gebhart/patrepeval huggingface dataset:
The universal stress protein paralogues of Escherichia coli are co‐ordinately regulated and co‐operate in the defence against DNA damage (2002)

We have cloned, characterized and inactivated genes encoding putative UspA paralogues in Escherichia coli. The yecG (uspC), yiiT (uspD) and ydaA (uspE) genes were demonstrated to encode protein pro-ducts and these were mapped to spots in the E. coli proteomic database. Expression analysis using chromosomal transcriptional lacZ fusions and two-dimensional gels revealed that all usp genes analysed are regulated in a similar fashion. Thus, uspC, D and E are all induced in stationary phase and by a variety of stresses causing growth arrest of cells. Induction is independent of rpoS but is abolished in a deltarelA deltaspoT (ppGpp0) background and rescued by suppressor mutations rendering the beta-subunit of RNA polymerase to behave like a stringent polymerase. Ectopic elevation of ppGpp levels in growing cells, by overproducing the RelA protein, triggered the induction of all usp genes. The expression of all usp genes was also elevated by a mutation in the ftsK cell division gene, and this super-induction could be suppressed by inactivating recA indicating that the usp paralogues are involved in the management of DNA. Indeed, uspC, uspD and uspE deletion mutants were all found to be sensitive to UV exposure. Overexpression of UspD could compensate for the lack of a chromosomal uspD gene but not a uspA gene. Similarly, UspA overproduction could only compensate for the lack of chromosomal uspA. Moreover, combination of usp mutations had no additive effect on UV sensitivity indicating that they are all co-operating and required in the same pathway, which could explain the co-ordinated regulation of the genes.
Efficient Synthesis of Aryl Hydroxylactams by Reducing Imides With Activated Zinc Dust (2006)

Abstract A series of aryl hydroxylactams (2a, 2b, 2d–2g, 2i–2k, 2m, and 2n) was synthesized by partially reducing aryl cyclic imides in moderate to excellent yields with activated zinc dust alone in acetic acid. This method was regiospecific and can be employed as an alternative for reported methods to partially reduce aryl cyclic imides. Keywords: Hydroxylactamsregiospecificsynthesiszinc dust
Kelly West Lecture 1991 Challenges in Diabetes Epidemiology—From West to the Rest (1992)

The application of epidemiology to the study of non-insulin-dependent diabetes mellitus (NIDDM) is providing new insights into many aspects of this major public-health problem, including its natural history, prevalence, incidence, morbidity, and mortality in diverse populations around the globe. The main impetus came from the late Kelly West's book Epidemiology of Diabetes and its Vascular Lesions. These studies are providing direction for research into the possible moleculardefect or defects and biochemical mechanism or mechanisms underlying NIDDM and important information on the extrinsic (social, cultural, environmental) risk determinants. Studies have highlighted the importance of regional adipose tissue distribution, particularly upper-body obesity, and physical inactivity in enhancing risk of NIDDM. These findings have important implications for the primary prevention of NIDDM, particularly in populations with increased genetic susceptibility such as Polynesians, Micronesians, American and Asian Indians, Mexican Americans, and Australian aborigines.
Automation of Solid form Screening Procedures in the Pharmaceutical Industry—How to Avoid the Bottlenecks (2004)

AbstractSolid form selection is one of the key milestones in the development of any new small molecule drug candidate. It is critical not only from a regulatory perspective but also from a drug substance manufacturing and drug product-processing viewpoint. High throughput systems provide a significant increase in the number and diversity of experiments performed on a given compound, and are becoming a central feature of drug development, especially in areas concerned with solid form selection. This paper reports our automation of the polymorph screening procedure in combination with automated isolation of samples. Particular focus is placed on the analysis by high throughput PXRD with associated strategies for analysis, clustering, pattern classification, and visualizationKeywords: PolymorphismAutomated crystallizationHigh throughput powder diffractionAutomated pattern comparison and classification
Spatially confined and temporally resolved refractive index and scattering evaluation in human skin performed with optical coherence tomography (2000)

The <i>Journal of Biomedical Optics</i> (JBO) is a Gold Open Access journal that publishes peer-reviewed papers on the use of novel optical systems and techniques for improved health care and biomedical research.
Interaction of Fc receptor (CD16) ligands induces transcription of interleukin 2 receptor (CD25) and lymphokine genes and expression of their products in human natural killer cells. (1988)

We report evidence that FcR(CD16) on human NK cells are signal-transducing molecules that, upon ligand binding, induce transcription of genes encoding surface activation molecules [IL-2-R(CD25)] and cytokines (IFN-gamma and TNF) relevant to NK cell biology and functions. Homogeneous NK and T cell populations purified from short-term bulk cultures of PBMC with irradiated B lymphoblastoid cell lines were cultured in the presence of FcR ligands (particulate immune complexes or immobilized anti-CD16 antibodies) alone or with rIL-2. Upon 18 h of stimulation, NK cells express Tac, TfR, and 4F2 antigens and produce IFN-gamma and TNF; both effects are synergistically enhanced in the presence of rIL-2, which is itself ineffective. Treatment of NK cells with FcR(CD16) ligands induces accumulation of mRNA for IFN-gamma and TNF and, to a lesser extent, IL-2-R with fast kinetics also in the absence of de novo protein synthesis. rIL-2 and FcR(CD16) ligands synergize to induce mRNA accumulation. mRNA accumulation and transcription of TNF and IFN-gamma genes induced by FcR(CD16) ligands are greater than those induced by rIL-2, and the reverse is true for IL-2-R. The two stimuli do not synergize at the transcriptional level. These observations indicate that the mechanisms through which FcR(CD16) ligands and rIL-2 induce NK cell activation are, in part, distinct. Both operate at the transcriptional level, although other mechanisms are probably induced by the FcR ligand stimulus per se or in combination with other lymphokines and synergize at a post-transcriptional or translational level to enhance NK cell activation.
Synthesis and Biological Evaluation of Some New Fused Heterobicyclic Derivatives Containing 1,2,4‐Triazolo/1,2,4‐Triazinopyridinone Moieties. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Dynamic Texture Recognition Using Local Binary Patterns with an Application to Facial Expressions (2007)

Dynamic texture (DT) is an extension of texture to the temporal domain. Description and recognition of DTs have attracted growing attention. In this paper, a novel approach for recognizing DTs is proposed and its simplifications and extensions to facial image analysis are also considered. First, the textures are modeled with volume local binary patterns (VLBP), which are an extension of the LBP operator widely used in ordinary texture analysis, combining motion and appearance. To make the approach computationally simple and easy to extend, only the co-occurrences of the local binary patterns on three orthogonal planes (LBP-TOP) are then considered. A block-based method is also proposed to deal with specific dynamic events such as facial expressions in which local information and its spatial locations should also be taken into account. In experiments with two DT databases, DynTex and Massachusetts Institute of Technology (MIT), both the VLBP and LBP-TOP clearly outperformed the earlier approaches. The proposed block-based method was evaluated with the Cohn-Kanade facial expression database with excellent results. The advantages of our approach include local processing, robustness to monotonic gray-scale changes, and simple computation.
Antibody response to Escherichia coli L-asparaginase. Prognostic significance and clinical utility of antibody measurement. (1986)

By using a modification of the microtiter solid-phase radioimmunoassay, we have measured Escherichia coli L-asparaginase (L-ASP) specific IgG, IgG4, and IgE antibodies in children who received L-ASP as part of their chemotherapy for leukemia and lymphoma. In 13 children with acute lymphoblastic leukemia induced with vincristine, prednisone, and L-ASP (10,000 IU/M2 i.v. each week for 3 weeks), seven developed high titer specific IgG antibodies. Four of the seven relapsed at the time of their peaking IgG response (6-10 months). None of the six with low or absent L-ASP antibody response have relapsed (followed for 20-35 months). In six children with allergic reactions to L-ASP reinduction, all had high titers of L-ASP specific IgG4 (greater than or equal to 20 U/ml) at the time of their reaction. In 16 other children with low L-ASP IgG4 (less than 13 U/ml), none demonstrated allergic reactions to rechallenge. Specific IgE was not consistently detectable in either group. In 21 patients with leukemia or lymphoma on L-ASP with cyclophosphamide-containing regimens, none developed significant IgG antibody response, compared with seven of 13 not receiving cyclophosphamide (p less than 0.001). We conclude: (a) development of L-ASP antibodies may have prognostic significance; (b) the detection of specific IgG4 can predict L-ASP allergy; and (c) cyclophosphamide-containing regimens reduce antibody formation to L-ASP and may allow repetitive (without anaphylaxis) and more effective (avoiding neutralizing antibodies) use of L-ASP.
Proof of the effect of testosterone on skeletal muscle (2001)

In spite of the widespread abuse of androgenic steroids by athletes and recreational body-builders, the effects of these agents on athletic performance and physical function remain poorly understood. Experimentally induced androgen deficiency is associated with a loss of fat-free mass; conversely, physiologic testosterone replacement of healthy, androgen-deficient men increases fat-free mass and muscle protein synthesis. Testosterone supplementation of HIV-infected men with low testosterone levels and of older men with normally low testosterone concentrations also increases muscle mass. However, we do not know whether physiologic testosterone replacement can improve physical function and health-related quality of life, and reduce the risk of falls and disability in older men or those with chronic illness. Testosterone increases maximal voluntary strength in a dose-dependent manner and thus might improve performance in power-lifting events. However, testosterone has not been shown to improve performance in endurance events. The mechanisms by which testosterone increases muscle mass are not known, but probably involve alterations in the expression of multiple muscle growth regulators.
Technology for just-in-time in-situ learning of facial affect for persons diagnosed with an autism spectrum disorder (2008)

Many first-hand accounts from individuals diagnosed with autism spectrum disorders (ASD) highlight the challenges inherent in processing high-speed, complex, and unpredictable social information such as facial expressions in real-time. In this paper, we describe a new technology aimed at helping people capture, analyze, and reflect on a set of social-emotional signals communicated by facial and head movements in live social interaction that occurs with their everyday social companions. We describe our development of a new combination of hardware using a miniature camera connected to an ultramobile PC together with custom software developed to track, capture, interpret, and intuitively present various interpretations of the facial-head movements (e.g., presenting that there is a high probability the person looks "confused"). This paper describes this new technology together with the results of a series of pilot studies conducted with adolescents diagnosed with ASD who used the technology in their peer-group setting and contributed to its development via their feedback.
Topographic antigenic determinants recognized by monoclonal antibodies to sperm whale myoglobin. (1982)

Monoclonal antibodies of high affinity (approximately 10(9) M-1) for sperm whale myoglobin were studied to pinpoint the antigenic determinants with which they interact. None of 6 different monoclonal antibodies tested reacted with any of the 3 CNBr cleavage fragments which encompass the whole sequence of myoglobin, an indication that they react with determinants present only on the native structure. To identify these sites, we compared the affinities of each antibody for a series of 14 mammalian myoglobins of known sequence and similar tertiary structure. Correlation of sequence differences with relative affinities allowed us, thus far, to identify critical antigenic residues recognized by 3 of the antibodies. Two of these antibodies recognize groups of residues which are far apart in primary structure but close together in the 3-dimensional structure of the native myoglobin molecule, i.e. topographic determinants. The third antibody distinguishes 140 Lys leads to Asn plus, probably, surface residues nearby. These determinants differ from previously reported antigenic sites on sperm whale myoglobin both in that they are topographic, rather than sequential, and in that almost all the critical residues recognized by these antibodies are outside the previously reported sites. Monoclonal antibodies are sensitive to subtle changes, e.g. Glu leads to Asp, in the antigenic site.
Plasminogen activator inhibitor-2: a molecular biomarker for head and neck cancer progression. (2003)

Head and neck squamous cell carcinoma (HNSCC) is an aggressive epithelial malignancy in which the early diagnosis of premalignant lesions is known to directly correlate with increased survival. However, only a portion of biopsies showing dysplasia will progress to cancer, and there are no currently accepted criteria for predicting which lesions will progress. Therefore, diagnostic protocols that can identify the lesions that are likely to become HNSCC are required. RNA was isolated from normal keratinocytes, the immortalized but nontumorigenic HaCat cell line, and the tumor cell lines SCC-4, SCC-9, SCC-25, and OSCC-3. The RNA was then labeled and used to probe nylon microarray filters that contained a total of 9184 genes (5295 named and 3889 Expression Sequence Tags). Genes whose expression demonstrated a 3-fold or greater change were considered significant. Comparison of expression profiles from normal, HaCat, and four tumor cell lines revealed changes in gene expression in a total of 508 genes. Of these, 16 genes showed a consistent loss of expression when comparing normal to immortalized keratinocytes. In addition, 10 genes demonstrated a consistent loss of expression in the tumor cell lines only. In this latter group of genes, plasminogen activator inhibitor-2 (PAI-2), a gene whose expression has been linked to cell invasion, was additionally investigated. Altered expression of PAI-2 in the different cultured cells was validated via real-time quantitative-PCR. In addition, immunohistochemical evaluation of biopsy samples revealed a high expression of PAI-2 in both normal and dysplastic epithelium with a marked decrease of expression in areas of the biopsies containing HNSCC. These data demonstrate that genomic profiling can then be used to identify potential genotypic/phenotypic biomarkers that may predict which dysplastic lesions are most likely to progress to HNSCC.
Magnetic Assembly of High-Density DNA Arrays for Genomic Analyses (2008)

A method for rapidly assembling high-density DNA arrays with near-perfect order is described. Photolithography is used to generate a wafer-scale array of microwells in a layer of photoresist on a chemically functionalized glass coverslip. The array is enclosed within a microfluidic device, and a suspension of superparamagnetic microbeads conjugated to DNA molecules is introduced into the chamber. A permanent magnet is used to direct the rapid assembly of the beads into the wells, with each well containing a single bead. These beads are immobilized on the glass surface via affinity binding, and excess beads can be recycled or washed away. Nonspecifically bound beads are removed by dissolving the photoresist. The result is a high-density array of beads with virtually no background. This method can be used to produce protein arrays for chip-based assays and DNA arrays for genotyping or genome sequencing.
IT-SOFC supported on Mixed Oxygen Ionic-Electronic Conducting Composites (2008)

Thin oxygen-ion-conducting films (5−10 µm) were prepared and characterized on mixed-conducting porous substrates. When this film is made of a pure ionic conductor, such as a gadolinia-doped ceria (Ce0.8Gd0.2O1.9) electrolyte material, the assembly can be used as a cathode-supported solid oxide fuel cell (SOFC) for operation at intermediate temperatures (500−600 °C). In this case, a porous anode comprising a Ni-CGO cermet or a Pt coating is deposited on top of the highly conductive electrolyte. Another structure with promising applications is created when the supported gastight layer includes a mixed conductor such as ferrite or cobaltite perovskites acting as oxygen-permeable membrane, which can be applied in the combustion of fuel with pure oxygen or in the intensification of other industrial processes currently using aerial catalytic oxidation. The different supported films and multilayer assemblies were characterized by SEM, EDS-WDX, SIMS, helium, and oxygen permeation, showing that gastight thin films can be achieved (values >1 × 10−6 mbar L s−1 cm−2) by inexpensive coating procedures (screen-printing or slip-casting). The electrochemical properties of thin CGO electrolytes were studied by impedance spectroscopy (EIS) and DC voltammetry on fully assembled fuel cells. It is concluded that thin CGO electrolytes under hydrogen atmosphere have enough n-type electronic conductivity to reduce the cell potential by 5−20% from the Nernst potential, which causes the consequent power density decrease. A possible solution to these leakage currents is the use of a thin electron-blocking layer as stabilized zirconia (YSZ or SSZ) deposited on the fuel-exposed CGO electrolyte side. Oxygen permeation of thin LSFC layers was measured using air and helium (sweep) in the range from 700 to 1000 °C. Supported thin films exhibit much better permeation fluxes than bulk thick membranes, especially when oxygen-reduction catalytic porous coatings were applied.
Etiology of Community-Acquired Pneumonia in Hospitalized School-Age Children: Evidence for High Prevalence of Viral Infections (2004)

The high prevalence of viral and mixed viral-bacterial infections supports the notion that the presence of a virus, acting either as a direct or an indirect pathogen, may be the rule rather than the exception in the development of CAP in school-age children requiring hospitalization.
Coherent image layout using an adaptive visual vocabulary (2013)

When querying a huge image database containing millions of images, the result of the query may still contain many thousands of images that need to be presented to the user. We consider the problem of arranging such a large set of images into a visually coherent layout, one that places similar images next to each other. Image similarity is determined using a bag-of-features model, and the layout is constructed from a hierarchical clustering of the image set by mapping an in-order traversal of the hierarchy tree into a space-filling curve. This layout method provides strong locality guarantees so we are able to quantitatively evaluate performance using standard image retrieval benchmarks. Performance of the bag-of-features method is best when the vocabulary is learned on the image set being clustered. Because learning a large, discriminative vocabulary is a computationally demanding task, we present a novel method for efficiently adapting a generic visual vocabulary to a particular dataset. We evaluate our clustering and vocabulary adaptation methods on a variety of image datasets and show that adapting a generic vocabulary to a particular set of images improves performance on both hierarchical clustering and image retrieval tasks.
Congestion Control and Traffic Management in ATM Networks: Recent Advances and a Survey (1995)

Congestion control mechanisms for ATM networks as selected by the ATM Forum traffic management group are described. Reasons behind these selections are explained. In particular, selection criteria for selection between rate-based and credit-based approach and the key points of the debate between the two approaches are presented. The approach that was finally selected and several other schemes that were considered are described.
An overview of cancer immunotherapy (2000)

The survival of patients with cancer has improved steadily but incrementally over the last century, with the advent of effective anticancer treatments such as chemotherapy and radiotherapy. However, the majority of patients with metastatic disease will not be cured by these measures and will eventually die of their disease. New and more effective methods of treating these patients are required urgently. The immune system is a potent force for rejecting transplanted organs or microbial pathogens, but effective spontaneous immunologically induced cancer remissions are very rare. In recent years, much has been discovered about the mechanisms by which the immune system recognizes and responds to cancers. The specific antigens involved have now been defined in many cases. Improved adjuvants are available. Means by which cancer cells overcome immunological attack can be exploited and overcome. Most importantly, the immunological control mechanisms responsible for initiating and maintaining an effective immune response are now much better understood. It is now possible to manipulate immunological effector cells or antigen-presenting cells ex vivo in order to induce an effective antitumour response. At the same time, it is possible to recruit other aspects of the immune system, both specific (e.g. antibody responses) and innate (natural killer cells and granulocytes).