gebhart/patrepeval huggingface dataset:
Full Resolution Image Compression with Recurrent Neural Networks (2017)

This paper presents a set of full-resolution lossy image compression methods based on neural networks. Each of the architectures we describe can provide variable compression rates during deployment without requiring retraining of the network: each network need only be trained once. All of our architectures consist of a recurrent neural network (RNN)-based encoder and decoder, a binarizer, and a neural network for entropy coding. We compare RNN types (LSTM, associative LSTM) and introduce a new hybrid of GRU and ResNet. We also study “one-shot” versus additive reconstruction architectures and introduce a new scaled-additive framework. We compare to previous work, showing improvements of 4.3%-8.8% AUC (area under the rate-distortion curve), depending on the perceptual metric used. As far as we know, this is the first neural network architecture that is able to outperform JPEG at image compression across most bitrates on the rate-distortion curve on the Kodak dataset images, with and without the aid of entropy coding.
Properties of Recombinant Human Cytosolic Sialidase HsNEU2 (2004)

Recombinant human cytosolic sialidase (HsNEU2), expressed in Escherichia coli, was purified to homogeneity, and its substrate specificity was studied. HsNEU2 hydrolyzed 4-methylumbelliferyl alpha-NeuAc, alpha 2-->3 sialyllactose, glycoproteins (fetuin, alpha-acid glycoprotein, transferrin, and bovine submaxillary gland mucin), micellar gangliosides GD1a, GD1b, GT1b, and alpha 2-->3 paragloboside, and vesicular GM3. alpha 2-->6 sialyllactose, colominic acid, GM1 oligosaccharide, whereas micellar GM2 and GM1 were resistant. The optimal pH was 5.6, kinetics Michaelis-Menten type, V(max) varying from 250 IU/mg protein (GD1a) to 0.7 IU/mg protein (alpha(1)-acid glycoprotein), and K(m) in the millimolar range. HsNEU2 was activated by detergents (Triton X-100) only with gangliosidic substrates; the change of GM3 from vesicular to mixed micellar aggregation led to a 8.5-fold V(max) increase. HsNEU2 acted on gangliosides (GD1a, GM1, and GM2) at nanomolar concentrations. With these dispersions (studied in detailed on GM1), where monomers are bound to the tube wall or dilutedly associated (1:2000, mol/mol) to Triton X-100 micelles, the V(max) values were 25 and 72 microIU/mg protein, and K(m) was 10 and 15 x 10(-9) m, respectively. Remarkably, GM1 and GM2 were recognized only as monomers. HsNEU2 worked at pH 7.0 with an efficiency (compared with that at pH 5.6) ranging from 4% (on GD1a) to 64% (on alpha(1)-acid glycoprotein), from 7% (on GD1a) to 45% (on GM3) in the presence of Triton X-100, and from 30 to 40% on GM1 monomeric dispersion. These results show that HsNEU2 differentially recognizes the type of sialosyl linkage, the aglycone part of the substrate, and the supramolecular organization (monomer/micelle/vesicle) of gangliosides. The last ability might be relevant in sialidase interactions with gangliosides under physiological conditions.
A Prototype Antibody Microarray Platform to Monitor Changes in Protein Tyrosine Phosphorylation (2004)

Reversible protein phosphorylation is a key regulatory process in all living cells. Deregulation of modification control mechanisms, especially in the case of tyrosine, may lead to malignant transformation and disease. Phosphotyrosine (p-Tyr) accounts for only 0.05% of the total cellular phospho-amino acid content, yet plays an unusually prominent role in eukaryotic signaling, development, and growth. Tracking temporal and positional p-Tyr changes across the cellular proteome, i.e. tyrosine phosphoproteomics, is therefore tremendously valuable. Here, we describe and evaluate a prototype antibody (Ab) microarray platform to monitor changes in protein Tyr phosphorylation. Availability permitting, a virtually unlimited number of Abs, each recognizing a specific cellular protein, may be arrayed on a chip, incubated with total cell or tissue extracts or with biological fluids, and then probed with a fluorescently labeled p-Tyr-specific monoclonal Ab, PY-KD1, specifically generated for this assay as part of the current study. The optimized protocol allowed detection of changes in the Tyr phosphorylation state of selected proteins using submicrogram to low nanogram of total protein extract, amounts that may conceivably be obtained from a thousand to a hundred thousand cells, or less, depending on the cell or tissue type. The assay platform was evaluated by assessing changes in a rationally selected subset of the Tyr phosphoproteome of Bcr-Abl-expressing cells treated with a specific inhibitor, Gleevec, and of epidermal growth factor (EGF)-treated HeLa cells. The results, ratiometric rather than strictly quantitative in nature, conformed with previous identifications of several Bcr-Abl and EGF receptor targets, and associated proteins, as detected by exhaustive mass spectrometric analyses. The Ab microarray method described here offers advantages of low sample and reagent consumption, scalability, detection multiplexing, and potential compatibility with microfluidic devices and automation. The system may hold particular promise for dissecting signaling pathways, molecular classification of tumors, and profiling of novel target-cancer drugs.
Discriminating Different Classes of Toxicants by Transcript Profiling (2004)

Male rats were treated with various model compounds or the appropriate vehicle controls. Most substances were either well-known hepatotoxicants or showed hepatotoxicity during preclinical testing. The aim of the present study was to determine if biological samples from rats treated with various compounds can be classified based on gene expression profiles. In addition to gene expression analysis using microarrays, a complete serum chemistry profile and liver and kidney histopathology were performed. We analyzed hepatic gene expression profiles using a supervised learning method (support vector machines; SVMs) to generate classification rules and combined this with recursive feature elimination to improve classification performance and to identify a compact subset of probe sets with potential use as biomarkers. Two different SVM algorithms were tested, and the models obtained were validated with a compound-based external cross-validation approach. Our predictive models were able to discriminate between hepatotoxic and nonhepatotoxic compounds. Furthermore, they predicted the correct class of hepatotoxicant in most cases. We provide an example showing that a predictive model built on transcript profiles from one rat strain can successfully classify profiles from another rat strain. In addition, we demonstrate that the predictive models identify nonresponders and are able to discriminate between gene changes related to pharmacology and toxicity. This work confirms the hypothesis that compound classification based on gene expression data is feasible.
Proxies for anonymous routing (2002)

Using traffic analysis, it is possible to infer who is talking to whom over a public network. This paper describes a flexible communications infrastructure, called onion routing, which is resistant to traffic analysis. Onion routing lies just beneath the application layer, and is designed to interface with a wide variety of unmodified Internet services by means of proxies. Onion routing has been implemented on a Sun Solaris 2.4; in addition, proxies for World Wide Web browsing (HTTP), remote logins (RLOGIN), e-mail (SMTP) and file transfers (FTP) have been implemented. Onion routing provides application-independent, real-time and bi-directional anonymous connections that are resistant to both eavesdropping and traffic analysis. Applications making use of onion routing's anonymous connections may (and usually should) identify their users over the anonymous connection. User anonymity may be layered on top of the anonymous connections by removing identifying information from the data stream. Our goal is anonymous connections, not anonymous communication. The use of a packet-switched public network should not automatically reveal who is talking to whom; this is the traffic analysis that onion routing complicates.
Aromatization of Androgens by Muscle and Adipose Tissue in Vivo* (1978)

[7-3HA1Androstenedione and [4-14C]estrone or [7-3H]testosterone and [14C]estradiol were infused at constant rates into brachial arm veins of 15 normal men. During the infusions blood samples were obtained from the brachial artery, a deep vein draining primarily muscle, and a superficial vein draining primarily adipose tissue of the arm contralateral to the infusion. In seven men the mean +/- SE value for the fractional conversion of androstene tissue. In eight men the mean +/- SE value for the fractional conversion of testosterone to estradiol was 0.0007 +/- 0.0001 for muscle and 0.0012 +/- 0.0002 for adipose tissue. Both of these values were significantly (P less than 0.01) less than the respective values of androstenedione aromatization to estrone. If constancy of tissue aromatization throughout the body is assumed, the muscle accounts for 25-30% and adipose tissue for 10-15% of the total extragonadal aromatization of androgens to estrogens.
Interaction between neurotransmitter antagonists and effects of sacral neuromodulation in rats with chronically hyperactive bladder (2005)

The results suggest that non-NMDA receptors are involved in the effects of sacral neuromodulation, whereas NMDA receptors appear to have no role. Nitric oxide is essential for maintaining the chronic hyperactive state of the urinary bladder.
Pathogenicity of a baculovirus infection causing white spot syndrome in cultured penaeid shrimp in Taiwan (1995)

Outbreaks of a disease causing serious losses among populations of cultured penaeid shrimp, including Penaeus monodon, P japonicus and P penicillatus, in Taiwan are characterized by obvious white spots on the carapace, appendages and the inside surface of the body. For this reason, we propose the name 'white spot syndrome' (WSS). Healthy juvenile kuruma shrimp P japonjcus were exposed by immersion to epidermal filtrate from diseased P japonicus and L? monodon which exhibited marked white spot signs. These experimentally infected shrimp resembled the spontaneously infected ones. Cumulative mortalities reached 100% within 5 to 7 d and were significantly affected by catching and temperature stress. A non-occluded rod-shaped viral particle was found by electron microscopy in the epidermis of both spontaneously and experimentally infected kuruma shrimp. Virions were enveloped, 330 + 20 nm in length and 87 * 7 nm in diameter. The close resemblance in external signs and viral morphology between spontaneously diseased and experimentally infected shrimp indicated that the rod-shaped virus may be the main causative agent of the disease characterized by white spot syndrome in Taiwan.
Doubly-True Alphametics (1994)

Alphametics (AMs) are crypted arithmetic problems; one or two are included in almost every collection of adult puzzles. They are a regular feature in the Journal of Recreational Mathematics (JRM). Precedent for including AMs as logology is provided by Dmitri Borgmann in "Language on Vacation."
Penile Metastasis Secondary to Esophageal Squamous Cell Carcinoma: A Case Report and Review of the Literature (2005)

Tumors that metastasize to the penis are very rare, especially primary esophageal carcinomas. A review of the literature showed that frequent primary sites are the genitourinary system (74.3%) and gastrointestinal tract (18.6%). We report a case of a metastatic penile tumor secondary to an esophageal carcinoma. To our knowledge, this is the second case of penile metastasis from an esophageal carcinoma reported in the literature so far.
There is no universally accepted treatment for metastatic penile malignancies. Whether tumor excision with a 2-cm margin-free status or palliative therapy can improve survival has not been definitively concluded. Generally, the prognosis of metastatic penile tumors from esophageal squamous cell carcinomas is poor. Our patient died 1 year after the diagnosis of his metastases. Improvement of the quality of life is the goal of treatment.
Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases (2011)

Zinc-finger nucleases and TALE nucleases are produced by combining a specific DNA-binding module and a non-specific DNA-cleavage module, resulting in nucleases able to cleave DNA at a unique sequence. Here a new approach for creating highly specific nucleases was pursued by fusing a catalytically inactive variant of the homing endonuclease I-SceI, as DNA binding-module, to the type IIP restriction enzyme PvuII, as cleavage module. The fusion enzymes were designed to recognize a composite site comprising the recognition site of PvuII flanked by the recognition site of I-SceI. In order to reduce activity on PvuII sites lacking the flanking I-SceI sites, the enzymes were optimized so that the binding of I-SceI to its sites positions PvuII for cleavage of the composite site. This was achieved by optimization of the linker and by introducing amino acid substitutions in PvuII which decrease its activity or disturb its dimer interface. The most specific variant showed a more than 1000-fold preference for the addressed composite site over an unaddressed PvuII site. These results indicate that using a specific restriction enzyme, such as PvuII, as cleavage module, offers an alternative to the otherwise often used catalytic domain of FokI, which by itself does not contribute to the specificity of the engineered nuclease.
Systematic review: faecal transplantation for the treatment of Clostridium difficile‐associated disease (2012)

Although these results appear to be promising, the treatment effects of faecal transplantation cannot be determined definitively in the absence of a control group. Results from randomised controlled trials that compare faecal transplantation to oral vancomycin without or with a taper regimen will help to better define the role of faecal transplantation in the management of recurrent CDAD.
Taurolidine: in vitro Activity against Multiple-Antibiotic-Resistant, Nosocomially Significant Clinical Isolates of <i>Staphylococcus aureus</i>, Enterococcus faecium, and Diverse Enterobacteriaceae (1993)

Taurolidine at < or = 1,250 micrograms/ml killed all 37 isolates of multiple-antibiotic-resistant Staphylococcus aureus (n = 9), Enterococcus faecium (n = 17), and Enterobacteriaceae (n = 11). Time-kill experiments disclosed that bovine serum (65% v/v) only marginally retarded the bactericidal activity of 2,000 and 1,000 micrograms/ml of taurolidine against the various strains. Taurolidine at 2,000 micrograms/ml did not antagonize the bactericidal activity of 50% (v/v) fresh human serum against promptly and delayed serum-sensitive test strains of Escherichia coli and Serratia marcescens. In the presence of 65% (v/v) of fresh defibrinated human blood from two donors, however, the bactericidal activity of this antimicrobial compound was delayed, i.e., manifested only following extended (overnight) incubation, against staphylococcal and enterococcal isolates, though less so in the case of Enterobacteriaceae. Taurolidine at 2,000 micrograms/ml killed ingested, i.e., intraphagocytic bacteria of human-serum-resistant S. marcescens strains CDC 06:H3 and P016:H-.
Enhanced Biodegradation of Toxic Organophosphate Compounds Using Recombinant Escherichia coli with Sec Pathway-Driven Periplasmic Secretion of Organophosphorus Hydrolase (2006)

Although Escherichia coli can be genetically engineered to degrade environmental toxic organophosphate compounds (OPs) to nontoxic materials, a critical problem in such whole cell systems is limited substrate diffusion. The present work examined whether periplasmic expression of organophosphorus hydrolase (OPH) resulted in better whole cell enzymatic activity compared to standard cytosolic expression. Recombinant OPH periplasmic expression was achieved using the general secretory (sec) pathway with the pelB signal sequence. We found that while total OPH activity in periplasmic-expressing cell lysates was lower compared to that in cytosolic-expressing cell lysates whole cell OPH activity was 1.8-fold greater at 12 h post-induction in the periplasmic-expressing cells as a result of OPH translocation into the periplasmic space ( approximately 67% of whole cell OPH activity was found in the periplasmic fraction). These data suggest that E. coli engineered to periplasmically secrete OPH via the sec pathway may provide an improved whole cell biodegradation system for destruction of environmental toxic OPs.
Xenopus Cyr61regulates gastrulation movements and modulates Wnt signalling (2003)

Cyr61 is a secreted, heparin-binding, extracellular matrix-associated protein whose activities include the promotion of adhesion and chemotaxis, and the stimulation of fibroblast and endothelial cell growth. Many, if not all, of these activities of Cyr61 are mediated through interactions with integrins. We explore the role of Cyr61 in the early development of Xenopus laevis. Gain- and loss-of-function experiments show that Xcyr61 is required for normal gastrulation movements. This role is mediated in part through the adhesive properties of Xcyr61 and its related ability to modulate assembly of the extracellular matrix. In addition, Xcyr61 can, in a context-dependent manner, stimulate or inhibit signalling through the Wnt pathway. These properties of Xcyr61 provide a mechanism for integrating cell signalling, cell adhesion and cell migration during gastrulation.
Protein–protein interaction in insulin signaling and the molecular mechanisms of insulin resistance (1999)

Schematic illustration of major signaling pathways of insulin action. The phosphorylated insulin receptor binds and phosphorylates IRS proteins and Shc, which bind differentially to various downstream signaling proteins. PI3-kinase is critical for metabolic actions of insulin, such as glucose transport, glycogen synthesis, and protein synthesis, whereas Grb-2/SOS complex, which activates the MAP kinase cascade, is critical in mitogenic response. PI3-kinase probably modulates the mitogenic response as well.
Isolation Set-Kernel and Its Application to Multi-Instance Learning (2019)

Set-level problems are as important as instance-level problems. The core in solving set-level problems is: how to measure the similarity between two sets. This paper investigates data-dependent kernels that are derived directly from data. We introduce Isolation Set-Kernel which is solely dependent on data distribution, requiring neither class information nor explicit learning. In contrast, most current set-similarities are not dependent on the underlying data distribution. We theoretically analyze the characteristic of Isolation Set-Kernel. As the set-kernel has a finite feature map, we show that it can be used to speed up the set-kernel computation significantly. We apply Isolation Set-Kernel to Multi-Instance Learning (MIL) using SVM classifier, and demonstrate that it outperforms other set-kernels or other solutions to the MIL problem.
Intralesional injection of mumps or Candida skin test antigens: a novel immunotherapy for warts. (2001)

Intralesional injection of mumps or Candida antigens into warts of immune individuals represents effective treatment. Observation of clearing of anatomically distinct and distant warts suggests acquisition of human papillomavirus-directed immunity in some patients. We conclude that this novel approach to immunotherapy may serve as first-line treatment in immune individuals with multiple or large warts and as second-line treatment in immune patients for whom cryotherapy fails.
Conserved and variable structural features in the lipopolysaccharide of <I>Pseudomonas aeruginosa</I> (2006)

The review is devoted to recent progress in the structural elucidation of the lipopolysaccharide of the bacterium Pseudomonas aeruginosa, including O-antigen biological repeats, core oligosaccharide, and lipid A. Data on biosynthesis, genetics and serology of the lipopolysaccharide isolated from various P. aeruginosa O-serogroups are discussed in relation to the chemical structures.
Human granulocyte-macrophage colony-stimulating factor induces expression of the tumor necrosis factor gene by the U937 cell line and by normal human monocytes. (1987)

Human granulocyte-macrophage colony-stimulating factor (GM-CSF) exerts profound effects on the proliferation, differentiation, and effector function of myeloid lineage cells. In contrast to its growth-promoting effects on normal myeloid progenitor cells, we found that GM-CSF unexpectedly inhibited the colony growth of U937 cells in agar culture. Furthermore, medium conditioned by recombinant GM-CSF(rGM-CSF)-treated U937 cells was found to exert an inhibitory effect on subsequent U937 colony growth that was partially due to the presence of tumor necrosis factor (TNF). By Northern blot analysis, rGM-CSF was shown to induce expression of the TNF gene in U937 cells and in T-lymphocyte-depleted, monocyte-enriched peripheral blood mononuclear cells. Furthermore, rGM-CSF was observed to significantly enhance TNF secretion by monocytes stimulated with endotoxin and phorbol myristate acetate (PMA). These data suggest that some of the biological effects of GM-CSF may be amplified through the release of monokines such as TNF.
Properties of a Highly Purified Human Plasma Factor IX:cTherapeutic Concentrate Prepared by Conventional Chromatography (1989)

We have characterized a highly purified (HP) factor IX concentrate intended for therapy of hemophilia B. The product has been prepared from pooled human plasma using a large-scale procedure combining three conventional chromatographic steps based on DEAE ion exchange and affinity on immobilized heparin. The specific activity of the product was 119±10 IU factor IX:c/mg protein (n = 15), corresponding to a purification factor of about 9,000. The concentrate was free of the vitamin K-dependent clotting factors II, VII and X and of proteins C and S. Most of the contaminants found in factor IX complex concentrate (PCC) were absent in this new product. High-molecular-weight kininogen, factors VIII, XI, XII or prekallikrein were not detected. There were no activated factors, such as factors IXa, and Xa, no thrombin and no phospholipids. Only two contaminants could be detected: C4 and inter-alpha-trypsin inhibitor (about 0.8 and 1.2mg/1,000IU factor IX:c, respectively). The purity of the product, as compared to PCC, was confirmed by sodium dodecylsulfate polyacrylamide gel electrophoresis, cellulose acetate electrophoresis, Grabar- Williams immunoelectrophoresis, and bidimensional immunoelectrophoresis. Thrombogenicity tests in rabbits revealed that the HP factor IX tested had a lower thrombogenic power than the PCC tested. The concentrate has been subjected to a 0.3% tri(n-butyl) phosphate-1% Tween 80 treatment for 6h at 25°C during its production to reduce or eliminate the risk of transmission of plasma-borne lipid-enveloped viruses. These conditions inactivated more than 3.8 log(10) of vesicular stomatitis virus and more than 4.3 log(10) of sindbis virus within 1 and 2 h of treatment, respectively. These data demonstrate that a highly purified therapeutic clotting factor IX concentrate can be prepared from human plasma by conventional chromatographic methods.