gebhart/patrepeval huggingface dataset:
Differences in the production of spliced antigenic peptides by the standard proteasome and the immunoproteasome (2010)

Peptide splicing allows the production of antigenic peptides composed of two fragments initially non-contiguous in the parental protein. The proposed mechanism of splicing is a transpeptidation occurring within the proteasome. Three spliced peptides, derived from FGF-5, melanoma protein gp100 and nuclear protein SP110, have been described. Here, we compared the production of these spliced peptides by the standard proteasome and the immunoproteasome. Differential isotope labelling was used to quantify (by mass spectrometry) the fragments contained in digests obtained with precursor peptides and purified proteasomes. The results show that both the standard and the immunoproteasomes can produce spliced peptides although they differ in their efficiency of production of each peptide. The FGF-5 and gp100 peptides are more efficiently produced by the standard proteasome, whereas the SP110 peptide is more efficiently produced by the immunoproteasome. This seems to result from differences in the production of the two splicing partners, which depends on a balance between cleavages liberating or destroying those fragments. By showing that splicing depends on the efficiency of production of the splicing partners, these results also support the transpeptidation model of peptide splicing. Furthermore, given the presence of immunoproteasomes in dendritic cells and cells exposed to IFN-γ, the findings may be relevant for vaccine design.
NSAID-induced gastric ulceration is dose related by weight: an endoscopic study with flurbiprofen. (1993)

Numerous studies have shown that higher doses of nonsteroidal anti-inflammatory drugs (NSAIDs) are associated with increased levels of mucosal injury and ulceration in both normal volunteers and patients. The present dose-ranging study was designed to determine whether escalating doses of a commonly prescribed NSAID, flurbiprofen, when expressed as mg/kg dosages, were associated with increased mucosal injury and ulceration. Subjects received either the recommended dose of 300 mg/day of flurbiprofen (N = 10), or the higher than recommended doses of 400 mg/day (N = 20) and 500 mg/day (N = 10), for a period of 7 days. Endoscopic examination was performed on day 0 and day 7, and the stomach was evaluated on day 7 for mucosal injury on a 0-4 scale, and for the presence or absence of ulcer. One gastric ulcer was seen in each of the 300- and 400-mg groups. However, in the 500 mg/day group, four gastric ulcers were seen (40%) (p = 0.04). Three of the six subjects developing gastric ulcer were of a fairly low body weight (two women, one man), and when the data were analyzed on a mg/kg basis, all six ulcers occurred in 19 of the 40 subjects receiving > 5.95 mg/kg, whereas no gastric ulcers were seen in the 21 subjects receiving dosages below that level (p < 0.01). These data suggest that, at least for this agent, a threshold level may exist above which gastric ulcers are much more likely to occur. This may in part explain why elderly debilitated, low-body-weight female patients are more prone to NSAID-related gastric ulcer.
Generation and reactivity of α-metalated vinyl ethers (2001)

Covering: 1951–1996.
Low-End General-Purpose Systems (1981)

Since the announcement of the IBM System/3 in 1969, IBM has been incorporating leading-edge technology in products referred to as small general-purpose systems. With the many models of the System/3, System/32, System/34, and System/38, IBM has introduced many technological advances addressing the needs of diverse customers, from the novice, first-time user to the experienced user in the distributed data processing account. By identifying the goals, objectives, design themes, major salient features, and development constraints, this paper reviews and highlights the technical evolution of these products in terms of their systems layout, processor architecture, machine structure, and programming support.
Involvement of waaY, waaQ, and waaP in the Modification of Escherichia coliLipopolysaccharide and Their Role in the Formation of a Stable Outer Membrane (1998)

The waaY, waaQ, and waaP genes are located in the central operon of the waa (formerly rfa) locus on the chromosome of Escherichia coli. This locus contains genes whose products are involved in the assembly of the core region of the lipopolysaccharide molecule. In the R1 core prototype strain, E. coli F470, there are nine genes in this operon, and all but waaY, waaQ, and waaP have been assigned function. In this study, the waaY, waaQ, and waaP genes were independently mutated by insertion of a non-polar antibiotic resistance cassette, and the structures of the resulting mutant core oligosaccharides were determined by chemical analyses and phosphorus-nuclear magnetic resonance spectroscopy. All three of these mutations were shown to affect the modification of the heptose region of the core, a region whose structure is critical to outer membrane stability. Mutation of waaY resulted in a core oligosaccharide devoid of phosphate on HepII. Mutation of waaQ resulted in loss of the branch HepIII residue on HepII and impeded the activity of WaaY. Mutation of waaP resulted in loss of phosphoryl substituents on HepI and obviated WaaQ and WaaY activity. Only mutation of waaP resulted in hypersensitivity to novobiocin and sodium dodecyl sulfate, a characteristic of deep-rough mutations.
First results of a dedicated breast PET imager, BPET, using NaI(Tl) curve plate detectors (2005)

We present the first imaging results from phantom measurements of a dedicated, breast-only positron emission imager, BPET, using NaI(Tl) Curve Plate detectors. The scanner uses 19 mm thick NaI(Tl) detectors in a split-ring design which surrounds the breast as the woman lies prone and the breast hangs down from the body. Because the detectors are close to the breast and the scanner detects photons that do not pass through the body, system sensitivity and spatial resolution are both optimized. The split ring design provides for flexibility for needle aspirations of masses or alternate viewing orientations. We have measured energy resolution, spatial resolution, scatter fraction, and system sensitivity. We have compared the BPET scanner's performance to our clinical whole-body scanner using a breast phantom with hot spheres simulating lesions. The results show that for activity concentrations that correspond to clinical FDG doses, the dedicated scanner has better lesion detectability than the whole-body scanner for the 20 cm detector separation used.
SUP-17, a <i>Caenorhabditis elegans</i> ADAM protein related to <i>Drosophila</i> KUZBANIAN, and its role in LIN-12/NOTCH signalling (1997)

LIN-12/NOTCH proteins mediate cell-cell interactions that specify cell fates. Previous work suggested that sup-17 facilitates lin-12 signalling in Caenorhabditis elegans. Here, we show that sup-17 encodes a member of the ADAM family of metalloproteases. SUP-17 is highly similar to Drosophila KUZBANIAN, which functions in Drosophila neurogenesis, and the vertebrate ADAM10 protein. Furthermore, we show by genetic analysis that the extracellular domain of LIN-12 appears to be necessary for sup-17 to facilitate lin-12 signalling and that sup-17 does not act downstream of lin-12. Finally, we show by cell ablation experiments that sup-17 can act cell autonomously to facilitate lin-12 activity. We discuss the implications of our observations for LIN-12/NOTCH signalling and how our results complement and extend results obtained from genetic analysis of kuz in Drosophila.
Potassium Iodide Reversal of Silver Diamine Fluoride Staining: A Case Report (2018)

This article describes the clinical protocol of using potassium iodide (KI) to reverse staining caused by silver diamine fluoride (SDF). SDF contains silver, fluoride, and ammonia. It has been used to arrest dental caries mainly in pediatric applications. The major drawback of SDF application is the dark staining of both teeth and restorative materials. Hence, its use on adult dentition is limited. Improving the esthetic outcome by stain reduction would greatly enhance the opportunity for SDF's universal use. This case demonstrates how KI can effectively reverse the staining.
A Simple Assay for Mammalian Spermine Oxidase: A Polyamine Catabolic Enzyme Implicated in Drug Response and Disease (2011)

Spermine oxidase (SMO), the most recently characterized polyamine metabolic enzyme, catalyzes the direct back-conversion of spermine to spermidine in an FAD-dependent reaction that also yields the byproducts hydrogen peroxide (H(2)O(2)) and 3-aminopropanal. These metabolites, particularly H(2)O(2), have been implicated in cytotoxic cellular responses to specific antitumor polyamine analogs, as well as in the inflammation-associated generation of DNA damage. This chapter describes a rapid, sensitive, and inexpensive method for the chemiluminescent measurement of SMO (or alternatively, N (1)-acetyl polyamine oxidase, APAO) enzyme activity in cultured cell lysates, without the need for radioactive reagents or the use of high performance liquid chromatography (HPLC). Specifically, H(2)O(2) production by SMO is coupled to chemiluminescence generated by the horseradish peroxidase-catalyzed oxidation of luminol. Detailed protocols for preparation of reagents, harvesting cell lysates, generation of a standard curve, assaying of samples, and calculation of SMO enzyme activity are presented.
Chip-n-Saw tackles small log conversion-head on. (1970)

Adaptation of movement may be driven by the difference between planned and actual motor performance, or the difference between expected and actual sensory consequences of movement. To identify how the nervous system differentially uses these signals, we asked: does motor adaptation occur when movement errors are irrelevant to the task goal? Participants reached on a digitizing tablet from a fixed start location to one of three targets: a point, an arc, or a ray. For the arc, reaches could be in any direction, but to a specific extent. For the ray, reaches could be to any distance, but in a targeted direction. After baseline reaching to the point, the direction or extent of continuous visual feedback was perturbed during training with either a cursor rotation or gain, respectively, while reaching to either the ray (goal = direction) or the arc (goal = extent). The perturbation, therefore, was either relevant or irrelevant to the task goal, depending on target type. During interspersed catch trials, the perturbation was removed and the target switched back to the point, identical to baseline. Although the goal of baseline and catch trials was the same, significant aftereffects in catch trials indicated behavioral adaptation in response to the perturbation. Adaptation occurred regardless of whether the perturbation was relevant to the task, and it was independent of feedback control. The presence of adaptation orthogonal to task demands supports the hypothesis that the nervous system can rely on sensory prediction to drive motor learning that can generalize across tasks.
Cell cycle control of c-kit+IL-7R+ B precursor cells by two distinct signals derived from IL-7 receptor and c-kit in a fully defined medium. (1995)

An important goal for the investigation of the proliferation of mammalian cells is to establish a fully defined condition for culturing them in vitro. Here, we report establishment of a fully defined culture condition that supports the primary culture of normal c-kit+IL-7 receptor (IL-7R)+ B precursor cells without the aid of stromal cell lines. This defined culture condition contains IL-7, the ligand for c-kit, transferrin, insulin, and bovine serum albumin as protein components. By using the cell lines derived from RAG2(-/-) mice, which do not differentiate into c-kit- stage, we have evaluated the role of each protein in the cell cycle progression of c-kit+IL-7R+ B precursor cells. Since B precursor cells can grow without insulin, c-kit remains a sole functional receptor tyrosine kinase for their growth. While both c-kit ligand (KL) and IL-7 are the requisite molecules for sustained proliferation of B precursor cells, each molecule plays distinct roles. IL-7 starvation results in prompt arrest of the cells at G1. An accumulation of the cells in the mitotic phase was also detected. Thus, the major role of IL-7 is to regulate the G1/S transition and the process of cytokinesis of B precursor cells. Although prolonged KL starvation over 48 h resulted in accumulation of G1 cells, its effect could not be detected within 24 h, which is long enough for all the cells to complete one cell cycle. This suggests that KL might be involved in the cell cycle progression of B precursor cells in a manner that its signal could still be effective in the one or two cell cycles that follow. Although molecular nature of the signals underlying the present observation awaits future investigation, the method described in this report would provide a useful model system for investigating the signaling pathways that are involved in the cell cycle progression of B precursor cells.
Dimerization of the DYT6 dystonia protein, THAP1, requires residues within the coiled‐coil domain (2011)

Thanatos-associated [THAP] domain-containing apoptosis-associated protein 1 (THAP1) is a DNA-binding protein that has been recently associated with DYT6 dystonia, a hereditary movement disorder involving sustained, involuntary muscle contractions. A large number of dystonia-related mutations have been identified in THAP1 in diverse patient populations worldwide. Previous reports have suggested that THAP1 oligomerizes with itself via a C-terminal coiled-coil domain, raising the possibility that DYT6 mutations in this region might affect this interaction. In this study, we examined the ability of wild-type THAP1 to bind itself and the effects on this interaction of the following disease mutations: C54Y, F81L, ΔF132, T142A, I149T, Q154fs180X, and A166T. The results confirmed that wild-type THAP1 associated with itself and most of the DYT6 mutants tested, except for the Q154fs180X variant, which loses most of the coiled-coil domain because of a frameshift at position 154. However, deletion of C-terminal residues after position 166 produced a truncated variant of THAP1 that was able to bind the wild-type protein. The interaction of THAP1 with itself therefore required residues within a 13-amino acid region (aa 154-166) of the coiled-coil domain. Further inspection of this sequence revealed elements highly consistent with previous descriptions of leucine zippers, which serve as dimerization domains in other transcription factor families. Based on this similarity, a structural model was generated to predict how hydrophobic residues in this region may mediate dimerization. These observations offer additional insight into the role of the coiled-coil domain in THAP1, which may facilitate future analyses of DYT6 mutations in this region.
A CNN-RNN Architecture for Multi-Label Weather Recognition (2019)

Weather Recognition plays an important role in our daily lives and many computer vision applications. However, recognizing the weather conditions from a single image remains challenging and has not been studied thoroughly. Generally, most previous works treat weather recognition as a single-label classification task, namely, determining whether an image belongs to a specific weather class or not. This treatment is not always appropriate, since more than one weather conditions may appear simultaneously in a single image. To address this problem, we make the first attempt to view weather recognition as a multi-label classification task, i.e., assigning an image more than one labels according to the displayed weather conditions. Specifically, a CNN-RNN based multi-label classification approach is proposed in this paper. The convolutional neural network (CNN) is extended with a channel-wise attention model to extract the most correlated visual features. The Recurrent Neural Network (RNN) further processes the features and excavates the dependencies among weather classes. Finally, the weather labels are predicted step by step. Besides, we construct two datasets for the weather recognition task and explore the relationships among different weather conditions. Experimental results demonstrate the superiority and effectiveness of the proposed approach. The new constructed datasets will be available at https://github.com/wzgwzg/Multi-Label-Weather-Recognition.
Abnormal Nerve Regeneration in Galactose Neuropathy (1986)

Nerve regeneration across a 10 mm gap through an implanted silicone tube was delayed in galactose-fed rats two and four weeks after transecting the nerve. This experimental metabolic neuropathy resembles diabetic neuropathy in which nerve regeneration is also delayed. Experiments were performed by introducing opposite ends of divided sciatic nerves into close-fitting silicone tubes, leaving a 10 mm gap. Growth of neurites across this gap was monitored by electron microscopy performed in sections at regular intervals of 2 mm from proximal to distal stumps. After two weeks some difference was apparent; axons advanced 1.4 +/- 0.4 mm in galactose-fed rats versus 3.5 +/- 1.5 mm in controls. Myelination did not progress beyond 1 mm in galactose-fed rats. Differences were greater between the two groups at four weeks. The growth of axons in galactose rats was 3.5 +/- 0.2 mm versus 9.4 +/- 0.1 mm in control nerves. In addition the size of the regenerating stump was much greater in control rats. Qualitative differences were also noticed during electron microscopic comparison of control and galactose-treated rats. The dystrophic axons seen in treated rats had abnormal electron-dense organelles, lamellated bodies, vesicles and tubular structures, as well as numerous glycogen granules. Abnormalities of spatial orientation were also noted. Unlike control axons which grew parallel with the long axis of the tube, regenerating axons in experimental animals were seen deviating from the axis at 90 degrees angles. Both immature sprouts and myelinating axons showed abnormal plasticity. Ultrastructural differences were also noted in Schwann cells, macrophages and vessels.
Effects of Endogenous <scp>d</scp> -Alanine Synthesis and Autoinhibition of <i>Bacillus anthracis</i> Germination on In Vitro and In Vivo Infections (2007)

Bacillus anthracis transitions from a dormant spore to a vegetative bacillus through a series of structural and biochemical changes collectively referred to as germination. The timing of germination is important during early steps in infection and may determine if B. anthracis survives or succumbs to responsive macrophages. In the current study experiments determined the contribution of endogenous D-alanine production to the efficiency and timing of B. anthracis spore germination under in vitro and in vivo conditions. Racemase-mediated production of endogenous D-alanine by B. anthracis altered the kinetics for initiation of germination over a range of spore densities and exhibited a threshold effect wherein small changes in spore number resulted in major changes in germination efficiency. This threshold effect correlated with D-alanine production, was prevented by an alanine racemase inhibitor, and required L-alanine. Interestingly, endogenous production of inhibitory levels of D-alanine was detected under experimental conditions that did not support germination and in a germination-deficient mutant of B. anthracis. Racemase-dependent production of D-alanine enhanced survival of B. anthracis during interaction with murine macrophages, suggesting a role for inhibition of germination during interaction with these cells. Finally, in vivo experiments revealed an approximately twofold decrease in the 50% lethal dose of B. anthracis spores administered in the presence of D-alanine, indicating that rates of germination may be directly influenced by the levels of this amino acid during early stages of disease.
One-dimensional processing for efficient optimal post-process/in-loop filtering in video coding (2008)

In this paper, efficient optimal post-process/inloop filtering in video coding is presented by applying two separate one-dimensional filters to significantly decrease the computational load of the optimal filtering process at the expense of only a slight quality loss. Furthermore, the compression of filter coefficients is evaluated using a Golomb-Rice (GR) coding approach together with differential encoding. Experimental results show that the proposed one dimensional processing approach reduces the computational complexity by at least 4 times compared to the formerly proposed two-dimensional optimal filtering case and enables real-time implementation. It is furthermore shown that, the filter coefficients can be compressed by up to 40% if GR coding is used together with differential encoding.
Modification of BPDA-ODA Polyimide Films by Diimides (2010)

Diimides 4,4′-oxydiphenylene diphthalylimide (PT-ODA-PT) and diphenylbiphenyltetracarboxyimide (A-BPDA-A) of an evident affinity to polyimides have been dispersed in a matrix of poly(4,4′-oxydiphenylene biphenyltetracarboxyimide) (BPDA-ODA). Changes in thermal and mechanical properties of BPDA-ODA films modified by diimides have been found to depend on the amount of diimide added and the conditions of film preparation (stretching). It has been established that diimides can play two different roles. When dissolved in polyimide, they act as plasticizers improving the segment mobility of BPDA-ODA chains, which may be critically needed to achieve the better molecular packing. The films plasticized by diimides show lower T g and the order–disorder transition temperature; the unstretched films exhibit better tensile properties, compared to unmodified films. However, dispersed beyond the limit of solubility in polyimides, diimides have detrimental effects on mechanical properties of the films. Though changes of the thermal properties of compositions derived from BPDA-ODA polyimide and microparticular diimides are less expressed than those of polyimide films plasticized by diimides, the compositions have poorer ultimate strength and shorter elongation at break. The conclusion may be drawn that the mechanical properties of the films modified by microparticular diimide are mainly controlled not by the interfacial interaction matrix–microparticles, but more likely by the much stronger macromolecular chain–chain interaction.
EphPub: Toward robust Ephemeral Publishing (2011)

The increasing amount of personal and sensitive information disseminated over the Internet prompts commen-surately growing privacy concerns. Digital data often lingers indefinitely and users lose its control. This motivates the desire to restrict content availability to an expiration time set by the data owner. This paper presents and formalizes the notion of Ephemeral Publishing (EphPub), to prevent the access to expired content. We propose an efficient and robust protocol that builds on the Domain Name System (DNS) and its caching mechanism. With EphPub, sensitive content is published encrypted and the key material is distributed, in a steganographic manner, to randomly selected and independent resolvers. The availability of content is then limited by the evanescence of DNS cache entries. The EphPub protocol is transparent to existing applications, and does not rely on trusted hardware, centralized servers, or user proactive actions. We analyze its robustness and show that it incurs a negligible overhead on the DNS infrastructure. We also perform a large-scale study of the caching behavior of 900K open DNS resolvers. Finally, we propose Firefox and Thunderbird extensions that provide ephemeral publishing capabilities, as well as a command-line tool to create ephemeral files.