required in only 2.9% of patients in the first 12 months after therapy.
Phase I Safety and Pharmacokinetic Study of Bavituximab, a Chimeric Phosphatidylserine-Targeting Monoclonal Antibody, in Patients with Advanced Solid Tumors (2011)

Bavituximab was well tolerated at doses ranging up to 3 mg/kg weekly. Pharmacokinetic studies support a weekly dosing regimen. Additional phase I and II clinical trials are in progress to investigate bavituximab in combination with chemotherapy and other molecularly targeted agents.
Targeting epidermal growth factor receptor in head and neck cancer (2002)

It is well known that growth factors play an important role in normal cell proliferation by means of stimulation of growth factor receptors located on the surface of cells. Tumor cells express high levels of growth factor receptors that can theoretically serve as therapeutic targets in cancer treatment. Tyrosine kinase (type 1) growth factor receptors include the family of erbB receptors. The most extensively studied receptor in the erbB family is the human epidermal growth factor receptor (EGFR), also known as erbB1. Studies have shown that overexpression of EGFR is involved in the development and progression of head and neck squamous cell carcinoma (HNSCC). Blocking this receptor in HNSCC cell lines and animal models inhibits tumor growth. Strategies have been developed to target EGFR, including monoclonal antibodies, tyrosine kinase-specific inhibitors, ligand-linked immunotoxins, and antisense approaches. Laboratory studies and clinical trials are under way to explore the safety and efficacy of these various approaches in a variety of cancers, including HNSCC. Preliminary results from early phase clinical trials are encouraging and may lead to the incorporation of these EGFR targeting strategies into the management of HNSCC.