gebhart/patrepeval huggingface dataset:
Model-based Halftoning (2005)

A model-based printing method and system for generating halftone output images corresponding to gray-scale-coded input signals. Models for individual two-level (e.g., black on white) printer types allow predicted printer error signals to be generated which can be used to modify the gray-scale coded signals in such manner as to produce binary signals which, when applied to the printer, create halftone images of enhanced quality. In an alternative embodiment binary signals are selected which minimize an error function based on the difference between (i) a predicted perceived image corresponding to the gray scale inputs as filtered by an eye-model filter and (ii) the halftone image resulting from filtering of the binary sequence by a filter modeling the printer followed by the eye-model filter.
The role of adhesion molecules and T cells in ischemic renal injury (2003)

The identification of T cells and new adhesion molecule pathways as modulators of ischemic acute renal failure offers novel and feasible therapeutic opportunities for both native and transplant acute renal failure. Rigorous clinical trials are required to translate these basic findings to the bedside. In addition, mechanistic studies are needed to elucidate the molecular mechanisms by which these pathways modulate kidney injury. The identification of T cell engagement in ischemic renal injury can also help explain long-standing observations linking alloantigen-independent and alloantigen-dependent renal damage.
Magnetic nanoparticle design for medical diagnosis and therapy (2004)

Magnetic nanoparticles have attracted attention because of their current and potential usefulness as contrast agents for magnetic resonance imaging (MRI) or colloidal mediators for cancer magnetic hyperthermia. This review examines these in vivo applications through an understanding of the involved problems and the current and future possibilities for resolving them. A special emphasis is made on magnetic nanoparticle requirements from a physical viewpoint (e.g. relaxivity for MRI and specific absorption rate for hyperthermia), the factors affecting their biodistribution (e.g. size, surface hydrophobic/hydrophilic balance, etc.) and the solutions envisaged for enhancing their half-life in the blood compartment and targeting tumour cells.
Genetic mapping of ada and adc mutations affecting the adaptive response of Escherichia coli to alkylating agents (1982)

The adaptive response to alkylating agents is an inducible repair system which protects Escherichia coli against the mutagenicity and toxicity of these agents. Four mutations, ada-3, ada-5, ada-6, and adc-1, which confer differing phenotypes as regards this response, were shown to be cotransducible with gyrA, and were located at 47 min on the E. coli genetic map. A mutation already shown on the map at 47 min as tag (B. J. Bachmann and K. B. Low, Microbiol. Rev. 44:1--56, 1980; Karran et al., J. Mol. Biol. 140:101--127, 1980) is now known to be an ada mutation (G. Evensen and E. Seeberg, personal communication).
Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis (2017)

Circular RNAs (circRNAs) constitute a family of transcripts with unique structures and still largely unknown functions. Their biogenesis, which proceeds via a back-splicing reaction, is fairly well characterized, whereas their role in the modulation of physiologically relevant processes is still unclear. Here we performed expression profiling of circRNAs during in vitro differentiation of murine and human myoblasts, and we identified conserved species regulated in myogenesis and altered in Duchenne muscular dystrophy. A high-content functional genomic screen allowed the study of their functional role in muscle differentiation. One of them, circ-ZNF609, resulted in specifically controlling myoblast proliferation. Circ-ZNF609 contains an open reading frame spanning from the start codon, in common with the linear transcript, and terminating at an in-frame STOP codon, created upon circularization. Circ-ZNF609 is associated with heavy polysomes, and it is translated into a protein in a splicing-dependent and cap-independent manner, providing an example of a protein-coding circRNA in eukaryotes.
The DNA Sequences of the Long Repeat Region and Adjoining Parts of the Long Unique Region in the Genome of Herpes Simplex Virus Type 1 (1988)

We have determined the DNA sequence of the long repeat region (RL) in the genome of herpes simplex virus type 1 (HSV-1) strain 17, as 9215 bp of composition 71.6% G + C. In addition, the sequences of parts of the long unique region (UL) adjacent to the terminal (TRL) and internal (IRL) copies of RL were determined (2611 and 3836 bp, respectively). Gene organization in these regions of UL was deduced from the sequences and other available data. It was proposed that the region of UL sequenced, adjacent to TRL, contains three complete genes, none with significant previous characterization, and that the region of UL adjacent to IRL also contains three genes, one encoding the immediate early protein IE63. The RL sequence contains one well characterized gene, for the protein IE110, whose organization we have described previously. Between the downstream end of the IE110 gene and UL there is a 3500 bp segment of RL in which we did not find convincing protein-coding sequences, and which thus remains of obscure functionality. Upstream of the IE110 gene is a region previously proposed by others to contain a gene. However, our sequence data are not compatible with their interpretation. We do consider it possible that the region is protein-coding, but regard gene organization here as still unresolved.
Pathogenesis and Treatment of Graft-Versus-Host Disease After Bone Marrow Transplant (2003)

Stem cell transplantation is being used to treat a number of hematologic malignancies as well as hematologic and immune deficiency states. The ages of patients being offered this therapy and the donor marrow sources have been expanded. One persistent problem has been graft-versus-host disease (GVHD). This article reviews the basic biology of GVHD, clinical manifestations of acute and chronic GVHD, prophylaxis and treatment of acute GVHD, and treatment of chronic GVHD.
Treatment of rheumatoid arthritis with platelet activating factor antagonist BN 50730. (1995)

These results need to be confirmed in a controlled study, but suggest an antiinflammatory effect. PAF antagonists could represent a new class of therapeutic agents in inflammatory arthropathies.
The unfolded protein response coordinates the production of endoplasmic reticulum protein and endoplasmic reticulum membrane. (1997)

The endoplasmic reticulum (ER) is a multifunctional organelle responsible for production of both lumenal and membrane components of secretory pathway compartments. Secretory proteins are folded, processed, and sorted in the ER lumen and lipid synthesis occurs on the ER membrane itself. In the yeast Saccharomyces cerevisiae, synthesis of ER components is highly regulated: the ER-resident proteins by the unfolded protein response and membrane lipid synthesis by the inositol response. We demonstrate that these two responses are intimately linked, forming different branches of the same pathway. Furthermore, we present evidence indicating that this coordinate regulation plays a role in ER biogenesis.
Deep neural networks for acoustic emotion recognition: Raising the benchmarks (2011)

Deep Neural Networks (DNNs) denote multilayer artificial neural networks with more than one hidden layer and millions of free parameters. We propose a Generalized Discriminant Analysis (GerDA) based on DNNs to learn discriminative features of low dimension optimized with respect to a fast classification from a large set of acoustic features for emotion recognition. On nine frequently used emotional speech corpora, we compare the performance of GerDA features and their subsequent linear classification with previously reported benchmarks obtained using the same set of acoustic features classified by Support Vector Machines (SVMs). Our results impressively show that low-dimensional GerDA features capture hidden information from the acoustic features leading to a significantly raised unweighted average recall and considerably raised weighted average recall.
Prediction of regulatory modules comprising microRNAs and target genes (2005)

A list of predicted modules is available from the authors upon request.
A Genetic Approach to Analyzing Membrane Protein Topology (1986)

Fusions of the secreted protein alkaline phosphatase to an integral cytoplasmic membrane protein of Escherichia coli showed different activities depending on where in the membrane protein the alkaline phosphatase was fused. Fusions to positions in or near the periplasmic domain led to high alkaline phosphatase activity, whereas those to positions in the cytoplasmic domain gave low activity. Analysis of alkaline phosphatase fusions to membrane proteins of unknown structure may thus be generally useful in determining their membrane topologies.
Symbiont-mediated insecticide resistance (2012)

Development of insecticide resistance has been a serious concern worldwide, whose mechanisms have been attributed to evolutionary changes in pest insect genomes such as alteration of drug target sites, up-regulation of degrading enzymes, and enhancement of drug excretion. Here, we report a previously unknown mechanism of insecticide resistance: Infection with an insecticide-degrading bacterial symbiont immediately establishes insecticide resistance in pest insects. The bean bug Riptortus pedestris and allied stinkbugs harbor mutualistic gut symbiotic bacteria of the genus Burkholderia, which are acquired by nymphal insects from environmental soil every generation. In agricultural fields, fenitrothion-degrading Burkolderia strains are present at very low densities. We demonstrated that the fenitrothion-degrading Burkholderia strains establish a specific and beneficial symbiosis with the stinkbugs and confer a resistance of the host insects against fenitrothion. Experimental applications of fenitrothion to field soils drastically enriched fenitrothion-degrading bacteria from undetectable levels to >80% of total culturable bacterial counts in the field soils, and >90% of stinkbugs reared with the enriched soil established symbiosis with fenitrothion-degrading Burkholderia. In a Japanese island where fenitrothion has been constantly applied to sugarcane fields, we identified a stinkbug population wherein the insects live on sugarcane and ≈8% of them host fenitrothion-degrading Burkholderia. Our finding suggests the possibility that the symbiont-mediated insecticide resistance may develop even in the absence of pest insects, quickly establish within a single insect generation, and potentially move around horizontally between different pest insects and other organisms.
Endocrine Therapy for Hormone Receptor–Positive Metastatic Breast Cancer: American Society of Clinical Oncology Guideline (2016)

Sequential hormone therapy is the preferential treatment for most women with HR-positive MBC. Except in cases of immediately life-threatening disease, hormone therapy, alone or in combination, should be used as initial treatment. Patients whose tumors express any level of hormone receptors should be offered hormone therapy. Treatment recommendations should be based on type of adjuvant treatment, disease-free interval, and organ function. Tumor markers should not be the sole criteria for determining tumor progression; use of additional biomarkers remains experimental. Assessment of menopausal status is critical; ovarian suppression or ablation should be included in premenopausal women. For postmenopausal women, aromatase inhibitors (AIs) are the preferred first-line endocrine therapy, with or without the cyclin-dependent kinase inhibitor palbociclib. As second-line therapy, fulvestrant should be administered at 500 mg with a loading schedule and may be administered with palbociclib. The mammalian target of rapamycin inhibitor everolimus may be administered with exemestane to postmenopausal women with MBC whose disease progresses while receiving nonsteroidal AIs. Among patients with HR-positive, human epidermal growth factor receptor 2-positive MBC, human epidermal growth factor receptor 2-targeted therapy plus an AI can be effective for those who are not chemotherapy candidates.
Comparison of the effects of FK-506, cyclosporin A and rapamycin on IL-2 production. (1991)

The immunosuppressive compounds FK-506, cyclosporin A (CsA) and rapamycin inhibit both the human and mouse mixed lymphocyte reactions (MLR) with IC50s of 2-5 x 10(-10) M for FK-506 and rapamycin and 10(-8) M for CsA. FK-506 and CsA were also potent inhibitors of A23187/PMA-stimulated IL-2 production by Jurkat and HuT-78 cells but had no effect on the response of mouse CTLL cells to IL-2. IC50 values for inhibition of IL-2 production closely matched those for inhibition of the MLR and both drugs were active only during the first 4-6 hr following stimulation. In contrast, rapamycin was a poor inhibitor of IL-2 production, although it inhibited cellular responses to IL-2. The IC50 values for these two activities indicated that neither alone accounted for rapamycin inhibition of the MLR. FK-506 and CsA affected IL-2 gene transcription in Jurkat cells by the same mechanism. Both inhibited the appearance of the transcription factor, NFAT, whereas rapamycin did not. The appearance of another transcription factor, NFK beta, was unaffected by all three drugs. The effects of FK-506 and CsA on IL-2 gene expression, therefore, are similar even though the two drugs act through distinct cytosolic receptors.
Examining e-health. (2002)

As part of its continuing mission to serve trustees and staff of health foundations and corporate giving programs, Grantmakers In Health (GIH) convened a small group of representatives from foundations, healthcare organizations, and the technology field to share their experiences and expertise on electronic health (e-health). This roundtable, held April 28, 2002, in Chicago, Illinois, highlighted emerging opportunities and challenges for foundations that wish to fund e-health initiatives. This report summarizes some of the key points from the day's discussion, providing both an introduction for grantmakers new to this area and offering the perspectives of some funders already experienced in funding e-health activities.
Bacteriolytic Activity and Specificity of Achromobacter -Lytic Protease (1998)

Achromobacter beta-lytic protease (blp), one of the bacteriolytic proteases secreted by Achromobacter lyticus, exhibited both peptidase and bacteriolytic activities at alkaline pH. The protease was strongly inhibited by 1,10-phenanthroline, and one zinc atom was detected in the molecule by ion-spray mass spectrometry. The zinc-protease specifically cleaved Gly-X bonds in peptides and possibly possessed subsites S2, S1, S1', and S2' for binding substrate [Schecter, I. and Berger, A. (1967) Biochem. Biophys. Res. Commun. 27, 157-162]. Blp lysed Staphylococcus aureus and Micrococcus luteus cells more efficiently than Achromobacter alpha-lytic protease (alp) and lysozyme, thus being responsible for the high bacteriolytic activity of A. lyticus. In the lysis of bacterial cell walls, blp hydrolyzed both the D-Ala-Gly/Ala bond at the linkage between the peptide subunit and the interpeptide and the Gly-Gly bond in the interpeptide bridge. These results indicate that blp is a highly active bacteriolytic enzyme with a broad bacteriolytic spectrum, which acts primarily by splitting the linkage between the peptide subunit and the interpeptide in the peptidoglycan.
Studies of apoptosis and bcl-2 in experimental atherosclerosis in rabbit and influence of selenium supplementation. (2002)

Apoptosis is a ubiquitous physiological mechanism of cell death regulating tissue mass and architecture. An attempt was made in the present study to see the occurrence of apoptotic cell death in three different treatment groups of rabbits viz. Control, HFD fed and HFD + Selenium fed. Apoptotic activity as checked by in situ DNA end labelling (TUNEL Assay) revealed excessive staining, mostly concentrated in plaque region both in fibrous as well as atheromatous plaque in HFD fed animals. However, in selenium (Se) supplemented animals, very little TUNEL staining could be seen, and even that confined to endothelial cells only. The control group on the other hand was totally devoid of any staining. Transmission Electron Microscopic (TEM) study also depicted the occurrence of apoptosis in aortic cells of HFD fed animals and very little in Se supplemented animals. Apoptotic activity has been discussed in relation to oxidative stress in HFD fed group. bcl-2, though an antiapoptotic oncoprotein, was found to be expressed more in atherogenic group as compared to control/HFD + Se treatment. On the whole, the study highlighted the occurrence of apoptotic process in atherosclerosis and the role of Se, a potent antioxidant, in inhibition of apoptotic process in HFD fed animals.
Interferon Gamma-1b for the Treatment of Idiopathic Pulmonary Fibrosis (1999)

Idiopathic pulmonary fibrosis is a chronic condition of the lung parenchyma involving progressive injury, inflammation, and fibrosis. Data collected from October 1988 through September 1990 in the population-based registry of patients with diffuse lung disease in Bernalillo County, New Mexico, suggest that the prevalence of this disease is roughly 20 cases per 100,000 men and 13 per 100,000 women.1 Idiopathic pulmonary fibrosis has the highest mortality of all of the diffuse lung diseases. Mortality rates from the disease almost doubled in England and Wales between 1979 and 1988,2 an increase that was not due to differences in the way the . . .
RF TAGS KEEP TRACK AUTOMATICALLY (1991)

Readers of this publication will be more aware than most of the fundamental changes that have occurred in the process of manufacturing. A combination of economic pressures and the advent of enabling technology, primarily driven by the development of IC microchips, have driven a conceptual re‐evaluation and restructuring of manufacturing and distribution.
Use of automated sequencing of polymerase chain reaction-generated amplicons to identify three types of cholera toxin subunit B in Vibrio cholerae O1 strains (1993)

Cholera toxin is the principal factor causing the profuse intestinal fluid secretion that is characteristic of cholera. The DNA sequences of the cholera toxin subunit B structural genes from 45 Vibrio cholerae O1 strains isolated in 29 countries over a period of 70 years were determined by automated DNA sequencing of polymerase chain reaction-generated amplicons. Three types of cholera toxin B subunit gene (ctxB) were identified. Genotype 1 was found in strains of classical biotype worldwide and El Tor biotype strains associated with the U.S. Gulf Coast, genotype 2 was found in El Tor biotype strains from Australia, and genotype 3 was found in El Tor biotype strains from the seventh pandemic and the recent Latin American epidemic. All base changes correspond to an amino acid substitution in the B subunit of the cholera toxin. Heterogenicity in the B subunit could have implications for vaccine development and diagnostic tests for cholera toxin and antitoxin. We conclude that this technology provides timely and potentially useful epidemiological information.
Trail of bytes (2010)

For the most part, forensic analysis of computer systems requires that one first identify suspicious objects or events, and then examine them in enough detail to form a hypothesis as to their cause and effect. Sadly, while our ability to gather vast amounts of data has improved significantly over the past two decades, it is all too often the case that we tend to lack detailed information just when we need it the most. Simply put, the current state of computer forensics leaves much to be desired. In this paper, we attempt to improve on the state of the art by providing a forensic platform that transparently monitors and records data access events within a virtualized environment using only the abstractions exposed by the hypervisor. Our approach monitors accesses to objects on disk and follows the causal chain of these accesses across processes, even after the objects are copied into memory. Our forensic layer records these transactions in a version-based audit log that allows for faithful, and efficient, reconstruction of the recorded events and the changes they induced. To demonstrate the utility of our approach, we provide an extensive empirical evaluation, including a real-world case study demonstrating how our platform can be used to reconstruct valuable information about the what, when, and how, after a compromised has been detected.
Isolation and structural mapping of a human c-src gene homologous to the transforming gene (v-src) of Rous sarcoma virus (1985)

We have utilized a lambda Charon 4A human genomic library to isolate recombinant clones harboring a highly conserved c-src locus containing nucleotide sequences homologous to the transforming gene of Rous sarcoma virus (v-src). Four overlapping clones spanning 24 kilobases of cellular DNA were analyzed by restriction endonuclease mapping. Human c-src sequences homologous to the entire v-src region are present in a 20-kilobase region that contains 11 exons as determined by restriction mapping studies utilizing hybridization to labeled DNA probes representing various subregions of the v-src gene and by preliminary DNA sequencing analyses. A considerable degree of similarity exists between the organization of the human c-src gene and that of the corresponding chicken c-src gene with respect to exon size and number. However, the human c-src locus is larger than the corresponding chicken c-src locus, because many human c-src introns are larger than those of chicken c-src. alu family repetitive sequences are present within several human c-src introns. This locus represents a highly conserved human c-src locus that is detectable in human cellular DNAs from various sources including placenta, HeLa cells, and WI-38 cells.
High Resolution Radial Distribution Function of Pure Amorphous Silicon (1999)

The structure factor $S(Q)$ of high purity amorphous Si membranes prepared by ion implantation was measured over an extended $Q$ range ( $0.03--55{\AA{}}^{\ensuremath{-}1}$). Calculation of the first neighbor shell coordination ( ${C}_{1}$) as a function of maximum $Q$ indicates that measurement of $S(Q)$ out to at least $40{\AA{}}^{\ensuremath{-}1}$ is required to reliably determine the radial distribution function (RDF). A $2%$ change in ${C}_{1}$ and subtle changes in the rest of the RDF were observed upon annealing, consistent with point defect removal. After annealing at 600 \ifmmode^\circ\else\textdegree\fi{}C, ${C}_{1}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}3.88$, which would explain why amorphous Si is less dense than crystalline Si.
Sequence Analysis and Characterization of Stutter Products at the Tetranucleotide Repeat Locus VWA (1996)

The PCR amplification of tetranucleotide short tandem repeat (STR) loci typically produces a minor product band 4 bp shorter than the corresponding main allele band; this is referred to as the stutter band. Sequence analysis of the main and stutter bands for two sample alleles of the STR locus vWA reveals that the stutter band lacks one repeat unit relative to the main allele. Sequencing results also indicate that the number and location of the different 4 bp repeat units vary between samples containing a typical verses low proportion of stutter product. The results also suggest that the proportion of stutter product relative to the main allele increases as the number of uninterrupted core repeat units increases. The sequence analysis and results obtained using various DNA polymerases appear to support the slipped strand displacement model as a potential explanation for how these stutter products are generated.