gebhart/patrepeval huggingface dataset:
Incorporation of Tumor Vasculature Targeting Motifs into Moloney Murine Leukemia Virus Env Escort Proteins Enhances Retrovirus Binding and Transduction of Human Endothelial Cells (2000)

Adhesion receptors expressed on the surfaces of tumor-activated endothelial cells provide an advantageous locus for targeting gene therapy vectors to angiogenic tissues and/or tumor vasculature. In this study, we engineered a series of Asn-Gly-Arg (NGR)-containing congeners of the presumptive cell binding motif contained within the ninth type III repeat of fibronectin and displayed these tumor vasculature targeting motifs (TVTMs) within the context of Moloney murine leukemia envelope "escort" proteins. Comparative studies of envelope incorporation into viral particles and evaluation of the cell binding properties of the targeted vectors revealed critical structural features, thus identifying a subset of optimal TVTMs. Utilizing a modified ELISA to evaluate viral binding to target cells, we observed a significant down-regulation of TVTM-virion binding to human endothelial cells following sustained (48-h) exposure to VEGF. Normalized for equivalent titers (10(6) CFU/ml), as assayed on NIH 3T3 cells, vectors displaying TVTM escort proteins significantly enhanced the transduction efficiency from 12.2 to 37.4% in human KSY-1 endothelial cell cultures (P < 0.001) and from 0.4 to 4.1% in human umbilical vein endothelial cell (HUVEC) cultures (P < 0.001). In summary, these studies utilized an engineering approach to identify a subset of TVTMs that are stably incorporated as envelope "escort" proteins into retroviral vectors and that, by functioning to improve the binding efficiency and transduction of both HUVEC and KSY1 endothelial cells, may have therapeutic potential for targeting gene delivery to the tumor-associated vasculature.
Impact of Porcine Islet Size on Cellular Structure and Engraftment After Transplantation (2005)

Large and well-structured islets, mainly found in adult pig pancreata, probably possess a better potential for cellular engraftment due to centralized vascularization and collagen distribution.
Identification of the two rotavirus genes determining neutralization specificities (1986)

Bovine rotavirus NCDV and simian rotavirus SA-11 represent two distinct rotavirus serotypes. A genetic approach was used to determine which viral gene segments segregated with serotype-specific viral neutralization. There were 16 reassortant rotaviruses derived by coinfection of MA-104 cells in vitro with the SA-11 and NCDV strains. The parental origin of reassortant rotavirus double-stranded RNA segments was determined by gene segment mobility in polyacrylamide gels and by hybridization with radioactively labeled parental viral transcripts. We found that two rotavirus gene segments found previously to code for outer capsid proteins vp3 and vp7 cosegregated with virus neutralization specificities.
Extrusion of polystyrene nanocomposite foams with supercritical CO2 (2003)

Abstract Intercalated and exfoliated polystyrene/nano‐clay composites were prepared by mechanical blending and in situ polymerization respectively. The composites were then foamed by using CO 2 as the foaming agent in an extrusion foaming process. The resulting foam structure is compared with that of pure polystyrene and polystyrene/talc composite. At a screw rotation speed of 10 rpm and a die temperature of 200°C, the addition of a small amount (i.e., 5 wt%) of intercalated nano‐clay greatly reduces cell size from 25.3 to 11.1 μm and increases cell density from 2.7 × 10 7 to 2.8 × 10 8 cells/cm 3 . Once exfoliated, the nanocomposite exhibits the highest cell density (1.5 × 10 9 cells/cm 3 ) and smallest cell size (4.9 μm) at the same particle concentration. Compared with polystyrene foams, the nanocomposite foams exhibit higher tensile modulus, improved fire retardance, and better barrier property. Combining nanocomposites and the extrusion foaming process provides a new technique for the design and control of cell structure in microcellular foams.
Bayesian approaches to failure prediction for disk drives (2001)

Hard disk drive failures are rare but are often costly. The ability to predict failures is important to consumers, drive manufacturers, and computer system manufacturers alike. In this paper we investigate the abilities of two Bayesian methods to predict disk drive failures based on measurements of drive internal conditions. We first view the problem from an anomaly detection stance. We introduce a mixture model of naive Bayes submodels (i.e. clusters) that is trained using expectation-maximization. The second method is a naive Bayes classifier, a supervised learning approach. Both methods are tested on realworld data concerning 1936 drives. The predictive accuracy of both algorithms is far higher than the accuracy of thresholding methods used in the disk drive industry today. 1.
Growth inhibition of MCF-7 cells by estrogen is dependent upon a serum factor. (2000)

MCF-7 cell growth is normally dependent upon estrogen, but if cells are maintained in serum-free medium estrogen inhibits cell growth with an IC50 of about 1 nM. Cells adapted to serum-free medium have approximately the same levels of estrogen receptor mRNA as control cells that are stimulated by estrogen. We have identified two serum components, one estrogen dependent and one not, that appear to be responsible for the inhibition of growth by estrogen. Our observations are consistent with the presence of a plasma membrane receptor which negatively regulates MCF-7 cell growth, and that can be inhibited by a serum protein that binds estrogen.
Molecular Changes Associated with Acquired Resistance to Crizotinib in ROS1 -Rearranged Non–Small Cell Lung Cancer (2015)

Molecular changes associated with acquired crizotinib resistance in ROS1-rearranged NSCLC are heterogeneous, including ROS1 tyrosine kinase mutations, EGFR activation, and epithelial-to-mesenchymal transition.
Molecular and immunological characterization of a novel timothy grass (Phleum pratense) pollen allergen, Phl p 11 (2002)

As the first representative of group 11 grass pollen allergens, Phl p 11 has been cloned and produced as a recombinant protein showing allergenic activity. One-third of grass pollen-sensitized subjects showed specific IgE reactivity to recombinant Phl p 11, corresponding in magnitude to a significant proportion of specific IgE to grass pollen extract.
Genetic association of an ( 2-macroglobulin (Val1000lle) polymorphism and Alzheimer's disease (1998)

alpha2-Macroglobulin (A2M) is a proteinase inhibitor found in association with senile plaques (SP) in Alzheimer's disease (AD). A2M has been implicated biochemically in binding and degradation of the amyloid beta (Abeta) protein which accumulates in SP. We studied the relationship between Alzheimer's disease and a common A2M polymorphism, Val1000 (GTC)/Ile1000 (ATC), which occurs near the thiolester active site of the molecule. In an initial exploratory data set (90 controls and 171 Alzheimer's disease) we noted an increased frequency of the G/G genotype from 0.07 to 0.12. We therefore tested the hypothesis that the G/G genotype is over-represented in Alzheimer's disease in an additional independent data set: a group of 359 controls and 566 Alzheimer's disease patients. In the hypothesis testing cohort, the G/G genotype increased from 0.07 in controls to 0.12 in Alzheimer's disease (P < 0.05, Fisher's exact test). The odds ratio for Alzheimer's disease associated with the G/G genotype was 1.77 (1.16-2.70, P < 0.01) and in combination with APOE4 was 9.68 (95% CI 3.91-24.0, P < 0.001). The presence of the G allele was associated with an increase in Abeta burden in a small series. The A2M receptor, A2M-r/LRP, is a multifunctional receptor whose ligands include apolipoprotein E and the amyloid precursor protein. These four proteins have each been genetically linked to Alzheimer's disease, suggesting that they may participate in a common disease pathway.
Extended depth of field using a logarithmic asphere (2003)

Imaging systems are described which use a logarithmic asphere and image processing in order to increase the depth of field substantially beyond classical limits. A nonparaxial form of the diffraction theory integral for an impulse response is derived and evaluated in order to establish a precise expression for the transmission function of this asphere. This nonparaxial physical optics formulation provides results of fractional wavelength accuracy that enable one immediately to complete the design and fabrication of the optical system. Circularly symmetric aspherical lenses, either for single-lens cameras or blurring phase filters for use with commercial photographic lenses, have been fabricated using advanced grinding and finishing machines. Computer simulation studies are presented to show that a logarithmic asphere is capable of diffraction-limited performance over an extended depth of field. Experimental imaging results including digital processing by an inverse filter show a tenfold increase in the depth of field.
The polymerase chain reaction in transfusion medicine (1990)

PCR is a sensitive and powerful diagnostic and research tool. Its diagnostic applications in infectious disease, genetics, and cancer will play a prominent role in transfusion medicine in the next several years. However, the indirect effect of PCR on transfusion medicine in terms of increasing our understanding of disease mechanisms and the development of therapeutic agents will be even greater.
A FAST RAY TRACING METHOD OF VISUALIZATION OF MEDICAL VOLUME DATA (1996)

This paper presents a fast ray tracing method of visualization of medical volume data.The method protype is based on image order volume rendering algorithm.But it is accelerated in object space to visual-ize medical 3D volurne data,In this paper,after a brief introduction of image order volume rendering techniques,we describe how to decrease tracing rays number using boundary box technique;At the end of this paper,the re-sult of this algorithm for visualizing multi-organ within the same medical volume data is given.
Serum levels of Th2 chemokines, CCL17, CCL22, and CCL27, were the important markers of severity in infantile atopic dermatitis (2008)

Atopic dermatitis (AD) is considered to be Th2 cell-mediated disorder. In most infants with AD, AD may be induced by food allergy. In the early stage of infantile AD, it is unclear whether there are changes in serum Th2 chemokines or in Th2 chemokine production by peripheral blood mononuclear cells (PBMC). Thirty-four patients with AD were examined (mean age, 4.5 months; female:male, 18:16). Ten age-matched infants with no history of allergic disease were used as controls. Thirty of these 34 patients were sensitized with ovalbumin (OVA; radioallergrosolvent score of >2). Serum levels of CCL17, CCL22, and CCL27 were measured with enzyme-linked immunosolvent assay (ELISA) kits and their correlation with the severity of skin lesions, defined by the scoring atopic dermatitis (SCORAD) index, was analyzed. The amounts of TNF-alpha, CCL17, CCL22, and CCL27 in the culture supernatants of PBMC from OVA-sensitized AD infants after stimulation with OVA were estimated with ELISA kits. Elevated serum CCL17, CCL22, and CCL27 levels significantly correlated with SCORAD index (r = 0.7181, p < 0.001; r = 0.5354, p < 0.005; r = 0.8312, p < 0.0001, respectively). CCL22 levels produced by PBMC from OVA-sensitized infants with AD reflected serum CCL22 levels. Only six of 30 OVA-sensitized patients in whom the skin signs increased immediately after OVA intake showed markedly high titers of TNF-alpha produced by PBMC after stimulation with OVA. These high TNF-alpha titers correlated significantly with serum CCL27 levels (r = 0.7181, p < 0.001). Serum concentrations of CCL17, CCL22, and CCL27 correlate well with the extent and intensity of AD in infants. Of the three Th2 chemokines examined, serum CCL27 correlated most significantly with the severity of AD. Thus, the peripheral immune responses of infantile AD patients are skewed to a Th2 dominant bias.
TSD: A Flexible Root of Trust for the Cloud (2012)

Due to the tight one-to-one binding relationship between the TPM and the single platform lacks of flexibility and scalability, the Trusted Platform Module (TPM) can not be directly applied to the cloud virtualization platform, on which concurrently running several user domains (VMs). For establishing the trust in the cloud, we propose the Trusted Service Domain (TSD), as a novel root of trust for the cloud. Being an independent functional domain, the TSD is able to provide the trusted service for the multiple user domains on the cloud virtualization platform. We firstly extend the existing trusted chain to secure the TSD, and generate the independent key hierarchies for the user domains in the TSD to support the cryptography service and secure storage. Then we design the secure communication mechanism to protect the inter-domain data, and present the migration scheme for the TSD in the cloud. Finally, we detailed our implementation of the prototype system and analyze the security of the TSD. Preliminary experiment results showed that the TSD has higher efficiency than the existing schemes on the trusted commands handling and the migration, which satisfied flexible deployment and rapidly migration requirements of the cloud virtualization platform.
Biodiversity of apidaecin-type peptide antibiotics. Prospects of manipulating the antibacterial spectrum and combating acquired resistance (1994)

Insects have a unique repertoire of peptide antibiotics but, to date, prospects of clinical applications are not clear. Apidaecin, a small peptide isolated from honeybees, inhibits viability of Gram-negative bacteria; lethal activity is near immediate, independent of a conventional "lytic" mechanism, and involves stereoselective recognition of target molecules. Here we report structural analysis of 14 naturally occurring apidaecin-type peptides and the existence of evolutionarily conserved ("constant") regions. By detailed analysis of activities against clinically relevant bacteria, we demonstrate that the diversity of the intervening ("variable") regions confers specificity to the antibacterial spectrum of each homolog. As a result, apidaecin-homolog-based antibiograms (using 16 peptides) differ markedly between bacterial strains, contrasting the most between Yersinia enterocolitica and Campylobacter jejuni. Furthermore, in at least one instance, acquired resistance to apidaecin could be negated by minor substitutions in the variable regions. The delineation in a short peptide of constant and variable regions, responsible for, respectively, general antibacterial capacity and specificity of the antibacterial spectrum, is unprecedented. Taken together, we provide evidence that antibacterial spectra of apidaecin-type peptides can be manipulated, and that, in some cases, resistance can be countered and perhaps prevented. The current findings will guide rational design of second generation peptide antibiotics for clinical trials.
Tumor Necrosis Factor Induces Adult Respiratory Distress Syndrome in Rats (1989)

To evaluate the effect of tumor necrosis factor (TNF), a major mediator of sepsis, on lung structure and function, we infused 200-g male Wistar rats with TNF (0, 2 x 10(5), or 4 x 10(5) U/kg of TNF) for 24 hours. Volume-pressure measurements were determined in the excised lungs using both air and saline, which eliminated surface tension forces. Total lung wet and dry weight, nitrogen level, and DNA and protein content were measured. Lungs of the rats that received TNF accepted significantly smaller volumes of air and saline at all pressures compared with the control group. Both the lung wet and dry weights increased with TNF. Lung DNA and protein content also increased, suggesting increased cellularity in the TNF-infused lungs. Thus, the lungs of the TNF-treated rats were stiffer, with reduced compliance values, and heavier due to increased water content and increased cellularity. These data indicate that sublethal administration of TNF in this rat model induces the adult respiratory distress syndrome and increases the work potential of respiration.
V H mutation status, CD38 expression level, genomic aberrations, and survival in chronic lymphocytic leukemia (2002)

In chronic lymphocytic leukemia (CLL), biologic risk factors such as immunoglobulin variable heavy chain gene (V(H)) mutation status, CD38 expression level, and genomic aberrations have recently been identified, but the relative prognostic impact of the individual parameters is unknown. In the current study, we analyzed V(H) mutation status by polymerase chain reaction and sequencing (n = 300), genomic aberrations by fluorescence in situ hybridization (+3q, 6q-, +8q, 11q-, +12q, 13q-, t(14q), 17p-) (n = 300), and CD38 expression by triple-color FACS (CD5, CD19, CD38) (n = 157) in a unicentric CLL cohort. The prognostic influence of V(H) mutation rate and CD38 expression level was tested by maximally selected log-rank statistics. A corrected P value (P(cor)) for a cutoff level allowing the best separation of 2 subgroups with different survival probabilities was identified at 97% V(H) homology (95% confidence interval [CI], 96%-98% homology, P(cor) <.001) and at 7% CD38 expression (95% CI, 20%-71% expression, P(cor) =.02). In univariate analyses, unmutated V(H) genes and high CD38 expression levels predicted for shorter survival times. The overall incidence of genomic aberrations was similar in the V(H) unmutated and V(H) mutated subgroups. High-risk genomic aberrations such as 17p- and 11q- occurred almost exclusively in the V(H) unmutated subgroup, whereas favorable aberrations such as 13q- and 13q- as single abnormalities were overrepresented in the V(H) mutated subgroup. In multivariate analysis, unmutated V(H), 17p deletion, 11q deletion, age, WBC, and LDH were identified as independent prognostic factors, indicating a complementary role of V(H) mutation status and genomic aberrations to predict outcome in CLL.
Enhanced shape-invariant pitch and time-scale modification for concatenative speech synthesis (2002)

To preserve shape invariance when performing pitch or time-scale modification of sinusoidally-modelled voiced speech, the phases of the sinusoids used to model the glottal excitation are made to add coherently at estimated excitation points. Previous methods achieved this by estimating excitation phases at synthesis frame boundaries, disregarding the frequency modulation that may occur between the frame boundary and the nearest modified excitation point. This approximation can produce a significant misalignment of the excitation phases, leading to distortion of the temporal structure of the synthetic speech. In this paper, a shape-invariant technique is proposed which aligns the excitation phases at excitation points, whilst allowing for variations in the frequency of the sinusoidal components.
A Randomized Trial of a Somatostatin Analog for Preserving Beta Cell Function in Children with Insulin Dependent Diabetes Mellitus (1994)

In an attempt to rest the beta cells of newly diagnosed children with type I diabetes mellitus (IDDM) and thus possibly preserve beta cell function, ten children were given Octreotide, a somatostatin analog, for the first 21 days after diagnosis. Ten age-matched diabetic children served as controls. Although there were no differences in either insulin requirements or in hemoglobin A1 levels, there were significant increases in the glucagon-stimulated C-peptide levels of the experimental group at six and 12 months after diagnosis, compared to control patients.
Treatment of traumatic brain injury in rats with erythropoietin and carbamylated erythropoietin (2007)

These data demonstrate that at the doses used, EPO and CEPO are equally effective in enhancing spatial learning and promoting neural plasticity after TBI.
Some remarks on confidence or fiducial limits (1954)

Journal Article Some remarks on confidence or fiducial limits Get access THEODORE E. STERNE THEODORE E. STERNE Ballistic Research LaboratoriesAberdeen Proving Ground, Maryland Search for other works by this author on: Oxford Academic Google Scholar Biometrika, Volume 41, Issue 1-2, June 1954, Pages 275–278, https://doi.org/10.1093/biomet/41.1-2.275 Published: 01 June 1954
Structural background of cyclodextrin-protein interactions (2003)

Cyclodextrins are cyclic oligosaccharides with the shape of a hollow truncated cone. Their exterior is hydrophilic and their cavity is hydrophobic, which gives cyclodextrins the ability to accommodate hydrophobic molecules/moieties in the cavity. This special molecular arrangement accounts for the variety of beneficial effects cyclodextrins have on proteins, which is widely used in pharmacological applications. We have studied the interaction between beta-cyclodextrin and four non-carbohydrate-binding model proteins: ubiquitin, chymotrypsin inhibitor 2 (CI2), S6 and insulin SerB9Asp by NMR spectroscopy at varying structural detail. We demonstrate that the interaction of beta-cyclodextrin and our model proteins takes place at specific sites on the protein surface, and that solvent accessibility of those sites is a necessary but not compelling condition for the occurrence of an interaction. If this behaviour can be generalized, it might explain the wide range of different effects of cyclodextrins on different proteins: aggregation suppression (if residues responsible for aggregation are highly solvent accessible), protection against degradation (if point of attack of a protease is sterically 'masked' by cyclodextrin), alteration of function (if residues involved in function are 'masked' by cyclodextrin). The exact effect of cyclodextrins on a given protein will always be related to the particular structure of this protein.
The Major Neutralizing Antibody Responses to Recombinant Anthrax Lethal and Edema Factors Are Directed to Non-Cross-Reactive Epitopes (2009)

Anthrax lethal and edema toxins (LeTx and EdTx, respectively) form by binding of lethal factor (LF) or edema factor (EF) to the pore-forming moiety protective antigen (PA). Immunity to LF and EF protects animals from anthrax spore challenge and neutralizes anthrax toxins. The goal of the present study is to identify linear B-cell epitopes of EF and to determine the relative contributions of cross-reactive antibodies of EF and LF to LeTx and EdTx neutralization. A/J mice were immunized with recombinant LF (rLF) or rEF. Pools of LF or EF immune sera were tested for reactivity to rLF or rEF by enzyme-linked immunosorbent assays, in vitro neutralization of LeTx and EdTx, and binding to solid-phase LF and EF decapeptides. Cross-reactive antibodies were isolated by column absorption of EF-binding antibodies from LF immune sera and by column absorption of LF-binding antibodies from EF immune sera. The resulting fractions were subjected to the same assays. Major cross-reactive epitopes were identified as EF amino acids (aa) 257 to 268 and LF aa 265 to 274. Whole LF and EF immune sera neutralized LeTx and EdTx, respectively. However, LF sera did not neutralize EdTx, nor did EF sera neutralize LeTx. Purified cross-reactive immunoglobulin G also failed to cross-neutralize. Cross-reactive B-cell epitopes in the PA-binding domains of whole rLF and rEF occur and have been identified; however, the major anthrax toxin-neutralizing humoral responses to these antigens are constituted by non-cross-reactive epitopes. This work increases understanding of the immunogenicity of EF and LF and offers perspective for the development of new strategies for vaccination against anthrax.