gebhart/patrepeval huggingface dataset:
Modeling and control of thermostatically controlled loads (2011)

As the penetration of intermittent energy sources grows substantially, loads will be required to play an increasingly important role in compensating the fast time-scale fluctuations in generated power. Recent numerical modeling of thermostatically controlled loads (TCLs) has demonstrated that such load following is feasible, but analytical models that satisfactorily quantify the aggregate power consumption of a group of TCLs are desired to enable controller design. We develop such a model for the aggregate power response of a homogeneous population of TCLs to uniform variation of all TCL setpoints. A linearized model of the response is derived, and a linear quadratic regulator (LQR) has been designed. Using the TCL setpoint as the control input, the LQR enables aggregate power to track reference signals that exhibit step, ramp and sinusoidal variations. Although much of the work assumes a homogeneous population of TCLs with deterministic dynamics, we also propose a method for probing the dynamics of systems where load characteristics are not well known.
Avoiding and controlling double transformation artifacts (2007)

This article describes a set of standard control experiments for the authentication of new protein variants isolated through library selection and site-directed mutagenesis. These controls are specifically designed to rule out artifacts derived from 'double transformants' -- i.e. cells transformed with, or infected by, two different plasmids simultaneously. These seem to have been the source of past artifacts and, as demonstrated here, are far more common than generally recognized. By following standard protocols for cloning, plasmid isolation, subcloning, in combination with functional assays, the presence of such artifacts can be ruled out. This protocol needs to be applied for any new variant isolated from heterogeneous gene repertoires, and in particular for variants isolated by selection for either enzymatic activity, or binding.
Evolution and Clinical Implications of the T Cell Repertoire Following Cord Blood Transplant (2013)

Cord blood transplant (CBT) recipients are at increased risk of transplant related mortality, in part due to delayed hematopoietic and immune system recovery resulting in increased infectious complications. However, without direct clinical measures of immunocompetence, the specific role of delayed immunity on CBT outcomes is not easily determined and intervention studies not possible. Blood samples were collected (pre-transplant and at days 28, 56, 100, 180 and 365 post-transplant) in 34 consecutive patients undergoing myeloablative CBT for treatment of hematologic malignancies. All samples were subjected to Immunoseq, a novel T cell receptor (TCR) sequencing assay that delivers an unprecedented depth of sequencing data. From these data, clonal expansion and contraction of hundreds of thousands of clones were tracked over time and TCR diversity was directly measured. Basic clinical outcomes for all patients were also determined, including GvHD, overall survival, disease free survival, regimen related toxicities and infectious complications. The ability to track clones demonstrated tremendous oscillation, with an almost entirely new T cell repertoire appearing at least monthly in CBT recipients. Furthermore, in contrast to healthy controls whose blood was sampled on a similar time-course, where the most frequent T cell clone at one time point remains the top clone at subsequent time points, the largest clones observed early post-transplant in CBT recipients subsequently dropped below detection within weeks of direct measurement. Of the 34 patients studied, six died of infectious complications between day 100 and one year. Notably, TCR diversity values for these six patients were far lower than those of the remaining patients (P-value = 0.015, see Figure 1). The TCR repertoire is exceptionally dynamic following CBT, with many T cell clones rising to high frequency and then receding to an undetectably low level in a matter of weeks. By two months after transplant, TCR diversity accurately predicted risk of death due to infection in this patient cohort, suggesting that diversity of the TCR is a direct measure of immunocompetence and may be useful as a test to guide clinical decision making in patients with acquired or congenital immunosuppression.
Impact of potassium citrate on urinary risk profile, glucose and lipid metabolism of kidney stone formers in Switzerland (2019)

Potassium citrate supplementation in KSFs in Switzerland resulted in a beneficial change of the urinary risk profile by particularly increasing anti-lithogenic factors. Fasting glucose, HbA<sub>1c</sub>, cholesterol levels and BMI were unaffected by potassium citrate therapy after 3 months, suggesting that potassium citrate is safe and not associated with unfavourable metabolic side effects. Lastly, 1,25(OH)<sub>2</sub> D<sub>3</sub> levels were not associated with urinary citrate excretion.
Reconstruction of xylose utilization pathway and regulons in Firmicutes (2010)

This study provided comprehensive insights to the xylose catabolism and its regulation in diverse Firmicutes bacteria especially Clostridia species, and paved ways for improving xylose utilization capability in C. acetobutylicum by genetic engineering in the future.
Negative Pressure Dressings as an Alternative Technique for the Treatment of Infected Wounds (2003)

Coverage of wounds caused by infection and subsequent treatment often are variable because of the location of the wound and wound size. Although much research has been done to expand the indications of negative pressure wound treatment systems, little investigation has been done to quantify the reduction of wound size for vacuum-assisted closure treatment in the presence of infection. In this series, 14 patients who had wounds caused by infections were treated with the vacuum-assisted wound closure system. All wounds were greater than 20 cm2. The duration of treatment averaged 10 days (range, 2-27 days), and the initial wound size averaged 70 cm2 (range, 22.5-288 cm2). After the course of treatment, the final wound size averaged 39 cm2 (range, 10-147 cm2). The average wound size reduction was 43%. This method seems to enhance the rapidity of wound reduction, and because it is a closed system of treatment, it has the added benefit of minimizing exposure of staff and other patients to communicable diseases. Vacuum-assisted wound closure systems add another option in the care of musculoskeletal infections.
Differential effects of interleukin-3 and interleukin-1 on the proliferation and interleukin-6 protein secretion of acute myeloid leukemic cells; the involvement of ERK, p38 and STAT5. (1999)

In the present study we examined whether the p38 and extracellular signal-regulated kinase (ERK) signal transduction pathways are involved in the interleukin-3 (IL-3)- or interleukin-1 (IL-1)-mediated proliferation and cytokine production of acute myeloid leukemic (AML) cells. The IL-3- and IL-1-mediated proliferation were both inhibited by the specific p38 and MEK1 inhibitors SB203580 and PD98059, respectively. Specificity of these inhibitors was demonstrated by in vitro kinase assays. Furthermore, we examined whether STAT5 (signal transducer and activator of transcription) activity is modulated by the p38 and ERK signal transduction pathways, since STAT5 activation has been linked to proliferation. We provide evidence that the p38 kinase pathway, but not the ERK pathway, is to a certain degree involved in the modulation of STAT5 transactivation since SB203580 and overexpression of an inactive MKK3 mutant inhibited the IL-3-induced STAT5 reporter transactivation. In addition, the p38 and ERK pathways are also involved in cytokine production. The IL-1-enhanced IL-6 protein secretion was strongly reduced by SB203580 and PD98059. Despite the fact that IL-3 did induce p38 and ERK kinase activity, it was not able to enhance IL-6 protein secretion, which coincided with the inability of IL-3 to induce NFkappaB (nuclear factor kappaB) activation and IkappaB (inhibitory protein kappaB) degradation. This study demonstrates that the p38 and ERK pathways play a functional role in cell proliferation and IL-6 secretion of AML cells which are dependent on the activated cytokine receptors.
A configuration tool to increase product competitiveness (1998)

The salesPLUS product configuration tool effectively solves complex configuration problems, reducing costs while meeting customer expectations in real-world applications. This commercial AI-based system effectively and intuitively models and configures products. It effectively produces and maintains consistent, accurate configurations that meet customer demands while significantly reducing costs.
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions (2010)

Panseq is freely available online at http://76.70.11.198/panseq. Panseq is written in Perl.
Application of microarray in breast cancer: An overview (2012)

There are more than 1.15 million cases of breast cancer diagnosed worldwide annually. At present, only small numbers of accurate prognostic and predictive factors are used clinically for managing the patients with breast cancer. DNA microarrays have the potential to assess the expression of thousands of genes simultaneously. Recent preliminary researches indicate that gene expression profiling based on DNA microarray can offer potential and independent prognostic information in patients with newly diagnosed breast cancer. In this paper, an overview upon the applications of microarray techniques in breast cancer is presented.
A Monosialoganglioside Is a Monoclonal Antibody-Defined Antigen of Colon Carcinoma (1981)

The antigen of a monoclonal antibody that is specific for cells of human carcinoma of the colon is a monosialoganglioside as determined by the direct binding of antibody to thin-layer chromatograms of total lipid extracts of tissues. Binding of antibody to chromatograms is detected by autoradiography after the application of iodine-125-labeled F(ab')2 of rabbit immunoglobulin G antibodies to mouse immunoglobulins.
Liaisons dangereuses? General anaesthetics and long-term toxicity in the CNS (2006)

We do not know how general anaesthetics cause their desired effects. Contrary to what has been thought until relatively recently, the clinical state of anaesthesia consists of multiple components that are mediated via interaction of the anaesthetic drugs with different targets on the molecular, the cellular, the network and the structural-anatomical levels. The mechanisms by which some of these drugs induce the different components of "anaesthesia" may be rather specific: discrete mutations of single amino acids in specific proteins profoundly affect the ability of certain anaesthetics to achieve specific endpoints. Despite this potential specificity, inhalational anaesthetics are present in the body at very high concentrations during surgical anaesthesia. Due to their lipid solubility, general anaesthetics dissolve in every membrane, penetrate into organelles and interact with numerous cellular structures in multiple ways. A priori, it is therefore not unreasonable to assume that these drugs have the potential to cause insidious changes in the body other than those acute and readily apparent ones that we routinely monitor for. Some changes may wane within a short time after removal of the drug (e.g. the suppression of immune cell function). Others may persist after complete removal of the drug and even become self-propagating (e.g. spread of malignant cells, the beta-oligomerization of proteins), still others may be irreversible (e.g. the induction of apoptosis in the central nervous system) but of unclear significance. This article will focus on evidence for anaesthetic toxicity in the central nervous system, which appears to be susceptible to anaesthetic neurotoxicity primarily at the extremes of ages but via different pathways: in the neonate, during the period of most intense synaptogenesis, anaesthetics can induce excessive apoptosis; in the aging brain subtle cognitive dysfunction can persist long after clearance of the drug and processes resembling neurodegenerative disorders may be accelerated. At all ages, anaesthetics affect gene expression regulating protein synthesis in poorly understood ways. While it seems reasonable to assume that the vast majority of our patients completely restore homeostasis after general anaesthesia, exposure to these drugs probably has more profound and longer-lasting effects on the brain than heretofore imagined.
Effects of Porcine Reproductive and Respiratory Syndrome Virus-Infected Antigen-Presenting Cells on T Cell Activation and Antiviral Cytokine Production (2006)

The ability of porcine reproductive and respiratory syndrome virus (PRRSV) to suppress T cell expression of CD25 (alpha chain of interleukin [IL]-2 receptor), interferon-gamma (IFN-gamma), and tumor necrosis factor-alpha (TNF-alpha) was determined by flow cytometry in naive porcine T cells in response to mitogen (concanavalin A) and cytokine inducers (phorbol 12-myristate 13-acetate plus ionomycin [PMA/I]). Four PRRSV isolates of varying clinical virulence and three different types of porcine myeloid antigen-presenting cells (APCs) were used. T cells cultured with monocytes infected with virulent PRRSV (VR-2385, SDSU-73, and VR-2332), but not with a vaccine strain (Ingelvac PRRS MLV; Boehringer Ingelheim Vetmedica, St. Joseph, MO), demonstrated significantly reduced CD25 expression (%CD25(+)) and IFN-gamma expression (%IFN-gamma (+)) compared with T cells incubated with uninoculated monocyte cultures. T cells cultured with monocytes infected with all four PRRSV isolates demonstrated significantly reduced %TNF-alpha (+). The significant reduction of %CD25(+), %IFN-gamma (+), and %TNF-alpha (+) was not detected in T cells cultured with monocyte-derived macrophages (MDMs) and immature monocyte-derived dendritic cells (MDCs) infected with any PRRSV isolates. Heat-inactivated PRRSV did not induce significantly reduced T cell responses in any APC cultures. The reduction of T cell response in monocyte cultures was not due to PRRSV-induced T cell death. Gene expression of IL-10 detected by semiquantitative reverse transcriptase-polymerase chain reaction was significantly increased in virulent PRRSV-infected monocyte cultures after PMA/I, but not concanavalin A, stimulation compared with IL-10 gene expression from uninoculated monocyte cultures. Increased IL-10 gene expression contributed to significantly reduced %IFN-gamma (+) and %TNF-alpha (+), but not %CD25(+), as determined by IL-10 neutralization assay. This study reports that PRRSV has the ability to suppress T cell responses. The suppressive ability of PRRSV is associated with viral virulence and is mediated by virus-infected monocytes, but not by virus-infected MDMs and immature MDCs.
Blocking the Monocyte Chemoattractant Protein-1/CCR2 Chemokine Pathway Induces Permanent Survival of Islet Allografts through a Programmed Death-1 Ligand-1-Dependent Mechanism (2003)

Abstract Islet allografts are subject to rapid rejection through host cellular immune responses involving mononuclear cell recruitment and tissue injury. Interruption of leukocyte recruitment through chemokine receptor targeting is of therapeutic benefit in various experimental models, but little is known about the contribution of chemokine pathways to islet allograft rejection. We found that murine islets produce monocyte chemoattractant protein-1 (MCP-1; CCL2) in vitro and that islet allograft rejection was associated with intragraft expression of MCP-1 and its receptor, CCR2. We therefore investigated whether MCP-1 and CCR2 are required for the rejection of fully MHC-disparate islet allografts. Wild-type mice treated with blocking anti-MCP-1 mAb plus a brief, subtherapeutic course of rapamycin had long-term islet allograft survival, in contrast to the effect of treatment with either mAb or rapamycin alone. CCR2−/− mice treated with rapamycin also maintained islet allografts long-term. Both MCP/CCR2- and rapamycin-sensitive signals were required for maximal proliferation of alloreactive T cells, suggesting that MCP-1/CCR2 induce rejection by promoting alloreactive T cell clonal expansion and homing and migration. Prolonged islet allograft survival achieved by blockade of the MCP-1/CCR2 pathway plus rapamycin therapy was accompanied by a mononuclear cell infiltrate expressing the inhibitory receptor, programmed death-1 (PD-1), and its ligand (PD-L1, B7-H1), and prolongation of islet allograft survival was abrogated by anti-PD-L1 mAb therapy. These data show that the blockade of MCP-1 binding to CCR2 in conjunction with subtherapeutic immunosuppression can have profound effects on islet allograft survival and implicate the expression of the PD-1/PD-L1 pathway in the regulation of physiologic responses in vivo.
High Doses of Multiple Antioxidant Vitamins: Essential Ingredients in Improving the Efficacy of Standard Cancer Therapy (1999)

Numerous articles and several reviews have been published on the role of antioxidants, and diet and lifestyle modifications in cancer prevention. However, the potential role of these factors in the management of human cancer have been largely ignored. Extensive in vitro studies and limited in vivo studies have revealed that individual antioxidants such as vitamin A (retinoids), vitamin E (primarily alpha-tocopheryl succinate), vitamin C (primarily sodium ascorbate) and carotenoids (primarily polar carotenoids) induce cell differentiation and growth inhibition to various degrees in rodent and human cancer cells by complex mechanisms. The proposed mechanisms for these effects include inhibition of protein kinase C activity, prostaglandin E1-stimulated adenylate cyclase activity, expression of c-myc, H-ras, and a transcription factor (E2F), and induction of transforming growth factor-beta and p21 genes. Furthermore, antioxidant vitamins individually or in combination enhance the growth-inhibitory effects of x-irradiation, chemotherapeutic agents, hyperthermia, and biological response modifiers on tumor cells, primarily in vitro. These vitamins, individually, also reduce the toxicity of several standard tumor therapeutic agents on normal cells. Low fat and high fiber diets can further enhance the efficacy of standard cancer therapeutic agents; the proposed mechanisms for these effects include the production of increased levels of butyric acid and binding of potential mutagens in the gastrointestinal tract by high fiber and reduced levels of growth promoting agents such as prostaglandins, certain fatty acids and estrogen by low fat. We propose, therefore, a working hypothesis that multiple antioxidant vitamin supplements together with diet and lifestyle modifications may improve the efficacy of standard and experimental cancer therapies.
The bacterial porin superfamily: sequence alignment and structure prediction (1991)

The porins of Gram-negative bacteria are responsible for the 'molecular sieve' properties of the outer membrane. They form large water-filled channels which allow the diffusion of hydrophilic molecules into the periplasmic space. Owing to the strong hydrophilicity of their amino acid sequence and the nature of their secondary structure (beta strands), conventional hydropathy methods for predicting membrane topology are useless for this class of protein. The large number of available porin amino acid sequences was exploited to improve the accuracy of the prediction in combination with tools detecting amphipathicity of secondary structure. Using the constraints of beta-sheet structure these porins are predicted to contain 16 membrane-spanning strands, 14 of which are common to the two (enteric and the neisserial) porin subfamilies.
Aptamer-Based Folding Fluorescent Sensor for Cocaine (2001)

We adapted in two steps a deoxyribonucleotide-based aptamer to signal the recognition of cocaine: an instability was engineered in one stem of a three-way junction that forms the cocaine-binding pocket and the resulting short stem was end labeled with a fluorophore and a quencher. In the absence of cocaine, two stems are open, but in its presence they close and the three-way junction forms. This major structural change brings fluorophore and quencher together thereby signaling the presence and concentration of ligand. The sensor is selective for cocaine over its metabolites, can operate in serum, and is useful for the screening of cocaine hydrolases.
Nanoporous Polyelectrolyte Spheres Prepared by Sequentially Coating Sacrificial Mesoporous Silica Spheres (2005)

Jede Menge Kugeln: Nanoporöse Polyelektrolyt(PE)-Kugeln sind durch schichtweises Abscheiden der entgegengesetzt geladenen Verbindungen Polyacrylsäure und Poly(allylaminhydrochlorid) auf mesoporöse Siliciumoxidkugeln (nach jedem Schritt wird durch Erhitzen vernetzt) und anschließendes Entfernen der Siliciumoxidtemplate mit Fluorwasserstoffsäure zugänglich (siehe Schema).
Laboratory Methods for the Detection of Mutations and Polymorphisms in DNA (1997)

Introduction, G.R. Taylor Arbitrarily Primed PCR Fingerprints, F. Mathieu-Daude, D. Ralph, and M. McClelland Minisatellite Analysis, G. Rysiecki, W.P. Childs, and N. Duxbury Microsatellite Analysis, S. Payne ARMS Analysis of Point Mutations, S. Little Solid Phase Minisequencing, A.C. Syvanen Oligonucleotide Ligation Assay, E.S. Winn-Deen Combined Single-Strand Conformation Polymorphism and Heteroduplex Analysis, A.J. Wallace Denaturing Gradient Gel Electrophoresis (DGGE), M. Loosekoot and R. Fodde Coupled Transcription-Translation, T. Hamzehleoi and S. West Peptide Nucleic Acids, H. Orum, T Koch, M. Egholm, H. O'Keefe, and J. Coull Orphan Peak Analysis, M. Hattori, H. Hagiwara, and Y. Sakaki Sequence-Specific Gene Signatures Produced by LSSP-PCR, A.J.G. Simpson and S.D.J. Pena Bisulphite Genomic Sequencing of Methylated Cytosines, S.J. Clark and M. Frommer Direct Sequencing of PCR Products, E. Werle Heterozygote Determination Using Automated DNA Sequencing Technology, M.N. Kronick A Robust Sequencing Protocol for PCR Products, M.D. Robinson and K.J. Leach Use of MutY and Thymine Glycosylase to Detect Point Mutations, I.C. Hsu MutS-Exonuclease Protection for the Detection of Mismatched Heteroduplexes, V.H. Laitinen, G.R. Taylor, S. Hamilton and P. Flick Enzyme Mismatch Cleavage-Bacterial Resolvases, R.D. Mashal and J. Sklar Chemical Cleavage of Mismatch in Heteroduplexes, J. Prosser Comparison of Mutation Detection by Chemical Cleavage of Mismatch (CCM) and Enzyme Mismatch Cleavage (EMC), R. Youil, S.J. Ramus, and R.G.H. Cotton Analysis of DNA Sequence Using Biosensors, P. Nilsson, B. Persson, M. Uhlen, and P.A. Nygren Repeat Expansion Detection, C. Zander, C. Erickson Burgess, J. Johansen, K. Lindblad, T. Hudson, and M. Schalling Comparative Genomic Hybridization, A Kallioniemi, R. Karhu, and O.-P. Kallioniemi Large-Scale Electrophoretic Studies: Microplate Array Diagonal Gel Electrophoresis (MADGE) and Profiling of Oligonucleotide Dissociation by Gel Electrophoresis (PODGE), I.N.M. Day, S.D. O'Dell, G.P. Weavind, and S.E. Humphries DNA Sequence Database Searches, Comparisons, and Primer Design, G. Williams Accessing Genome Data: The Human Genome Database, Internet, and WWW, G. Williams List of Suppliers Index