gebhart/patrepeval huggingface dataset:
Cholesterol masks membrane glycosphingolipid tumor-associated antigens to reduce their immunodetection in human cancer biopsies (2013)

Glycosphingolipids (GSLs) are neoplastic and normal/cancer stem cell markers and GSL/cholesterol-containing membrane rafts are increased in cancer cell plasma membranes. We define a novel means by which cancer cells can restrict tumor-associated GSL immunoreactivity. The GSL-cholesterol complex reorients GSL carbohydrate to a membrane parallel, rather than perpendicular conformation, largely unavailable for antibody recognition. Methyl-β-cyclodextrin cholesterol extraction of all primary human tumor frozen sections tested (ovarian, testicular, neuroblastoma, prostate, breast, colon, pheochromocytoma and ganglioneuroma), unmasked previously "invisible" membrane GSLs for immunodetection. In ovarian carcinoma, globotriaosyl ceramide (Gb3), the GSL receptor for the antineoplastic Escherichia coli-derived verotoxin, was increased throughout the tumor. In colon carcinoma, Gb3 detection was vastly increased within the neovasculature and perivascular stroma. In tumors considered Gb3 negative (neuroblastoma, Leydig testicular tumor and pheochromocytoma), neovascular Gb3 was unmasked. Tumor-associated GSL stage-specific embryonic antigen (SSEA)-1, SSEA-3, SSEA-4 and globoH were unmasked according to tumor: SSEA-1 in prostate/colon; SSEA-3 in prostate; SSEA-4 in pheochromocytoma/some colon tumors; globoH in prostate/some colon tumors. In colon, anti-SSEA-1 was tumor cell specific. Within the GSL-cholesterol complex, filipin-cholesterol binding was also reduced. These results may relate to the ill-defined benefit of statins on cancer prognosis, for example, prostate carcinoma. We found novel anti-tumor GSL antibodies circulating in 3/5 statin-treated, but not untreated, prostate cancer patients. Lowering tumor membrane cholesterol may permit immune recognition of otherwise unavailable tumor-associated GSL carbohydrate, for more effective immunosurveillance and active/passive immunotherapy. Our results show standard immunodetection of tumor GSLs significantly under assesses tumor membrane GSL content, impinging on the current use of such antigens as cancer vaccines.
Dose‐finding study of 153Sm‐EDTMP in patients with poor‐prognosis osteosarcoma (2009)

Patients with osteosarcoma who have previously been heavily treated with chemotherapy can be safely administered (153)Sm-EDTMP with rapid hematologic recovery. The data from the current study support the development of a future trial to assess the efficacy of combining targeted radiotherapy with cytotoxic chemotherapy as a treatment option for patients with high-risk osteosarcoma.
Organization and expression of the Escherichia coli K-12 dad operon encoding the smaller subunit of D-amino acid dehydrogenase and the catabolic alanine racemase (1994)

A fragment of the Escherichia coli K-12 chromosome complementing the D-amino acid dehydrogenase and catabolic alanine racemase deficiency of a dad operon deletion mutant was cloned in a mini-Mu plasmid. The dadA and dadX genes were localized to a 3.5-kb part of the plasmid insert. The nucleotide sequence of this fragment revealed two open reading frames encoding 432- and 356-amino-acid-long proteins. We show here that they correspond to the dadA and dadX genes. The dadA gene can encode only the smaller of the two subunits of D-amino acid dehydrogenase. A computer search revealed the presence of a flavin adenine dinucleotide-binding motif in the N-terminal domain of the deduced DadA protein sequence. This is in agreement with biochemical data showing that the D-amino acid dehydrogenase contains flavin adenine dinucleotide in its active center. The predicted dadX gene product appeared to be 85% identical to a dadB-encoded catabolic alanine racemase of Salmonella typhimurium. The organization of the dadA and dadX genes confirmed our previous conclusion based on the genetic data (J. Wild, J. Hennig, M. Lobocka, W. Walczak, and T. Kłopotowski, Mol. Gen. Genet. 198:315-322, 1985) that these genes form an operon. The main transcription start points of the dad operon were determined by primer extension. They are preceded by a putative sigma 70 promoter sequence and two cyclic AMP-cyclic AMP receptor protein (cAMP-CRP) binding sites, one of higher and one of lower affinity to CRP. We propose that the high-affinity site, centered 59.5 bp upstream of the main transcription start point, plays a role in cAMP-CRP-mediated activation of dad operon expression in the absence of glucose.
The Effects of Cellular Glutathione Elevation on the Oxygen Enhancement Ratio (1985)

The radiation responses at various oxygen tensions were evaluated in V79 Chinese hamster cells under conditions where their nonprotein thiols, primarily glutathione (GSH), were elevated by 2-oxothiazolidine-4-carboxylate (OTZ). OTZ, when cleaved by intracellular oxoprolinase, provides the cell with cysteine which stimulates GSH synthesis. A 2-hr pretreatment with 10 mM OTZ elevated GSH to 200% of controls. This elevation in GSH offered no protection to aerated cells; however, for O2 tensions less than or equal to 40,000 ppm modest protection was observed as evidenced by an increase in oxygen enhancement ratio. GSH elevation afforded maximal protection between 1000 and 10,000 ppm O2; however, the extent of protection was relatively small (protection factor = 1.3).
Maximum Entropy Density Estimation with Generalized Regularization and an Application to Species Distribution Modeling (2007)

We present a unified and complete account of maximum entropy density estimation subject to constraints represented by convex potential functions or, alternatively, by convex regularization. We provide fully general performance guarantees and an algorithm with a complete convergence proof. As special cases, we easily derive performance guarantees for many known regularization types, including l1, l2, l22, and l2 + l22 style regularization. We propose an algorithm solving a large and general subclass of generalized maximum entropy problems, including all discussed in the paper, and prove its convergence. Our approach generalizes and unifies techniques based on information geometry and Bregman divergences as well as those based more directly on compactness. Our work is motivated by a novel application of maximum entropy to species distribution modeling, an important problem in conservation biology and ecology. In a set of experiments on real-world data, we demonstrate the utility of maximum entropy in this setting. We explore effects of different feature types, sample sizes, and regularization levels on the performance of maxent, and discuss interpretability of the resulting models.
Growth and applications of Group III-nitrides (1998)

Recent research results pertaining to InN, GaN and AlN are reviewed, focusing on the different growth techniques of Group III-nitride crystals and epitaxial films, heterostructures and devices. The chemical and thermal stability of epitaxial nitride films is discussed in relation to the problems of deposition processes and the advantages for applications in high-power and high-temperature devices. The development of growth methods like metalorganic chemical vapour deposition and plasma-induced molecular beam epitaxy has resulted in remarkable improvements in the structural, optical and electrical properties. New developments in precursor chemistry, plasma-based nitrogen sources, substrates, the growth of nucleation layers and selective growth are covered. Deposition conditions and methods used to grow alloys for optical bandgap and lattice engineering are introduced. The review is concluded with a description of recent Group III-nitride semiconductor devices such as bright blue and white light-emitting diodes, the first blue-emitting laser, high-power transistors, and a discussion of further applications in surface acoustic wave devices and sensors.
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures (2016)

Our analysis sheds light on the immune infiltration patterns of 19 human cancers and unravels mRNA signatures with prognostic utility and immunotherapeutic biomarker potential in ccRCC.
Characterization of a prokaryotic SMC protein involved in chromosome partitioning (1998)

smc of Bacillus subtilis encodes a homolog of eukaryotic SMC proteins involved in chromosome condensation, pairing, and partitioning. A null mutation in B. subtilis smc caused a temperature-sensitive-lethal phenotype in rich medium. Under permissive conditions, the mutant had abnormal nucleoids, approximately 10% of the cells were anucleate, and assembly of foci of the chromosome partitioning protein Spo0J was altered. In combination with a null mutation in spo0J, the smc mutation caused a synthetic phenotype; cell growth was slower and approximately 25% of the cells were anucleate. Our results demonstrate that the B. subtilis Smc protein, like its eukaryotic counterpart, plays an important role in chromosome structure and partitioning.
Magnetic Iron Oxide Nanoparticles: Synthesis, Stabilization, Vectorization, Physicochemical Characterizations, and Biological Applications (2008)

peer reviewed
Integrated DFM framework for dynamic yield optimization (2006)

We present a new methodology for a balanced yield-optimization and a new DFM framework which implements it. Our approach allows designers to dynamically balance multiple factors contributing to yield loss and select optimal combination of DFM enhancements based on the current information about the IC layout, the manufacturing process, and known causes of failures. We bring together the information gained from layout analysis, layout-aware circuit analysis, resolution enhancement and optical proximity correction tools, parasitics extraction, timing estimates, and other tools, to suggest the DFM solution which is optimized within the existing constraints on design time and available data. The framework allows us to integrate all available sources of yield information, characterize and compare proposed DFM solutions, quickly adjust them when new data or new analysis tools become available, fine-tune DFM optimization for a particular design and process and provide the IC designer with a customized solution which characterizes the manufacturability of the design, identifies and classifies areas with the most opportunities for improvement, and suggests DFM improvements. The proposed methodology replaces the ad-hoc approach to DFM which targets one yield loss cause at the expense of other factors with a comprehensive analysis of competing DFM techniques and trade-offs between them.
Immunological Responses of Mice following Administration of Natural Rubber Latex Proteins by Different Routes of Exposure (2000)

Although the prevalence of IgE-mediated latex allergy has increased over the past decade, the circumstances which culminate in sensitization remain uncertain. The objective of these studies was to evaluate the role which sensitization route plays in the development of latex allergy using murine models representative of potential exposure routes by which health care workers (topical and respiratory) and spina bifida patients (subcutaneous) may be sensitized. BALB/c mice administered latex proteins by the subcutaneous, topical, intranasal, or intratracheal routes exhibited dose-responsive elevations in total IgE. In vitro splenocyte stimulation initially demonstrated specificity of the murine immune response to latex proteins. Subsequently, immunoblot analysis was used to compare latex-specific IgE production amongst sensitization routes. Immunoblots of IgE from subcutaneously sensitized mice demonstrated recognition of latex proteins with molecular weights near 14 kDa and 27 kDa. These protein sizes are consistent with the molecular weights of major latex allergens (Hev b 1 and Hev b 3), to which high percentages of spina bifida patients develop antibodies. Mice sensitized by intratracheal or topical administration exhibited combined IgE recognition of latex proteins near 14 kDa, 35 kDa, and 92 kDa. These molecular weights are similar to other latex allergens (Hev b 6, Hev b 2, and Hev b 4) commonly recognized by IgE of health care workers. Mice sensitized to latex proteins by topical, intranasal, or intratracheal exposures exhibited bronchoconstriction as evaluated by whole body plethysmography following respiratory challenge with latex proteins. Subcutaneously sensitized mice were unresponsive. These differences in latex-specific IgE immunoblot profiles and altered pulmonary function amongst the four different sensitization routes suggest that exposure routes leading to sensitization may play a role in determining the primary allergen(s), and the clinical manifestation of the allergic responses.
Complete cDNA sequence encoding human β-galactoside α-2, 6-sialyltransferase (1990)

Journal Article Complete cDNA sequence encoding human β-galactoside α-2, 6-sialyltransferase Get access Ulrich Grundmann, Ulrich Grundmann Department of Molecular Biology, Research InstitutesBerhringwerke AG, Postfach 1140, 3550 Marburg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Claudia Nerlich, Claudia Nerlich Department of Molecular Biology, Research InstitutesBerhringwerke AG, Postfach 1140, 3550 Marburg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Thomas Rein, Thomas Rein Department of Molecular Biology, Research InstitutesBerhringwerke AG, Postfach 1140, 3550 Marburg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Gerd Zettlmeissl Gerd Zettlmeissl Department of Molecular Biology, Research InstitutesBerhringwerke AG, Postfach 1140, 3550 Marburg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 3, 11 February 1990, Page 667, https://doi.org/10.1093/nar/18.3.667 Published: 11 February 1990 Article history Accepted: 05 January 1990 Published: 11 February 1990
COSMIC 2005 (2006)

The Catalogue Of Somatic Mutations In Cancer (COSMIC) database and web site was developed to preserve somatic mutation data and share it with the community. Over the past 25 years, approximately 350 cancer genes have been identified, of which 311 are somatically mutated. COSMIC has been expanded and now holds data previously reported in the scientific literature for 28 known cancer genes. In addition, there is data from the systematic sequencing of 518 protein kinase genes. The total gene count in COSMIC stands at 538; 25 have a mutation frequency above 5% in one or more tumour type, no mutations were found in 333 genes and 180 are rarely mutated with frequencies <5% in any tumour set. The COSMIC web site has been expanded to give more views and summaries of the data and provide faster query routes and downloads. In addition, there is a new section describing mutations found through a screen of known cancer genes in 728 cancer cell lines including the NCI-60 set of cancer cell lines.
Biopolymers and biodegradable smart implants for tissue regeneration after spinal cord injury. (2003)

Biosynthetic conduits carrying extracellular matrix molecules and different cell lines, and supplemented with neurotrophic growth factors have yielded encouraging results in the treatment of experimental spinal cord injury. These findings provide a basis for further development of techniques aimed at spinal cord repair in humans.
GSAEC — Acoustic echo cancellation embedded into the generalized sidelobe canceller (2000)

In this paper, we examine the integration of acoustic echo cancellation (AEC) with a robust generalized side-lobe canceller (GSC) [2, 3] with regard to exploitable synergies. Since the AEC is located behind the fixed beamformer (FBF) of the GSC only one AEC is required for an arbitrary number of array elements. System analysis shows that ideal suppression of local interferers and of acoustic echoes cannot be achieved simultaneously. However, experiments confirm that the interference reduction (IR) is degraded by less than 3 dB compared to a cascade of AEC and GSC and that the echo reduction is improved by more than 13 dB relative to the GSC in echoic environments.
Synthesis of an Eight-Membered Cyclic Pseudo-Dipeptide Using Ring Closing Metathesis (2001)

Ring closing metathesis of diallylglycine 6 provided cyclic Z-olefin 7 in 80% yield. The reaction was promoted by substitution of the amide nitrogen with the 2,4-dimethoxybenzyl group allowing for the required cis diallylglycine amide rotamer. Removal of the protecting groups provided cyclic dipeptide 2, a constrained scaffold useful in peptidomimetic research.
The B-cell-specific Oct-2 protein contains POU box- and homeo box-type domains. (1988)

Transcription of promoters of immunoglobulin genes is controlled by an octanucleotide sequence element. The sequence of a cDNA encoding a B-cell-specific protein, Oct-2, has been determined. This protein specifically recognizes the octanucleotide element and is part of the previously identified NF-A2 family of proteins. The DNA-binding domain of Oct-2 is structurally related to the homeo box consensus and thus contains a potential helix-turn-helix sequence. Oct-2 also possesses a potential 'leucine zipper' domain, where four leucines are each separated by exactly seven residues. Comparisons of Oct-2 with protein Oct-1, which also recognizes the octanucleotide element but is constitutively expressed in all cell types, show high sequence conservation through the 60-residue DNA-binding domain, as well as an adjacent tract of 75 residues. The latter conserved region is also found in regulatory genes expressed in pituitary cells and nematodes and has been termed a POU box. Because two different cDNAs were isolated, it is proposed that the oct-2 gene is expressed as multiple mRNAs that vary in splicing patterns. Most interestingly, the oct-2 cDNA contains a second overlapping open reading frame, 278 residues in length, which might also specify a protein important for B-cell development.
Death-effector Filaments: Novel Cytoplasmic Structures that Recruit Caspases and Trigger Apoptosis (1998)

The death-effector domain (DED) is a critical protein interaction domain that recruits caspases into complexes with members of the TNF-receptor superfamily. Apoptosis can also be induced by expressing certain DED-containing proteins without surface receptor cross-linking. Using Green Fluorescent Protein to examine DED-containing proteins in living cells, we show that these proteins cause apoptosis by forming novel cytoplasmic filaments that recruit and activate pro-caspase zymogens. Formation of these filaments, which we term death-effector filaments, was blocked by coexpression of viral antiapoptotic DED-containing proteins, but not by bcl-2 family proteins. Thus, formation of death-effector filaments allows a regulated intracellular assembly of apoptosis-signaling complexes that can initiate or amplify apoptotic stimuli independently of receptors at the plasma membrane.
Learning to Compose Domain-Specific Transformations for Data Augmentation. (2017)

Data augmentation is a ubiquitous technique for increasing the size of labeled training sets by leveraging task-specific data transformations that preserve class labels. While it is often easy for domain experts to specify individual transformations, constructing and tuning the more sophisticated compositions typically needed to achieve state-of-the-art results is a time-consuming manual task in practice. We propose a method for automating this process by learning a generative sequence model over user-specified transformation functions using a generative adversarial approach. Our method can make use of arbitrary, non-deterministic transformation functions, is robust to misspecified user input, and is trained on unlabeled data. The learned transformation model can then be used to perform data augmentation for any end discriminative model. In our experiments, we show the efficacy of our approach on both image and text datasets, achieving improvements of 4.0 accuracy points on CIFAR-10, 1.4 F1 points on the ACE relation extraction task, and 3.4 accuracy points when using domain-specific transformation operations on a medical imaging dataset as compared to standard heuristic augmentation approaches.
Bin size and linear v(z) (1996)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1996Bin size and linear v(z)Authors: Christopher L. LinerRalph GobeliChristopher L. LinerUniversity of Tulsa and Ralph GobeliMercury International Technologyhttps://doi.org/10.1190/1.1826680 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1826680FiguresReferencesRelatedDetailsCited ByReferences26 September 20163-D seismic survey design for linear v ( z ) mediaGEOPHYSICS, Vol. 64, No. 23‐D seismic survey design and linear v(z)Christopher L. Liner and Ralph Gobeli10 February 2005 SEG Technical Program Expanded Abstracts 1996ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1996 Pages: 2106 publication data© 1996 Copyright © 1996 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 10 Feb 2005 CITATION INFORMATION Christopher L. Liner and Ralph Gobeli, (1996), "Bin size and linear v(z)," SEG Technical Program Expanded Abstracts : 47-50. https://doi.org/10.1190/1.1826680 Plain-Language Summary PDF DownloadLoading ...
The rs738409 (I148M) variant of the PNPLA3 gene and cirrhosis: a meta-analysis (2014)

The human patatin-like phospholipase domain-containing-3 (PNPLA3) gene rs738409 C>G polymorphism is associated with several types of liver disease. The aim of this meta-analysis was to assess the risk of cirrhosis on the basis of rs738409 allele frequency and genotype. Medline, the Cochrane Library, EMBASE, and Google Scholar were searched for prospective and retrospective studies assessing the effect of the rs738409 polymorphism on liver cirrhosis. Seven studies, involving 2,023 patients with cirrhosis, were included. The G allele was associated with a significantly increased risk of cirrhosis versus the C allele [pooled odds ratio (OR) = 1.86, 95% confidence interval (CI) = 1.64-2.12, Z = 9.55, P < 0.001]. Both the GC and GG genotypes were associated with a significantly increased risk of cirrhosis versus the CC genotype (GC vs. CC: pooled OR = 1.73, 95% CI = 1.51-1.98, Z = 7.86, P < 0.001; GG vs. CC: pooled OR = 3.41, 95% CI = 2.77-4.18, Z = 11.65, P < 0.001). There was no evidence of publication bias. Our findings suggest that patients at risk for liver cirrhosis may benefit from PNPLA3 genotyping and thus more intensive monitoring if the rs738409 C>G polymorphism is identified.