gebhart/patrepeval huggingface dataset:
Identification of protein IT of the intestinal cytoskeleton as a novel type I cytokeratin with unusual properties and expression patterns. (1990)

A major cytoskeletal polypeptide (Mr approximately 46,000; protein IT) of human intestinal epithelium was characterized by biochemical and immunological methods. The polypeptide, which was identified as a specific and genuine mRNA product by translation in vitro, reacted, in immunoblotting after SDS-PAGE, only with one of numerous cytokeratin (CK) antisera tested but with none of many monoclonal CK antibodies. In vitro, it formed heterotypic complexes with the type II CK 8, as shown by blot binding assays and gel electrophoresis in 4 M urea, and these complexes assembled into intermediate filaments (IFs) under appropriate conditions. A chymotrypsin-resistant Mr approximately 38,000 core fragment of protein IT could be obtained from cytoskeletal IFs, indicating its inclusion in a coiled coil. Antibodies raised against protein IT decorated typical CK fibril arrays in normal and transformed intestinal cells. Four proteolytic peptide fragments obtained from purified polypeptide IT exhibited significant amino acid sequence homology with corresponding regions of coils I and II of the rod domain of several other type I CKs. Immunocytochemically, the protein was specifically detected as a prominent component of intestinal and gastric foveolar epithelium, urothelial umbrella cells, and Merkel cells of epidermis. Sparse positive epithelial cells were noted in the thymus, bronchus, gall bladder, and prostate gland. The expression of protein IT was generally maintained in primary and metastatic colorectal carcinomas as well as in cell cultures derived therefrom. A corresponding protein was also found in several other mammalian species. We conclude that polypeptide IT is an integral IF component which is related, though somewhat distantly, to type I CKs, and, therefore, we propose to add it to the human CK catalogue as CK 20.
Steroidal regulation of oestradiol-17β dehydrogenase activity of the human breast cancer cell line MCF-7 (1988)

We have examined the direct effects of progestins, oestrogens, peptide hormones and growth factors on oestradiol-17 beta dehydrogenase (OE2DH) activity of cultures of the human breast cancer cell line MCF-7. Cells were cultured in the presence of steroid or peptide for 6 days, after which the number of cells was determined and cellular OE2DH activity assessed. Progesterone, 6 alpha-methyl-17 alpha-hydroxyprogesterone acetate, norethisterone and D(-)-norgestrel all profoundly inhibited cell mitosis and stimulated reductive (oestrone----oestradiol-17 beta) and oxidative (oestradiol-17 beta----oestrone) OE2DH activity. Both oestrone and oestradiol-17 beta directly stimulated reductive OE2DH activity, but had no effect on the oxidative direction. Oestradiol-17 beta stimulated cell growth only in phenol-red free culture medium. Ovine prolactin, LH, epidermal growth factor and transforming growth factor did not alter OE2DH activity but small stimulatory effects on the growth of MCF-7 cells were exerted by prolactin and a combination of transforming growth factor with epidermal growth factor. It is concluded that these results may explain, at least in part, the alterations in mitotic activity and tissue oestradiol-17 beta levels observed in breast tissue during varying physiological and pathological conditions, such as during the menstrual cycle and in breast cancers.
Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences (1995)

To demonstrate the extent of phylogenetic diversity of diazotrophic bacteria associated with rice roots, we characterized phylogenetically 23 nifH gene sequences obtained by PCR amplification of mixed organism DNA extracted directly from rice roots without culturing the organisms. The analyses document the presence of eight novel NifH types, which appear to be a variety of significant components of the diazotrophic community, dominated mainly by proteobacteria.
Orientation-based FRET sensor for real-time imaging of cellular forces (2012)

Mechanical stress is an unmapped source of free energy in cells. Mapping the stress fields in a heterogeneous time-dependent environment like that found in cells requires probes that are specific for different proteins and respond to biologically relevant forces with minimal disturbance to the host system. To meet these goals, we have designed a genetically encoded stress sensor with minimal volume and high sensitivity and dynamic range. The new FRET-based sensor, called cpstFRET, is designed to be modulated by the angles between the donor and acceptor rather than the distance between them. Relative to other probes, it is physically smaller and exhibits a greater dynamic range and sensitivity and expresses well. For in vivo testing, we measured stress gradients in time and space in non-erythroid spectrin in several different cell types and found that spectrin is under constitutive stress in some cells but not in others. Stresses appear to be generated by both F-actin and tubulin. The probe revealed, for the first time, that spectrin undergoes time-dependent force modulation during cell migration. cpstFRET can be employed in vitro, in vivo and in situ, and when incorporated into biologically expressed extracellular polymers such as collagen, it can report multidimensional stress fields.
Diagonal recurrent neural network for controller designs (2002)

A new neural network paradigm called diagonal recurrent neural network (DRNN) structure is presented, and is used to design a neural network controller, which includes both a neuroidentifier (DRNI) and a neurocontroller (DRNC). An unknown plant is identified by a neuroidentifier, which provides the sensitivity information of the plant to a neurocontroller. A generalized dynamical backpropagation algorithm (DBP) is developed to train both DRNC and DRNI. An approach to use an adaptive learning rate scheme based on the Lyapunov function is developed. The use of adaptive learning rates not only accelerates the learning speed but also guarantees the convergence of the neural network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Midazolam pharmacokinetics following intravenous and buccal administration (1998)

Aims Midazolam has good anxiolytic qualities and is a well established premedication agent before anaesthesia or short surgical procedures. The objective of the present study was to determine pharmacokinetic data from individual plasma concentration profiles obtained following intravenous and buccal administration of midazolam. Methods Eight young healthy volunteers received single doses of 5 mg midazolam i.v. and after a period of 1 week buccally in a cross over manner. Blood samples were obtained up to 480 min. The measurement of plasma midazolam concentrations was by gas‐chromatography. Results The maximum plasma concentration was 55.9 ng ml −1 (range 35.6–77.9 ng ml −1 ) at 30 min (range 15–90 min) following buccal administration. AUC was calculated to be 15 016 ng ml −1 min (s.d. 3778 ng ml −1 min) following i.v. and 11191 ng ml −1 min (s.d. 1777 ng ml −1 min) following buccal midazolam. This gave a mean midazolam bioavailabilty of 74.5%. Conclusions The pharmacokinetic data presented in this study demonstrate a high bioavailability and reliable plasma concentrations following buccal midazolam. The clinical benefit of buccal midazolam may be in particular patient controlled premedication or sedation in adults.
RGD-Human Serum Albumin Conjugates as Efficient Tumor Targeting Probes (2009)

Cyclic arginine-glycine-aspartate (RGD) peptides and their derivatives have been intensively studied as tumor targeting probes. One major drawback, however, is their short blood circulation half-lives, which greatly compromises their targeting efficacy. To address this issue, a cyclic peptide, c(RGDyK), and an organic dye (IRDye800 or Cy5.5) were covalently conjugated onto human serum albumin (HSA). The conjugates were subjected to in vitro cell staining, in vivo near-infrared fluorescence (NIRF) imaging, ex vivo NIRF imaging, and histologic studies to evaluate their feasibility as tumor imaging probes. As a control, RAD peptide was also coupled with HSA and labeled with IRDye800 for in vivo imaging. The HSA-RGD-IRDye800 exhibited integrin alpha(v)beta(3)-specific binding in cell staining experiment. In vivo NIRF imaging showed higher tumor accumulation and tumor to background contrast of HSA-RGD-IRDye800 over RGD-IRDye800. The integrin specificity of HSA-RGD-IRDye800 is confirmed by both successful inhibition of tumor uptake in the presence of c(RGDyK) and the inability to accumulate in integrin-positive tumors by RAD-HSA-IRDye800. Histologic examination revealed initial tumor vascular binding and eventually both tumor vasculature and tumor cell integrin binding in vivo. In summary, we successfully developed an RGD-based protein conjugate with prolonged circulation half-life for NIRF imaging of tumor integrin alpha(v)beta(3) expression. The success of this study may be generalizable for other peptide-based probes to be conjugated with HSA for prolonged tumor contrast and improved pharmacokinetics.
Autophagy and Lysosomes in Pompe Disease (2006)

In Pompe disease, a deficiency of lysosomal acid alpha-glucosidase, intralysosomal glycogen accumulates in multiple tissues, with skeletal and cardiac muscle most severely affected.(1) Complete enzyme deficiency results in rapidly progressive infantile cardiomyopathy and skeletal muscle myopathy that is fatal within the first two years of life. Patients with partial enzyme deficiency suffer from skeletal muscle myopathy and experience shortened lifespan due to respiratory failure. The major advance has been the development of enzyme replacement therapy, which recently became available for Pompe patients. However, the effective clearance of skeletal muscle glycogen, as shown by both clinical and preclinical studies, has proven more difficult than anticipated.(2-4) Our recent work published in Annals of Neurology(5) was designed to cast light on the problem, and was an attempt to look beyond the lysosomes by analyzing the downstream events affected by the accumulation of undigested substrate in lysosomes. We have found that the cellular pathology in Pompe disease spreads to affect both endocytic (the route of the therapeutic enzyme) and autophagic (the route of glycogen) pathways, leading to excessive autophagic buildup in therapy-resistant skeletal muscle fibers of the knockout mice.
Expression of αB‐crystallin in human brain tumors (1993)

We have previously shown that alpha B-crystallin is a heat-shock protein which specifically accumulates in response to the expression of c-Ha-ras and v-mos oncogenes in mouse NIH 3T3 fibroblasts. Elevated levels of alpha B-crystallin mRNA or protein were shown to be associated with pathological conditions of the brain. Therefore, we have examined the expression of alpha B-crystallin in normal human brains and brain tumors by Western blot analysis. alpha B-crystallin is moderately expressed in adult but not fetal brain. Elevated levels of alpha B-crystallin expression are observed in glial tumors such as astrocytoma, glioblastoma multiforme, and oligodendroglioma. alpha B-crystallin in these tumors is predominately unphosphorylated. High amounts of accumulated alpha B-crystallin in astrocytic tumors are preferentially found in the more aggressive stages. Glioblastoma multiforme is exceptional in that high alpha B-crystallin expression is observed in only one half of the analyzed samples whereas no alpha B-crystallin could be detected in the other. These results indicate that alpha B-crystallin may be a useful biochemical marker for studying the pathogenesis of various human brain tumors.
Compiler Transformations for High-Performance Computing (1993)

In the last three decades a large number of compiler transformations for optimizing programs have been implemented. Most optimizations for uniprocessors reduce the number of instructions executed by the program, and analyze the properties of scalar quantities using flow analysis techniques. In contrast, optimizations for high-performance vector and parallel processors maximize parallelism and memory locality, mostly by tracking the properties of arrays using loop dependence analysis. &lt;p&gt;In this survey we give an overview of the important high-level program restructuring techniques for imperative languages such as C and Fortran, and to describe how and when they should be applied on high-performance uniprocessors and on vector and multiprocessor machines. The basic issues involved in optimization are discussed, and the compiler analysis required for the transformations is described in some detail. A basic familiarity with modern computer architecture and program compilation is assumed
Pitfalls of Liver Stiffness Measurement: A 5-Year Prospective Study of 13,369 Examinations (2009)

In our experience, liver stiffness measurements are uninterpretable in nearly one in five cases. The principal reasons are obesity, particularly increased waist circumference, and limited operator experience. These results emphasize the need for adequate operator training and for technological improvements in specific patient subpopulations.
Helical periodicity of (PNA)2.(DNA) triplexes in strand displacement complexes (1999)

To study the helical structure in a P-loop formed by an invasion of oligopyrimidine peptide nucleic acid (PNA) into DNA duplex, bent DNA fragments containing a homopurine.homopyrimidine sequence between two bent DNA loci were prepared. As the spacer DNA length between the two bent loci varied by 1 bp over one helical turn, the electrophoretic mobility, reflecting the overall extent of DNA bending, was modulated sinusoidally in non-denaturing 5% polyacrylamide gel. When the bent DNA fragments differing in the spacer DNA length were preincubated with an oligopyrimidine PNA, the gel mobilities were changed due to a P-loop formation. By analyzing the gel mobility data with variations of the P-loop size, average helical parameters at the P-loop structure were determined. (PNA)2. (DNA) triplex within a P-loop had the helical periodicities of 15. 6(0.2) bp per turn at 20 degrees C and 17.4(0.7) bp per turn at 10 degrees C. In addition, the results indicate that a helical unwinding by 57(7) degrees at 20 degrees C and 37(13) degrees at 10 degrees C is present at the two junctions between a P-loop and its adjacent DNA duplex.
Contact Angle Hysteresis Explained (2006)

A view of contact angle hysteresis from the perspectives of the three-phase contact line and of the kinetics of contact line motion is given. Arguments are made that advancing and receding are discrete events that have different activation energies. That hysteresis can be quantified as an activation energy by the changes in interfacial area is argued. That this is an appropriate way of viewing hysteresis is demonstrated with examples.
Differential Role of the Lectin Pathway of Complement Activation in Susceptibility to Neonatal Sepsis (2010)

BACKGROUND. The incidence of bacterial sepsis during the neonatal period is high. Mannan-binding lectin (MBL), L-ficolin, and H-ficolin recognize microorganisms and activate the complement system via MBL-associated serine proteases (MASPs). This study investigated whether cord blood concentrations of the lectin pathway proteins are associated with neonatal sepsis. METHODS. This was a case-control study including 47 infants with culture-proven sepsis during the first month of life and 94 matched controls. MBL, L-ficolin, H-ficolin, MASP-2, and MASP-3 levels were measured in cord blood with use of enzyme-linked immunosorbent assay and time-resolved immunofluorometric assay. Multivariate logistic regression was performed. RESULTS. Infants with gram-positive sepsis had significantly lower H-ficolin cord blood concentrations than controls (multivariate odds ratio [OR], 4.00; 95% confidence interval [CI], 1.51-10.56; P = .005), whereas infants with gram-negative sepsis had lower MBL cord blood concentrations (OR, 2.99; 95% CI, 0.86-10.33; P = .084). When excluding patients with postoperative sepsis, multivariate analysis confirmed that low H-ficolin was associated with a significantly higher risk of gram-positive sepsis (OR, 3.71; 95% CI, 1.26-10.92; P = .017) and late-onset sepsis (OR, 3.14; 95% CI, 1.07-9.21; P = .037). In contrast, low MBL was associated with a significantly higher risk of gram-negative sepsis (OR, 4.39; 95% CI, 1.10-17.45; P = .036) and early-onset sepsis (OR, 3.87; 95% CI, 1.05-14.29; P = .042). The concentrations of all the lectin pathway proteins increased with gestational age (P < .01). CONCLUSIONS. These preliminary results indicate that low MBL concentrations are a susceptibility factor for gram-negative sepsis, and low H-ficolin concentrations indicate susceptibility to gram-positive sepsis. The decreased expression of lectin pathway proteins in neonates must be considered to be an additional form of neonatal immunodeficiency.
Lack of type 2 T cell-independent B cell responses and defect in isotype switching in TNF-lymphotoxin alpha-deficient mice (1997)

TNF is implicated in in vitro Ig production, but its role in vivo is not clearly defined. Our previous studies had shown that TNF-LT alpha double-deficient mice have defective IgM and IgG primary Ab responses to the T cell-dependent (TD) Ag SRBC. We now extend these studies to secondary responses and to T cell-independent (TI) B cell responses. Injections of the TD Ag SRBC did not induce germinal center formation in the spleen of TNF-LT alpha-deficient mice. Associated with the morphologic defect, there was a defective IgG Ab response and a secondary hyper-IgM response to the TD Ag in TNF-LT alpha-deficient mice. The response to the TI Ag type 2 DNP-alanyl-glycyl-glycyl-Ficoll was essentially absent in TNF-LT alpha-deficient mice, while that to the TI Ag type 1 TNP-LPS was significantly reduced only for IgG2b isotype. Transplantation of bone marrow cells from wild-type mice into irradiated TNF-LT alpha-deficient mice restored the formation of splenic germinal centers and corrected the IgM and IgG responses to both TD and TI Ags. These data suggest that TNF and/or LT alpha signaling are critically required for germinal center formation and for the IgM and IgG responses to both TD and TI type 2 Ags.
Abrogation of tumorigenicity and metastasis of murine and human tumor cells by transfection with the murine IFN-beta gene: possible role of nitric oxide. (1997)

The purpose of this study was to determine whether sustained local production of murine IFN-beta (mIFN-beta) could inhibit the tumorigenicity and metastasis of human and murine tumor cells implanted into nude mice. Human melanoma cells (A375SM), renal carcinoma cells (SN12PM6), and colon carcinoma cells (KM12SM) were transfected with mIFN-beta or a control neomycin resistance vector. All cell lines grew well in culture. Tumor cells were injected into the subcutis, kidney, spleen, or lateral tail vein of nude mice. Parental or control transfected cells produced local tumors and experimental or spontaneous lung metastases, whereas mIFN-beta-transfected cells did not. In vivo survival experiments using [125I]IdUdR-labeled cells showed that by day 7 after s.c. implantation, all IFN-beta-transfected cells died. IFN-beta transfection prevented the outgrowth of parental or control-transfected cells only when they were injected together with transfected cells into one site, suggesting that IFN-beta promoted a local lysis of the bystander cells. Similar indirect antitumor activity was demonstrated in various human (KM12SM and SN12PM6) and murine (CT-26 colon carcinoma, RENCA renal cell carcinoma, and 3LL Lewis lung carcinoma) tumors. The IFN-beta-transfected tumor cells stimulated a high level of nitric oxide production by murine macrophages under in vitro and in vivo conditions, which correlated with the vigorous nonspecific antitumor activity. Collectively, these results demonstrate that local production of IFN-beta can eradicate tumor cells of different histology by inducing inducible nitric oxide synthase expression in infiltrating cells.
High-speed policy-based packet forwarding using efficient multi-dimensional range matching (1998)

The ability to provide differentiated services to users with widely varying requirements is becoming increasingly important, and Internet Service Providers would like to provide these differentiated services using the same shared network infrastructure. The key mechanism, that enables differentiation in a connectionless network, is the packet classification function that parses the headers of the packets, and after determining their context, classifies them based on administrative policies or real-time reservation decisions. Packet classification, however, is a complex operation that can become the bottleneck in routers that try to support gigabit link capacities. Hence, many proposals for differentiated services only require classification at lower speed edge routers and also avoid classification based on multiple fields in the packet header even if it might be advantageous to service providers. In this paper, we present new packet classification schemes that, with a worst-case and traffic-independent performance metric, can classify packets, by checking amongst a few thousand filtering rules, at rates of a million packets per second using range matches on more than 4 packet header fields. For a special case of classification in two dimensions, we present an algorithm that can handle more than 128K rules at these speeds in a traffic independent manner. We emphasize worst-case performance over average case performance because providing differentiated services requires intelligent queueing and scheduling of packets that precludes any significant queueing before the differentiating step (i.e., before packet classification). The presented filtering or classification schemes can be used to classify packets for security policy enforcement, applying resource management decisions, flow identification for RSVP reservations, multicast look-ups, and for source-destination and policy based routing. The scalability and performance of the algorithms have been demonstrated by implementation and testing in a prototype system.
Targeted Macrophage Cytotoxicity Using a Nonreplicative Live Vector Expressing a Tumor-Specific Single-Chain Variable Region Fragment (2000)

Antigen-specific recognition and subsequent destruction of tumor cells is the goal of vaccine-based immunotherapy of cancer. Often, however, tumor antigen-specific cytotoxic T lymphocytes (CTLs) are either not available or in a state of anergy. In addition, MHCI expression on tumor cells is often downregulated. Either or both of these situations can allow tumor growth to proceed unchecked by CTL control. We have shown previously that tumor antigen-specific monoclonal antibodies can be expressed in vaccinia virus and that activated macrophages infected with this virus acquire the ability to kill tumor cells expressing that antigen. Here we show that a membrane-anchored form of the scFv portion of the MUC1 tumor antigen-specific monoclonal antibody, SM3, can be expressed on activated macrophages with the highly attenuated poxvirus, modified vaccinia Ankara (MVA), as a gene transfer vector. Cells infected with the MVA-scFv construct were shown to express the membrane-bound scFv by Western blot and FACS analysis. That cells expressing the membrane-anchored scFv specifically bind antigen was shown by FACS and by BIAcore analysis. GM-CSF-activated macrophages were infected with the construct and shown to recognize specifically MUC1-expressing tumor cells as measured by IL-12 release. Furthermore, activated macrophages expressing the membrane-bound scFv specifically lyse target cells expressing the MUC1 antigen but not cells that do not express MUC1.