gebhart/patrepeval huggingface dataset:
Major alterations in the nucleotide structure of DNA in cancer of the female breast. (1991)

DNA of invasive ductal carcinomas from five women was analyzed for structural alterations in the purine nucleotides using gas chromatography-mass spectrometry with selected ion monitoring. The results were compared to those for a normal DNA control. The carcinoma DNA showed dramatically higher concentrations of the base modifications 8-hydroxy-guanine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, and 8-hydroxyadenine. For example, the concentration of total identified base modifications represented a more than 9-fold increase over the control value. Base modifications of this type, which arise from radical-induced hydroxylation and cleavage reactions of the purine ring, likely play a major role in initiation and probably contribute to the further transformation of neoplastic cells in cancer of the female breast.
Functional Meta-Optics and Nanophotonics Governed by Mie Resonances (2017)

Scattering of electromagnetic waves by subwavelength objects is accompanied by the excitation of electric and magnetic Mie resonances that may modify substantially the scattering intensity and radiation pattern. Scattered fields can be decomposed into electric and magnetic multipoles, and the magnetic multipoles define magnetic response of structured materials underpinning the new field of all-dielectric resonant meta-optics. Here we review the recent developments in meta-optics and nanophotonics and demonstrate that the Mie resonances can play a crucial role offering novel ways for the enhancement of many optical effects near magnetic and electric multipolar resonances, as well as driving a variety of interference phenomena which govern recently discovered novel effects in nanophotonics. We further discuss the frontiers of all-dielectric meta-optics for flexible and advanced control of light with full phase and amplitude engineering, including nonlinear nanophotonics, anapole nanolasers, quantum optics, and topological photonics.
Amplification of the metallothionein-I gene in cadmium-resistant mouse cells. (1981)

Friend leukemia cells resistant to cadmium toxicity were selected. More than 70% of total cysteine incorporation in these cells was into the metal-binding protein, metallothionein. We used cDNA and genomic DNA clones containing the metallothionein-I gene to measure the concentration of its mRNA, the rate of gene transcription, and the number of genes. On a per cell basis, optimally induced, cadmium-resistant cells have a 14-fold more metallothionein-I mRNA, a 6-fold higher rate of metallothionein-I gene transcription, and 6-fold more metallothionein-I genes than do nonresistant cells. Metaphase spreads revealed that the resistant cells are nearly tetraploid and contain, on the average, three very small chromosomes that are absent from non-resistant Friend cells.
The expanding family of regulatory B cells (2015)

Over the last decade it has become evident that in addition to producing antibody, B cells activate the immune system by producing cytokines and via antigen presentation. In addition, B cells also exhibit immunosuppressive functions via diverse regulatory mechanisms. This subset of B cells, known as regulatory B cells (Bregs), contributes to the maintenance of tolerance, primarily via the production of IL-10. Studies in experimental animal models, as well as in patients with autoimmune diseases, have identified multiple Breg subsets exhibiting diverse mechanisms of immune suppression. In this review, we describe the different Breg subsets identified in mice and humans, and their diverse mechanisms of suppression in different disease settings.
Estimated Prevalence of Autism and Other Developmental Disabilities Following Questionnaire Changes in the 2014 National Health Interview Survey. (2015)

The revised question ordering and new approach to asking about developmental disabilities in the 2014 NHIS likely affected the prevalence estimates of these conditions. In previous years, it is likely that some parents of children diagnosed with ASD reported this developmental disability as other DD instead of, or in addition to, ASD. Following these changes, the 2014 ASD estimate was more similar to ASD prevalence estimates from other sources.
Accumulation of fetal fibronectin mRNAs during the development of rat cardiac hypertrophy induced by pressure overload. (1991)

Cardiac pressure overload induces a shift towards the fetal form of major proteins expressed by the myocytes, and an accumulation of extracellular matrix proteins. One of them, fibronectin (FN), accumulates soon after the imposition of pressure overload. Because FN exists both as cellular FN (c-FN) locally synthesized by nonmuscle cells and as "plasma-FN" (p-FN) synthesized by the hepatocytes, the first issue of this study was to determine whether FN accumulation within the myocardium in response to pressure overload is paralleled by a local increase in mRNA. The expression of c-FN isoforms being developmentally regulated in a tissue-specific manner, the types of FN exons expressed by cardiac cells were analyzed. Pressure overload was induced in 25-d-old rats by stenosis of the thoracic aorta. Using in situ hybridization, we show that the mRNAs encoding the fetal forms of c-FN are accumulated in the interstitial tissue of fetal rat hearts but are absent in adult. 1-3 d after aortic stenosis, the fetal forms of c-FN mRNAs were found in the wall of coronary arteries and in focal areas of the myocardium. Thus nonmuscle cells and smooth muscle cells, like myocytes, do respond to pressure overload by reexpressing fetal gene transcripts.
Development and Application of the Controlled-Freeze-Zone Process (1989)

Summary The controlled-freeze-zone (CFZ) process is a cryogenic distillation technique for separating CO2 and heavier compounds from methane (C1). This paper describes how the process controls the freezing and melting of CO2 in a specially designed section of an otherwise conventional distillation tower. In addition to describing the process, this paper compares the CFZ process to other gas-treating processes, discusses pilot-plant operational results, and gives examples of potential CFZ applications. The CFZ process is a simple, cost-effective method to process gas streams containing CO2 using proven facilities, equipment, and control philosophies and has been demonstrated through the operation of a large-scale pilot plant.
Animal‐cell culture media: History, characteristics, and current issues (2017)

Further improvements of culture media are desirable, which will certainly contribute to a reduction in the experimental variation, enhance productivity among biopharmaceuticals, improve treatment outcomes of assisted reproductive technologies, and facilitate implementation and popularization of regenerative medicine.
RObust Header Compression (ROHC): Framework and four profiles (2001)

This document specifies a highly robust and efficient header compression scheme for RTP/UDP/IP (Real-Time Transport Protocol, User Datagram Protocol, Internet Protocol), UDP/IP, and ESP/IP (Encapsulating Security Payload) headers.
Astrocytes play a key role in EAE pathophysiology by orchestrating in the CNS the inflammatory response of resident and peripheral immune cells and by suppressing remyelination (2013)

Astrocytes respond to insult with a process of cellular activation known as reactive astrogliosis. One of the key signals regulating this phenomenon is the transcription factor nuclear factor-kappa B (NF-κB), which is responsible for modulating inflammation, cell survival, and cell death. In astrocytes, following trauma or disease, the expression of NF-κB-dependent genes is highly activated. We previously demonstrated that inactivation of astroglial NF-κB in vivo (GFAP-IκBα-dn mice) leads to improved functional outcome in experimental autoimmune encephalomyelitis (EAE), and this is accompanied by reduction of pro-inflammatory gene expression in the CNS. Here we extend our studies to show that recovery from EAE in GFAP-IκBα-dn mice is associated with reduction of peripheral immune cell infiltration into the CNS at the chronic phase of EAE. This is not dependent on a less permeable blood-brain barrier, but rather on a reduced immune cell mobilization from the periphery. Furthermore, once inside the CNS, the ability of T cells to produce pro-inflammatory cytokines is diminished during acute disease. In parallel, we found that the number of total and activated microglial cells is reduced, suggesting that functional improvement in GFAP-IκBα-dn mice is dependent upon reduction of the overall inflammatory response within the CNS sustained by both resident and infiltrating cells. This results in preservation of myelin compaction and enhanced remyelination, as shown by electron microscopy analysis of the spinal cord. Collectively our data indicate that astrocytes are key players in driving CNS inflammation and are directly implicated in the pathophysiology of EAE, since blocking their pro-inflammatory capability results in protection from the disease.
Dominant negative selection of heterologous genes: isolation of Candida albicans genes that interfere with Saccharomyces cerevisiae mating factor-induced cell cycle arrest. (1992)

We have used a genomic library of Candida albicans to transform Saccharomyces cerevisiae and screened for genes that act similarly to dominant negative mutations by interfering with pheromone-mediated cell cycle arrest. Six different plasmids were identified from 2000 transformants; four have been sequenced. One gene (CZF1) encodes a protein with structural motifs characteristic of a transcription factor. A second gene (CCN1) encodes a cyclin homologue, a third (CRL1) encodes a protein with sequence similarity to GTP-binding proteins of the RHO family, and a fourth (CEK1) encodes a putative kinase of the ERK family. Since CEK1 confers a phenotype similar to that of the structurally related S. cerevisiae gene KSS1 but cannot complement a KSS1 defect, it is evident that dominant negative selection can identify proteins that complementation screens would miss. Because dominant negative mutations exert their influence even in wild-type strain backgrounds, this approach should be a general method for the analysis of complex cellular processes in organisms not amenable to direct genetic analysis.
Fabric sensors for the measurement of physiological parameters (2003)

In this paper, we present fabric sensors for the recording of electrocardiogram (ECG) and respiration rate. Special attention is given to the dedicated sensor interface circuits. The sensors are integrated in a prototype belt for an intelligent suit. The suit will contain not only the sensors, but also the interface, data handling, storage and transmission circuitry. The suit is intended for the monitoring of children in a hospital environment.
Specific binding to cultured cells of 125I-labeled type beta transforming growth factor from human platelets. (1984)

Purified type beta transforming growth factor from human platelets (TGF beta) radioiodinated with 125I-labeled Bolton and Hunter reagent was found to bind to a variety of cultured cells of both epithelial and mesenchymal origin, including normal human fibroblasts and keratinocytes. TGF beta binding sites have also been found on three mouse embryo-derived fibroblast-like cell lines with lower levels of TGF beta binding on the chemically transformed derivatives of these cell lines. A variety of human tumor cell lines was shown to have an inverse correlation between their level of TGF beta binding and their ability to form colonies in soft agar. The mouse embryo-derived AKR-2B (clone 84A) cells reached maximal binding of 125I-labeled TGF beta after 2 hr at 22 degrees C. Scatchard analysis of the equilibrium binding of TGF beta to AKR-2B (clone 84A) cells gives a Kd of 33 pM with approximately equal to 10,500 binding sites per cell. This Kd for TGF beta binding to AKR-2B (clone 84A) cells agreed well with the ED50 of 40 pM for stimulation of colony formation of these cells by TGF beta. The TGF beta binding sites on the AKR-2B cells were shown to be specific for TGF beta with no significant competition with epidermal growth factor, fibroblast growth factor, or insulin and only a small level of competition with high concentrations of platelet-derived growth factor. Partially purified preparations with TGF beta-like activity from mouse embryos and medium conditioned by mouse embryo-derived cells competed effectively for binding to the TGF beta receptor.
Corneal cell adhesion and proliferation on hydrogel sheets bound with cell-adhesive proteins (1991)

The efficiency of protein immobilization to provide a hydrogel surface with a high affinity for corneal epithelial cells was investigated. The cell adhesive proteins collagen and fibronectin, and the cell adhesive oligopeptide RGDS (arginine-glycine-aspartic acid-serine) were successfully covalently immobilized on poly(vinyl alcohol) (PVA) hydrogel sheets. Corneal epithelial cells and L-929 cells were applied to these surfaces. A large number of cells did adhere and proliferate on these protein-bound surfaces in comparison with the virgin PVA not so immobilized.
Clinical potential of monoclonal antibodies against gamma interferon. (1990)

Interferon-gamma (IFN-gamma) is a cytokine discovered by its ability to inhibit virus replication in cells. Although it exerts many different actions on different cells, the most prominent action is its macrophage activating effect. Macrophages, in turn, fulfill various regulatory and effector functions in inflammation. It can therefore be expected that interference with the action of IFN-gamma will affect inflammatory reactions. The studies reported here show that administration of neutralizing monoclonal antibodies directed against murine IFN-gamma modifies inflammatory reactions in various experimental models, in particular local LPS-induced inflammation in a footpad swelling model, LPS-induced lethal shock in a generalized Shwartzman type model, and experimental allergic encephalitis. These and other observations justify the hope that administration of monoclonal antibodies against IFN-gamma will be useful to treat or prevent certain inflammatory disorders.
Crystal Structure of Streptococcus pyogenes Csn2 Reveals Calcium-Dependent Conformational Changes in Its Tertiary and Quaternary Structure (2012)

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute a microbial immune system against invading genetic elements, such as plasmids and phages. Csn2 is an Nmeni subtype-specific Cas protein, and was suggested to function in the adaptation process, during which parts of foreign nucleic acids are integrated into the host microbial genome to enable immunity against future invasion. Here, we report a 2.2 Å crystal structure of Streptococcus pyogenes Csn2. The structure revealed previously unseen calcium-dependent conformational changes in its tertiary and quaternary structure. This supports the proposed double-stranded DNA-binding function of S. pyogenes Csn2.
Preparation and Characterization of Multiwalled Carbon Nanotube-Supported Platinum for Cathode Catalysts of Direct Methanol Fuel Cells (2003)

Multiwalled carbon nanotube-supported Pt (Pt/MWNT) nanocomposites were prepared by both the aqueous solution reduction of a Pt salt (HCHO reduction) and the reduction of a Pt ion salt in ethylene glycol solution. For comparison, a Pt/XC-72 nanocomposite was also prepared by the EG method. The Pt/MWNT catalyst prepared by the EG method has a high and homogeneous dispersion of spherical Pt metal particles with a narrow particle-size distribution. TEM images show that the Pt particle size is in the range of 2−5 nm with a peak at 2.6 nm, which is consistent with 2.5 nm obtained from the XRD broadening calculation. Surface chemical modifications of MWNTs and water content in EG solvent are found to be the key factors in depositing Pt particles on MWNTs. In the case of the direct methanol fuel cell (DMFC) test, the Pt/MWNT catalyst prepared by EG reduction is slightly superior to the catalyst prepared by aqueous reduction and displays significantly higher performance than the Pt/XC-72 catalyst. These differences in catalytic performance between the MWNT-supported or the carbon black XC-72-supported catalysts are attributed to a greater dispersion of the supported Pt particles when the EG method is used, in contrast to aqueous HCHO reduction and to possible unique structural and higher electrical properties when contrasting MWNTs to carbon black XC-72 as a support.
Allosteric changes in thrombin's activity produced by peptides corresponding to segments of natural inhibitors and substrates. (1991)

Acidic synthetic peptides corresponding to segments of several nonhomologous proteins (hirudin, residues 54-65; heparin cofactor II, residues 54-75; and fibrinogen, residues 410-427 of the gamma B-chain) inhibit thrombin's cleavage of fibrinogen without blocking the enzyme's active site. Here, we examined effects of these peptides on thrombin's cleavage of protein C and small peptides. Activation of protein C by thrombin in the absence of calcium was inhibited by all of the peptides. Maximal inhibition was 60%, and no greater inhibition was produced by higher peptide concentrations. This differed from progressive inhibition of protein C activation by increasing peptide concentrations in the presence of thrombomodulin and calcium. Potencies of the peptides were in the order hirudin-(54-65) greater than heparin cofactor II-(54-75) greater than gamma B-chain-(410-427). Sulfation of the tyrosine residue in hirudin-(54-65) increased its potency about 10-fold, similar to changes in anticlotting activity. The peptides were activators rather than inhibitors of the cleavage of small chromogenic substrates. In the presence of the peptides, the affinity of thrombin for the substrates S-2366 (pyro-Glu-Pro-Arg-4-nitroanilide), Chromozyme TH (tosyl-Gly-Pro-Arg-4-nitroanilide), and S-2251 (D-Val-Leu-Lys-4-nitroanilide) increased 1.5-2-fold with little change in the Vmax of substrate cleavage. Potencies of peptides in these allosteric effects on thrombin was in the same order as for their other effects. The similar actions of these nonhomologous peptides, which are believed to bind to thrombin's anion-binding exosite, suggest that binding of any peptide to this site exerts the same allosteric effect on thrombin's active site. Interactions of these peptides with thrombin may serve as models for regulation of thrombin's interactions with natural substrates and inhibitors.
Tumor angiogenesis activity in cells grown in tissue culture. (1976)

Normal, viral transformed and tumor-derived cells grown in tissue culture and representing different species were tested for their ability to produce an extracellular tumor angiogenesis factor (TAF). TAF was assayed by measuring the host-mediated vascular response of the chorioallantoic membrane to TAF preparations. All of the viral transformed and tumor-derived cells tested, including SVT2, SVW126, Welker 256 rat carcinoma, B-16 mouse melanoma, human glioblastoma, and human meningioma cells, produced TAF. The potency of the TAF preparations, as measured by the number of cells needed to induce a positive vascular response on the chorioallantoic membrane, varied from cell line to cell line. The most potent cells tested were the glioblastoma and maningioma brain tumor cells. Since these brain tumors are found to be the most highly vascularized tumors in vivo, it was concluded that a correlation exists between the vascularity of a tumor in vivo and the potency of TAF in vitro. There was no detectable angiogenesis activity induced by density-inhibited BALB/c primary mouse embryo or early-passage human skin fibroblasts, even when relatively large numbers of cells were used to make a sample. However, density-inhibited BALB/c 3T3 aan W138 human embryonic lung fibroblasts, two cell lines widely regarded as demonstrating "normal" growth behavior in culture, produced TAF. From these and other observations, it was suggested that BALB/c 3T3 and W138 are not fully "normal" cells. Furthermore, it was suggested that the production of TAF is an early event in the cell transformation process that precedes the loss of density inhibition of growth in vitro.
Biochemical analysis of the recombinant Fur (ferric uptake regulator) protein from Anabaena PCC 7119: factors affecting its oligomerization state (2002)

Fur (ferric uptake regulator) protein is a DNA-binding protein which regulates iron-responsive genes. Recombinant Fur from the nitrogen-fixing cyanobacterium Anabaena PCC 7119 has been purified and characterized, and polyclonal antibodies obtained. The experimental data show that Fur from Anabaena dimerizes in solution with the involvement of disulphide bridges. Cross-linking experiments and MALDI-TOF (matrix-assisted laser desorption/ionization time of flight) MS also show several oligomerization states of Fur, and the equilibrium of these forms depends on protein concentration and ionic strength. In intact recombinant Fur, four cysteine residues out of five were inert towards DTNB [5,5'-dithiobis-(2-nitrobenzoic acid)], and their modification required sodium borohydride. Metal analysis and electrospray ionization MS revealed that neither zinc nor other metals are present in this Fur protein. Purified recombinant Fur bound to its own promoter in gel-shift assays. Fur was shown to be a constitutive protein in Anabaena cells, with no significant difference in its expression in cells grown under iron-sufficient compared with iron-deficient conditions.
Freezing immunoglobulins to see them move (2004)

The issue of protein dynamics and its implications in the biological function of proteins are arousing greater and greater interest in different fields of molecular biology. In cryo-electron tomography experiments one may take several snapshots of a given biological macromolecule. In principle, a large enough collection of snapshots of the molecule may then be used to calculate its equilibrium configuration in terms of the experimentally accessible degrees of freedom and, hence, to estimate its potential energy. This information would be crucial in order to analyze the biological functions of biomolecules by directly accessing the relevant dynamical indicators. In this article, we analyze the results of cryo-electron tomography experiments performed on monoclonal murine IgG2a antibodies. We measure the equilibrium distribution of the molecule in terms of the relevant angular coordinates and build a mechanical model of the antibody dynamics. This approach enables us to derive an explicit expression of the IgG potential energy. Furthermore, we discuss the configuration space at equilibrium in relation to results from other techniques, and we set our discussion in the context of the current debate regarding conformation and flexibility of antibodies.
Rickettsial vaccines: the old and the new (2004)

In the past century vaccine development for prevention of rickettsial diseases has been prolific. However, in the past 20 years no new rickettsial vaccine has been manufactured and there are currently no new or old rickettsial vaccines licensed. Early rickettsial vaccines were difficult, expensive and very hazardous to produce. Molecular biology techniques of today are currently being used to develop new rickettsial vaccines that are standardized, inexpensive, nonhazardous and efficacious.