gebhart/patrepeval huggingface dataset:
Molecular cloning and expression of Rickettsia tsutsugamushi genes for two major protein antigens in Escherichia coli (1987)

Several polypeptide antigens of Rickettsia tsutsugamushi are recognized by human or primate convalescent sera and may be important protective immunogens. Molecular cloning and expression of the genes encoding the 110K (110 kilodalton) and 56K polypeptide antigens of R. tsutsugamushi Karp were accomplished in the lambda gt11 expression vector system. Southern blot analysis with the cloned fragments for the 56K polypeptide antigen (0.7 kilobases) and the 110K polypeptide antigen (5.4 kilobases) confirmed that the insert DNA was rickettsial and not host cell in origin. Expression of a complete 110K polypeptide was shown to be independent of isopropyl-beta-D-thiogalactopyranoside induction, suggesting that an intact rickettsial promoter was operational. Epitopes of the 56K polypeptide were expressed as lac promoter-dependent beta-galactosidase fusion proteins. Polyclonal antibody, affinity purified against the recombinant 110K and 56K polypeptides, reacted with polypeptides of similar size in the Kato and Gilliam strains of R. tsutsugamushi. Group-reactive, but not strain-specific, monoclonal antibodies against the 56K polypeptide reacted with the cloned portion of the 56K polypeptide. Western blot analysis demonstrated that the cloned 56K Karp antigen gene product is recognized by human convalescent serum.
Plasmodium falciparum Histones Induce Endothelial Proinflammatory Response and Barrier Dysfunction (2012)

Plasmodium falciparum is a protozoan parasite of human erythrocytes that causes the most severe form of malaria. Severe P. falciparum infection is associated with endothelial activation and permeability, which are important determinants of the outcome of the infection. How endothelial cells become activated is not fully understood, particularly with regard to the effects of parasite subcomponents. We demonstrated that P. falciparum histones extracted from merozoites (HeH) directly stimulated the production of IL-8 and other inflammatory mediators by primary human dermal microvascular endothelial cells through a signaling pathway that involves Src family kinases and p38 MAPK. The stimulatory effect of HeH and recombinant P. falciparum H3 (PfH3) was abrogated by histone-specific antibodies. The release of nuclear contents on rupture of infected erythrocytes was captured by live cell imaging and confirmed by detecting nucleosomes in the supernatants of parasite cultures. HeH and recombinant parasite histones also induced endothelial permeability through a charge-dependent mechanism that resulted in disruption of junctional protein expression and cell death. Recombinant human activated protein C cleaved HeH and PfH3 and abrogated their proinflammatory effects. Circulating nucleosomes of both human and parasite origin were detected in the plasma of patients with falciparum malaria and correlated positively with disease severity. These results support a pathogenic role for both host- and pathogen-derived histones in P. falciparum-caused malaria.
Toward an ICPMS-Linked DNA Assay Based on Gold Nanoparticles Immunoconnected through Peptide Sequences (2005)

Gold nanoparticles modified with anti-mouse IgG have been used to trace oligonucleotides carrying a c-myc peptide. Two strategies, a dot-blot format as well as inductively coupled plasma mass spectrometry (ICPMS) have been used to detect the nanoparticle tracer. For both cases, oligonucleotide-peptide conjugates were first applied to a nitrocellulose membrane using a manifold attached to a suction device. After immobilization of the oligonucleotide by UV radiation, the samples were incubated with an anti-c-myc monoclonal antibody. In the case of the dot-blot format strategy, it was followed by incubation with a secondary antibody conjugated to horseradish peroxidase and development with luminol as chemiluminescent substrate. In the case of ICPMS strategy, it was followed by incubation with the secondary antibody (anti-mouse IgG) conjugated to gold nanoparticles and their ICPMS detection after dissolving. The nonspecific adsorptions were found to be around zero. The limit of detection for peptide-modified DNA was 0.2 pmol. The method may have significant potential as an important ICPMS-based nonradioactive DNA detection method for the simultaneous determination of various sequences by labeling different kinds of inorganic nanoparticles.
Axiomatic Design of Mechanical Systems (1995)

Design is done in many fields. Although the design practices in different fields appear to be distinct from each other, all fields use a common thought process and design principles. Consequently, the true differences between these fields are minor, often consisting of the definitions of words, the specific data, and knowledge. In comparison, larger differences can exist within a given field between simple systems and large systems due to the size and the time dependent nature of functional requirements. The axiomatic approach to design provides a general theoretical framework for all these design fields, including mechanical design. The key concepts of axiomatic design are: the existence of domains, the characteristic vectors within the domains that can be decomposed into hierarchies through zigzagging between the domains, and the design axioms (i.e., the Independence Axiom and the Information Axiom). Based on the two design axioms, corollaries and theorems can be stated or derived for simple systems, large systems, and organizations. These theorems and corollaries can be used as design rules or guidelines for designers. The basic concepts are illustrated using simple mechanical design examples. When design is viewed axiomatically, not only product design but all other designs, including design of process, systems, software, organizations, and materials, are amenable to systematic treatment.
Brassica Oilseeds: Production and Utilization (1995)

Part 1 The field crop: physiology agronomy diseases weeds and their control pests plant breeding biotechnology environmental aspects. Part 2 Processing and utilization: seed chemistry seed analysis processing oil utilization and human nutrition meal utilization and animal nutrition utilization as a condiment industrial uses.
Improvement of serological diagnosis of neonatal cytomegalovirus infection by simultaneously testing for specific immunoglobulins E and M by antibody-capture enzyme-linked immunosorbent assay (1987)

This study describes the results of testing 92 serum samples, including 10 umbilical cord serum samples, from 38 cytomegalovirus (CMV)-infected neonates for CMV-specific immunoglobulins E (IgE) and M by antibody-capture enzyme-linked immunosorbent assays with enzyme-labeled CMV antigen. All infants excreted CMV in the urine. It was demonstrated that the CMV IgE test was more sensitive than the CMV IgM test in diagnosing CMV infection in neonates by serology. Thus, the sensitivity for the IgE test was 82%, whereas for the IgM test it was only 66%. Furthermore, the CMV-specific IgE response, expressed as absorbance, was higher than the specific IgM response in 91% of the 76 sera which contained antibodies of either one or both immunoglobulin classes. Forty-six control sera, including 18 umbilical cord sera, from 46 neonates from whom CMV was not isolated were also tested. Most sera were negative. Three infants, however, had CMV antibodies of one or both classes, indicating infection. The level of total serum IgE was controlled in 24 of the sera from the CMV-infected neonates, but in none of the cases was the level elevated. No correlation was found between the reactivity of the antibodies in the two immunoglobulin classes and the level of CMV in urine.
Calmodulin‐dependent protein kinase II (1990)

Three multifunctional protein kinases, cyclic AMP-dependent protein kinase, protein kinase C, and calmodulin-dependent protein kinase II, are involved in signal transduction in response to their respective second messengers, cyclic AMP, diacylglycerol, and Ca2+. This review will summarize the key findings on calmodulin-dependent protein kinase II.
Structural requirements for time-dependent inhibition of prostaglandin biosynthesis by anti-inflammatory drugs. (1975)

Several anti-inflammatory drugs have been examined for their ability to cause a time-dependent destruction of the fatty acid oxygenase that produces prostaglandins. All of the time-dependent inhibitors contained carboxylic acid moieties, and in addition all but one of the drugs contained a halogen atom. Structural analogs (of the time-dependent inhibitors) lacking halogen atoms were unable to cause a time-dependent destruction of the enzyme. The time-dependent property of an inhibitor was totally eliminated after methylation of the carboxylate group. Methylation did not, however, alter the ability of the inhibitors to competitively inhibit the oxygenase. Thus, the reversible binding of the agents at the active site was not appreciably dependent upon the free carboxyl group, whereas the subsequent irreversible process was.
CD69 expression on primitive progenitor cells and hematopoietic malignancies (1996)

CD69 is an early activation antigen of peripheral blood lymphocytes and is constitutively expressed on a wide variety of bone marrow-derived cells. To further characterize the distribution and understand the potential biological role of the molecule in normal and malignant hematopoiesis, we used a novel high affinity anti-CD69 mAb (UN6) and analyzed hematopoietic progenitor cells together with a panel of myeloid and lymphoid malignancies. We report that mobilized peripheral blood CD34+ cells display detectable levels of CD69 and that the density of membrane expression correlates with the immature phenotype CD34bright Thy-1bright cells. Furthermore, during cytokine-induced differentiation, the expression of CD69 is moderately down-regulated. Analysis of hematopoietic malignancies revealed that CD69 expression correlates with the immature myeloid phenotype. Taken together these data suggest a role of CD69 during the early phase of hematopoiesis and in the leukemic transformation.
Nucleotide Bias Observed with a Short SELEX RNA Aptamer Library (2011)

Systematic evolution of ligands by exponential enrichment (SELEX) is a powerful in vitro selection process used for over 2 decades to identify oligonucleotide sequences (aptamers) with desired properties (usually high affinity for a protein target) from randomized nucleic acid libraries. In the case of RNA aptamers, several highly complex RNA libraries have been described with RNA sequences ranging from 71 to 81 nucleotides (nt) in length. In this study, we used high-throughput sequencing combined with bioinformatics analysis to thoroughly examine the nucleotide composition of the sequence pools derived from several selections that employed an RNA library (Sel2N20) with an abbreviated variable region. The Sel2N20 yields RNAs 51 nt in length, which unlike longer RNAs, are more amenable to large-scale chemical synthesis for therapeutic development. Our analysis revealed a consistent and early bias against inclusion of adenine, resulting in aptamers with lower predicted minimum free energies (ΔG) (higher structural stability). This bias was also observed in control, "nontargeted" selections in which the partition step (against the target) was omitted, suggesting that the bias occurred in 1 or more of the amplification and propagation steps of the SELEX process.
The Role of RANTES in Meningococcal Disease (2000)

The chemokine RANTES (regulated on activation, normal T cell expressed and secreted) is a potent regulator of leukocyte trafficking. RANTES preferentially attracts mature CD4 cells as well as macrophages and eosinophils, but not neutrophils. In total, 128 children with meningococcal disease were prospectively studied, and the role of RANTES in the pathophysiology of meningococcal disease was assessed. Plasma RANTES, interleukin (IL)-8, IL-6, IL-1 receptor agonist, and tumor necrosis factor-alpha were measured at admission. Severity of disease was stratified by the Glasgow meningococcal septicemia prognostic score (GMSPS). RANTES levels correlated significantly with IL-8 levels, admission lactate levels, platelets, prothrombin time, and activated partial thromboplastin time. RANTES levels were lower in children with severe disease (GMSPS>/=8; P=.001), in those with septic shock (P<.0005), and in nonsurvivors (P=.048; Mann-Whitney test). RANTES is a potential mediator in the pathophysiology of meningococcal disease.
Mycobacterium shottsii sp. nov., a slowly growing species isolated from Chesapeake Bay striped bass (Morone saxatilis) (2003)

Slowly growing, non-pigmented mycobacteria were isolated from striped bass (Morone saxatilis) during an epizootic of mycobacteriosis in the Chesapeake Bay. Growth characteristics, acid-fastness and results of 16S rRNA gene sequencing were consistent with those of the genus Mycobacterium. A unique profile of biochemical reactions was observed among the 21 isolates. A single cluster of eight peaks identified by analysis of mycolic acids (HPLC) resembled those of reference patterns but differed in peak elution times from profiles of reference species of the Mycobacterium tuberculosis complex. One isolate (M1 75T) was placed within the slowly growing mycobacteria by analysis of aligned 168S rRNA gene sequences and was proximate in phylogeny to Mycobacterium ulcerans and Mycobacterium marinum. However, distinct nucleotide differences were detected in the 16S rRNA gene sequence among M175T, M. ulcerans and M. marinum (99.2% similarity). Isolate M175T could be differentiated from other slowly growing, non-pigmented mycobacteria by its inability to grow at 37 degrees C, production of niacin and urease, absence of nitrate reductase and resistance to isoniazid (1 microg ml(-1)), thiacetazone and thiophene-2-carboxylic hydrazide. Based upon these genetic and phenotypic differences, isolate M175T (=ATCC 700981T =NCTC 13215T) is proposed as the type strain of a novel species, Mycobacterium shottsii sp. nov.
Evidence for a Signaling System in Helicobacter pylori : Detection of a luxS -Encoded Autoinducer (2000)

Helicobacter pylori possesses a homolog of the luxS gene, initially identified by its role in autoinducer production for the quorum-sensing system 2 in Vibrio harveyi. The genomes of several other species of bacteria, notably Escherichia coli, Salmonella enterica serovar Typhimurium, and Vibrio cholerae, also include luxS homologs. All of these bacteria have been shown to produce active autoinducers capable of stimulating the expression of the luciferase operon in V. harveyi. In this report, we demonstrate that H. pylori also synthesizes a functional autoinducer (AI-2) that can specifically activate signaling system 2 in V. harveyi. Maximal activity is produced during early log phase, and the activity is diminished when cells enter stationary phase. We show that AI-2 is not involved in modulating any of the known or putative virulence factors in H. pylori and that a luxS null mutant has a two-dimensional protein profile identical to that of its isogenic parent strain. We discuss the implications of having an AI-2-like quorum-sensing system in H. pylori and suggest possible roles that it may play in H. pylori infection.
Stretchable ultrasonic transducer arrays for three-dimensional imaging on complex surfaces (2018)

Ultrasonic imaging has been implemented as a powerful tool for noninvasive subsurface inspections of both structural and biological media. Current ultrasound probes are rigid and bulky and cannot readily image through nonplanar three-dimensional (3D) surfaces. However, imaging through these complicated surfaces is vital because stress concentrations at geometrical discontinuities render these surfaces highly prone to defects. This study reports a stretchable ultrasound probe that can conform to and detect nonplanar complex surfaces. The probe consists of a 10 × 10 array of piezoelectric transducers that exploit an "island-bridge" layout with multilayer electrodes, encapsulated by thin and compliant silicone elastomers. The stretchable probe shows excellent electromechanical coupling, minimal cross-talk, and more than 50% stretchability. Its performance is demonstrated by reconstructing defects in 3D space with high spatial resolution through flat, concave, and convex surfaces. The results hold great implications for applications of ultrasound that require imaging through complex surfaces.
Mucin-based Targeted Pancreatic Cancer Therapy (2012)

The prognosis of pancreatic cancer (PC) patients is very poor with a five-year survival of less than 5%. One of the major challenges in developing new therapies for PC is the lack of expression of specific markers by pancreatic tumor cells. Mucins are heavily Oglycosylated proteins characterized by the presence of short stretches of amino acid sequences repeated several times in tandem. The expression of several mucins including MUC1, MUC4, MUC5AC, and MUC16 is strongly upregulated in PC. Recent studies have also demonstrated a link between the aberrant expression and differential overexpression of mucin glycoproteins to the initiation, progression, and poor prognosis of the disease. These studies have led to increasing recognition of mucins as potential diagnostic markers and therapeutic targets in PC. In this focused review we present an overview of the therapies targeting mucins in PC, including immunotherapy (i.e. vaccines, antibodies, and radioimmunoconjugates), gene therapy, and other novel therapeutic strategies.
A ticket to ride: peptide radiopharmaceuticals. (1993)

Over the past three decades, biospecific imaging agents have evolved from large proteins (i.e., antibodies) to antibody fragments (i.e., F(ab')2 and Fab fragments) to smaller "molecular recognition units" such as Fv fragments, antigen binding domain fragments and small biologically active peptides. The smaller size of these molecules confers desirable pharmacokinetic properties, such as higher target-to-background ratios and faster blood clearance, that are favorable for imaging. Molecular engineering techniques now permit the peptide to carry the radionuclide-binding group in its structure while maintaining high-affinity binding to the receptor site. An important component to this system is the ability to radiolabel these agents with high specific activity using short-lived radionuclides, particularly 99mTc. Recently, the application of small radiolabeled biologically active peptides for external imaging of a variety of biological processes has received considerable interest. These applications have ranged from the current widespread use of somatostatin analogs for imaging numerous types of tumors to the development of radiolabeled chemotactic peptides for infection imaging. In this review, we will describe many of the parameters for the rational development of peptide-based imaging agents, including: classes of peptides for imaging, methods for radiolabeling peptides, current biologically active peptide-based radiopharmaceuticals and future prospects for this new technology.
ELLA: An Efficient Lifelong Learning Algorithm (2013)

The problem of learning multiple consecutive tasks, known as lifelong learning, is of great importance to the creation of intelligent, general-purpose, and flexible machines. In this paper, we develop a method for online multi-task learning in the lifelong learning setting. The proposed Efficient Lifelong Learning Algorithm (ELLA) maintains a sparsely shared basis for all task models, transfers knowledge from the basis to learn each new task, and refines the basis over time to maximize performance across all tasks. We show that ELLA has strong connections to both online dictionary learning for sparse coding and state-of-the-art batch multi-task learning methods, and provide robust theoretical performance guarantees. We show empirically that ELLA yields nearly identical performance to batch multi-task learning while learning tasks sequentially in three orders of magnitude (over 1,000x) less time. 1.
Transdermal fentanyl for improvement of pain and functioning in osteoarthritis: A randomized, placebo‐controlled trial (2006)

TDF can reduce pain and improve function in patients with knee or hip OA.
Transplantation of Mobilized Peripheral Blood Stem Cells: Role of Filgrastim (1994)

Autologous bone marrow transplantation, although successful, is limited in the rate of hematopoietic recovery achieved. Myeloablative chemotherapy results in prolonged pancytopenia with standard autologous bone marrow support. High-dose myelosuppressive chemotherapy results in severe but short-term pancytopenia, and hematopoietic recovery is routine without cellular support. Cellular support becomes necessary when multiple-cycle, severely myelosuppressive regimens are used because of the cumulative stem cell damage and unacceptably long duration of severe pancytopenia. Peripheral blood progenitor cells (PBPCs) may be used as cellular support, and colony-stimulating factors with or without chemotherapy are currently the most potent available PBPC-mobilizing tools. Filgrastim (rmethG-CSF) has been shown to enhance the number of PBPCs for harvest in both cancer patients and normal donors. When Filgrastim is used in conjunction with chemotherapy, there appears to be greater PBPC mobilization, which seems to be dependent on dose and schedule of chemotherapy as well as the type of chemotherapeutic agent used. Platelet recovery has been shown to be more rapid when PBPCs are used compared with historical controls given autologous bone marrow infusions. It may be concluded that PBPC transplantation is useful supportive care following myeloablative chemotherapy.
New electronic method for measuring hematocrit: clinical evaluation. (1961)

Abstract A new rapid electronic method for measuring hematocrit utilizes the principle that the electrical resistance of a column of blood is a function of the relative volume per cent of erythrocytes. A description is presented of a small light electronic instrument which is portable, completely transistorized, and powered only by a standard transistor radio battery; it measures the resistance of a small column of blood in a plastic cuvette. A clinical evaluation of this instrument compared the hematocrit of eighty-seven patients' finger-tip capillary blood measured by this instrument with that measured by a standard centrifuged microhematocrit technique. There was no clinically significant systematic difference between the two methods (mean difference of 1.0 hematocrit per cent units); the standard deviation was ± 3.0 hematocrit per cent units. In experiments using reconstituted blood of different protein concentration, it is shown that the reading is subject to correction in patients suspected of having abnormally large deviation in total serum protein concentration. This new technique is useful in circumstances requiring very rapid hematocrit determination or where a centrifuge or electric power source is not available.