gebhart/patrepeval huggingface dataset:
Oncogene Protein Co-Expression Value of Ha-ras, c-myc, c-fos, and p53 as Prognostic Discriminants for Breast Carcinoma (1995)

Approximately one fifth of the breast cancer patients in this analysis (disease-free and recurrent) expressed only a single oncogene marker (c-fos, c-myc, Ha-ras, or p53); one quarter of patients with recurrent disease expressed only one oncogene protein. Single oncogene expression did not possess independent prognostic significance for prediction of recurrence. Further, p53 mutations did not function as independent correlates for prognosis. The co-expression of the studied proto-oncogenes (c-myc, Ha-ras) and the nuclear transcriptional protein (c-fos) functioned as a strong prognostic correlate for recurrence and survival; the effect of individual oncogenes to predict survival was greatest for Ha-ras and c-fos. Immediate or early co-expression of three oncogene proteins in neoplastic transformation endowed cells of invasive carcinoma with an aggressive phenotype. This aggressive phenotype was evident in a small percentage of the studied population (11%) and predicted adverse disease-free and overall survival. These findings suggest that oncogene co-expression possesses significant prognostic and potential therapeutic value; incorporation of this molecular technology into future prospective randomized trials is advisable.
Characterization of a diffuse field in a reverberant room (1997)

An efficient modal approach to characterize the diffuseness of the sound field in a rectangular room is presented. Using two simple descriptors, the correlation function and the spatial uniformity of the pressure field, a practical and convenient tool is proposed to study the diffuse field in the room. A precise criterion has been given in terms of the least permissible number of room modes to achieve an adequate diffusion. It has been shown that the criterion is in great accordance with the well-known “Schroeder frequency” limit for the diffuse field. Detailed calculations of the correlation function are presented to show the importance of the Δk/k correction terms to the well-known sin(kR)/kR prediction. A new closed form for the correlation function is thus derived. A discussion about the importance of having more than one descriptors is also presented. It is shown that a diffuse field can be established in a room with strong modal behavior under certain assumptions.
Autotaxin inhibitors: a perspective on initial medicinal chemistry efforts (2010)

The lysophospholipase D enzyme, autotaxin (ATX), has been linked to numerous human diseases including cancer, neurophatic pain, obesity and Alzheimer's disease. Although the ATX protein was initially purified and characterized in 1992, a link to bioactive lipid metabolism was not made until 2002. In the past decade, metal chelators, lysophospholipid product analogs, and more recently, small non-lipid inhibitors of the enzyme were successfully identified. The majority of these inhibitors have been characterized using recombinant purified ATX in vitro, with very few examples studied in more complex systems. Translation of ATX inhibitors from the hands of medicinal chemists to clinical use will require substantially expanded characterization of ATX inhibitors in vivo.
Activity Assays for Receptor-Interacting Protein Kinase 1:A Key Regulator of Necroptosis (2013)

Necroptosis is a novel form of regulated non-apoptotic cell death, which displays morphological features of necrosis. The kinase activity of receptor-interacting protein kinase 1 (RIP1) is a critical component in signaling for necroptosis. The development of assays to evaluate RIP1 kinase activity is important in the further development of existing and novel inhibitors of necroptosis. Here, we describe RIP1 protein expression and purification from mammalian and insect cells as well as two in vitro kinase assays to detect RIP1 kinase activity and inhibition.
Feedback Inhibition of l -Glutamine d -Fructose 6-Phosphate Amidotransferase by Uridine Diphosphate N -Acetylglucosamine in Neurospora crassa (1970)

The enzyme, l-glutamine d-fructose 6-phosphate amidotransferase (EC 2.6.1.16) of Neurospora crassa, which catalyzes the formation of glucosamine 6-phosphate was shown to be subject to feedback inhibition by uridine diphosphate N-acetyl-d-glucosamine (UDP-GlcNAc). The conclusion is based on the following observations. UDP-GlcNAc, the direct precursor of chitin, did not accumulate in the cell even when its utilization for the synthesis of cell wall chitin was interrupted by the antibiotic polyoxin D, a competitive inhibitor of the chitin synthetase (EC 2.4.1.16). Furthermore, the cellular level of UDP-GlcNAc rose in a short period of time when the amidotransferase was bypassed in vivo by the addition of glucosamine to the growing medium of the fungus. The amidotransferase was purified from N. crassa approximately 85-fold. Kinetic studies showed that UDP-GlcNAc was a potent and specific inhibitor of the amidotransferase, and that it did not alter the Michaelis constant for either l-glutamine or d-fructose 6-phosphate, suggesting that the inhibitor binds at a site on the enzyme distinct from the active site.
A guided tour to approximate string matching (2001)

We survey the current techniques to cope with the problem of string matching that allows errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices. We conclude with some directions for future work and open problems.
Identification of pro-angiogenic markers in blood vessels from stroked-affected brain tissue using laser-capture microdissection (2009)

In this work we have identified concurrent activation of key angiogenic molecules associated with endothelial cell migration, differentiation and tube-formation, vessel stabilization and stem cell homing mechanisms in areas of revascularization. Therapeutic stimulation of these processes in all areas of damaged tissue might improve morbidity and mortality from stroke.
Iridium-Catalyzed, Silyl-Directed Borylation of Nitrogen-Containing Heterocycles (2010)

Selective methods for the functionalization of indoles and other nitrogen heterocycles would provide access to the core structures of many natural products and pharmaceuticals. Although there are many methods and strategies for the synthesis of substituted indoles or functionalization of the azole ring, strategies for the selective functionalization of the benzo-fused portion of the indole skeleton, particularly the 7-position, are less common. We report a one-pot, iridium-catalyzed, silyl-directed C-H borylation of indoles at the 7-position. This process occurs in high yield with a variety of substituted indoles, and conversions of the 7-borylindole products to 7-aryl-, 7-cinnamyl-, and 7-haloindoles are demonstrated. The Ir-catalyzed, silyl-directed C-H borylation also occurs with several other nitrogen heterocycles, including carbazole, phenothiazines, and tetrahydroquinoline. The utility of this methodology is highlighted by the one-pot synthesis of a member of the pyrrolophenanthridone class of alkaloid natural products.
User identification based on finger-vein patterns for consumer electronics devices (2010)

With the development of consumer electronics technologies, many more powerful consumer devices such as cell phone, PDA and laptop have brought consumers an unprecedented level of convenience and flexibility. However, how to protect personal private information stored in the consumer electronics devices from misuses owing to theft or loss is becoming a major issue. To solve the problem, more secure and reliable user identification mechanisms using biometrics technology should be equipped into the consumer electronics devices. This paper presents a user identification system framework using finger-vein technology for consumer electronics devices. The finger-vein identification system is one of the biometrics sensor technologies, which provides high security and reliability than other identification technology. The algorithm of the proposed system compose a feature extraction using Radon transform and singular value decomposition (SVD) and classification using a normalized distance measure. The experimental results indicate that the proposed system performs well for user identification and achieves good performance in terms of the false acceptance rate (FAR) and the false rejection rate (FRR).
C-Terminal Sequence Analysis with Carboxypeptidase Y (1996)

To date there is no chemical method that provides the ability to determine extensive lengths of amino acid sequence sequentially at the C-terminus of a protein or a peptide, although the thiocyanate method described in Chapter 92 is showing great promise following recent developments (extensive sequence data from the N-terminus can of course be achieved using the Edman degradation). However, limited C-terminal sequence data can be obtained fairly quickly and easily using a class of enzymes called carboxypeptidases. Such limited information can be useful, for example, in determining positions of proteolytic cleavage in proteins, or for confirming sequence data toward the end of a peptide or protein sequence.
Oxygen Radicals in Influenza-Induced Pathogenesis and Treatment with Pyran Polymer-Conjugated SOD (1989)

The pathogenicity of influenza virus infection in the mice involves, at least in part, overreaction of the immune responses of the host rather than a direct effect of virus multiplication. Xanthine oxidase, which is responsible for the generation of oxygen free radicals, was elevated in serum and lung tissue of mice infected with influenza virus. To test the theory that oxygen-free radicals are involved in pathogenesis, free radicals were removed by injecting superoxide dismutase (SOD), a specific superoxide radical scavenger, which was conjugated with a pyran copolymer. The conjugate protected mice against a potentially lethal influenza virus infection if administered 5 to 8 days after infection. These findings indicate that oxygen radicals are important in the pathogenesis of influenza virus infection, and that a polymer-conjugated SOD has therapeutic potential for this virus infection and other diseases associated with free radicals.
Directed establishment of rat brain cell lines with the phenotypic characteristics of type 1 astrocytes. (1992)

Interest in obtaining cell lines for use in studies on the development and biochemistry of the central nervous system has motivated efforts to establish cells from primary brain cultures by the use of oncogene-transfer techniques. In previous reports, cell lines derived from astrocytes in this way have had immature or abnormal phenotypes. We have explored the possibility of specifically "targeting" expression of exogenous oncogenes to differentiated astrocytes by using the promoter of the gene encoding glial fibrillary acidic protein, which is expressed almost exclusively in such cells. We report here that cell lines displaying the phenotypic characteristics of type 1 astrocytes can be established reproducibly in this manner. Given the heterogeneity of primary cultures, the availability of clonal cell lines displaying characteristics of type 1 astrocytes should greatly facilitate our understanding of the biology of these cells.
Comparison between Cultured Small-Intestinal and Fecal Microbiotas in Beagle Dogs (2005)

The microbiota of the small intestine is poorly known because of difficulties in sampling. In this study, we examined whether the organisms cultured from the jejunum and feces resemble each other. Small-intestinal fluid samples were collected from 22 beagle dogs with a permanent jejunal fistula in parallel with fecal samples. In addition, corresponding samples from seven of the dogs were collected during a 4-week period (days 4, 10, 14, and 28) to examine the stability of the microbiota. In the jejunal samples, aerobic/facultative and anaerobic bacteria were equally represented, whereas anaerobes dominated in the fecal samples. Despite lower numbers of bacteria in the jejunum (range, 10(2) to 10(6) CFU/g) than in feces (range, 10(8) to 10(11) CFU/g), some microbial groups were more prevalent in the small intestine: staphylococci, 64% versus 36%; nonfermentative gram-negative rods, 27% versus 9%; and yeasts, 27% versus 5%, respectively. In contrast, part of the fecal dominant microbiota (bile-resistant Bacteroides spp., Clostridium hiranonis-like organisms, and lactobacilli) was practically absent in the jejunum. Many species were seldom isolated simultaneously from both sample types, regardless of their overall prevalence. In conclusion, the small intestine contains a few bacterial species at a time with vastly fluctuating counts, opposite to the results obtained for the colon, where the major bacterial groups remain relatively constant over time. Qualitative and quantitative differences between the corresponding jejunal and fecal samples indicate the inability of fecal samples to represent the microbiotas present in the upper gut.
Generation of CD19-chimeric antigen receptor modified CD8+ T cells derived from virus-specific central memory T cells (2011)

The adoptive transfer of donor T cells that have been genetically modified to recognize leukemia could prevent or treat leukemia relapse after allogeneic HSCT (allo-HSCT). However, adoptive therapy after allo-HSCT should be performed with T cells that have a defined endogenous TCR specificity to avoid GVHD. Ideally, T cells selected for genetic modification would also have the capacity to persist in vivo to ensure leukemia eradication. Here, we provide a strategy for deriving virus-specific T cells from CD45RA(-)CD62L(+)CD8(+) central memory T (T(CM)) cells purified from donor blood with clinical grade reagents, and redirect their specificity to the B-cell lineage marker CD19 through lentiviral transfer of a gene encoding a CD19-chimeric Ag receptor (CAR). Virus-specific T(CM) were selectively transduced by exposure to the CD19 CAR lentivirus after peptide stimulation, and bi-specific cells were subsequently enriched to high purity using MHC streptamers. Activation of bi-specific T cells through the CAR or the virus-specific TCR elicited phosphorylation of downstream signaling molecules with similar kinetics, and induced comparable cytokine secretion, proliferation, and lytic activity. These studies identify a strategy for tumor-specific therapy with CAR-modified T cells after allo-HSCT, and for comparative studies of CAR and TCR signaling.
Simplification and repair of polygonal models using volumetric techniques (2003)

Two important tools for manipulating polygonal models are simplification and repair and we present voxel-based methods for performing both of these tasks. We describe a method for converting polygonal models to a volumetric representation in a way that handles models with holes, double walls, and intersecting parts. This allows us to perform polygon model repair simply by converting a model to and from the volumetric domain. We also describe a new topology-altering simplification method that is based on 3D morphological operators. Visually unimportant features such as tubes and holes may be eliminated from a model by the open and close morphological operators. Our simplification approach accepts polygonal models as input, scan converts these to create a volumetric description, performs topology modification, and then converts the results back to polygons. We then apply a topology-preserving polygon simplification technique to produce a final model. Our simplification method produces results that are everywhere manifold.
A Cell Cycle Regulator Potentially Involved in Genesis of Many Tumor Types (1994)

A putative tumor suppressor locus on the short arm of human chromosome 9 has been localized to a region of less than 40 kilobases by means of homozygous deletions in melanoma cell lines. This region contained a gene, Multiple Tumor Suppressor 1 (MTS1), that encodes a previously identified inhibitor (p16) of cyclin-dependent kinase 4. MTS1 was homozygously deleted at high frequency in cell lines derived from tumors of lung, breast, brain, bone, skin, bladder, kidney, ovary, and lymphocyte. Melanoma cell lines that carried at least one copy of MTS1 frequently carried nonsense, missense, or frameshift mutations in the gene. These findings suggest that MTS1 mutations are involved in tumor formation in a wide range of tissues.
Real-Time, Noninvasive Recording And Three-Dimensional Display Of The Functional Movements Of An Arbitrary Mandible Point (1986)

The monitoring of the motion of an arbitrary mandibular point is essential in dentistry in order to extract from typical motion patterns relevant parameters indicating normal or abnormal masticatory function. After first experiences of nonrestrictive jaw motion quantification with the help of a Selspot I we designed a new real-time optoelectronic system. The recording system includes three cameras. Each camera contains a cylindrical lens and a linear optosensor (CCD). Two extra-oral lightweight target frames (2g) containing each three light emitting diodes are fixed on the patients&apos;s teeth. The system fires each LED cyclically and computes their three-dimensional coordinates in a reconstruction unit. From these coordinates another processing unit computes the three-dimensional coordinates of an arbitrary jaw point in a head fixed coordinate system. The computed trajectories are drawn on-line with the help of a dedicated 3D viewing hardware on a CRT where they can be directly rotated and zoomed to follow intricate motion details. The system is easy to handle, low-cost, stand-alone, has an excellent linearity and a resolution better than 0.1 mm.
Comparison of Methods for Sequential Screening of Large Compound Sets (2006)

Sequential screening is an iterative procedure that can greatly increase hit rates over random screening or non-iterative procedures. We studied the effects of three factors on enrichment rates: the method used to rank compounds, the molecular descriptor set and the selection of initial training set. The primary factor influencing recovery rates was the method of selecting the initial training set. Rates for recovering active compounds were substantially lower with the diverse training sets than they were with training sets selected by other methods. Because structure-activity information is incrementally enhanced in intermediate training sets, sequential screening provides significant improvement in the average rate of recovery of active compounds when compared with non-iterative selection procedures.
Plasmonic nanopatch array with integrated metal–organic framework for enhanced infrared absorption gas sensing (2017)

In this letter, we present a nanophotonic device consisting of plasmonic nanopatch array (NPA) with integrated metal-organic framework (MOF) for enhanced infrared absorption gas sensing. By designing a gold NPA on a sapphire substrate, we are able to achieve enhanced optical field that spatially overlaps with the MOF layer, which can adsorb carbon dioxide (CO<sub>2</sub>) with high capacity. Experimental results show that this hybrid plasmonic-MOF device can effectively increase the infrared absorption path of on-chip gas sensors by more than 1100-fold. The demonstration of infrared absorption spectroscopy of CO<sub>2</sub> using the hybrid plasmonic-MOF device proves a promising strategy for future on-chip gas sensing with ultra-compact size.
Complement-mediated lysis of Plasmodium falciparum gametes by malaria-immune human sera is associated with antibodies to the gamete surface antigen Pfs230 (1997)

Antibodies to the sexual-stage surface antigens of Plasmodium falciparum, Pfs230 and Pfs48/45, can abolish the infectivity of gametes to mosquitoes; these antigens have been proposed as candidates for inclusion in a malaria transmission-blocking vaccine. One possible mechanism of antibody-mediated transmission blocking is complement-mediated gamete lysis. We have used a panel of human sera from geographically distinct regions where malaria is endemic to investigate whether this may be a mechanism of naturally acquired transmission-blocking immunity to P. falciparum. By immunoprecipitation, we have shown that antibody recognition of Pfs230 and Pfs48/45 is limited, despite universal exposure to P. falciparum gametocytes. In vitro complement-mediated lysis of P. falciparum gametes was positively associated with the presence of antibodies to Pfs230 but not with antibodies to the N-terminal region of the precursor molecule (Pfs260), which is shed from the gametocyte surface at the time of gametogenesis. Similarly, antibodies to two other gametocyte-specific proteins, Pfs48/45 and Pfg27/25, were not associated with gamete lysis. All sera which mediate gamete lysis contain immunoglobulin G1 (IgG1) and/or IgG3 antibodies to gamete surface proteins as determined by an enzyme-linked immunosorbent assay. These data suggest that Pfs230 is a major target of complement-fixing antibodies which may be important for antibody-mediated transmission-blocking immunity.
Single cell manipulation using ferromagnetic composite microtransporters (2010)

For biomedical applications, such as single cell manipulation, it is important to fabricate microstructures that can be powered and controlled wirelessly in fluidic environments. In this letter, we describe the construction and operation of truly micron-sized, biocompatible ferromagnetic microtransporters driven by external magnetic fields. Microtransporters were fabricated using a simple, single step fabrication method and can be produced in large numbers. We demonstrate that they can be navigated to manipulate single cells with micron-size precision without disturbing the local environment.
Protection against LethalAspergillus fumigatusInfection in Mice by Allogeneic Myeloid Progenitors Is Not Major Histocompatibility Complex Restricted (2005)

Invasive fungal infections are a leading cause of morbidity and mortality after myelotoxic chemotherapy or radiation exposure. The resulting depletion of myeloid precursors under these conditions appears to be the factor that limits approaches to accelerate immune reconstitution. In a murine model of myeloablation after radiation exposure, we demonstrated that highly purified common myeloid and granulocyte-monocyte progenitors (CMPs/GMPs) accelerated myeloid recovery and, thus, enhanced innate immunity as measured by survival after a lethal challenge with Aspergillus fumigatus. Of greatest significance was the demonstration that the protection afforded by CMPs/GMPs was not major histocompatibility complex restricted. Furthermore, the effect of CMP/GMP cellular therapy was additive with that of liposomal amphotericin B treatment. These observations greatly expand the potential donor pool and, thus, the clinical utility of CMP/GMP cellular therapy in patients with myeloid depletion.