gebhart/patrepeval huggingface dataset:
Adaptive 2D cylindrical section phased array system for ultrasonic hyperthermia (2003)

A prototype 2D cylindrical section phased array, as part of an adaptive hyperthermia system, is used to examine the role of implantable acoustic sensors for phase aberration correction and motion compensation in ultrasound hyperthermia. After phase aberration correction and motion compensation, enhanced focal patterns are achieved even in the presence of significant aberration and motion. The limited number of acoustic sensors implanted inside a tumor in the clinic requires phase aberrations measured at one point to be extrapolated to other neighboring focal points. Significantly improved focal patterns can be obtained if phase aberrations and beam shifts are mainly caused by aberrators close to the array surface, and extrapolated focal points are close to measured points.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Evolution of Pandemic Clones of Methicillin-Resistant Staphylococcus aureus : Identification of Two Ancestral Genetic Backgrounds and the Associated mec Elements (2001)

Previous surveillance studies carried out by our laboratories, primarily in Southern and Eastern Europe, Latin America, and the United States, have characterized 3,067 methicillin-resistant Staphylococcus aureus (MRSA) hospital isolates by a combination of molecular typing methods. Nearly 70% of these isolates could be classified into five clonal types showing extensive geographic spread. Representative isolates of these clonal types were now reexamined for their genetic relatedness by multilocus sequence typing (MLST) and by sequencing the polymorphic region of protein A (spaA typing), and also for the type of the Staphylococcal Chromosomal Cassette (SCCmec) resident in the bacteria. Three of the previously classified clonal types (Iberian, Brazilian, and Hungarian clones) shared a common or closely related genetic background A, which was the same as the background of the earliest European isolates of MRSA from England and Denmark. The Pediatric and New York/Japan clones belonged to a completely different genetic background B. The three recently described SCCmec types were specifically associated with different pandemic clones: types I and III with isolates of genetic background A and type II with isolates of genetic background B. A novel SCCmec related to type I, called SCCmec type IV, was identified in some MRSA strains belonging to genetic background A as well as B. Structural variations in SCCmec types I and III were also observed. The data allow tentative identification of an evolutionary pathway for the emergence of pandemic MRSA clones and also provide evidence for the multiple, yet restricted, numbers of acquisition of the mec element by S. aureus.
A Tissue-Specific Coactivator of Steroid Receptors, Identified in a Functional Genetic Screen (2000)

Steroid receptors mediate responses to lipophilic hormones in a tissue- and ligand-specific manner. To identify nonreceptor proteins that confer specificity or regulate steroid signaling, we screened a human cDNA library in a steroid-responsive yeast strain. One of the identified cDNAs, isolated in the screen as ligand effect modulator 6, showed no homology to yeast or Caenorhabditis elegans proteins but high similarity to the recently described mouse coactivator PGC-1 and was accordingly termed hPGC-1. The hPGC-1 DNA encodes a nuclear protein that is expressed in a tissue-specific manner and carries novel motifs for transcriptional regulators. The expression of hPGC-1 in mammalian cells enhanced potently the transcriptional response to several steroids in a receptor-specific manner. hPGC-1-mediated enhancement required the receptor hormone-binding domain and was dependent on agonist ligands. Functional analysis of hPGC-1 revealed two domains that interact with steroid receptors in a hormone-dependent manner, a potent transcriptional activation function, and a putative dimerization domain. Our findings suggest a regulatory function for hPGC-1 as a tissue-specific coactivator for a subset of nuclear receptors.
Therapeutic Vaccination with Simian Immunodeficiency Virus (SIV)-DNA+IL-12 or IL-15 Induces Distinct CD8 Memory Subsets in SIV-Infected Macaques (2008)

DNA vaccination is an invaluable approach for immune therapy in that it lacks vector interference and thus permits repeated vaccination boosts. However, by themselves, DNA-based vaccines are typically poor inducers of Ag-specific immunity in humans and non-human primates. Cytokines, such as IL-12 and IL-15, have been shown to be potent adjuvants for the induction and maintenance of cellular immune responses, in particular during HIV infection. In this study, we examined the ability of therapeutic vaccination with SIV-DNA+IL-12 or IL-15 as molecular adjuvants to improve DNA vaccine potency and to enhance memory immune responses in SIV-infected macaques. Our results demonstrate that incorporating IL-12 into the vaccine induces SIV-specific CD8 effector memory T cell (T(EM)) functional responses and enhances the capacity of IFN-gamma-producing CD8 T(EM) cells to produce TNF. Lower levels of PD-1 were expressed on T cells acquiring dual function upon vaccination as compared with mono-functional CD8 T(EM) cells. Finally, a boost with SIV-DNA+IL-15 triggered most T cell memory subsets in macaques primed with either DNA-SIV or placebo but only CD8 T(EM) in macaques primed with SIV-DNA+IL-12. These results indicate that plasmid IL-12 and IL-15 cytokines represent a significant addition to enhance the ability of therapeutic DNA vaccines to induce better immunity.
Duplications in theDMD gene (2006)

The detection of duplications in Duchenne (DMD)/Becker Muscular Dystrophy (BMD) has long been a neglected issue. However, recent technological advancements have significantly simplified screening for such rearrangements. We report here the detection and analysis of 118 duplications in the DMD gene of DMD/BMD patients. In an unselected patient series the duplication frequency was 7%. In patients already screened for deletions and point mutations, duplications were detected in 87% of cases. There were four complex, noncontiguous rearrangements, with two also involving a partial triplication. In one of the few cases where RNA was analyzed, a seemingly contiguous duplication turned out to be a duplication/deletion case generating a transcript with an unexpected single-exon deletion and an initially undetected duplication. These findings indicate that for clinical diagnosis, duplications should be treated with special care, and without further analysis the reading frame rule should not be applied. As with deletions, duplications occur nonrandomly but with a dramatically different distribution. Duplication frequency is highest near the 5' end of the gene, with a duplication of exon 2 being the single most common duplication identified. Analysis of the extent of 11 exon 2 duplications revealed two intron 2 recombination hotspots. Sequencing four of the breakpoints showed that they did not arise from unequal sister chromatid exchange, but more likely from synthesis-dependent nonhomologous end joining. There appear to be fundamental differences therefore in the origin of deletions and duplications in the DMD gene.
Detection of Cell-Surface Antigens Using Antibody-Conjugated Fluorospheres (ACF): Application for Six-Color Immunofluorescence (1996)

Antibody-conjugated fluorospheres (ACF) were used to phenotype murine leukocytes by flow cytometric analysis. Multicolor immunofluoresence (beyond simultaneous 4-color analysis) is limited by the availability of specific antibody-fluorochrome chrome conjugates and even further restricted by the spectral emission overlap of many of the fluorochromes when used in combination. Fluorospheres possessing unique excitation/emission spectra can provide much needed versatility to existing protocols of multicolor fluorescence. SKY BLUE (647 nm excitation, 730 nm emission) fluorospheres conjugated to CD11b monoclonal antibody were used in combination with the monoclonal antibodies IAd-FITC, L3T4 (CD4)-PE, LYT2 (CD8)-APC, THY1.2 (CD90)-biotin and B220 (CD45R)-RED613 for the simultaneous detection of six distinct cell-surface antigens in a mixed cell population. All fluorescence signals were resolved, and comparison of results from five-, six- and single-color samples indicated that the percentages of cells positive for specific surface antigens were equivalent.
Loss of Plasma Proprotein Convertase Subtilisin/Kexin 9 (PCSK9) After Lipoprotein Apheresis (2013)

Our results show, for the first time, that modulation of LDL levels by LA directly affects plasma PCSK9 levels, and suggest that PCSK9 reduction is an additional benefit of LA. Because the loss of PCSK9 could contribute to the LDL-lowering effect of LA, then (1) anti-PCSK9 therapies may reduce frequency of LA in patients currently approved for therapy, and (2) LA and anti-PCSK9 therapies may be used synergistically to reduce treatment burden.
Properties and medical applications of shape memory alloys. (2009)

One of the most known intelligent material is nitinol, which offers many functional advantages over conventional implantable alloys. Applications of SMA to the biomedical field have been successful because of their functional qualities, enhancing both the possibility and the execution of less invasive surgeries. The biocompatibility of these alloys is one of their most important features. Different applications exploit the shape memory effect (one-way or two-way) and the super elasticity, so that they can be employed in orthopedic and cardiovascular applications, as well as in the manufacture of new surgical tools. Therefore, one can say that smart materials, especially SMA, are becoming noticeable in the biomedical field. Super elastic NiTi has become a material of strategic importance as it allows to overcome a wide range of technical and design issues relating to the miniaturization of medical devices and the increasing trend for less invasive and therefore less traumatic procedures. This paper will consider just why the main properties of shape memory alloys hold so many opportunities for medical devices and will review a selection of current applications.
Architecture validation for processors (1995)

Modem, high performance microprocessors are extremely complex machines which require substantial validation effort to ensure functional correctness prior to tapeout. Generating the corner cases to test these designs is a mostly manual process, where completion is hard to judge. Experience shows that the errors that are caught late in the design, many post-silicon, are interactions between different components in very improbable corner case situations. In this paper we present a technique that targets such error-causing interactions by automatically generat- ing test vectors that will cause the processor to exercise all transitions of the control logic in simulation. We use techniques from formal verification to derive transition tours of a fully enumerated state graph of the control logic of the processor. Our system works from a Verilog description of the original machine and is currently being used to validate an embedded dual-issue processor in the node controller of the Stanford FLASH Multiprocessor. Modeling the processor control results in 200K states and an 8M instruction trace to check all transitions of control arcs.
Causes and Consequences of Increased Glucose Metabolism of Cancers (2008)

In this review we examine the mechanisms (causes) underlying the increased glucose consumption observed in tumors within a teleological context (consequences). In other words, we will ask not only "How do cancers have high glycolysis?" but also, "Why?" We believe that the insights gained from answering the latter question support the conclusion that elevated glucose consumption is a necessary component of carcinogenesis. Specifically we propose that glycolysis is elevated because it produces acid, which provides an evolutionary advantage to cancer cells vis-à-vis normal parenchyma into which they invade.
Chylomicron remnant cholesteryl esters as the major constituent of very low density lipoproteins in plasma of cholesterol-fed rabbits (1977)

Feeding rabbits 500 mg of cholesterol daily for 4 to 15 days greatly increased the concentration of esterified cholesterol in lipoproteins of d less than 1.006 g/ml. The origin of hypercholesterolemic very low density lipoproteins was investigated by monitoring the degradation of labeled lymph chyomicrons administered to normal and cholesterol-fed rabbits. Chylomicrons were labeled in vivo by feeding either 1) [3H]cholesterol and [14C]oleic acid or 2) [14C]cholesterol and [3H]retinyl acetate. After intravenous injection of labeled chylomicrons to recipient rabbits, [14C]triglyceride hydrolysis was equally rapid in normal and cholesterol-fed animals. Normal rabbits rapidly removed from plasma both labeled cholesteryl and retinyl esters, whereas cholesterol-fed rabbits retained nearly 50% of doubly labeled remnants in plasma 25 min after chylomicron injection. Ultracentrifugal separation of plasma into subfractions of very low density lipoproteins showed that chylomicron remnants in cholesterol-fed animals are found among all subclasses of very low density lipoproteins. Analysis of cholesteryl ester specific activity-time curves for the very low density lipoproteins subfraction from hypercholesterolemic plasma showed that nearly all esterified cholesterol in large very low density lipoproteins and approximately 30% of esterified cholesterol in small very low density lipoproteins was derived from chylomicron degradation. Apparently, nearly two-thirds of the esterified cholesterol in total very low density lipoproteins from moderately hypercholesterolemic rabbits is of dietary origin.
The Molecular Biology of Human Immunodeficiency Virus Type 1 Infection (1991)

HUMAN immunodeficiency virus type 1 (HIV-1) has been clearly identified as the primary cause of the acquired immunodeficiency syndrome (AIDS).1 , 2 Unlike any other infectious disease in modern medical history, AIDS has galvanized the concern and efforts of physicians, scientists, and the lay public alike. The magnitude of the mounting AIDS problem is indeed sobering. Since the initial clinical reports in the summer of 1981, over 132,000 cases of AIDS have been diagnosed in the United States, and nearly half the patients have died as a result of their disease.3 In addition, between 1 and 2 million Americans are now infected . . .
Association of the type II cAMP-dependent protein kinase with a human thyroid RII-anchoring protein. Cloning and characterization of the RII-binding domain. (1992)

The type II cAMP-dependent protein kinase (PKA) is localized to specific subcellular environments through binding of the dimeric regulatory subunit (RII) to anchoring proteins. Subcellular localization is likely to influence which substrates are most accessible to the catalytic subunit upon activation. We have previously shown that the RII-binding domains of four anchoring proteins contain sequences which exhibit a high probability of amphipathic helix formation (Carr, D. W., Stofko-Hahn, R. E., Fraser, I. D. C., Bishop, S. M., Acott, T. E., Brennan, R. G., and Scott J. D. (1991) J. Biol. Chem. 266, 14188-14192). In the present study we describe the cloning of a cDNA which encodes a 1015-amino acid segment of Ht 31. A synthetic peptide (Asp-Leu-Ile-Glu-Glu-Ala-Ala-Ser-Arg-Ile-Val-Asp-Ala-Val-Ile-Glu-Gln-Val -Lys-Ala-Ala-Tyr) representing residues 493-515 encompasses the minimum region of Ht 31 required for RII binding and blocks anchoring protein interaction with RII as detected by band-shift analysis. Structural analysis by circular dichroism suggests that this peptide can adopt an alpha-helical conformation. Both Ht 31 (493-515) peptide and its parent protein bind RII alpha or the type II PKA holoenzyme with high affinity. Equilibrium dialysis was used to calculate dissociation constants of 4.0 and 3.8 nM for Ht 31 peptide interaction with RII alpha and the type II PKA, respectively. A survey of nine different bovine tissues was conducted to identify RII binding proteins. Several bands were detected in each tissues using a 32P-RII overlay method. Addition of 0.4 microM Ht 31 (493-515) peptide to the reaction mixture blocked all RII binding. These data suggest that all anchoring proteins bind RII alpha at the same site as the Ht 31 peptide. The nanomolar affinity constant and the different patterns of RII-anchoring proteins in each tissue suggest that the type II alpha PKA holoenzyme may be specifically targeted to different locations in each type of cell.
Caprine beta-mannosidosis: clinical and pathological features. (1983)

Beta-mannosidosis, an inherited defect of glycoprotein catabolism associated with deficiency of tissue beta-mannosidase and accumulation of Man(beta 1-4)GlcNAc and Man(beta 1-4)GlcNAc(beta 1-4)GlcNAc, appeared in four of 13 offspring of a single pair of clinically normal, related Nubian goats. Neurological examinations revealed that all four affected goats were unable to rise or walk. All had facial dysmorphism, dome-shaped skulls, small palpebral fissures, carpal contractures, hyperextension of the pastern joints, proximal muscle atrophy, intermittent ocular oscillations resembling pendular nystagmus, marked intention tremor, and deafness. With intensive care, three affected kids were hand-reared and then killed at 1, 7, and 21 days of age. Macroscopically, there were paucity of myelin in the cerebral and cerebellar hemispheres and ventricular dilatation. Microscopically, the extent and distribution of cytoplasmic vacuolation, myelin paucity, axonal spheroids, and filamentous expansions were evaluated in the cerebrum, cerebellum, brainstem, spinal cord, and peripheral nerves of the four affected kids and two age-matched, clinically normal kids. Widespread cytoplasmic vacuolation correlated with the previously reported accumulation of oligosaccharides in the brain and kidney and the deficiency of tissue beta-mannosidase. beta-Mannosidosis, not yet identified in man or other species, is characterized by distinctive neonatal clinical, pathological and biochemical features which differentiate it from the alpha-mannosidosis and other inherited diseases of glycoprotein catabolism.
The 2012 AHS/AAN Guidelines for Prevention of Episodic Migraine: A Summary and Comparison With Other Recent Clinical Practice Guidelines (2012)

The AHS/AAN and Canadian guidelines are recommended for use on the basis of the AGREE-II quality assessment. Recommendations for the future development of clinical practice guidelines in migraine are provided. In particular, efforts should be made to ensure that guidelines are regularly updated and that guideline developers strive to locate and incorporate unpublished clinical trial evidence.
A single-pass, in-situ planarization process utilizing TEOS for double-poly, double-metal CMOS technologies (2003)

A planarization technique utilizing in situ etching of TEOS-based CVD oxide is presented. The process includes TEOS/O/sub 2/-based PECVD oxide, TEOS/O/sub 3/-based LPCVD oxide, Ar/sup +/ sputter etching, and CF/sub 4/-based reactive ion etching, all in a single pumpdown. This planarization process has been successfully used to fabricate advanced double-poly double-metal circuits on 0.8- mu m CMOS technologies. E-test structures indicate low via resistance (0.15 Omega /via) and the absence of any metal opens or shorts. Custom-designed defect monitors show extremely low defect densities for both vias and metal. Comparison of die yields for the new in situ TEOS-etchback process and an SOG-etchback process indicates that much higher yields can be obtained by the use of the new process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Transforming Growth Factor-β1 Induces Nuclear to Cytoplasmic Distribution of Androgen Receptor and Inhibits Androgen Response in Prostate Smooth Muscle Cells1 (1998)

Stromal-epithelial interactions in the prostate gland are dependent on androgen regulation of prostate stromal cells, yet little is known about androgen action in these cell types. Recent reports have demonstrated that androgen-regulated gene transcription can be stimulated or inhibited by certain growth factors, indicating cross-talk mechanisms. To address potential cross-talk in signaling pathways between androgen and transforming growth factor-beta1 (TGFbeta1) in prostate stromal cells, the PS-1 prostate smooth muscle cell line was examined. In the presence of physiological concentrations of androgen, PS-1 cell proliferation was stimulated, and androgen receptor (AR) exhibited a nuclear localization pattern. The addition of TGFbeta1 (25 pM) was capable of blocking androgen-induced proliferation, but had no direct effect in cultures without androgen. Immunocytochemistry to localize AR subcellular distribution showed that TGFbeta1 (5-100 pM) altered the distribution of AR from the nucleus to the cytoplasm. Other growth factors, including fibroblast growth factor-2, epidermal growth factor, and TGFbeta2 had no effect on AR distribution. The TGFbeta1-induced nuclear to cytoplasmic change in receptor localization was rapid (initiated within 30 min), was neutralized by TGFbeta1 antibodies, did not require new protein synthesis, and was complete by 6 h. Removal of TGFbeta1 from the culture medium resulted in a rapid redistribution of AR to the nucleus, indicating reversible mechanisms. Northern analysis of the ddp17 marker transcript for androgen action in PS-1 cells showed that androgen-stimulated ddp17 expression was inhibited in the presence of TGFbeta1 (25 pM). TGFbeta1 induced a similar nuclear to cytoplasmic distribution of AR in primary cultures of rat prostate stromal cells. TGFbeta1, however, had no effect on AR distribution in either the LNCaP prostatic carcinoma cell line or the DDT1MF-2 leiomyosarcoma cell line. Specific cross-talk between TGFbeta1 and AR signaling pathways in prostate stromal cells may play a significant role in prostate development and stromal cell response in carcinoma progression.
Theory of the Interface between Immiscible Polymers. II (1972)

A theory is developed to predict the interfacial properties between two immiscible polymers. A self-consistent-field approach is employed to describe the configurational statistics of polymer molecules in the interfacial region. The density profiles and surface tension are calculated, and compare well with experiments. The interfaces are found to be much broader than for ordinary liquids. Also discussed are the distribution of chain ends and block-copolymer joints in the interface, and the effects of adding moderate amounts of solvent.
Defects in XRCC4 and KU80 differentially affect the joining of distal nonhomologous ends (2007)

XRCC4-null mice have a more severe phenotype than KU80-null mice. Here, we address whether this difference in phenotype is connected to nonhomologous end-joining (NHEJ). We used intrachromosomal substrates to monitor NHEJ of two distal double-strand breaks (DSBs) targeted by I-SceI, in living cells. In xrcc4-defective XR-1 cells, a residual but significant end-joining process exists, which primarily uses microhomologies distal from the DSB. However, NHEJ efficiency was strongly reduced in xrcc4-defective XR-1 cells versus complemented cells, contrasting with KU-deficient xrs6 cells, which showed levels of end-joining similar to those of complemented cells. Nevertheless, sequence analysis of the repair junctions indicated that the accuracy of end-joining was strongly affected in both xrcc4-deficient and KU-deficient cells. More specifically, these data showed that the KU80/XRCC4 pathway is conservative and not intrinsically error-prone but can accommodate non-fully complementary ends at the cost of limited mutagenesis.