gebhart/patrepeval huggingface dataset:
Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation (2004)

Bacteroides are predominant human colonic commensals, but the principal pathogenic species, Bacteroides fragilis (BF), lives closely associated with the mucosal surface, whereas a second major species, Bacteroides thetaiotaomicron (BT), concentrates within the colon. We find corresponding differences in their genomes, based on determination of the genome sequence of BF and comparative analysis with BT. Both species have acquired two mechanisms that contribute to their dominance among the colonic microbiota: an exceptional capability to use a wide range of dietary polysaccharides by gene amplification and the capacity to create variable surface antigenicities by multiple DNA inversion systems. However, the gene amplification for polysaccharide assimilation is more developed in BT, in keeping with its internal localization. In contrast, external antigenic structures can be changed more systematically in BF. Thereby, at the mucosal surface, where microbes encounter continuous attack by host defenses, BF evasion of the immune system is favored, and its colonization and infectious potential are increased.
Specific absorption rate and temperature elevation in a subject exposed in the far-field of radio-frequency sources operating in the 10-900-MHz range (2003)

The exposure of a subject in the far field of radiofrequency sources operating in the 10-900-MHz range has been studied. The electromagnetic field inside an anatomical heterogeneous model of the human body has been computed by using the finite-difference time-domain method; the corresponding temperature increase has been evaluated through an explicit finite-difference formulation of the bio-heat equation. The thermal model used, which takes into account the thermoregulatory system of the human body, has been validated through a comparison with experimental data. The results show that the peak specific absorption rate (SAR) as averaged over 10 g has about a 25-fold increase in the trunk and a 50-fold increase in the limbs with respect to the whole body averaged SAR (SAR/sub WB/). The peak SAR as averaged over 1 g, instead, has a 30- to 60-fold increase in the trunk, and up to 135-fold increase in the ankles, with respect to SAR/sub WB/. With reference to temperature increases, at the body resonance frequency of 40 MHz, for the ICNIRP incident power density maximum permissible value, a temperature increase of about 0.7/spl deg/C is obtained in the ankles muscle. The presence of the thermoregulatory system strongly limits temperature elevations, particularly in the body core.
Ensemble approaches for regression (2012)

The goal of ensemble regression is to combine several models in order to improve the prediction accuracy in learning problems with a numerical target variable. The process of ensemble learning can be divided into three phases: the generation phase, the pruning phase, and the integration phase. We discuss different approaches to each of these phases that are able to deal with the regression problem, categorizing them in terms of their relevant characteristics and linking them to contributions from different fields. Furthermore, this work makes it possible to identify interesting areas for future research.
Rho GTPases are over-expressed in human tumors (1999)

Small GTPases of the Rho family are involved in the regulation of a variety of cellular processes, such as the organization of the microfilamental network, cell-cell contact and malignant transformation. To address the question of whether Rho proteins are involved in carcinogenesis in man, we compared their expression in tumors from colon, breast and lung with that of the corresponding normal tissue originating from the same patient. As shown by Rho-specific 32P-ADP-ribosylation, as well as Western-blot analysis, the amount of RhoA protein was largely increased in all 3 types of tumors tested. The most dramatic differences in the expression of Rho GTPases were observed in breast tissue. All breast tumors analyzed showed high levels of RhoA, Rac and Cdc42 proteins, whereas in the corresponding normal tissue these Rho proteins were hardly or not detectable. Progression of breast tumors from WHO grade I to grade III was accompanied by a significant average increase in RhoA protein. Overall, increase in the amount of Rho GTPases, in particular RhoA, appears to be a frequent event in different types of human tumors. This supports the view that Rho GTPases are involved in human carcinogenesis.
Particle swarm optimization (2002)

A concept for the optimization of nonlinear functions using particle swarm methodology is introduced. The evolution of several paradigms is outlined, and an implementation of one of the paradigms is discussed. Benchmark testing of the paradigm is described, and applications, including nonlinear function optimization and neural network training, are proposed. The relationships between particle swarm optimization and both artificial life and genetic algorithms are described.
Induction of ovulation and superovulation in mares using equine LH and FSH separated by hydrophobic interaction chromatography (1993)

Pharmacological control of reproduction in mares requires the use of equine gonadotrophins to avoid induced immunological resistance. Crude equine gonadotrophins (CEG) have been used but the presence of equine luteinizing hormone (eLH) and follicle-stimulating hormone (eFSH) in CEG has led to disappointing results in superovulation studies. Separation of eLH and eFSH activities from CEG is necessary to overcome this problem. The hydrophobic properties of the two hormones were sufficiently different to permit their separation by hydrophobic interaction chromatography (HIC) on a phenyl Sepharose matrix. Good yields of separate FSH and LH fractions were readily obtained by stepwise elution and the method was adapted for large scale preparations of enriched fractions of eLH and eFSH. Two experiments were performed in vivo to evaluate the biological activity of the HIC fractions. Experiment 1 showed that biological activity of the LH fraction in inducing ovulation of preovulatory follicles was similar to that obtained with CEG, indicating that LH bioactivity was not altered by HIC. Experiment 2 demonstrated that biological activity of the FSH fraction was identical (as far as rate of ovulation was concerned) to that of CEG in superovulating mares, indicating that FSH activity was also not altered by HIC. Although we have not obtained better results with the separate equine gonadotrophins than with CEG, it is potentially advantageous to use preparations with single activity to obtain a controlled balance of FSH and LH activity. The HIC technique was chosen because it could easily be scaled up to provide the large amounts of the separate hormones needed for the treatment of a large number of mares.
On global sequence alignment (1994)

We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time. We also describe a multiple alignment algorithm based on the pairwise algorithm. Both algorithms have been implemented as portable C programs. Experimental results indicate that for a commonly used set of gap penalties, the new programs produce more satisfactory alignments on sequences of various lengths than some existing pairwise and multiple programs based on the dynamic programming algorithm of Needleman and Wunsch.
Mlc of Thermus thermophilus : a Glucose-Specific Regulator for a Glucose/Mannose ABC Transporter in the Absence of the Phosphotransferase System (2006)

We report the presence of Mlc in a thermophilic bacterium. Mlc is known as a global regulator of sugar metabolism in gram-negative enteric bacteria that is controlled by sequestration to a glucose-transporting EII(Glc) of the phosphotransferase system (PTS). Since thermophilic bacteria do not possess PTS, Mlc in Thermus thermophilus must be differently controlled. DNA sequence alignments between Mlc from T. thermophilus (Mlc(Tth)) and Mlc from E. coli (Mlc(Eco)) revealed that Mlc(Tth) conserved five residues of the glucose-binding motif of glucokinases. Here we show that Mlc(Tth) is not a glucokinase but is indeed able to bind glucose (K(D) = 20 microM), unlike Mlc(Eco). We found that mlc of T. thermophilus is the first gene within an operon encoding an ABC transporter for glucose and mannose, including a glucose/mannose-binding protein and two permeases. malK1, encoding the cognate ATP-hydrolyzing subunit, is located elsewhere on the chromosome. The system transports glucose at 70 degrees C with a K(m) of 0.15 microM and a V(max) of 4.22 nmol per min per ml at an optical density (OD) of 1. Mlc(Tth) negatively regulates itself and the entire glucose/mannose ABC transport system operon but not malK1, with glucose acting as an inducer. MalK1 is shared with the ABC transporter for trehalose, maltose, sucrose, and palatinose (TMSP). Mutants lacking malK1 do not transport either glucose or maltose. The TMSP transporter is also able to transport glucose with a K(m) of 1.4 microM and a V(max) of 7.6 nmol per min per ml at an OD of 1, but it does not transport mannose.
A least-squares approach to blind channel identification (1995)

Conventional blind channel identification algorithms are based on channel outputs and knowledge of the probabilistic model of channel input. In some practical applications, however, the input statistical model may not be known, or there may not be sufficient data to obtain accurate enough estimates of certain statistics. In this paper, we consider the system input to be an unknown deterministic signal and study the problem of blind identification of multichannel FIR systems without requiring the knowledge of the input statistical model. A new blind identification algorithm based solely on the system outputs is proposed. Necessary and sufficient identifiability conditions in terms of the multichannel systems and the deterministic input signal are also presented.
Things that blink: Computationally augmented name tags (1996)

The conventional name tag automatically dispenses information at a time when it is useful and relevant. The name of the person wearing the tag is visible in a face-to-face encounter. The information presented on a name tag changes according to who is wearing the name tag, but it does not depend on who is viewing the name tag. This paper presents a computationally augmented name tag-the "Thinking Tag"-that is capable of displaying different information depending on who is viewing it. When two participants at an event face each other, their name tags change to reflect a simple measure of how much they have in common. A goal of the Thinking Tag technology design is to create an augmented name tag that does not interfere with the social mechanisms that normally operate among groups of people. Therefore, the communication and computation technology are hidden within the tag.
Selection of high-affinity Centyrin FN3 domains from a simple library diversified at a combination of strand and loop positions (2014)

Alternative scaffold molecules represent a class of proteins important to the study of protein design and mechanisms of protein-protein interactions, as well as for the development of therapeutic proteins. Here, we describe the generation of a library built upon the framework of a consensus FN3 domain sequence resulting in binding proteins we call Centyrins. This new library employs diversified positions within the C-strand, CD-loop, F-strand and FG-loop of the FN3 domain. CIS display was used to select high-affinity Centyrin variants against three targets; c-MET, murine IL-17A and rat TNFα and scanning mutagenesis studies were used to define the positions of the library most important for target binding. Contributions from both the strand and loop positions were noted, although the pattern was different for each molecule. In addition, an affinity maturation scheme is described that resulted in a significant improvement in the affinity of one selected Centyrin variant. Together, this work provides important data contributing to our understanding of potential FN3 binding interfaces and a new tool for generating high-affinity scaffold molecules.
Improving the current output of GaInNAs solar cells using distributed Bragg reflectors (2016)

The influence of AlGaAs-based distributed Bragg reflector (DBR) on the performance of a GaInNAs n-i-p solar cells is reported. The DBR increased the short circuit current density by ~1 mA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , owing to increased external quantum efficiency in the wavelength range from 1120 nm to 1240 nm. As a result of the incorporation of the DBR structure, the series resistance of the cell was increased by 4 mOhm-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Early Detection of Tumor Cells by Innate Immune Cells Leads to Treg Recruitment through CCL22 Production by Tumor Cells (2011)

In breast carcinomas, patient survival seems to be negatively affected by the recruitment of regulatory T cells (T(reg)) within lymphoid aggregates by CCL22. However, the mechanisms underpinning this process, which may be of broader significance in solid tumors, have yet to be described. In this study, we determined how CCL22 production is controlled in tumor cells. In human breast carcinoma cell lines, CCL22 was secreted at low basal levels that were strongly increased in response to inflammatory signals [TNF-α, IFN-γ, and interleukin (IL)-1β], contrasting with CCL17. Primary breast tumors and CD45(+) infiltrating immune cells appeared to cooperate in driving CCL22 secretion, as shown clearly in cocultures of breast tumor cell lines and peripheral blood mononuclear cells (PBMC) or their supernatants. We determined that monocyte-derived IL-1β and TNF-α are key players as monocyte depletion or neutralization of these cytokines attenuated secretion of CCL22. However, when purified monocytes were used, exogenous human IFN-γ was also required to generate this response suggesting a role for IFN-γ-producing cells within PBMCs. In this setting, we found that human IFN-γ could be replaced by the addition of (i) IL-2 or K562-activated natural killer (NK) cells or (ii) resting NK cells in the presence of anti-MHC class I antibody. Taken together, our results show a dialogue between NK and tumor cells leading to IFN-γ secretion, which in turn associates with monocyte-derived IL-1β and TNF-α to drive production of CCL22 by tumor cells and subsequent recruitment of T(reg). As one validation of this conclusion in primary breast tumors, we showed that NK cells and macrophages tend to colocalize within tumors. In summary, our findings suggest that at early times during tumorigenesis, the detection of tumor cells by innate effectors (monocytes and NK cells) imposes a selection for CCL22 secretion that recruits T(reg) to evade this early antitumor immune response.
Human natural killer cells: a unique innate immunoregulatory role for the CD56bright subset (2001)

During the innate immune response to infection, monocyte-derived cytokines (monokines), stimulate natural killer (NK) cells to produce immunoregulatory cytokines that are important to the host's early defense. Human NK cell subsets can be distinguished by CD56 surface density expression (ie, CD56(bright) and CD56(dim)). In this report, it is shown that CD56(bright) NK cells produce significantly greater levels of interferon-gamma, tumor necrosis factor-beta, granulocyte macrophage-colony-stimulating factor, IL-10, and IL-13 protein in response to monokine stimulation than do CD56(dim) NK cells, which produce negligible amounts of these cytokines. Further, qualitative differences in CD56(bright) NK-derived cytokines are shown to be dependent on the specific monokines present. For example, the monokine IL-15 appears to be required for type 2 cytokine production by CD56(bright) NK cells. It is proposed that human CD56(bright) NK cells have a unique functional role in the innate immune response as the primary source of NK cell-derived immunoregulatory cytokines, regulated in part by differential monokine production.
MOSBY'S MEDICAL, NURSING, AND ALLIED HEALTH DICTIONARY : illusteated in full color throughout (1994)

Contents A-Z. Appendices: normal reference values clinical calculations units of measurement symbols and abbreviations medical terminology language translation guide - Spanish-French-English tabular atlas of human anatomy and physiology leading health problems assessment guides guidelines for relating to patients from different cultures nutrition paediatrics pharmacology health organizations communicable diseases guidelines for advance directives diagnosis-related groups DSM-III-R classification nursing diagnoses blood normal values (adult) urine normal values (adult) the UKCC Code of Professional Conduct for the Nurse, Midwife and Health Visitor (1992) district and regional drug services directory of health care organizations and voluntary groups.
Natural Killer Cells Generated from Cord Blood Hematopoietic Progenitor Cells Efficiently Target Bone Marrow-Residing Human Leukemia Cells in NOD/SCID/IL2Rgnull Mice (2013)

Natural killer (NK) cell-based adoptive immunotherapy is an attractive adjuvant treatment option for patients with acute myeloid leukemia. Recently, we reported a clinical-grade, cytokine-based culture method for the generation of NK cells from umbilical cord blood (UCB) CD34⁺ hematopoietic progenitor cells with high yield, purity and in vitro functionality. The present study was designed to evaluate the in vivo anti-leukemic potential of UCB-NK cells generated with our GMP-compliant culture system in terms of biodistribution, survival and cytolytic activity following adoptive transfer in immunodeficient NOD/SCID/IL2Rg(null) mice. Using single photon emission computed tomography, we first demonstrated active migration of UCB-NK cells to bone marrow, spleen and liver within 24 h after infusion. Analysis of the chemokine receptor expression profile of UCB-NK cells matched in vivo findings. Particularly, a firm proportion of UCB-NK cells functionally expressed CXCR4, what could trigger BM homing in response to its ligand CXCL12. In addition, high expression of CXCR3 and CCR6 supported the capacity of UCB-NK cells to migrate to inflamed tissues via the CXCR3/CXCL10-11 and CCR6/CCL20 axis. Thereafter, we showed that low dose IL-15 mediates efficient survival, expansion and maturation of UCB-NK cells in vivo. Most importantly, we demonstrate that a single UCB-NK cell infusion combined with supportive IL-15 administration efficiently inhibited growth of human leukemia cells implanted in the femur of mice, resulting in significant prolongation of mice survival. These preclinical studies strongly support the therapeutic potential of ex vivo-generated UCB-NK cells in the treatment of myeloid leukemia after immunosuppressive chemotherapy.
Measuring the metabolome: current analytical technologies (2005)

The post-genomics era has brought with it ever increasing demands to observe and characterise variation within biological systems. This variation has been studied at the genomic (gene function), proteomic (protein regulation) and the metabolomic (small molecular weight metabolite) levels. Whilst genomics and proteomics are generally studied using microarrays (genomics) and 2D-gels or mass spectrometry (proteomics), the technique of choice is less obvious in the area of metabolomics. Much work has been published employing mass spectrometry, NMR spectroscopy and vibrational spectroscopic techniques, amongst others, for the study of variations within the metabolome in many animal, plant and microbial systems. This review discusses the advantages and disadvantages of each technique, putting the current status of the field of metabolomics in context, and providing examples of applications for each technique employed.
Distribution and processing of the polymeric immunoglobulin receptor in the rat hepatocyte: morphological and biochemical characterization of subcellular fractions. (1986)

The transepithelial transport of polymeric immunoglobulins is an essential process in the mucosal immune system. Transport across the epithelial cells of mucous or exocrine glands is affected by an integral membrane glycoprotein receptor known as membrane secretory component (SCm) or as polymeric immunoglobulin receptor (pIgR). This receptor binds polymeric immunoglobulins at the basolateral cell surface and mediates their transcellular translocation and their release from the apical plasma membrane into external secretions. Release depends on cleavage of the membrane-anchoring domain of the receptor, resulting in liberation of polymeric immunoglobulin bound to the ectoplasmic domain of the receptor (secreted SC or SCs) into extracellular secretions. Using a monoclonal antibody directed against the cytoplasmic tail of the receptor and a polyclonal antibody directed against the secreted ectoplasmic domain, we have combined cell fractionation and Western blotting techniques to examine the fate of these receptor domains in the hepatocyte. In this study, we characterize biochemically and morphologically the various subcellular components separated by our fractionation scheme, and correlate this with biochemical analysis of the receptor in each fraction.
Controlled Synthesis of III–V Quantum Dots in Microfluidic Reactors (2009)

Defined properties: Microfluidic reactors have recently emerged as near-ideal systems for the growth of high quality colloidal nanoparticles due to the unprecedented control they offer over reaction conditions (see figure). High quality InP quantum dots are synthesized in simple microfluidic devices, and their spectral characteristics are easily tuned. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Warner-Lambert/Parke-Davis award lecture. Cytokine-mediated activation of vascular endothelium. Physiology and pathology. (1988)

The concept of endothelial cell activation has been extremely useful in understanding endothelial cell function. The morphologic definition of activation from the 1960s has been replaced by a cell biologic definition in the 1980s, but recent studies have suggested that these phenomena are two aspects of the same processes. Moreover, the initial distinction of endothelial cell activation, a beneficial reaction, from injury and dysfunction, a harmful sequence, has become more complex as clinical studies have revealed that activation can produce dysfunction, with or without injury. Most importantly, as our in vivo studies indicate, the concept of activation is a testable hypothesis, as modern immunochemical and molecular biologic techniques have been employed to bridge the gap between in vitro culture experiments and patient-based clinical research.