gebhart/patrepeval huggingface dataset:
Bioengineering of Bacterial Magnetic Particles and their Applications in Biotechnology (2010)

Magnetic particles have attracted much attention for their versatile uses in biotechnology, especially in medical applications. The major advantage of magnetic particles is that they can be easily manipulated by magnetic forces. Magnetotactic bacteria synthesize nano-sized biomagnetites, otherwise known as bacterial magnetic particles (BacMPs) that are individually enveloped by a lipid bilayer membrane. The mechanisms of BacMP synthesis have been analyzed by genomic, proteomic, and bioinformatic approaches. Based on those studies in Magnetospirillum magneticum AMB-1, functional nanomaterials have been designed and produced. Through genetic engineering, functional proteins such as enzymes, antibodies, and receptors have been successfully displayed on BacMPs. These functional BacMPs have been utilized in various biosensors and bio-separation processes. Here, recent papers and patents for bioengineering of BacMPs and their applications in biotechnology are reviewed. The elucidation of the mechanism of magnetic particle synthesis has provided a roadmap for the design of novel biomaterials that can play useful roles in multiple disciplinary fields.
Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (<i>Glycine max</i>) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (<i>Heterodera glycines</i>) (2010)

Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.
Phthalic Anhydride from<i>o</i>-Xylene Catalysis: Science and Engineering (1991)

Abstract Phthalic anhydride is one of the most important products of modem large-scale organic synthesis, and it has a wide application in various branches of chemical industry. It is mostly used (60% of the world production) for preparation plasticizers for PVC. The rapid development of the industrial production of polymeric materials during the last two decades increased the need of phthalic anhydride, which resulted in an increase of its production [1, 2].
The type III effector repertoire of <i>Pseudomonas syringae</i> pv. <i>syringae</i> B728a and its role in survival and disease on host and non‐host plants (2006)

The bacterial plant pathogen Pseudomonas syringae injects a large repertoire of effector proteins into plant cells using a type III secretion apparatus. Effectors can trigger or suppress defences in a host-dependent fashion. Host defences are often accompanied by programmed cell death, while interference with defences is sometimes associated with cell death suppression. We previously predicted the effector repertoire of the sequenced bean pathogen P. syringae pv. syringae (Psy) B728a using bioinformatics. Here we show that PsyB728a is also pathogenic on the model plant species Nicotiana benthamiana (tobacco). We confirm our effector predictions and clone the nearly complete PsyB728a effector repertoire. We find effectors to have different cell death-modulating activities and distinct roles during the infection of the susceptible bean and tobacco hosts. Unexpectedly, we do not find a strict correlation between cell death-eliciting and defence-eliciting activity and between cell death-suppressing activity and defence-interfering activity. Furthermore, we find several effectors with quantitative avirulence activities on their susceptible hosts, but with growth-promoting effects on Arabidopsis thaliana, a species on which PsyB728a does not cause disease. We conclude that P. syringae strains may have evolved large effector repertoires to extend their host ranges or increase their survival on various unrelated plant species.
Electromechanical Restoration of the Micturition Reflex (1971)

Techniques for reflex simulation as a treatment for the neurologically impaired bladder must restore volitional control of bladder function. This paper outlines the engineering commitments necessitated by biological considerations and the exclusive biological problems that must be dealt with in order to accomplish this. An electromechanical system that includes patient controllable mechanisms to provide for retention of intravesical content interrupted by intermittent expulsion is then described.
European maize landraces made accessible for plant breeding and genome-based studies (2019)

Doubled-haploid libraries from landraces capture native genetic diversity for a multitude of quantitative traits and make it accessible for breeding and genome-based studies. Maize landraces comprise large allelic diversity. We created doubled-haploid (DH) libraries from three European flint maize landraces and characterized them with respect to their molecular diversity, population structure, trait means, variances, and trait correlations. In total, 899 DH lines were evaluated using high-quality genotypic and multi-environment phenotypic data from up to 11 environments. The DH lines covered 95% of the molecular variation present in 35 landraces of an earlier study and represent the original three landrace populations in an unbiased manner. A comprehensive analysis of the target trait plant development at early growth stages as well as other important agronomic traits revealed large genetic variation for line per se and testcross performance. The majority of the 378 DH lines evaluated as testcrosses outperformed the commercial hybrids for early development. For total biomass yield, we observed a yield gap of 15% between mean testcross yield of the commercial hybrids and mean testcross yield of the DH lines. The DH lines also exhibited genetic variation for undesirable traits like root lodging and tillering, but correlations with target traits early development and yield were low or nonsignificant. The presented diversity atlas is a valuable, publicly available resource for genome-based studies to identify novel trait variation and evaluate the prospects of genomic prediction in landrace-derived material.
nippon kagaku kaishi (1975)

チタン中の微量のマンガン,鉄を沈殿分離-ケィ光X線で迅速,簡単に同時定量する方法を検討した。試料を硫酸,フヅ化水素酸および硝酸で加熱溶解しち,ホウ酸を加えて水で-定量に希釈する。この溶液の-定量(チタン50mg,マンガン10μ9,鉄200μ9以下)に内漂準としてコパルト50μ9と10%クエン酸ナトリウム溶液5m1を添加したのち,アンモニア水でpHを7～9に調節する。この溶液に10%ジエチルジチオカルバミド酸ナトリウム(DDTC)溶液5mZを添加し,生成したDDTC錯体の沈殿をメンブラZフィルターでミ戸過,赤外線ランプで乾燥する。コバルトに対する各元素のK.線の強度比を測定し,マンガン,鉄を定量した。マンガン100μ9,鉄200μ9まで良好な直線関係が得られた。チタンβOm玄の共存でマンガン50μgl鉄100μ9における5回のくり返し実験め変動率はそれぞれα鰯鵠4彫であ?た諮灘より冴タ沖の耀伽ンガン,鋤聴瀞に同時定量することができ,その分析結果礁原子吸光分析溝や吸光光度法による結果ともほぼ-致した。
Continuous Curvature Trajectory Design and Feedforward Control for Parking a Car (2007)

In this paper, a two-step trajectory planning algorithm from robotics literature is applied to generate suitable trajectories for an autonomous parking maneuver of a car. First, a collision-free curve between a given start and a desired goal configuration within the parking space is planned ignoring the kinematic restrictions on the movement of the car. Second, the collision-free curve is converted into a feasible collision-free trajectory, which can be exactly followed by the car. It is shown how this general planning scheme must be adapted to meet the requirements of the automotive industry
Tumor necrosis factor (TNF) up-regulates the expression of p75 but not p55 TNF receptors, and both receptors mediate, independently of each other, up-regulation of transforming growth factor alpha and epidermal growth factor receptor mRNA. (1993)

The expression and cytokine-mediated regulation of the two different receptors for tumor necrosis factor, TNF-R-75 and TNF-R-55, was investigated in human malignant epithelial cell lines. Here we show that cells treated with TNF-alpha up-regulate the TNF-R-75 mRNA and protein levels. No changes were seen regarding the level of TNF-R-55 transcripts. Phospholipase and protein kinase C inhibitors abrogated the signal transduction pathway of TNF-mediated TNF-R-75 mRNA up-regulation which proceeded in the absence of transcriptional activation. This process was also elicited by an agonistic antibody binding specifically to TNF-R-55. Ligand binding assays using specific inhibitory antibodies showed a marked shift in active binding sites from p55 to p75 without significant changes in the total binding for TNF-alpha after up-regulation of p75 TNF-R. This ligand-induced regulation of one of the corresponding receptors has so far only been detected in malignant epithelial cells and not in hematopoietic cell lines. In our search for a specific function we were able to show that p75 is the specific receptor for TNF-mediated up-regulation of transforming growth factor alpha mRNA, whereas p55 is the signal transducer for TNF-induced up-regulation of epidermal growth factor receptor mRNA. This is the first demonstration of an exclusive function of TNF-R-75 in cells of epithelial origin.
DNA Damage by Free Radical Production by Aminoguanidine (2006)

Aminoguanidine (AG), a prototype therapeutic dicarbonyl scavenger, is the most potent drug available today to inhibit the formation of advanced glycation endproducts (AGEs) and to reverse glycation-mediated damage in normal aging. This paper examines the ability of AG to cause damage to supercoiled plasmid DNA in the presence of the transition metal, Fe(+3). Damage to DNA was dependent on the concentrations of both the transition metal and AG. We could detect hydroxyl radical as well as hydrogen peroxide during the incubation of AG with Fe(+3). Thus this finding further cautions against the indiscriminate use of AG in clinical prophylaxis in diabetes and questions its use as a therapeutic agent.
BACTERICIDAL ACTION OF SELECTED PHENANTHROLINE CHELATES AND RELATED COMPOUNDS (1969)

Summary Selected 1, 10‐phenanthroline hydrochlorides, quaternary salts and metal chelates are bactericidal to Staphylococcus aureus, Streptococcus pyogenes (Group A), Clostridium perfringens, Escherichia coli and Proteus vulgaris in serum broth in that general order of decreasing sensitivity; certain hydro‐ chlorides and metal chelates are also bactericidal to Staphylococcus aureus in distilled water in the absence of added metal ion. Metal chelates with similar or identical bactericidal titres following 48 hours' incubation with Staphylococcus aureus, Streptococcus pyogenes (Group A) or Escherichia coli differ greatly in their rate of kill. Generally, the labile Cu(II), Cd(II), Zn(II) and Mn(II) phenanthroline chelates are rapidly lethal to these bacteria while the corresponding more inert Fe(II), Ni(II) and Ru(II) compounds are more slowly bactericidal; the Co(II) analogues are the most slowly lethal, probably owing to the formation of highly inert cobalt (III) species. These results suggest that the kinetic reactivity of the metal chelate is more important than its thermodynamic stability in governing rate of bactericidal action. Other important factors are the lipophilia of the active species, which may be the phenanthroline ligand or a metal‐containing derivative, and the permeability of the organism to it. Comparison of the bactericidal activity and rate of kill of Staphylococcus aureus and Escherichia coli by selected metal chelates and by a series of un‐ related but clinically‐useful antibacterials suggests that the former compounds warrant investigation for the sterilization of skin surfaces both prophylactically and therapeutically.
The Development of a Neurotropic Strain of Measles Virus in Hamsters and Mice (1964)

Journal Article The Development of a Neurotropic Strain of Measles Virus in Hamsters and Mice Get access Theodore Burnstein, Theodore Burnstein Department of Veterinary Microbiology, Pathology, and Public Health, Purdue University School of Veterinary Science and Medicine, Lafayette, Indiana; and from the Department of Bacteriology and Immunology, Harvard University Medical School, and the Neurology Service, Massachusetts General Hospital, Boston, Massachusetts Search for other works by this author on: Oxford Academic PubMed Google Scholar John H. Jensen, John H. Jensen Department of Veterinary Microbiology, Pathology, and Public Health, Purdue University School of Veterinary Science and Medicine, Lafayette, Indiana; and from the Department of Bacteriology and Immunology, Harvard University Medical School, and the Neurology Service, Massachusetts General Hospital, Boston, Massachusetts Search for other works by this author on: Oxford Academic PubMed Google Scholar Byron H. Waksman Byron H. Waksman Department of Veterinary Microbiology, Pathology, and Public Health, Purdue University School of Veterinary Science and Medicine, Lafayette, Indiana; and from the Department of Bacteriology and Immunology, Harvard University Medical School, and the Neurology Service, Massachusetts General Hospital, Boston, Massachusetts Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 114, Issue 3, June 1964, Pages 265–272, https://doi.org/10.1093/infdis/114.3.265 Published: 01 June 1964 Article history Received: 07 January 1964 Published: 01 June 1964
Matrix-M adjuvanted virosomal H5N1 vaccine confers protection against lethal viral challenge in a murine model (2011)

IM vaccination provided protection irrespective of dose and the presence of Matrix-M adjuvant, whilst the IN vaccine required adjuvant to protect against the challenge. The Matrix-M adjuvanted vaccine induced a strong and cross-reactive serum antibody response indicative of seroprotection after both IM and IN administration. In addition, the IM vaccine induced the highest frequencies of influenza specific CD4+ and CD8+ T-cells. The results confirm a high potential of Matrix-M adjuvanted virosomal vaccines and support the progress of this vaccine into a phase 1 clinical trial.
Neuroimaging of obesity (2010)

Functional neuroimaging techniques have been used to assess the link between intake of food ingredients (i.e. glucose) and changes in hypothalamus, and to compare responses in lean and obese individuals. Several functional magnetic resonance imaging (fMRI) studies reported transient changes of the blood oxygen level dependent (BOLD) signals in the hypothalamus after administration of glucose in rats and humans. Many peripheral metabolic signals directly or indirectly interact with brain dopamine (DA) pathways. This chapter discusses the relation of DA in brain regions during sensory perception of food. These regions include insular cortex, somatosensory cortex, orbitofrontal cortex (OFC), and amygdala. These brain imaging studies have the potential to facilitate the understanding of mechanisms underlying obesity and overeating behaviors and provide scientific bases for the assessment of the efficacy of drug treatments and for the development of novel pharmacological approaches.
A Drug of Such Damned Nature.1 Challenges and Opportunities in Translational Platinum Drug Research (2017)

The platinum-based anticancer agents cisplatin, carboplatin, and oxaliplatin represent a spectacular translational science achievement. The basic research observations that led to the discovery of Pt complexes as DNA-binding agents that elicit cell arrest, the preclinical tumor regression studies, and the inorganic medicinal chemistry that led to clinical implementation of effective platinum complexes in the clinic have fueled multidisciplinary research into platinum-based drugs. While the successes are clear and the research activity continues, a significant window of time has passed since a new Pt drug has been approved for clinical use. Here we assess the current Pt drug landscape and challenges for future Pt development and discuss opportunities for improving our understanding of Pt drugs that utilize contemporary translational science tools such as chemical biology and real-time imaging. The underexplored spaces may reveal new opportunities for Pt drug development.
Dynamic Infrared Imaging of Newly Diagnosed Malignant Lymphoma Compared with Gallium-67 and Fluorine-18 Fluorodeoxyglucose (FDG) Positron Emission Tomography (2003)

Staging and therapy monitoring of malignant lymphomas relies heavily on imaging using arbitrary size criteria from computed tomography (CT) and sometimes non-specific radionuclide studies to assess the activity of the disease. Treatment decisions are based on early assessment of the response to therapy and the residual volume of the disease. Our initial experience is reported using a new noninvasive, inexpensive, and reproducible passive imaging modality, Dynamic Infrared Imaging (DIRI), which may add a new dimension to functional imaging. This system relies on its ability to filter the raw infrared signal using biological oscillatory behavior. It detects and analyzes minute oscillations of temperature and heat distribution in tumors.
Characterization of clays by organic compounds (1981)

Abstract Many problems—from soil research to ceramics—require a reliable characterization of the clay minerals involved. This can be done using four clay-organic reactions: (i) staining tests and dye adsorption; (ii) glycerol and glycol adsorption; (iii) intercalation; (iv) alkylammonium ion exchange. Dye adsorption (staining tests) and glycerol adsorption allow a preliminary identification of the clay mineral groups. Intercalation reactions indicate minute differences between kaolins which cannot be detected by XRD and DTA. Alkylammonium ion exchange provides the best method for characterizing smectites and is sensitive to changes in the layer charge.
Synthetic crude oil and transportation fuels from oil shale (1981)

The importance of assessment of disease activity and its prognosis in PMR or GCA patients via ultrasonographic evaluation of exudate in peripheral joints and resistance index of temporal artery as well as the analysis of T-cell distribution in peripheral blood and incidence of HLA-antigens has not been proved yet. Practical significance of monitoring the above-mentioned parameters can be verified only by further prospective study performed with a larger sample of patients.
Treatment of Cytomegalovirus Retinitis with 9-[2-Hydroxy-1-(hydroxymethyl)ethoxymethyl]guanine (1985)

Cytomegalovirus infections can cause significant morbidity and mortality in immunosuppressed patients, and present antiviral agents have had little efficacy against these infections. We describe the use of an acyclic nucleoside 9-[2-hydroxy-1-(hydroxymethyl) ethoxy methyl]guanine (BW B759U), in the treatment of two patients with cytomegalovirus retinitis. The efficacy of this agent was evident, with healing of retinal lesions and resolution of viremia and viral shedding. BW B759U appears to be similar pharmacokinetically to intravenous acyclovir in terms of half-life, peak serum levels, and renal excretion.
High-mobility group box 1 represents a potential marker of disease activity and novel therapeutic target in systemic lupus erythematosus (2011)

High-mobility group box 1 (HMGB1) protein is a nuclear DNA-binding protein, which functions as an alarmin when released from cells. Recent studies implicate extracellular HMGB1 in the pathogenesis of systemic lupus erythematosus (SLE), a prototypical autoimmune disease characterized by the formation of multiple autoantibodies, especially those directed against nucleosomes and double-stranded (ds)DNA. Elevated concentrations of HMGB1 are observed in sera as well as in skin lesions of patients with lupus. Of importance, serum HMGB1 and anti-HMGB1 autoantibody levels correlate with disease activity. In the blood of patients with SLE, HMGB1 is complexed with nucleosomes, at least partially. Moreover, HMGB1-nucleosome complexes from apoptotic cells activate antigen-presenting cells. Injection of HMGB1-nucleosome complexes into nonautoimmune mice results in the formation of autoantibodies against dsDNA and histones in a Toll-like receptor (TLR) 2-dependent manner. Additionally, HMGB1, as a part of DNA-anti-DNA immune complexes, can interact with receptor for advanced glycation end products (RAGE) on the surface of plasmacytoid dendritic cells and B cells leading to TLR9-dependent interferon (IFN)α release and activation of autoreactive B cells, respectively. HMGB1 attached to neutrophil extracellular traps may contribute to IFNα production by facilitating the recognition of self-nucleic acids. Furthermore, HMGB1, complexed with DNA and pathogenic anti-DNA autoantibodies, activates its receptors, TLR2, TLR4 and RAGE, and may thereby be involved in anti-DNA autoantibody-induced kidney damage in lupus nephritis. Collectively, these findings suggest that HMGB1 is a potential marker of disease activity and, because of its probable involvement in the pathogenesis, a novel therapeutic target in SLE.
Nonsteroidal Anti-Inflammatory Drugs and Inflammatory Bowel Disease (1993)

Nonsteroidal anti-inflammatory drugs (NSA!Ds)adversely affect the entire gastrointesrinal tract. The small intestinal side effects of NSAIDs arc well-characterized and are a source of bleeding and protein loss which contributes co iron deficiency and hypoalbuminE>mia, respectively. NSAIDs rarely cause strictures, but these may be pathognomic when they occur. There arc only isolated reports of small intestinal perforations and massive bleeding. The pathogenesis ofNSAID cnteroparhy can be divided into two stages. The first stage is characterized by specific biochemical damage, principally to cmerocyte mitochondria, followed by inhibition of generation of reparative prostaglandins. Collectively this causes a breach in mucosa! integrity with increased intestinal permeability, which leads Lo the second, nonspecific tissue stage, representing an interplay between luminal aggressive tactors and mucosa! defences. This results in inflammation and macroscopic damage. The large intestine is not subjected co the same type of damage, presumably because of the completeness of drug absorption from the small intestine. However, NSAIDs have been implicated in colonic perforations and bleeding, diverticulitis and occasionally colitis. NSAIDs arc recognized as one of four mam causes of relapse in inflammatory bowel disease (IBO), all of which may have the potential to increase intestinal permeability. Extensive studies in patients with Crohn's disease -including sequential changes in intestinal inflammation, intestinal permeability and T cell activation in response to treatment with elemental diets, along with comparative studies on the site ufneutrophil chemoattractants in lBD and NSAID enteropathy -suggest that the clinical spectrum of Crohn's disease can be viewed as two separate events. It is suggested that the relapse of Crohn's disease ( with ia; unchecked inflammation) involves mechanisms identical to the nonspecific second stage of NSAID enteropathy, fundamentally unrelated to the Departments of Clnucal B1ocl1emistry and Medicine, King's