gebhart/patrepeval huggingface dataset:
Structural and functional studies of a 39,000-Mr immunodominant protein of vaccinia virus (1987)

Little is known about the nature of poxvirus proteins involved in the host immune response. Screening a lambda gt11 expression library of genomic rabbit poxvirus DNA with hyperimmune rabbit anti-vaccinia virus serum and selection of monospecific antibodies identified a highly antigenic viral protein of about 39,000 molecular weight (39K protein). The same-size protein of vaccinia virus was also identified with a monoclonal antibody (MAb B6) obtained from hybridomas generated after fusion of hyperimmunized mouse spleen cells with mouse myeloma cells. Structural analysis revealed that the 39K protein is an acidic polypeptide, that it can exist in two molecular forms because of intramolecular disulfide linkages, and that it is part of the virus core. This protein shares antigenic determinants with a cytoplasmic component(s) from uninfected cells. Functional studies revealed that the 39K protein is synthesized at late times postinfection and appears to be required for virus assembly. This protein is highly conserved in members of the Orthopoxvirus group, but in cowpox virus, a 41K virion protein was specifically recognized by antibodies that reacted against the vaccinia virus 39K protein. Significantly, during long-term passages of Friend erythroleukemia cells persistently infected with vaccinia virus, some virus mutants were found to increase or decrease by about 2 kilodaltons the size of the 39K protein. Mapping analysis localized sequences encoding the 39K protein in a rifampin-sensitive gene cluster between the two major core-associated viral polypeptides, 4a and 4b. The fact that the 39K core protein of vaccinia virus elicits strong humoral immune response, induces antibodies that react against a host component(s), and is subjected to genetic variability suggests that this protein has important biological functions.
Development of bioactive polyurethaneureas to support endothelialization (2004)

Vascular diseases are responsible for the majority of deaths in the United States. Synthetic materials have been developed for blood vessel substitutes but not suitable for small diameter vascular applications such as coronary artery bypass grafting (CABG). Polyurethaneureas (PUU) have been widely used for biomedical applications due to their excellent mechanical properties and relatively good biocompatibility. However, like other synthetic materials, they are generally thrombogenic on exposure to blood. Endothelialization of synthetic grafts is a good strategy to improve graft patency. However, the graft patency is dependent on retention of endothelial cells on exposure to physiological shear stress. In this study, we developed bioactive polyurethaneureas to support endothelialization. First, we have demonstrated that endothelial cell behaviors could be altered by the surface YIGSR peptide concentrations. Bioactive polyurethanureas (PUUYIGSR) have been developed by incorporating YIGSR peptide sequences into polymer main chain, and improved endothelialization has been observed on the surface. In addition, PEG- and YIGSR-modified polyurethaneureas (PUUYIGSR-PEG) have been developed, and enhanced endothelialization and improved thromboresistance have been obtained simultaneously. Our bulk modification strategy allowed us to fabricate microporous scaffolds without interfering bioactivity of incorporated peptide sequences. Microporous scaffolds have been also used as a carrier of vascular endothelial growth factor (VEGF). The synergistic effects of peptide sequences, microporous structure, and incorporated VEGF on endothelialization have been observed. Additionally, nitric oxide (NO) releasing polyurethanes (PUBD-NO) have been developed by incorporating NO donor into the polymer main chain. NO was successfully released from the PUBD-NO in controlled manner and reduced platelet adhesion and smooth muscle cell proliferation but improved endothelialization proliferation.
Immunocytochemical localization of protein kinases Yes and Src in amoeboid microglia in culture: association of Yes kinase with vimentin intermediate filaments. (1995)

Amoeboid microglia isolated from primary cultures of neonatal rat brain correspond to a transient form of activated microglia, a resident population of macrophage-like cells. In order to understand the molecular aspects of microglial activation, we have studied amoeboid microglia in primary culture for the presence of Yes and Src protein tyrosine kinases, two kinases which have been implicated in signal transduction process during monocyte/macrophage activation. Immunofluorescence with an antibody raised against the peptide from unique N-terminal domains of Yes and Src demonstrated that Yes and Src kinases are enriched in perinuclear areas of amoeboid microglia. In addition, the antibody to c-yes peptide had a cytoplasmic distribution which coincided with the distribution of vimentin-containing intermediate filaments. Preadsorption of anti-c-yes antibody with an excess of antigenic peptide inhibited anti-c-yes immunofluorescence, while vimentin immunofluorescence remained unchanged. Double immunofluorescence images analyzed with the two-dimensional intensity distribution program (2-D scattered histograms) on Zeiss confocal scanning laser microscope demonstrate the colocalization of c-yes with vimentin. The extent of colocalization was more prominent after exposure of intact cultured microglia to dibutyryl cyclic AMP (dBcAMP), or to phorbol ester TPA (12-O-tetradecanoylphorbol-13-acetate) or to okadaic acid, an inhibitor of protein phosphatases. The findings suggest that vimentin might serve as molecular support for Yes kinase and, since previous studies have shown that vimentin in amoeboid microglia is one of the major protein substrates of serine/threonine protein kinases, this function could be regulated by phosphorylation.
Many NK cell receptors activate ERK2 and JNK1 to trigger microtubule organizing center and granule polarization and cytotoxicity (2007)

Natural killer (NK) cells are components of the innate immune system that recognize and kill tumor or virus-infected target cells through specific NK activating receptor/ligand interactions. Lymphocyte function-associated antigen (LFA)-1 and its ligand ICAM-1 are also required to initiate conjugation and actin cytoskeletal remodeling. The NK activating receptors, many of which are expressed on a single NK cell, signal the polarization of the microtubule organizing center (MTOC) together with cytolytic granules to the synapse with target cells. After ligation of any one of these receptors, Src family kinases initiate activation of two signal pathways, the phosphoinositide-3 kinase --> ERK2 and the phospholipase Cgamma --> JNK1 pathways. Both are required for polarization of the MTOC and cytolytic granules, a prerequisite for killing the targets. Crosslinking of CD28, NKG2D, NKp30, NKp46, NKG2C/CD94, or 2B4 leads to the phosphorylation of both ERK2 and JNK1, although they use different proximal signaling modules. Thus, many, if not all, activating receptors stimulate these two distal pathways, independent of the proximal signaling module used. By contrast, CD2, DNAM-1, and beta(1)-integrin crosslinking do not activate either pathway; they may be costimulatory molecules or have another function in the synapse.
Regulation of PD-1/PD-L1 pathway and resistance to PD-1/PD-L1 blockade (2017)

Immune checkpoint blockades, such as inhibitors against programmed death 1 (PD-1) and its ligand (PD-L1), have received extensive attention in the past decade because of their dramatic clinical outcomes in advanced malignancies. However, both primary and acquired resistance becomes one of the major obstacles, which greatly limits the long-lasting effects and wide application of PD-1/PD-L1 blockade therapy. PD-1/PD-L1 both regulates and is regulated by cellular signaling pathways and epigenetic modification, thus inhibiting the proliferation and effector function of T and B cells. The lack of tumor antigens and effective antigen presentation, aberrant activation of oncogenic pathways, mutations in IFN-γ signaling, immunosuppressive tumor microenvironment such as regulatory T cells, myeloid-derived suppressor cells, M2 macrophages, and immunoinhibitory cytokines can lead to resistance to PD-1/PD-L1 blockade. In this review, we describe PD-1 related signaling pathways, essential factors contributing to the resistance of PD-1 blockade, and discuss strategies to increase the efficacy of immunotherapy. Furthermore, we discuss the possibility of combined epigenetic therapy with PD-1 blockade as a potential promising approach for cancer treatment.
Development of an endotoxin-specific Limulus amebocyte lysate test blocking .BETA.-glucan-mediated pathway by carboxymethylated curdlan and its application. (1990)

We developed a simple new endotoxin-specific assay method that uses Limulus amebocyte lysate (LAL) containing a sufficient amount of a water-soluble (1----3)-beta-D-glucan derivative as a blocker of the (1----3)-beta-D-glucan-mediated coagulation pathway. The addition of 0.1 mg/ml or more of carboxymethylated (1----3)-beta-D-glucan completely blocked the activation of LAL by (1----3)-beta-D-glucan itself. The assay of endotoxin was unaffected by the presence of 1 mg/ml carboxymethylated (1----3)-beta-D-glucan. Spiked endotoxin was recovered well from beta-glucans by the turbidimetric kinetic method with LAL containing 1 mg/ml of carboxymethylated (1----3)-beta-D-glucan. Besides, this new LAL formulation was applied for an endotoxin-specific assay by the conventional gel-clot method or the chromogenic method. Gram-negative bacteria were specifically detected by the turbidimetric kinetic method with the LAL formulation. This LAL formulation may be used for an endotoxin-specific assay not only in pharmacology but also in clinical microbiology.
Deficit of <i>in vivo</i> mitochondrial ATP production in patients with Friedreich ataxia (1999)

Friedreich ataxia (FRDA), the most common of the inherited ataxias, is an autosomal recessive degenerative disorder, characterized clinically by onset before the age of 25 of progressive gait and limb ataxia, absence of deep tendon reflexes, extensor plantar responses, and loss of position and vibration sense in the lower limbs. FRDA is caused by a GAA triplet expansion in the first intron of the FRDA gene on chromosome 9q13 in 97% of patients. The FRDA gene encodes a widely expressed 210-aa protein, frataxin, which is located in mitochondria and is severely reduced in FRDA patients. Frataxin function is still unknown but the knockout of the yeast frataxin homologue gene (YFH1) showed a severe defect of mitochondrial respiration and loss of mtDNA associated with elevated intramitochondrial iron. Here we report in vivo evidence of impaired mitochondrial respiration in skeletal muscle of FRDA patients. Using phosphorus magnetic resonance spectroscopy we demonstrated a maximum rate of muscle mitochondrial ATP production (V(max)) below the normal range in all 12 FRDA patients and a strong negative correlation between mitochondrial V(max) and the number of GAA repeats in the smaller allele. Our results show that FRDA is a nuclear-encoded mitochondrial disorder affecting oxidative phosphorylation and give a rationale for treatments aimed to improve mitochondrial function in this condition.
Variability of Venom-Neutralizing Properties of Serum from Snakes of the Colubrid Genus Lampropeltis (1992)

Scott A. Weinstein, Clement F. DeWitt, Leonard A. Smith, Variability of Venom-Neutralizing Properties of Serum from Snakes of the Colubrid Genus Lampropeltis, Journal of Herpetology, Vol. 26, No. 4 (Dec., 1992), pp. 452-461
Conservative management or closed nailing for tibial shaft fractures. A randomised prospective trial (1991)

We performed a prospective randomised trial on matched groups of patients with displaced tibial shaft fractures to compare conservative treatment with closed intramedullary nailing. The results showed conclusively that intramedullary nailing gave more rapid union with less malunion and shortening. Nailed patients had less time off work with a more predictable and rapid return to full function. We therefore consider that closed intramedullary nailing is the most efficient treatment for displaced fractures of the tibial shaft.
Radiation-Sensitive Diselenide Block Co-polymer Micellar Aggregates: Toward the Combination of Radiotherapy and Chemotherapy (2011)

We have developed a potential radiation-sensitive drug-delivery system using active diselenide-containing block co-polymer aggregates in aqueous solution that can load and release anticancer drugs. These aggregates were sensitive to even a low dose of γ-radiation, such as 5 Gy, which is close to the radiation dose received by patients during a single radiotherapy treatment. This line of research may open an avenue for the combination of radiotherapy and chemotherapy.
Efficient ECC-Based Directory Implementations for Scalable Multiprocessors (2000)

With increasing chip densities, next-generation micro-processor design have the opportunity to integrate many of the traditional system-level moules onto the same chip as the processor. This integration changes some of the design trade-offs for how and where to store directory information. One extremely attractive option is to support directory data with virtually no memory space overhead by computing memory ECC at a coarser granularity and utilizing the usused bits for storing the directory information. Compared to providing a dedicated memory and datapath for directory atorage, this approach leads to lower cost and a simpler design by requiring fewer components and pins. Furthermore, this approach leverages the low latency, high bandwidth path to memory provided by the integration of memory controllers onto the processor chip. However, without careful design, maintaining data and directory bits together can lead to potential inefficiencies in the form of extra memory bandwidth usage and memory controller occupancy, and extra memory latency. This paper describes the techniques used in the context of the Piranha design [3] to provide an efficient ECC-based directory implementation which addresses the occupancy/bandwidth and latency issues. Our approach for dealing with the occupancy/bandwidth issues involves either eliminating the extra read and write operations or performing partial memory accesses (instead of accessing the whole block). Thi is achieved by a combination of techniques which include (i) augmenting the L2 caching state to keep track of some critical directory state, (ii) making up dummy data for protocol transactions with a stale momory copy, and (iii) maintaining a partial ECC that is used to compute the combined ECC of the data and the modified directory bits without needing the actual data bits. To address the latency issues, we replicate critical directory state in different segments of the momory line which allows us to efficiently support the critical-word-first optimization by pipelining data from memory to the requester before all the data is read from memory. The combination of the above techniques also eliminates all the inefficiencies that arise due to maintaining a combined ECC for directory and data bits. Therefore, we benefit from the more efficient use of bits provided by the combined ECC with virtually no performance penalty compared to maintaining separe ECC bits for data and directory. Finally, the optimizations used in Piranha are general and applicable to other designs that use ECC-based directories.
Rectilinearity measurements for polygons (2003)

The paper introduces a shape measure intended to describe the extent to which a closed polygon is rectilinear. Other than somewhat obvious measures of rectilinearity (e.g., the sum of the differences of each corner's angle from multiples of 90/spl deg/), there has been little work in deriving a measure that is straightforward to compute, is invariant under scale, rotation, and translation, and corresponds with the intuitive notion of rectilinear shapes. There are applications in a number of different areas of computer vision and photogrammetry. Rectilinear structures often correspond to human-made objects and are therefore justified as attentional cues for further processing. For instance, in aerial image processing and reconstruction, where building footprints are often rectilinear on the local ground plane, building structures, once recognized as rectilinear, can be matched to corresponding shapes in other views for stereo reconstruction. Perceptual grouping algorithms may seek to complete shapes based on the assumption that the object in question is rectilinear. Using the proposed measure, such systems can verity this assumption.
Time Out: The Cricket Season (1986)

The cricket season is upon us again. We are relaxed, on holidays, well-disposed to share a Toohey's or two with our working class hero Doug Walters, eager to be told of the famous Gatting 'grittiness' and to view with pleasure the inevitable Border boundaries. We are prepared, in other words, to be entertained.
Therapeutic antimicrobial peptides may compromise natural immunity (2012)

Antimicrobial peptides (AMPs) have been proposed as a promising new class of antimicrobials despite warnings that therapeutic use could drive the evolution of pathogens resistant to our own immunity peptides. Using experimental evolution, we demonstrate that Staphylococcus aureus rapidly evolved resistance to pexiganan, a drug-candidate for diabetic leg ulcer infections. Evolved resistance was costly in terms of impaired growth rate, but costs-of-resistance were completely ameliorated by compensatory adaptation. Crucially, we show that, in some populations, experimentally evolved resistance to pexiganan provided S. aureus with cross-resistance to human-neutrophil-defensin-1, a key component of the innate immune response to infection. This unintended consequence of therapeutic use could drastically undermine our innate immune system's ability to control and clear microbial infections. Our results therefore highlight grave potential risks of AMP therapies, with implications for their development.
Heterogeneous Knowledge-Based Attentive Neural Networks for Short-Term Music Recommendations (2018)

The current existing data in online music service platforms are heterogeneous, extensive, and disorganized. Finding an effective method to use these data in recommending appropriate music to users during a short-term session is a significant challenge. Another serious problem is that most of the data, in reality, obey the long-tailed distribution, which consequently leads to traditional music recommendation systems recommending a lot of popular music that users do not like on a specific occasion. To solve these problems, we propose a heterogeneous knowledge-based attentive neural network model for short-term music recommendations. First, we collect three types of data for modeling entities in user–music interaction network, i.e., graphic, textual, and visual data, and then embed them into high-dimensional spaces using the TransR, distributed memory version of paragraph vector, and variational autoencoder methods, respectively. The concatenation of these embedding results is an abstract representation of the entity. Based on this, a recurrent neural network with an attention mechanism is built, which is capable of obtaining users’ preferences in the current session and consequently making recommendations. The experimental results show that our proposed approach outperforms the current state-of-the-art short-term music recommendation systems on one real-world dataset. In addition, it can also recommend more relatively unpopular songs compared with classic models.
Complete Nucleotide Sequence of KPC-3-Encoding Plasmid pKpQIL in the Epidemic <i>Klebsiella pneumoniae</i> Sequence Type 258 (2010)

We have determined the entire DNA sequence of plasmid pKpQIL, the bla(KPC-3)-carrying plasmid harbored by the carbapenem-resistant Klebsiella pneumoniae clone sequence type 258 (ST 258) in Israel. pKpQIL is a 113,637-bp, self-transmissible plasmid that belongs to the incompatibility group IncFII. It consists of a large backbone of a pKPN4-like plasmid and carries the bla(KPC-3)-containing Tn4401a transposon of a pNYC-like plasmid.
112. Chemistry of hop constituents. Part XIII. The hydrogenation of isohumulone (1959)

P. M. Brown, G. A. Howard and A. R. Tatchell, J. Chem. Soc., 1959, 545 DOI: 10.1039/JR9590000545
Exploratory Analysis of the Way to Realizing China’s Service-Oriented Police Affairs (2016)

As society changes, traditional types of police affairs can no longer adapt to the development and demand of the times. Service-oriented police affairs in the new era closely follows the government’s pace of reform, and is an effective way to solve the problem caused by numerous types of police affairs losing effectiveness at present. This article discusses the meaning, theoretical basis, characteristics and way to the realization of China’s service-oriented police affairs. In short, in the process of constructing China’s service-oriented police affairs, what are needed include changing the idea of police service, improving public security organizations, structuring highly efficient police affairs operation mechanism, etc..
Impeding CAPTCHA breakers with visual decryption (2010)

Abuse of free Internet resources and services from false account creation, to spam, to identity theft, ex-cessive bandwidth usage, or even vote stuffing online polls is a big problem. The Completely Automatic Public Turing Test to tell Computers and Humans Apart (CAPTCHA) controls access to resources but automated systems are increasingly adept at over-coming them. In this paper a method of access con-trol is introduced as an extra layer of security on top of existing CAPTCHA implementations. It uses visual encryption to encrypt images, which are pre-sented to clients like a CAPTCHA. It’s purpose is to compress many sub-images into a small image format that humans can decode visually but is hard for auto-mated systems due to decrypting overhead, and hav-ing to process more images to find the hidden image. This paper introduces visual encryption as a viable method to encrypt CAPTCHAs, and tests a proto-type to measure how efficiently users can find them. It also measures whether this method could impede a real CAPTCHA breaker. Results show humans de-tect images within 16-33 seconds, and deciphering images is almost 100%. Estimates on CAPTCHA breaking benchmarks show automated systems would be slowed significantly, even assuming the image is found and decoded. As sub-images increase, humans can process the visually encrypted images faster than automated systems can.
Solubility, stability, and electrochemical studies of sulfur-sulfide solutions in organic solvents (1978)

A preliminary study of the sulfur electrode in organic solvents suggests that the system warrants further investigation for use in a low temperature (100 deg to 120 C) Na-S secondary battery. A qualitative screening was undertaken at 120 C to determine the solubilities and stabilities of Na2S and Na2S2 in representatives of many classes of organic solvents. From the screening and quantitative studies, two classes of solvents were selected for work; amides and cyclic polyalcohols. Voltammetric and Na-S cell charge discharge studies of sulfide solutions in organic solvents (e.g., N, N-dimethylformamide) at 120 C suggested that the reversibilities of the reactions on Pt or high density graphite were moderately poor. However, the sulfur electrode was indeed reducible (and oxidizable) through the range of elemental sulfur to Na2S. Reactions and mechanisms are proposed for the oxidation reduction processes occurring at the sulfur electrode.
Application of hydraulic fracturing in the recovery of oil by waterflooding: a summary (1963)

The results and conclusions reached by various investigators who have attempted to determine the extent to which hydraulic fracturing will affect the secondary recovery of crude oil by waterflooding are summarized. The most advantageous use of the well-stimulation method in waterflood projects is discussed.