gebhart/patrepeval huggingface dataset:
Tumor escape mechanisms from immunosurveillance: induction of unresponsiveness in a specific MHC-restricted CD4+; human T cell clone by the autologous MHC class II+ melanoma (1993)

The co-existence of tumor specific immunity with a progressing tumor is observed in a variety of experimental systems and remains one of the major paradoxes of tumor immunology. We now report that a human melanoma cell line (SMC) expressing MHC class II was able to induce clonal anergy in a specific, MHC-restricted CD4+ T cell clone (STC3). Clonal anergy is a mechanism of T lymphocyte tolerance induced by antigen receptor stimulation in the absence of co-stimulation. We observed that a CD4+ T cell clone and an autologous melanoma cell line form conjugates with each other that leads to an increase of [Ca++]i in the T cell clone; however, this interaction failed to induce IL-2 production or proliferation of the T cell clone. Furthermore, this interaction rendered this T cell clone unresponsive to subsequent stimulation. All these effects were MHC class II restricted. Therefore, the human melanoma cell line SMC was capable of delivering antigen-specific signals to the T cell clone, but did not deliver the co-stimulatory signals, e.g. a B7/CD28 interaction, necessary for full T cell activation. Transfection of the melanoma cells with an expression vector containing a B7 cDNA that resulted in subsequent expression of B7 on its cell surface rendered it into a fully competent antigen presenting cell, which is able to induce a nuclear factor binding to the IL-2 promoter in the specific T cell clone resulting in enhanced IL-2 transcription, synthesis, and T cell proliferation. These findings suggest that manipulation of co-stimulation may offer new strategies for future tumor immunotherapy.
The Human CC Chemokine Receptor 5 (CCR5) Gene (1997)

Human CC chemokine receptor 5 (CCR5), mediates the activation of cells by the chemokines macrophage inflammatory protein-1alpha, macrophage inflammatory protein-1beta, and RANTES, and serves as a fusion cofactor for macrophage-tropic strains of human immunodeficiency virus type 1. To understand the molecular mechanisms that regulate human CCR5 gene expression, we initiated studies to determine its genomic and mRNA organization. Previous studies have identified a single CCR5 mRNA isoform whose open reading frame is intronless. We now report the following novel findings. 1) Complex alternative splicing and multiple transcription start sites give rise to several distinct CCR5 transcripts that differ in their 5'-untranslated regions (UTR). 2) The gene is organized into four exons and two introns. Exons 2 and 3 are not interrupted by an intron. Exon 4 and portions of exon 3 are shared by all isoforms. Exon 4 contains the open reading frame, 11 nucleotides of the 5'-UTR and the complete 3'-UTR. 3) The transcripts appear to be initiated from two distinct promoters: an upstream promoter (PU), upstream of exon 1, and a downstream promoter (PD), that includes the "intronic" region between exons 1 and 3. 4) PU and PD lacked the canonical TATA or CAAT motifs, and are AT-rich. 5) PD demonstrated strong constitutive promoter activity, whereas PU was a weak promoter in all three leukocyte cell environments tested (THP-1, Jurkat, and K562). 6) We provide evidence for polymorphisms in the noncoding sequences, including the regulatory regions and 5'-UTRs. The structure of CCR5 was strikingly reminiscent of the overall structure of other chemokine/chemoattractant receptors, underscoring an important evolutionarily conserved function for a prototypical gene structure. This is the first description of functional promoters for any CC chemokine receptor gene, and we speculate that the complex pattern of splicing events and dual promoter usage may function as a versatile mechanism to create diversity and flexibility in the regulation of CCR5 expression.
A high-performance monolithic multiplier using active feedback (1974)

Since its conception in 1967, the linearized transconductance multiplier (LTM) has rapidly gained acceptance as the preferred approach to the realization of monolithic analog multipliers, and its simplicity has commended it for use in low-cost modular designs. Accuracies of these units have been limited to about 0.5 to 2 percent, and drift and noise performance have generally been worse than that possible using the dominant alternative technique of pulse-width-height modulation. This paper shows that when careful attention is given to all the sources of error it is possible to attain a five-fold improvement in accuracy and corresponding reductions in the drift and noise levels. Odd-order nonlinearities can be reduced to negligible magnitudes by the use of active feedback, by substituting the usual resistive-bridge feedback path by an amplifier identical to that used as the input stages.
Exon array data analysis using Affymetrix power tools and R statistical software (2011)

The use of microarray technology to measure gene expression on a genome-wide scale has been well established for more than a decade. Methods to process and analyse the vast quantity of expression data generated by a typical microarray experiment are similarly well-established. The Affymetrix Exon 1.0 ST array is a relatively new type of array, which has the capability to assess expression at the individual exon level. This allows a more comprehensive analysis of the transcriptome, and in particular enables the study of alternative splicing, a gene regulation mechanism important in both normal conditions and in diseases. Some aspects of exon array data analysis are shared with those for standard gene expression data but others present new challenges that have required development of novel tools. Here, I will introduce the exon array and present a detailed example tutorial for analysis of data generated using this platform.
Structure–activity studies of normal and retro pig cecropin–melittin hybrids (1999)

Chimeric analogs of cecropin P1 and melittin with normal and retro sequences were synthesized to explore the effect of sequence, amide bond direction (helical dipole), charge, amphipathicity and hydrophobicity on their antibacterial activity and channel-forming ability. When viewed from the opposite end by rotation in the plane 180 degrees retro analogs have the same sequence as the parent with reversed amide bond and helical dipole directions. The expected activities were related to the important structural features and a series of assumptions were made. Retro analogs are expected to be inactive if both sequence and amide bond direction make critical contributions to the activity. CP1(1-10)M(2-9) amide, (SWLSKTAKKLIGAVLKVL), showed a broad antibacterial spectrum with high activity against the two Gram-negative and three Gram-positive bacteria tested. Retro-CP1(1-10)M(2-9) was less active compared to its normal peptide. CP1(1-9)M(1-8) and CP1(1-9)M(2-8) amides were found to be active against Gram-negative Escherichia coli and also Gram-positive Streptococcus pyogenes, but inactive against the other test organisms. The corresponding retro analogs were inactive against all the five bacteria tested. These results suggest that both sequence and amide bond direction (helix dipole) are important structural requirements for the activity of CP1-M hybrids. Acetylation of the N-terminal amine in both normal and retro analogs lowered their activity, indicating the contribution of free amine to the activity. These analogs form ion-conducting channels in lipid bilayers. The action of the peptides may be explained by self-aggregation and formation of ion-conducting pores across bacterial membranes. Conformational analysis obtained from CD measurements showed that all analogs form amphipathic alpha-helices in presence of 12-20% hexafluoro isopropanol. The retro CP1(1-10)M(2-9) amide showed higher helicity and is more potent compared to other retro analogs synthesized. These studies show the effect of small sequence modifications on the biological activity of the peptides and on their alpha-helical conformation in HFIP, the structure-inducing organic solvent.
Abstract 570: Heart Failure Imaging in the Rat With LMI1195: A New PET Cardiac Neuronal Imaging Agent (2009)

LMI1195 is a new 18F-benzylguanidine analog being developed to assess cardiac neuronal function by targeting the norepinephrine transporter. The objective of this study was to evaluate the prognost...
Origin of Vascular Smooth Muscle Cells and the Role of Circulating Stem Cells in Transplant Arteriosclerosis (2003)

To date, clinical solid-organ transplantation has not achieved its goals as a long-term treatment for patients with end-stage organ failure. Development of so-called chronic transplant dysfunction (CTD) is now recognized as the predominant cause of allograft loss long term (after the first postoperative year) after transplantation. CTD has the remarkable histological feature that the luminal areas of intragraft arteries become obliterated, predominantly with vascular smooth muscle cells (VSMCs) intermingled with some inflammatory cells (transplant arteriosclerosis, or TA). The development of TA is a multifactorial process, and many risk factors have been identified. However, the precise pathogenetic mechanisms leading to TA are largely unknown and, as a result, adequate prevention and treatment protocols are still lacking. This review discusses the origin (donor versus recipient, bone marrow versus nonbone marrow) of the VSMCs in TA lesions. Poorly controlled influx and subsequent proliferative behavior of these VSMCs are considered to be critical elements in the development of TA. Available data show heterogeneity when analyzing the origin of neointimal VSMCs in various transplant models and species, indicating the existence of multiple sites of origin. Based on these findings, a model considering plasticity of VSMC origin in TA in relation to severity and extent of graft damage is proposed.
Digestive physiological outcomes related to polydextrose and soluble maize fibre consumption by healthy adult men (2011)

The objective of the present study was to evaluate digestive physiological outcomes elicited by functional fibres fed to healthy adult men. A total of twenty-one healthy adult men were utilised in a cross-over design. Each subject received polydextrose (PDX) or soluble maize fibre (SCF) (21 g/d) or no supplemental fibre (no fibre control; NFC) in a snack bar. Periods were 21 d and faeces were collected during the last 5 d of each period. Food intake, including fibre intake, did not differ among treatments. Flatulence (P = 0·001) and distention (P = 0·07) were greatest when subjects consumed PDX or SCF. Reflux was greater (P = 0·04) when subjects consumed SCF compared with NFC. All tolerance scores were low ( < 2·5), indicating only slight discomfort. Faecal ammonia, 4-methylphenol, indole and branched-chain fatty acid concentrations were decreased (P < 0·01) when subjects consumed the functional fibre sources compared with NFC. Faecal acetate, propionate and butyrate concentrations were lower (P < 0·05) when subjects consumed PDX compared with SCF and NFC. Faecal pH was lower (P = 0·01) when subjects consumed SCF compared with NFC, while PDX was intermediate. Faecal wet weight was greatest (P = 0·03) when subjects consumed SCF compared with NFC. Faecal dry weight tended to be greater (P = 0·07) when subjects consumed PDX compared with NFC. The functional fibres led to 1·4 and 0·9 g (PDX and SCF, respectively) increases in faecal dry mass per g supplemental fibre intake. Bifidobacterium spp. concentrations were greater (P < 0·05) when subjects consumed SCF compared with NFC. These functional fibres appear to be beneficial to gut health while leading to minimal gastrointestinal upset.
Hypothesis (1999)

Volatile anesthetics may produce immobility by a concurrent action on two sites five carbon atom lengths apart.
Relaxation and clustering in a local search framework (1999)

This paper presents two primary results relevant to physical design problems in CAD/VLSI through a case study of the linear placement problem. First a local search mechanism which incorporates a neighborhood operator based on constraint relaxation is proposed. The strategy exhibits many of the desirable features of analytical placement while retaining the flexibility and non-determinism of local search. The second and orthogonal contribution is in netlist clustering. We characterize local optima in the linear placement problem through a simple visualization toolthe displacement graph. This characterization reveals the relationship between clusters and local optima and motivates a dynamic clustering scheme designed specifically for escaping such local optima. Promising experimental results are reported.
Production of Ethanol from d -Xylose by Using d -Xylose Isomerase and Yeasts (1981)

d-Xylulose, an intermediate of d-xylose catabolism, was observed to be fermentable to ethanol and carbon dioxide in a yield of greater than 80% by yeasts (including industrial bakers' yeast) under fermentative conditions. This conversion appears to be carried out by many yeasts known for d-glucose fermentation. In some yeasts, xylitol, in addition to ethanol, was produced from d-xylulose. Fermenting yeasts are also able to produce ethanol from d-xylose when d-xylose isomerizing enzyme is present. The results indicate that ethanol could be produced from d-xylose in a yield of greater than 80% by a two-step process. First, d-xylose is converted to d-xylulose by xylose isomerase. d-Xylulose is then fermented to ethanol by yeasts.
A Survey on Wearable Sensor-Based Systems for Health Monitoring and Prognosis (2009)

The design and development of wearable biosensor systems for health monitoring has garnered lots of attention in the scientific community and the industry during the last years. Mainly motivated by increasing healthcare costs and propelled by recent technological advances in miniature biosensing devices, smart textiles, microelectronics, and wireless communications, the continuous advance of wearable sensor-based systems will potentially transform the future of healthcare by enabling proactive personal health management and ubiquitous monitoring of a patient's health condition. These systems can comprise various types of small physiological sensors, transmission modules and processing capabilities, and can thus facilitate low-cost wearable unobtrusive solutions for continuous all-day and any-place health, mental and activity status monitoring. This paper attempts to comprehensively review the current research and development on wearable biosensor systems for health monitoring. A variety of system implementations are compared in an approach to identify the technological shortcomings of the current state-of-the-art in wearable biosensor solutions. An emphasis is given to multiparameter physiological sensing system designs, providing reliable vital signs measurements and incorporating real-time decision support for early detection of symptoms or context awareness. In order to evaluate the maturity level of the top current achievements in wearable health-monitoring systems, a set of significant features, that best describe the functionality and the characteristics of the systems, has been selected to derive a thorough study. The aim of this survey is not to criticize, but to serve as a reference for researchers and developers in this scientific area and to provide direction for future research improvements.
Transgenic mice expressing a functional human photopigment. (1998)

The human L photopigment transduces light efficiently in mouse cones, implying that all protein domains necessary for efficient interaction with intracellular transport and signal transduction machineries in mouse cones have been conserved through evolution. The expression of the human L photopigment gene in both classes of cone of the mouse retina indicates that the transgene did not have the regulatory elements necessary for restricting its expression to mouse M cones or that such elements are not recognized in mouse UV-sensitive cones.
NOD/scid IL-2Rgnull mice: a preclinical model system to evaluate human dendritic cell-based vaccine strategies in vivo (2012)

This humanized mouse model system enables comparisons among different DC vaccine types to be rapidly assessed in vivo. In addition, ex vivo analyses of human CD3+ T cells recovered from the spleens of these mice are also possible, including studies on lymphocyte subsets, Th1/Th2 polarization, presence of regulatory T cells and the impact of DC vaccination on their functions.
Grid-Based Environment Estimation Using Evidential Mapping and Particle Tracking (2018)

Modeling and estimating the current local environment by processing sensor measurement data is essential for intelligent vehicles. Static obstacles, dynamic objects, and free space have to be appropriately represented, classified, and filtered. Occupancy grids, known for mapping static environments, provide a common low-level representation using occupancy probabilities with an implicit data association through the discrete grid structure. Extending this idea toward dynamic environments with moving objects requires a static/dynamic classification of measured occupancy and a tracking of the dynamic state of grid cells. In this paper, we propose a new dynamic grid mapping approach. An evidential representation using the Dempster-Shafer framework is used to model hypotheses for static occupancy, dynamic occupancy, free space, and their combined hypotheses. These hypotheses are consistently estimated and accumulated in a dynamic grid map by an adapted evidential filtering, allowing one to distinguish static and dynamic occupancy. The evidential grid mapping is combined with a low-level particle filter tracking that is used to estimate cell velocity distributions and predict dynamic occupancy of the grid map. Static occupancy is directly modeled in the grid map without requiring particles, increasing efficiency, and improving the static/dynamic classification due to the persistent map accumulation. Experimental results with real sensor data show the effectiveness of the proposed approach in challenging scenarios with occlusions and dense traffic.
Carnitine-dependent β Oxidation of Prostaglandins (1972)

Abstract The oxygen polarograph was used to follow prostaglandin oxidation by rat liver mitochondria. This system exhibits an absolute requirement for exogenous carnitine and ATP, in contrast to the oxidation of prostanoyl carnitine which is stimulated by ADP in a very similar manner to palmityl carnitine. Prostaglandin E1, prostaglandin E2, prostaglandin F1α, prostaglandin F2α, prostaglandin A2, and 15-dehydroprostaglandin E2 exhibited ADP:O ratios in the range of 1.3 to 2.0, which is typical of normal fatty acids. Our data thus indicate that prostaglandins utilize the common carnitine-dependent system for the β oxidation of long chain fatty acids.
Experimental models of multiple sclerosis (2011)

The animal models have their advantages and disadvantages, but no model fully reproduces the spectrum of the human disease.
Reaction of Arynes with Sulfoxides (2015)

A S-O bond insertion reaction of sulfoxides with arynes is reported. This reaction represents a rare instance of semipolar single bond insertion in aryne chemistry. The study of mechanism indicates that a sulfur ylide triggered by aryne is the key intermediate, which further transfers its methylene group to carbonyl compounds to give epoxides and thioethers through a sequential process.
Peptide models for the membrane destabilizing actions of viral fusion proteins (1992)

The fusion of enveloped viruses to target membranes is promoted by certain viral fusion proteins. However, many other proteins and peptides stabilize bilayer membranes and inhibit membrane fusion. We have evaluated some characteristics of the interaction of peptides that are models of segments of measles and influenza fusion proteins with membranes. Our results indicate that these models of the fusogenic domains of viral fusion proteins promote conversion of model membrane bilayers to nonbilayer phases. This is opposite to the effects of peptides and proteins that inhibit viral fusion. A peptide model for the fusion segment of the HA protein of influenza increased membrane leakage as well as promoted the formation of nonbilayer phases upon acidification from pH 7-5. We analyze the gross conformational features of the peptides, and speculate on how these conformational features relate to the structures of the intact proteins and to their role in promoting membrane fusion.
Selective functionalisation of TNT for sensitive detection by SERRSElectronic supplementary information (ESI) available: full experimental details on the synthesis and analysis of the reported compounds. See http://www.rsc.org/suppdata/cc/b1/b110972c/ (2002)

Selective chemical functionalisation of 2,4,6-trinitrotoluene to a surface enhanced resonance Raman active species for sensitive detection.
Alteration of the glutamate and GABA transporters in the hippocampus of the Niemann‐Pick disease, type C mouse using proteomic analysis (2006)

Niemann-Pick disease type C (NPC) is a fatal autosomal recessive cholesterol disorder characterized by severe progressive neurodegeneration. To unveil the mechanism of neurodegeneration, proteomic and morphological approaches were applied to the hippocampus in NPC -/- mouse. Two-DE was utilized to resolve the hippocampal protein expression profiles of 4- and 8-week-old NPC +/+ and -/- mice. Differentially expressed protein spots were identified by MALDI-TOF MS and database searching. At 4 weeks of age, there was no significant difference in protein profiles between NPC +/+ and -/- mice. However, at the age of 8 weeks, NPC +/+ and -/- mice showed marked difference in protein expressions. Among these, glutamate receptor 2 precursor was identified. The immunohistochemical study on neurotransporters showed that glial GABA transporter (GAT-3) increased in both 4- and 8-week-old NPC -/- mouse and glutamic acid decarboxylase (GAD-6) increased in 8-week-old NPC -/- mouse. Glial glutamate transporter, excitatory amino acids carrier-1 (EAAC1), decreased in 8-week-old NPC -/- mouse. In conclusion, our data may provide insight into the understanding of the basic mechanism through perturbation of protein networks and neurotransporter systems in a single gene knockout model of NPC disease.
Efficient Gene Editing in Tomato in the First Generation Using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated9 System (2014)

The CRISPR/Cas9 system is highly efficient at generating targeted mutations in stable transgenic tomato plants, and homozygous deletions of a desired size can be created in the first generation.