gebhart/patrepeval huggingface dataset:
3'-Azido-3'-deoxythymidine (BW A509U): an antiviral agent that inhibits the infectivity and cytopathic effect of human T-lymphotropic virus type III/lymphadenopathy-associated virus in vitro. (1985)

The acquired immune deficiency syndrome (AIDS) is thought to result from infection of T cells by a pathogenic human retrovirus, human T-lymphotropic virus type III (HTLV-III) or lymphadenopathy-associated virus (LAV). In this report, we describe the antiviral effects of a thymidine analogue,3'-azido-3'-deoxythymidine (BW A509U), which, as a triphosphate, inhibits the reverse transcriptase of HTLV-III/LAV. This agent blocks the expression of the p24 gag protein of HTLV-III/LAV in H9 cells following exposure to virus. The drug also inhibits the cytopathic effect of HTLV-IIIB (a virus derived from a pool of American patients) and HTLV-III/RF-II (an isolate obtained from a Haitian patient that differs by about 20% in the amino acid sequence of the envelope gene from several isolates of HTLV-III/LAV, including HTLV-IIIB, analyzed so far). 3'-Azido-3'-deoxythymidine also completely blocks viral replication as assessed by reverse transcriptase production in normal human peripheral blood mononuclear cells exposed to HTLV-IIIB. Finally, at concentrations of 3'-azido-3'-deoxythymidine that block the in vitro infectivity and cytopathic effect of HTLV-IIIB, the in vitro immune functions of normal T cells remain basically intact.
Androgen-dependent hereditary mouse keratoconus: linkage to an MHC region. (2002)

SKC mouse keratoconus is a potential model for a subset of human keratoconus, which is a disease entity with heterogeneous pathogeneses. Alternatively, SKC mouse keratoconus could be a model for other human or mouse-specific keratopathies.
Whole-genome shotgun assembly and comparison of human genome assemblies (2004)

We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-sequencing 2-kbp, 10-kbp, and 50-kbp inserts from shotgun clone libraries. The quality-trimmed reads covered the genome 5.3 times, and the inserts from which pairs of reads were obtained covered the genome 39 times. With the nearly complete human DNA sequence [National Center for Biotechnology Information (NCBI) Build 34] now available, it is possible to directly assess the quality, accuracy, and completeness of WGSA and of the first reconstructions of the human genome reported in two landmark papers in February 2001 [Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) Science 291, 1304-1351; International Human Genome Sequencing Consortium (2001) Nature 409, 860-921]. The analysis of WGSA shows 97% order and orientation agreement with NCBI Build 34, where most of the 3% of sequence out of order is due to scaffold placement problems as opposed to assembly errors within the scaffolds themselves. In addition, WGSA fills some of the remaining gaps in NCBI Build 34. The early genome sequences all covered about the same amount of the genome, but they did so in different ways. The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats.
Managing server energy and operational costs in hosting centers (2005)

The growing cost of tuning and managing computer systems is leading to out-sourcing of commercial services to hosting centers. These centers provision thousands of dense servers within a relatively small real-estate in order to host the applications/services of different customers who may have been assured by a service-level agreement (SLA). Power consumption of these servers is becoming a serious concern in the design and operation of the hosting centers. The effects of high power consumption manifest not only in the costs spent in designing effective cooling systems to ward off the generated heat, but in the cost of electricity consumption itself. It is crucial to deploy power management strategies in these hosting centers to lower these costs towards enhancing profitability. At the same time, techniques for power management that include shutting down these servers and/or modulating their operational speed, can impact the ability of the hosting center to meet SLAs. In addition, repeated on-off cycles can increase the wear-and-tear of server components, incurring costs for their procurement and replacement. This paper presents a formalism to this problem, and proposes three new online solution strategies based on steady state queuing analysis, feedback control theory, and a hybrid mechanism borrowing ideas from these two. Using real web server traces, we show that these solutions are more adaptive to workload behavior when performing server provisioning and speed control than earlier heuristics towards minimizing operational costs while meeting the SLAs.
Isolation and Characterization of a Novel Ribosome-Inactivating Protein from Root Cultures of Pokeweed and Its Mechanism of Secretion from Roots (2002)

Ribosome-inactivating proteins are N-glycosidases that remove a specific adenine from the sarcin/ricin loop of the large rRNA, thus arresting protein synthesis at the translocation step. In the present study, a novel type I ribosome-inactivating protein, termed PAP-H, was purified from Agrobacterium rhizogenes-transformed hairy roots of pokeweed (Phytolacca americana). The protein was purified by anion- and cation-exchange chromatography. PAP-H has a molecular mass of 29.5 kD as detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and its isoelectric point was determined to be 7.8. Yeast (Saccharomyces cerevisiae) ribosomes incubated with PAP-H released the 360-nucleotide diagnostic fragment from the 26S rRNA upon aniline treatment, an indication of its ribosome-inactivating activity. Using immunofluorescence microscopy, PAP-H was found to be located in the cell walls of hairy roots and root border cells. PAP-H was determined to be constitutively secreted as part of the root exudates, with its secretion enhanced by a mechanism mediated by ethylene induction. Purified PAP-H did not show in vitro antifungal activity against soil-borne fungi. In contrast, root exudates containing PAP-H as well as additional chitinase, beta-1,3-glucanase, and protease activities did inhibit the growth of soil-borne fungi. We found that PAP-H depurinates fungal ribosomes in vitro and in vivo, suggesting an additive mechanism that enables PAP-H to penetrate fungal cells.
Viewpoint: Climate change and planning: carbon control and spatial regulation (2008)

After a decade of false starts, the goal of radically reducing emissions of greenhouse gases, and particularly carbon dioxide, is rising up the political agenda. The renewed urgency of the 'carbon control' agenda reflects a tipping point in political, public and media acceptance of the reality of global warming, its human causes, and the future economic and social costs of inaction. Political commitment to carbon control is also
Human trophoblast cell-surface antigens defined by monoclonal antibodies. (1981)

A series of monoclonal antibodies has been raised against the human choriocarcinoma cell-line, BeWo. Four antigens, Trop-1, -2, -3, and -4, are defined on normal and malignant trophoblast cells. Trop-1 and Trop-2 appear to be specifically expressed on syncytio- and cytotrophoblasts, whereas Trop-3 and Trop-4 are also detected on various tumor cell lines, normal lymphocytes, and monocytes. Anti-Trop-1 and anti-Trop-2 antibodies might prove useful for detection and isolation of fetal trophoblast cells circulating in pregnant women's blood and for diagnosis and therapy in patients having choriocarcinomas and other germ-cell neoplasms.
Inhibition of growth ofl-cystine crystals by N-acetyl-l-cysteine (2016)

N-Acetyl-L-cysteine, a thiol drug used commonly as an expectorant, was used to inhibit the growth of L-cystine crystals. Dual effects of a chemical decomposition reaction and crystallization inhibition ensure that N-acetyl-L-cysteine has an unusual inhibitory effect on the growth of L-cystine crystals, and could aid its development as a new drug for the treatment of L-cystine stones.
A Ras activation pathway dependent on Syk phosphorylation of protein kinase C (2003)

Protein kinase C (PKC) and Syk protein tyrosine kinase play critical roles in immune cell activation including that through the high-affinity IgE receptor, FcepsilonRI. Mechanisms by which PKC activation leads to the activation of Ras, a family of GTPases essential for immune cell activation, have been elusive. We present evidence that Tyr-662 and Tyr-658 of PKCbetaI and PKCalpha, respectively, are phosphorylated by Syk in the membrane compartment of FcepsilonRI-stimulated mast cells. These phosphorylations require prior PKC autophosphorylation of the adjacent serine residues (Ser-661 and Ser-657, respectively) and generate a binding site for the SH2 domain of the adaptor protein Grb-2. By recruiting the Grb-2/Sos complex to the plasma membrane, these conventional PKC isoforms contribute to the full activation of the Ras/extracellular signal-regulated kinase signaling pathway in FcepsilonRI-stimulated mast cells.
Crystal Structure of the Intrinsically Flexible Addiction Antidote MazE (2003)

A specific camel VHH (variable domain of dromedary heavy chain antibody) fragment was used to crystallize the intrinsically flexible addiction antidote MazE. Only 45% of the polypeptide chain is found ordered in the crystal. The MazE monomer consisting of two beta-hairpins connected by a short alpha-helix has no hydrophobic core on its own and represents only one half of a typical protein domain. A complete domain structure is formed by the association of two chains, creating a hydrophobic core between two four-stranded beta-sheets. This hydrophobic core consists exclusively of short aliphatic residues. The folded part of MazE contains a novel DNA binding motif. A model for DNA binding that is consistent with the available biochemical data is presented.
<title>Overlapped block motion compensation</title> (1992)

Block motion compensation is a critical component of most efficient video compression algorithms. Applications range from real-time low bit rate teleconferencing codecs to moderate and high bit-rate coding standards currently being considered for CD-ROM video storage and packet video. Recent research has suggested that blocking artifacts can be reduced by applying block motion compensation on overlapped blocks in image frames. In this paper, we formulate overlapped block motion compensation as an optimal linear estimator of pixel intensities given the neighboring block motion estimate in the frame. Applying this framework, we propose a procedure for designing optimal windows for overlapped block motion compensation. When applying block motion compensation with overlapped blocks, the optimal motion vector to apply at each block in an image depends on values of motion vectors in a non-causal neighborhood of that block. Thus, unlike for standard block-based compensation, optimal motion estimates cannot be computed with exhaustive search block- matching algorithms, even with the overlap window incorporated. Instead, we defined a simple iterative procedure for computing optimal motion estimates for overlapped block motion compensation. The performance gains achieved by both optimal motion estimation and optimal overlapped windows are demonstrated in simulations. Together, reductions of up to 30% in displaced frame difference energy are demonstrated compared with standard block motion compensation.
Regulation of Integrin Function by CD47 Ligands (2002)

We examined the regulation of alpha4beta1 integrin function in melanoma cells and T cells by ligands of CD47. A CD47 antibody (B6H12) that inhibited alphavbeta3-mediated adhesion of melanoma cells induced by CD47-binding peptides from thrombospondin-1 directly stimulated alpha4beta1-mediated adhesion of the same cells to vascular cell adhesion molecule-1 and N-terminal regions of thrombospondin-1 or thrombospondin-2. B6H12 also stimulated alpha4beta1- as well as alpha2beta1- and alpha5beta1-mediated adhesion of CD47-expressing T cells but not of CD47-deficient T cells. alpha4beta1 and CD47 co-purified as a detergent-stable complex on a CD47 antibody affinity column. CD47-binding peptides based on C-terminal sequences of thrombospondin-1 also specifically enhanced adhesion of melanoma cells and T cells to alpha4beta1 ligands. Unexpectedly, activation of alpha4beta1 function by the thrombospondin-1 CD47-binding peptides also occurred in CD47-deficient T cells. CD47-independent activation of alpha4beta1 required the Val-Val-Met (VVM) motif of the peptides and was sensitive to inhibition by pertussis toxin. These results indicate that activation of alpha4beta1 by the CD47 antibody B6H12 and by VVM peptides occurs by different mechanisms. The antibody directly activates a CD47-alpha4beta1 complex, whereas VVM peptides may target an unidentified Gi-linked receptor that regulates alpha4beta1.
A Gold Nanoparticle-Based Microfluidic Protein Chip for Tumor Markers (2009)

A cancer protein chip has been developed incorporating with signal amplification technology based on gold nanoparticles (AuNPs) and microfluidic technology. The chip was a reversed phase one that deposited the target proteins directly onto chip surface. At first, a tumor marker protein, carcinoma embryonic antigen (CEA), was captured on the chip with the help of first layer microfluidic channel. Then, monoclonal antibody was reacted with the CEA through the second layer microfluidic channel at upright direction against the first layer. In the end, AuNPs labeled secondary antibody and silver enhancement regent were added to creating positive or negative signals in crossed areas, depending on the amounts of tumor marker protein. Using the protein chip based on nanotechnology, we could detect CEA at a wide range of concentration (5-50,000 ng/mL) and also had high sensitivity (LOD < 1 pM). Because of its quick detection procedure and no need for high-cost instruments, the protein chip showed potential use for point-of-care (POC) diagnostics.
Induction of Inflammation byWest Nile virusCapsid through the Caspase-9 Apoptotic Pathway (2002)

West Nile virus (WNV) is a member of the Flaviviridae family of vector-borne pathogens. Clinical signs of WNV infection include neurologic symptoms, limb weakness, and encephalitis, which can result in paralysis or death. We report that the WNV-capsid by itself induces rapid nuclear condensation and cell death in tissue culture. Apoptosis is induced through the mitochondrial pathway resulting in caspase-9 activation and downstream caspase-3 activation. Capsid gene delivery into the striatum of mouse brain or interskeletal muscle resulted in cell death and inflammation, likely through capsid-induced apoptosis in vivo. These studies demonstrate that the capsid protein of WNV may be responsible for aspects of viral pathogenesis through induction of the apoptotic cascade.
Compound image compression for real-time computer screen image transmission (2005)

We present a compound image compression algorithm for real-time applications of computer screen image transmission. It is called shape primitive extraction and coding (SPEC). Real-time image transmission requires that the compression algorithm should not only achieve high compression ratio, but also have low complexity and provide excellent visual quality. SPEC first segments a compound image into text/graphics pixels and pictorial pixels, and then compresses the text/graphics pixels with a new lossless coding algorithm and the pictorial pixels with the standard lossy JPEG, respectively. The segmentation first classifies image blocks into picture and text/graphics blocks by thresholding the number of colors of each block, then extracts shape primitives of text/graphics from picture blocks. Dynamic color palette that tracks recent text/graphics colors is used to separate small shape primitives of text/graphics from pictorial pixels. Shape primitives are also extracted from text/graphics blocks. All shape primitives from both block types are losslessly compressed by using a combined shape-based and palette-based coding algorithm. Then, the losslessly coded bitstream is fed into a LZW coder. Experimental results show that the SPEC has very low complexity and provides visually lossless quality while keeping competitive compression ratios.
Rapid gridding reconstruction with a minimal oversampling ratio (2005)

Reconstruction of magnetic resonance images from data not falling on a Cartesian grid is a Fourier inversion problem typically solved using convolution interpolation, also known as gridding. Gridding is simple and robust and has parameters, the grid oversampling ratio and the kernel width, that can be used to trade accuracy for computational memory and time reductions. We have found that significant reductions in computation memory and time can be obtained while maintaining high accuracy by using a minimal oversampling ratio, from 1.125 to 1.375, instead of the typically employed grid oversampling ratio of two. When using a minimal oversampling ratio, appropriate design of the convolution kernel is important for maintaining high accuracy. We derive a simple equation for choosing the optimal Kaiser-Bessel convolution kernel for a given oversampling ratio and kernel width. As well, we evaluate the effect of presampling the kernel, a common technique used to reduce the computation time, and find that using linear interpolation between samples adds negligible error with far less samples than is necessary with nearest-neighbor interpolation. We also develop a new method for choosing the optimal presampled kernel. Using a minimal oversampling ratio and presampled kernel, we are able to perform a three-dimensional (3-D) reconstruction in one-eighth the time and requiring one-third the computer memory versus using an oversampling ratio of two and a Kaiser-Bessel convolution kernel, while maintaining the same level of accuracy.
Caffeine protects mice against whole-body lethal dose of gamma-irradiation (1999)

Administration of caffeine (1,3,7-trimethylxanthine), a major component of coffee, to Swiss mice at doses of 80 or 100 mg/kg body weight 60 min prior to whole-body lethal dose of gamma-irradiation (7.5 Gy) resulted in the survival of 70 and 63% of animals, respectively, at the above doses in contrast to absolutely no survivors (LD-100/25 days) in the group exposed to radiation alone. Pre-treatment with a lower concentration of caffeine (50 mg/kg) did not confer any radioprotection. The protection exerted by caffeine (80 mg/kg), however, was reduced from 70 to 50% if administered 30 min prior to irradiation. The trend statistics reveal that a dose of 80 mg/kg administered 60 min before whole-body exposure to 7.5 Gy is optimal for maximal radioprotection. However, caffeine (80 mg/kg) administered within 3 min after irradiation offered no protection. While there is documentation in the literature that caffeine is an antioxidant and radioprotector against the oxic pathway of radiation damage in a wide range of cells and organisms, this is the first report demonstrating unequivocally its potent radioprotective action in terms of survival of lethally whole-body irradiated mice.
A One‐Pot Total Synthesis of Crambin (2004)

Making up for lost time: The one-pot synthesis of crambin (see structure) with only a single final purification step gave the target protein of exceptional purity in only two days with an overall yield of ≈40 %. Three unprotected peptide segments were linked by native chemical ligation, and the polypeptide chain assumed its 3D structure without intermediate purification steps. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z53540_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Triple Component Carbon Epoxy pH Probe (2007)

Abstract A pH probe based on a carbon‐epoxy electrode design is discussed. The electrode consists of three redox active components within a carbon epoxy matrix. These are the pH sensitive species anthraquinone and phenanthrenequinone, along with the pH insensitive ferrocene reference compound. The values of the peak potentials when combined are shown to shift by 120 mV/pH unit at 25 °C with respect to the ferrocene reference potential.
Route of Adenovirus-Based HIV-1 Vaccine Delivery Impacts the Phenotype and Trafficking of Vaccine-Elicited CD8 + T Lymphocytes (2010)

Candidate HIV-1 vaccine regimens utilizing intramuscularly (i.m.) administered recombinant adenovirus (rAd)-based vectors can induce potent mucosal cellular immunity. However, the degree to which mucosal rAd vaccine routing might alter the quality and anatomic distribution of vaccine-elicited CD8(+) T lymphocytes remains unclear. We show that the route of vaccination critically impacts not only the magnitude but also the phenotype and trafficking of antigen-specific CD8(+) T lymphocytes in mice. I.m. rAd immunization induced robust local transgene expression and elicited high-frequency, polyfunctional CD8(+) T lymphocytes that trafficked broadly to both systemic and mucosal compartments. In contrast, intranasal (i.n.) rAd immunization led to similarly robust local transgene expression but generated low-frequency, monofunctional CD8(+) T lymphocytes with restricted anatomic trafficking patterns. Respiratory rAd immunization elicited systemic and mucosal CD8(+) T lymphocytes with phenotypes and trafficking properties distinct from those elicited by i.m. or i.n. rAd immunization. Our findings indicate that the anatomic microenvironment of antigen expression critically impacts the phenotype and trafficking of antigen-specific CD8(+) T lymphocytes.
THE COMPONENT REFLEXES OF MICTURITION IN THE CAT (1931)

Journal Article THE COMPONENT REFLEXES OF MICTURITION IN THE CAT: PARTS I AND II Get access F. J. F. BARRINGTON F. J. F. BARRINGTON Laboratories of the Surgical Unit, University College Hospital Medical School Search for other works by this author on: Oxford Academic PubMed Google Scholar Brain, Volume 54, Issue 2, June 1931, Pages 177–188, https://doi.org/10.1093/brain/54.2.177 Published: 01 June 1931
Do Deep Neural Networks Learn Facial Action Units When Doing Expression Recognition? (2015)

Despite being the appearance-based classifier of choice in recent years, relatively few works have examined how much convolutional neural networks (CNNs) can improve performance on accepted expression recognition benchmarks and, more importantly, examine what it is they actually learn. In this work, not only do we show that CNNs can achieve strong performance, but we also introduce an approach to decipher which portions of the face influence the CNN's predictions. First, we train a zero-bias CNN on facial expression data and achieve, to our knowledge, state-of-the-art performance on two expression recognition benchmarks: the extended Cohn-Kanade (CK+) dataset and the Toronto Face Dataset (TFD). We then qualitatively analyze the network by visualizing the spatial patterns that maximally excite different neurons in the convolutional layers and show how they resemble Facial Action Units (FAUs). Finally, we use the FAU labels provided in the CK+ dataset to verify that the FAUs observed in our filter visualizations indeed align with the subject's facial movements.