gebhart/patrepeval huggingface dataset:
CHLAMYDIA PNEUMONIAE STRAIN TWAR, MYCOPLASMA PNEUMONIAE, AND VIRAL INFECTIONS IN ACUTE RESPIRATORY DISEASE IN A UNIVERSITY STUDENT HEALTH CLINIC POPULATION (1990)

Clinical and serologic data were collected on 667 University of Washington students who presented to the David Hall Student Health Center between 1983 and 1987 with acute respiratory disease. Sera were tested for evidence of acute or past infections with Chlamydia pneumoniae strain TWAR, Chlamydia trachomatis, Mycoplasma pneumoniae, influenza A virus, influenza B virus, adenovirus, and respiratory syncytial virus. Pharyngeal swab specimens were cultured for C. pneumoniae and C. trachomatis, but not for the other agents. Evidence of acute infection with C. pneumoniae was found in 20 patients and evidence of an acute infection with M. pneumoniae in 29 patients. C. pneumoniae was associated with 9% and M. pneumoniae with 11% of 149 pneumonias diagnosed clinically, and with 20% and 22%, respectively, of the 59 pneumonias confirmed on chest radiograph. There was no evidence of seasonality in C. pneumoniae or M. pneumoniae infections. Compared with patients with M. pneumoniae, patients with C. pneumoniae were less likely to have a temperature greater than 37.8 degrees C (10% vs. 34%), but were more likely to present with a sore throat (80% vs. 52%) or hoarseness (30% vs. 3%). The mean number of days from onset of symptoms until enrollment was longer in patients with C. pneumoniae infections than in those with M. pneumoniae (12.8 vs. 7.9 days), or those with a viral infection (12.8 vs. 7.3 days), suggesting a more gradual onset of disease caused by C. pneumoniae.
Isolation of glycine betaine and proline betaine from human urine. Assessment of their role as osmoprotective agents for bacteria and the kidney. (1987)

Human urine is osmoprotective for enteric bacteria, permitting E. coli to grow with high concentrations of NaCl and other salts and even higher concentrations of sucrose and mannitol but not urea. The active material in urine is soluble in methanol and is precipitated by ammonium reineckate at acid pH. Using gel filtration and high-pressure liquid chromatography, we have identified two major osmoprotective compounds in urine. One is glycine betaine; the other is proline betaine as demonstrated by nuclear magnetic resonance, mass spectrum scanning, and chemical synthesis. Proline betaine has not been described previously to our knowledge in vertebrate tissues. It is known to be a cell volume-regulating agent for marine red algae and the euryhaline mollusk Elysia chloritica. We suggest that the presence of glycine and proline betaines in human urine may reflect an osmoprotective role for the kidney and that they protect bacteria in the urine only fortuitously.
Chemical studies on tobacco smoke LXVIII. Analysis of volatile and tobacco-specific nitrosamines in tobacco products. (1980)

The yields of volatile N-nitrosamines in cigarette smoke are primarily dependent upon the nitrate content of the tobacco and, to some extent, on the protein content. Cellulose acetate tips, such as those found on most commercial filter cigarettes, selectively remove at least 70% of the volatile N-nitrosamines, independently of the pH of the weakly acidic or weakly alkaline smoke. So far, three tobacco-specific N-nitrosamines have been detected in tobacco and tobacco smoke. During tobacco processing and smoking, N'-nitrosonornicotine is formed by nitrosation of nicotine and, to a minor degree, by nitrosation of nornicotine, whereas 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone originates from oxidative nitrosation of nicotine. N'-Nitrosoanatabine is formed by nitrosation of the second most abundant tobacco alkaloid, anatabine. The tobacco-specific N-nitrosamines in the smoke arise partly from the tobacco by transfer and partly by nitrosation of the alkaloids during smoking (pyrosynthesis). Preliminary results indicate that cellulose acetate filter tips may selectively remove considerable amounts of the nonvolatile nitrosamines from the smoke.
Expression, Purification, and Inhibitory Properties of Human Proteinase Inhibitor 8 (1997)

In a previous report, the cDNA for human proteinase inhibitor 8 (PI8) was first identified, isolated, and subcloned into a mammalian expression vector and expressed in baby hamster kidney cells. Initial studies indicated that PI8 was able to inhibit the amidolytic activity of trypsin and form an SDS-stable approximately 67-kDa complex with human thrombin [Sprecher, C. A., et al. (1995) J. Biol Chem. 270, 29854-29861]. In the present study, we have expressed recombinant PI8 in the methylotropic yeast Pichia pastoris, purified the inhibitor to homogeneity, and investigated its ability to inhibit a variety of proteinases. PI8 inhibited the amidolytic activities of porcine trypsin, human thrombin, human coagulation factor Xa, and the Bacillus subtilis dibasic endoproteinase subtilisin A through different mechanisms but failed to inhibit the Staphylococcus aureus endoproteinase Glu-C. PI8 inhibited trypsin in a purely competitive manner, with an equilibrium inhibition constant (Ki) of less than 3.8 nM. The interaction between PI8 and thrombin occurred with a second-order association rate constant (kassoc) of 1.0 x 10(5) M-1 s-1 and a Ki of 350 pM. A slow-binding kinetics approach was used to determine the kinetic constants for the interactions of PI8 with factor Xa and subtilisin A. PI8 inhibited factor Xa via a two-step mechanism with a kassoc of 7.5 x 10(4) M-1 s-1 and an overall Ki of 272 pM. PI8 was a potent inhibitor of subtilisin A via a single-step mechanism with a kassoc of 1.16 x 10(6) M-1 s-1 and an overall Ki of 8.4 pM. The interaction between PI8 and subtilisin A may be of physiological significance, since subtilisin A is an evolutionary precursor to the intracellular mammalian dibasic processing endoproteinases.
Long-Term Control of Recurrent Anaplastic Ependymoma With Extracranial Metastasis: Importance of Multiple Surgery and Stereotactic Radiosurgery Procedures-Case Report- (2004)

An 11-year-old Japanese girl presented with a right frontal lobe anaplastic ependymoma. The tumor was removed surgically. However, she developed a secondary lesion and extracranial metastasis in the cervical lymph node. In total, she underwent eight intracranial tumor removal procedures, five stereotactic radiosurgeries with six targets, and five cervical lymph node removal surgeries during the course of 7 years. She is currently alive with a good quality of life, and has no major neurological deficits except right facial nerve palsy. The combination of surgery and radiosurgery can achieve local control of anaplastic ependymoma. Multiple surgery or radiosurgery procedures can result in good outcome, if the tumor does not involve crucial structures, even if extracranial metastasis occurs.
The Tomato Transcription Factor Pti4 Regulates Defense-Related Gene Expression via GCC Box and Non-GCC BoxcisElements[W] (2003)

The tomato transcription factor Pti4, an ethylene-responsive factor (ERF), interacts physically with the disease resistance protein Pto and binds the GCC box cis element that is present in the promoters of many pathogenesis-related (PR) genes. We reported previously that Arabidopsis plants expressing Pti4 constitutively express several GCC box-containing PR genes and show reduced disease symptoms compared with wild-type plants after inoculation with Pseudomonas syringae pv tomato or Erysiphe orontii. To gain insight into how genome-wide gene expression is affected by Pti4, we used serial analysis of gene expression (SAGE) to compare transcripts in wild-type and Pti4-expressing Arabidopsis plants. SAGE provided quantitative measurements of >20,000 transcripts and identified the 50 most highly expressed genes in Arabidopsis vegetative tissues. Comparison of the profiles from wild-type and Pti4-expressing Arabidopsis plants revealed 78 differentially abundant transcripts encoding defense-related proteins, protein kinases, ribosomal proteins, transporters, and two transcription factors (TFs). Many of the genes identified were expressed differentially in wild-type Arabidopsis during infection by Pseudomonas syringae pv tomato, supporting a role for them in defense-related processes. Unexpectedly, the promoters of most Pti4-regulated genes did not have a GCC box. Chromatin immunoprecipitation experiments confirmed that Pti4 binds in vivo to promoters lacking this cis element. Potential binding sites for ERF, MYB, and GBF TFs were present in statistically significantly increased numbers in promoters regulated by Pti4. Thus, Pti4 appears to regulate gene expression directly by binding the GCC box and possibly a non-GCC box element and indirectly by either activating the expression of TF genes or interacting physically with other TFs.
Electrophoresis of slender particles (1994)

The hydrodynamic theory of slender bodies is used to model electrophoretic motion of a slender particle having a charge (zeta potential) that varies with position along its length. The theory is limited to systems where the Debye screening length of the solution is much less than the typical cross-sectional dimension of the particle. A stokeslet representation of the hydrodynamic force is combined with the Lorentz reciprocal theorem for Stokes flow to develop a set of linear equations which must be solved for the components of the translational and angular velocities of the particle. Sample calculations are presented for the electrophoretic motion of straight spheroids and cylinders and a torus in a uniform electric field. The theory is also applied to a straight uniformly charged particle in a spatially varying electric field. The uniformly charged particle rotates into alignment with the principal axes of ∇ E ∞ ; we suggest that such alignment can lead to electrophoretic transport of particles through a small aperture in an otherwise impermeable wall. The theory developed here is more general than just for electrophoresis, since the final result is expressed in terms of a general 'slip velocity’ at the surface of the particle. Thus, the results are applicable to diffusiophoresis of slender particles if the proper slip-velocity coefficient is used.
Semantic role labeling using different syntactic views (2005)

Semantic role labeling is the process of annotating the predicate-argument structure in text with semantic labels. In this paper we present a state-of-the-art baseline semantic role labeling system based on Support Vector Machine classifiers. We show improvements on this system by: i) adding new features including features extracted from dependency parses, ii) performing feature selection and calibration and iii) combining parses obtained from semantic parsers trained using different syntactic views. Error analysis of the baseline system showed that approximately half of the argument identification errors resulted from parse errors in which there was no syntactic constituent that aligned with the correct argument. In order to address this problem, we combined semantic parses from a Minipar syntactic parse and from a chunked syntactic representation with our original baseline system which was based on Charniak parses. All of the reported techniques resulted in performance improvements.
The live oral typhoid vaccine Ty21a is a rpoS mutant and is susceptible to various environmental stresses (1995)

The rpoS (katF) gene, which encodes a RNA polymerase σ factor (σs), regulates the virulence of Salmonella typhimurium in mice. In the present study, we show that rpoS mutants can be frequently found among laboratory strains of Salmonella. In addition, a rpoS mutation was identified in the S. typhi live oral vaccine Ty21a. Introduction of a wild-type rpoS gene in Ty21a allowed the bacteria to survive better under starvation conditions and increased their resistance to other stresses. These results contribute to a better understanding of the genetic background of the live typhoid oral vaccine Ty21a and suggest that the rpoS mutation may contribute to the safety of this strain in humans.
An adenovirus type 5 early gene function regulates expression of other early viral genes. (1979)

We have identified an adenovirus type 5(Ad5) early gene function located in early region 1 which is required for the production of early cytoplasmic mRNAs corresponding to early regions 2, 3, and 4. Mutant dl312 (lacks the segment between 1.5 and 4.5 map units) grows as well as wild-type virus in 293 cells (Ad5-transformed human embryonic kidney cells), but its growth is severely restricted in HeLa cells. We detect no viral RNAs in the cytoplasm of dl312-infected HeLa cells. Viral RNA sequences are present, however, in dl312-infected HeLa cell nuclei.
Vector Texture Maps on the GPU (2006)

Figure 1: Vector Texture Maps applied onto an object. The ACM logo is represented by four gradient shaders, combined by VTMs. By indexing characters in a font represented by a compressed VTM (that uses 128 KB), the anti-aliased text on the paper roll only uses 8 bytes per character (two RGBA texels). Performances are 54 FPS (3DLabs Wildcat Realizm 200). This paper presents VTMs (Vector Texture Maps), a novel representation of vector images that can be used as a texture by the GPU for real-time rendering. A VTM decomposes texture space into different regions, represented in an analytic way, by a set of implicit degree 3 polynomials. Each region can be rendered by a different fragment shading function. Accurate anti-aliasing is performed in real-time, based on an estimate of fragment coverage. As a consequence, infinite zooming can be applied without any pixel discretization artifact. Based on a hierarchical data structure, our representation has low memory requirements. Its versatility is demonstrated in various settings, including a font engine completely implemented in the GPU.
Normal physiological values for conscious pigs used in biomedical research. (1990)

Although the domestic pig is rapidly becoming an animal of choice in certain areas of biomedical research requiring a large animal model, effective utilization of the species is often encumbered by a lack of reference values for common functional variables. To address this problem, normal data for over 100 physiologic or related variables were collected from conscious chronically instrumented animals that were maintained under near basal conditions. Included were measurements of body composition, fluid volumes, blood physical and biochemical characteristics, blood gas and acid-base status, plasma hormone levels, energy metabolism, renal function, hemodynamics and pulmonary function. Most porcine values were similar to those collected under comparable conditions from humans. Compared to adult man, however, pigs had higher values for extracellular space, plasma volume, arterial pH, plasma bicarbonate, cardiac output, arterial pressure, expired ventilation, heat production, and core temperature, and lower values for red cell volume, hemoglobin level, plasma osmotic and oncotic pressure, arterial O2 content, renal blood flow and glomerular filtration rate. Many of these deviations were due to immaturity. Nevertheless, we have found pigs to be an excellent large animal model for a variety of functional studies.
Optical Spectra of Ni2+, Co2+, and Cu2+ in Tetrahedral Sites in Crystals (1962)

The polarized absorption spectra of Ni2+ and Co2+ in crystals of ZnO, ZnS, and CdS; Ni2+ in crystals of Cs2ZnCl4 and Cs2ZnBr4; and Cu2+ in ZnO have been measured at 4°K, 77°K, and room temperature. The spectra have been interpreted by the use of crystal field theory for the states of the (3d)n configuration acted on by a potential of predominately Td symmetry. Certain details of the spectra are accounted for by smaller contributions from fields of lower symmetry, notably a C3v potential contribution for the transition metal ions in ZnO. Crystal field, electrostatic repulsion, and spin-orbit parameters have been obtained for all these cases. An empirical correlation between the electrostatic repulsion parameter, B, for the ions in the crystals and the ligand polarizibility has been obtained. Although the configuration mixing between the states of the configurations (3d)n and (3d)n—1 (4p) has been found to give a negligible contribution to the calculated relative energies of the levels, it does partially explain the large values of the observed intensities of the transitions. The relative intensities of transitions between the spin-orbit components have been calculated by using models for both p—d mixing and σ bonding with the ligands. Neither model gives a quantitatively good account of the observed relative intensities and there is evidence, at least for the Ni2+ spectra, that the observed low energy, intense charge transfer absorptions play a predominant role in the intensity mechanisms of the d—d transitions.
Hematopoietic Differentiation of Human Induced Pluripotent Stem Cells (2008)

Abstract Induced pluripotent stem cells (iPSCs) provide an unprecedented opportunity for modeling of human diseases in vitro as well as for developing novel approaches for regenerative therapy based on immunologically compatible cells. In the present study, we employed an OP9 differentiation system to characterize the hematopoietic differentiation potential of seven human iPSC lines obtained from human fetal, neonatal, and adult fibroblasts through reprogramming with POU5F1, SOX2, NANOG, and LIN28 and compared it with the differentiation potential of five human embryonic stem cell lines (hESC; H1, H7, H9, H13, and H14). Similar to hESCs, all iPSCs in coculture with OP9 generated all types of colony forming cells (CFCs) as well as CD34+ cells that can be separated into distinct subsets based on differential expression of CD43 and CD31. CD34+CD31+CD43− cells obtained from all iPSCs expressed molecules present on endothelial cells and readily formed a monolayer when placed in endothelial conditions, while hematopoietic CFC potential was restricted to CD43+ cells. iPSC-derived CD43+ cells could be separated into three major subsets based on differential expression of CD235a/CD41a and CD45: CD235a+CD41a+/− (erythro-megakaryocytic progenitors), and lin-CD34+CD43+CD45− (multipotent), and lin-CD34+CD43+CD45+ (myeloid-skewed) primitive hematopoietic cells. Both subsets of primitive hematopoietic cells expressed genes associated with myeloid and lymphoid development, although myeloid genes were upregulated in CD45+ cells, which are skewed toward myeloid differentiation. Cytogenetic analysis demonstrated that iPSCs and derived from them CD43+ cells maintained normal karyotype. In addition short tandem repeat analysis of CFCs generated from IMR90-1 cells has been performed to confirm that blood cells are in fact derived from reprogrammed IMR90 cells, and not from contaminating hESCs. While we observed some variations in the efficiency of hematopoietic differentiation between different iPSCs, the pattern of differentiation was very similar in all seven tested iPSC and five hESC lines. Using different cytokine combinations and culture conditions we were able to expand iPSC-derived myeloid progenitors and induce their differentiation toward red blood cells, neutrophils, eosinophils, macrophages, ostoeclasts, dendritic and Langerhans cells. Although several issues remain to be resolved before iPSC-derived blood cells can be administered to humans for therapeutic purposes, patient-specific iPSCs can already be used for characterization of mechanisms of blood diseases and to identify molecules that can correct affected genetic networks.
A 20 mV Colpitts Oscillator powered by a thermoelectric generator (2012)

In this paper, we present a MOSFET-based Colpitts oscillator based on a “zero-threshold” transistor operating at a supply voltage below 20 mV. The circuit was carefully analyzed and expressions relating the start-up conditions and the voltage supply, as well as the oscillation frequency were developed. Measurement results obtained on a discrete prototype confirmed the low-voltage operation of the oscillator, which sustained oscillations of 130 mV (peak-to-peak) at 97 kHz when the voltage supply was 19.8 mV. The circuit was also powered from a thermoelectric generator (TEG) connected to a persons arm in a room with temperature of 24°C room. Under these conditions, the TEG supplied 22 mV and the circuit operated as expected.
A new bone to pick: osteoblasts and the haematopoietic stem‐cell niche (2004)

Two recent publications highlight the role of bone-forming cells, the osteoblasts, in controlling the development of neighboring haematopoietic stem cells (HSCs).1,2 Using two distinct transgenic mouse models, one using the conditional deletion of the Bone Morphogenetic Protein Receptor 1A (BMPR1A) gene, the other using over-expression of an active PTH/PTHrP receptor (PPR) mutant within osteoblasts, the authors show parallel, concordant increases in the generation of trabecular osteoblasts and the number of HSCs. In situ staining showed that rarely cycling HSCs sporadically attach to endosteal osteoblasts, while in vitro assays indicated that ligation of Jag1 on osteoblasts by Notch1 on HSCs promotes HSC proliferation. These two independent works have revived and revitalized the notion that osteoblasts are a major, defining component of the HSC niche within the bone marrow (BM). This minireview discusses these results in the context of other recent studies of mesenchymal cells within the BM microenvironment, presents one potential unified model of the functional anatomy of the BM HSC niche, and highlights new questions raised by these and other studies of osteoblasts and HSCs.
N-isopropyl-[123I] p-iodoamphetamine: single-pass brain uptake and washout; binding to brain synaptosomes; and localization in dog and monkey brain. (1980)

The kinetics of N-isopropyl-p-[123I]iodoamphetamine in rat brains were determined by serial measurements of brain uptake index (BUI) after intracarotid injection; also studied were its effects on amine uptake and release in rat's brain cortical synaptosomes; and its in vivo distribution in the dog and monkey. Serial BUI correspond to a first-pass extraction efficiency of 100% and a washout half-time of approximately 318 sec. The S-(+)-isomer inhibited norepinephrine uptake in synaptosomes as strongly as D-amphetamine, but was more potent in inhibiting synaptosomal uptake of serotonin. Both isomers were comparable to D-amphetamine in causing release of serotonin from synaptosomes, but the S-(+)-isomer promoted release of dopamine, whereas D-amphetamine did not. No specific localization in brain nuclei of the dog was seen, but there was progressive accumulation in the eyes. Rapid initial brain uptake in the ketamine-sedated monkey was noted, and further slow brain uptake occurred during the next 20 min but without retinal localization. High levels of brain activity were maintained for several hours. The quantitative initial single-pass clearance of the agent in the brain suggests its use in evaluation of regional brain perfusion. Its interaction with brain amine-binding sites suggests its possible application in studies of cerebral amine metabolism.
Resistance of a subset of red blood cells to clearance by antibodies in a mouse model of incompatible transfusion (2012)

These studies demonstrate that surviving RBCs during incompatible transfusion can represent a population that is resistant to clearance.