gebhart/patrepeval huggingface dataset:
Pulsed-field electrophoresis: application of a computer model to the separation of large DNA molecules. (1987)

The biased reptation theory has been applied to the pulsed-field electrophoresis of DNA in agarose gels. A computer simulation of the theoretical model that calculates the mobility of large DNA molecules as a function of agarose pore size, DNA chain properties, and electric field conditions has been used to generate mobility curves for DNA molecules in the size range of the larger yeast chromosomes. Pulsed-field electrophoresis experiments resulting in the establishment of an electrophoretic karyotype for yeast, where the mobility of the DNA fragments is a monotonic function of molecular size for the entire size range that is resolved (200-2200 kilobase pairs), has been compared to the theoretical mobility curves generated by the computer model. The various physical mechanisms and experimental conditions responsible for band inversion and improved electrophoretic separation are identified and discussed in the framework of the model.
The complete genomic sequence of Nocardia farcinica IFM 10152 (2004)

We determined the genomic sequence of Nocardia farcinica IFM 10152, a clinical isolate, and revealed the molecular basis of its versatility. The genome consists of a single circular chromosome of 6,021,225 bp with an average G+C content of 70.8% and two plasmids of 184,027 (pNF1) and 87,093 (pNF2) bp with average G+C contents of 67.2% and 68.4%, respectively. The chromosome encoded 5,674 putative protein-coding sequences, including many candidate genes for virulence and multidrug resistance as well as secondary metabolism. Analyses of paralogous protein families suggest that gene duplications have resulted in a bacterium that can survive not only in soil environments but also in animal tissues, resulting in disease.
Inhibition of platelet adhesion to fibronectin, fibrinogen, and von Willebrand factor substrates by a synthetic tetrapeptide derived from the cell-binding domain of fibronectin (1985)

The role in platelet function of the cell-binding region of fibronectin was explored by the use of synthetic peptides. The prototypical peptide gly-arg-gly-asp-ser was capable of inhibiting thrombin-induced platelet aggregation without altering the degree of platelet activation as judged by the secretion of 14C-serotonin. The peptide also effectively inhibited, in a concentration-dependent manner, the binding of radiolabeled fibronectin to platelets and the adhesion of platelets to fibronectin substrates. The smallest peptide from the cell-binding region of fibronectin which retained full activity was arg-gly-asp-ser. Transposition of amino acids or conservative substitutions of amino acids within this short sequence resulted in inactive peptides. Peptides containing the arg-gly-asp-ser sequence were also capable of inhibiting the adhesion of platelets to fibrinogen and von Willebrand factor substrates. Examination of the entire panel of synthetic peptides for ability to inhibit adhesion to fibrinogen or von Willebrand factor substrates revealed the same structure-function relationships that had been determined in the studies with fibronectin.
The Fumarase Genes of Escherichia coli: Location of the fumB Gene and Discovery of a New Gene (fumC) (1985)

The fumB gene of Escherichia coli, which complements the fumarase deficiency of a fumA mutant when present in multiple copies, has been located at 93.5 min in the E. coli linkage map and its product has been identified as a polypeptide of 61 kDal. Four overlapping ColE1-fumB+ plasmids representing a continuous segment of 23.3 kb of bacterial DNA have been isolated from the Clarke-Carbon E. coli gene bank and the location of the fumB gene relative to the restriction map and the adjacent mel operon has been defined. Hybridization studies have shown that the fumB gene is homologous to the fumA gene, which complements the fumA1 mutation in single and multi-copy situations, and encodes an analogous 61 kDal product formerly regarded as the E. coli fumarase. The hybridization studies also showed that the Bacillus subtilis fumarase gene (citG) is homologous to an independent gene, fumC (formerly g48), which lies adjacent to the fumA gene at 35.5 min in the E. coli linkage map. The N-terminal sequences of the citG and fumC products exhibit a 51% identity over 88 residues. It is possible that the fumC and citG genes are fumarase structural genes of E. coli and B. subtilis, and that the fumA gene may encode a differentially-regulated fumarase or be a positive regulator gene which is essential for the expression of fumC (but not citG). If so, the fumB gene may encode a related enzyme or activator that can replace the fumA function when amplified.
Semisynthetic Cyclopamine Analogues as Potent and Orally Bioavailable Hedgehog Pathway Antagonists (2008)

Herein is reported the synthesis of a novel class of hedgehog antagonists derived from cyclopamine. The acid sensitive D-ring of cyclopamine was homologated utilizing a sequence of chemoselective cyclopropanation and stereoselective acid-catalyzed rearrangement. Further modification of the A/B-ring homoallylic alcohol to the conjugated ketone led to the discovery of new cyclopamine analogues with improved pharmaceutical properties and in vitro potency (EC 50) ranging from 10 to 1000 nM.
Diversity Combining for Signals of Different Medians (1961)

Over-the-horizon communication systems normally use two identical antennas at each end. It is shown that an asymmetrical arrangement, for example, 6o'( )60' 30'( )30' is better than a symmetrical arrangement when both antennas at one end are used for diversity reception and the larger antenna at the other end is used for transmitting. This arrangement is important because for a given performance it costs less than the symmetrical arrangement. Depending on the exact relationship between cost and antenna gain, the cost is a minimum when the difference in antenna gains lies between 3.2 and 4.8 db. Statistical performance for various combining methods and degrees of diversity are presented. As for the case of equal medians derived previously, selector diversity combining is decidedly inferior to equal gain combining, which in turn is about one db worse than maximal ratio combining. The "instantaneous" SNR's (applicable to data transmission) are derived and compared to the usual short-term SNR's applicable to telephony.
Graphene Plasmonics: A Platform for Strong Light–Matter Interactions (2011)

Graphene plasmons provide a suitable alternative to noble-metal plasmons because they exhibit much tighter confinement and relatively long propagation distances, with the advantage of being highly tunable via electrostatic gating. Here, we propose to use graphene plasmons as a platform for strongly enhanced light-matter interactions. Specifically, we predict unprecedented high decay rates of quantum emitters in the proximity of a carbon sheet, observable vacuum Rabi splittings, and extinction cross sections exceeding the geometrical area in graphene nanoribbons and nanodisks. Our theoretical results provide the basis for the emerging and potentially far-reaching field of graphene plasmonics, offering an ideal platform for cavity quantum electrodynamics, and supporting the possibility of single-molecule, single-plasmon devices.
Preparation of Layered Li[Ni1⁄3Mn1⁄3Co1⁄3]O2 as a Cathode for Lithium Secondary Battery by Carbonate Coprecipitation Method (2004)

Abstract Layered Li[Mn1⁄3Ni1⁄3Co1⁄3]O2 cathode material was synthesized by carbonate coprecipitation method. SEM observation and X-ray diffraction experiment showed that the material with spherical particle morphology was successfully synthesized by the method. The cathode material delivered 180 mAh/g as an initial discharge capacity at 0.2 mA/cm2 and showed high average capacity retention ratio of 99.85%/cycle over 40 cycles.
Susceptibility of Mice Deficient in CD1D or TAP1 to Infection with Mycobacterium tuberculosis (1999)

Cellular immunity against Mycobacterium tuberculosis controls infection in the majority of infected humans. Studies in mice have delineated an important role for CD4(+) T cells and cytokines including interferon gamma and tumor necrosis factor alpha in the response to infection with mycobacteria. Recently, the identification of CD8(+) CD1-restricted T cells that kill M. tuberculosis organisms via granulysin and the rapid death after infection of beta2 microglobulin deficient mice in humans has drawn attention to a critical role for CD8(+) T cells. The nature of mycobacterial-specific CD8(+) T cells has been an enigma because few have been identified in any species. Here, we delineate the contribution of class I MHC-restricted T cells in the defense against tuberculosis as transporter associated with antigen processing (TAP)1-deficient mice died rapidly, bore a greater bacterial burden, and had more severe tissue pathology than control mice. In contrast, CD1D-/- mice were not significantly different in their susceptibility to infection than control mice. This data demonstrates a critical role for TAP-dependent peptide antigen presentation and provides further evidence that class I MHC-restricted CD8(+) T cells, the major T cell subset activated by this antigen processing pathway, play an essential role in immunity to tuberculosis.
Stability of Gadolinium-Based Magnetic Resonance Imaging Contrast Agents in Human Serum at 37°C (2008)

The release of Gd from all linear Gd3+ complexes in human serum was several orders of magnitude greater than predicted by the conditional stability constants. After 15 days, release of Gd3+ from the nonionic linear GBCAs was about 10 times higher than from the ionic linear GBCAs. Elevated serum phosphate levels accelerated the release of Gd3+ from nonionic linear GBCAs and, to a lesser degree, from the ionic linear GBCAs. All 3 macrocyclic GBCAs remained stable in human serum at both normal and elevated phosphate levels.
Cellulose-binding domains: potential for purification of complex proteins (1992)

The endoglucanase CenA and the exoglucanase Cex from Cellulomonas fimi each contain a discrete cellulose-binding domain (CBD), at the amino-terminus or carboxyl-terminus respectively. The gene fragment encoding the CBD can be fused to the gene of a protein of interest. Using this approach hybrid proteins can be engineered which bind reversibly to cellulose and exhibit the biological activity of the protein partner. Alkaline phosphatase (PhoA) from Escherichia coli, and a beta-glucosidase (Abg) from an Agrobacterium sp. are dimeric proteins. The fusion polypeptides CenA-PhoA and Abg-CBC(Cex) are sensitive to proteolysis at the junctions between the fusion partners. Proteolysis results in a mixture of homo- and heterodimers; these bind to cellulose if one or both of the monomers carry a CBD, e.g. CenA-PhoA/CenA-PhoA and CenA-PhoA/PhoA. CBD fusion polypeptides could be used in this way to purify polypeptides which associate with the fusion partner.
Alkaloids as Anticancer Agents: A Review of Chinese Patents in Recent 5 Years (2020)

More than one hundred anticancer alkaloids were disclosed in Chinese patents and their mode of action referred to arresting cell cycle, inhibiting protein kinases, affecting DNA synthesis and p53 expression, etc. Conclusion: Many newly found alkaloids displayed potent anticancer activity both in vitro and in vivo, and some of the anticancer alkaloids acted as protein kinase inhibitors or CDK inhibitors possess the potential for developing as novel anticancer agents.
Separation, purification, partial characterization and comparison of the heavy and light chains of botulinum neurotoxin types A, B, and E. (1985)

Clostridium botulinum produces botulinum neurotoxin (NT) in antigenically distinct forms. When isolated from bacterial cultures type E is a single chain, type B is a mixture of single and two-chain molecules, and type A is essentially a two-chain molecule (Mr approximately 150,000). Protease(s) in the cultures or trypsin nick single-chain NT to the two-chain form. The heavy (Mr approximately 100,000) and light (Mr approximately 50,000) chains of the two-chain molecule remain held together by -S-S-bond(s). The two chains are presumed to have different functions. NT binds to nerve cells via the heavy chain and then light chain enters the cell and blocks release of acetylcholine (Simpson, L. L. (1981) Pharmacol. Rev. 33, 155-188). We nicked single-chain NT to form the two-chain form with trypsin, minimizing secondary cleavages, then separated and purified the heavy and light chains using ion-exchange chromatography. The technique, with minor modifications, is a generalized method for types A, B, and E. These subunit chains (each a single band in sodium dodecyl sulfatepolyacrylamide gel electrophoresis) were analyzed for their complete amino acid compositions. The amino acid contents of the heavy and light chains agreed well with the parent two-chain molecule. This affirms that NT is composed of two chains. The two subunit chains are now usable for amino acid sequence and other studies. Comparison of the amino acid contents indicates more similarity among the light chains than the heavy chains of the three NT types, a similarity that agrees with our published partial amino acid sequences (first 13-18 residues) of these chains. Several (up to 9) different amino acid residues of the heavy chain (which is twice the size of the light chain) are present in double the number of corresponding residues in the light chain.
Myofibroblasts revert to an inactive phenotype during regression of liver fibrosis (2012)

Myofibroblasts produce the fibrous scar in hepatic fibrosis. In the carbon tetrachloride (CCl(4)) model of liver fibrosis, quiescent hepatic stellate cells (HSC) are activated to become myofibroblasts. When the underlying etiological agent is removed, clinical and experimental fibrosis undergoes a remarkable regression with complete disappearance of these myofibroblasts. Although some myofibroblasts apoptose, it is unknown whether other myofibroblasts may revert to an inactive phenotype during regression of fibrosis. We elucidated the fate of HSCs/myofibroblasts during recovery from CCl(4)- and alcohol-induced liver fibrosis using Cre-LoxP-based genetic labeling of myofibroblasts. Here we demonstrate that half of the myofibroblasts escape apoptosis during regression of liver fibrosis, down-regulate fibrogenic genes, and acquire a phenotype similar to, but distinct from, quiescent HSCs in their ability to more rapidly reactivate into myofibroblasts in response to fibrogenic stimuli and strongly contribute to liver fibrosis. Inactivation of HSCs was associated with up-regulation of the anti-apoptotic genes Hspa1a/b, which participate in the survival of HSCs in culture and in vivo.
Heparin-Binding-Hemagglutinin-Induced IFN-γ Release as a Diagnostic Tool for Latent Tuberculosis (2007)

The use of ESAT-6- and CFP-10-based IGRAs may underestimate the incidence of LTBI, whereas the use of HBHA may combine the operational advantages of IGRAs with high sensitivity and specificity for latent infection.
Comparison of Madin-Darby canine kidney cells (MDCK) with a green monkey continuous cell line (Vero) and human lung embryonated cells (MRC-5) in the isolation of influenza A virus from nasopharyngeal aspirates by shell vial culture (1997)

We report a comparative study of the MDCK, Vero, and MRC-5 cell lines in the isolation of the influenza A (IA) virus. We studied 746 samples in which 63 IA viruses were isolated. The MDCK line displayed 100% sensitivity, the Vero line displayed 71.4%, and the MRC-5 displayed 57.1%. The MDCK line showed a statistically significant difference with respect to the Vero line (P = 0.001) and the MRC-5 line (P = 0.001). The quantitative sensitivity analysis showed the MDCK line to be superior to the other lines. It seems that the MDCK line is still one of the most recommendable for the isolation of the IA virus from respiratory samples.
Structure And Function Of Porins From Gram Negative Bacteria (1988)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
Levels of expression of CD19 and CD20 in chronic B cell leukaemias. (1998)

Quantitative determination of CD19 and CD20 may provide useful diagnostic information for the study of B lymphoproliferative disorders.
The immunological barriers to xenotransplantation (2015)

The availability of cells, tissues and organs from a non-human species such as the pig could, at least in theory, meet the demand of organs necessary for clinical transplantation. At this stage, the important goal of getting over the first year of survival has been reported for both cellular and solid organ xenotransplantation in relevant preclinical primate models. In addition, xenotransplantation is already in the clinic as shown by the broad use of animal-derived medical devices, such as bioprosthetic heart valves and biological materials used for surgical tissue repair. At this stage, however, prior to starting a wide-scale clinical application of xenotransplantation of viable cells and organs, the important obstacle represented by the humoral immune response will need to be overcome. Likewise, the barriers posed by the activation of the innate immune system and coagulative pathway will have to be controlled. As far as xenogeneic nonviable xenografts, increasing evidence suggests that considerable immune reactions, mediated by both innate and adaptive immunity, take place and influence the long-term outcome of xenogeneic materials in patients, possibly precluding the use of bioprosthetic heart valves in young individuals. In this context, the present article provides an overview of current knowledge on the immune processes following xenotransplantation and on the possible therapeutic interventions to overcome the immunological drawbacks involved in xenotransplantation.
Hole-driven MIT theory, Mott transition in VO_2, MoBRiK (2006)

For inhomogeneous high-T_c superconductors, hole-driven metal-insulator transition (MIT) theory explains that the gradual increase of conductivity with increasing hole doping is due to inhomogeneity with the local Mott system undergoing the first-order MIT and the local non-Mott system. For VO_2, a monoclinic and correlated metal (MCM) phase showing the linear characteristic as evidence of the Mott MIT is newly observed by applying electric field and temperature. The structural phase transition occurs between MCM and Rutile metal phases. Devices using the MIT are named MoBRiK.
Use of biological treatments in patients with hidradenitis suppurativa (2017)

Pilosebaceous unit occlusion and secondary inflammatory perifollicular lympho-histiocytic infiltration seem to be the underlying etiopathogenic mechanisms giving rise to hidradenitis suppurativa (HS). Increased levels of tumor necrosis factor (TNF)-alpha and other cytokines such as interleukins 12 and 23 (IL12/23) and interleukins 10 and 17 have been observed in HS lesional skin. Biological drugs have been reported to be effective for HS, but the level and duration of the response are quite variable. Among anti-TNF drugs, adalimumab and infliximab seem to obtain better results in HS. Adalimumab is the only registered systemic agent for HS and results from multicenter clinical trials demonstrate that 58.9% of patients may achieve clinical response without significant adverse events. Continuous treatment seems to maintain the therapeutic response, but discontinuation of the treatment usually results in a rapid relapse of the disease. Infliximab may also obtain a good response profile with 50% improvement of HS lesions. Treatment with ustekinumab for HS resulted in variable results showing a moderate-to-marked improvement in 82% of patients. Anakinra, a recombinant IL-1 receptor antagonist, has been also been postulated as a potential systemic treatment for HS. A reduction in the disease activity in 67% of patients has been reported. Biological drugs seem to represent an effective therapeutic option for HS, but complete and persistent resolution of the disease is rarely achieved. Flares of the disease usually develop regardless the prescribed treatment. Combined treatments including antibiotics and retinoids seem to be a potential additional therapeutic approach. In chronic and severe cases, a surgical approach is mandatory in order to remove persistent scarring tissue. New drugs are currently being evaluated as new insights in the pathogenesis of the disease are elucidated. Several clinical trials with apremilast, anti-IL17 drugs and anti-interleukin-1 alpha are currently ongoing.
Vignette and Exposure Calibration and Compensation (2010)

We discuss calibration and removal of "vignetting" (radial falloff) and exposure (gain) variations from sequences of images. Even when the response curve is known, spatially varying ambiguities prevent us from recovering the vignetting, exposure, and scene radiances uniquely. However, the vignetting and exposure variations can nonetheless be removed from the images without resolving these ambiguities or the previously known scale and gamma ambiguities. Applications include panoramic image mosaics, photometry for material reconstruction, image-based rendering, and preprocessing for correlation-based vision algorithms.
Isolation and Characterization of Skin-type, Type I Antifreeze Polypeptides from the Longhorn Sculpin, Myoxocephalus octodecemspinosus (2001)

The antifreeze polypeptides (AFPs) are found in several marine fish and have been grouped into four distinct biochemical classes (type I-IV). Recently, the new subclass of skin-type, type I AFPs that are produced intracellularly as mature polypeptides have been identified in the winter flounder (Pleuronectes americanus) and the shorthorn sculpin (Myoxocephalus scorpius). This study demonstrates the presence of skin-type AFPs in the longhorn sculpin (Myoxocephalus octodecemspinosus), which produces type IV serum AFPs. Using polymerase chain reaction-based methods, a clone that encoded for a type I AFP was identified. The clone lacked a signal sequence, indicating that the mature polypeptide is produced in the cytosol. A recombinant protein was produced in Escherichia coli and antifreeze activity was characterized. Four individual Ala-rich polypeptides with antifreeze activity were isolated from the skin tissue. One polypeptide was completely sequenced by tandem MS. This study provides the first evidence of a fish species that produces two different biochemical classes of antifreeze proteins (type I and type IV), and enforces the notion that skin-type AFPs are a widespread biological phenomenon in fish.
Analysis of knee joint sound signals for non-invasive diagnosis of cartilage pathology (1990)

The need for a safe, objective, noninvasive tool for the early detection, localization, and quantification of both hyaline articular cartilage and meniscal pathology in the knee is discussed, and the possible use of joint sounds for this purpose is examined. A historical survey of joint sound analysis is given, and the authors' own research is described. The analysis of the knee joint sounds, using time-domain signal plots and three-dimensional spectral plots, supported the authors' assumptions regarding the nature of various degrees of chondromalacia and meniscal lesions, and the associated sounds. Quantitative features such as energy, frequency peaks, duration of signal components, and bandwidths can be easily computed from the data. Further subclassification, however, would require more accurate quantification or parametric representation of signal features, which should be possible by modeling techniques such as linear prediction.