gebhart/patrepeval huggingface dataset:
Bordetella parapertussis Infection in Children: Epidemiology, Clinical Symptoms, and Molecular Characteristics of Isolates (1998)

The clinical trial conducted in Italy to evaluate the efficacy of acellular pertussis vaccines provided an opportunity to estimate the frequency of clinical infections with Bordetella parapertussis and to compare the clinical characteristics of children suffering from Bordetella pertussis illness with those of children with B. parapertussis illness. This study dealt with 76 B. parapertussis infections diagnosed from a population of 15,601 children participating in the follow-up of suspected cases of pertussis. An overall incidence of 2.1 cases of laboratory-confirmed parapertussis per 1,000 person-years was observed. Children affected by B. parapertussis infections showed a less severe clinical picture both in the duration of symptoms and in the percentage of patients affected, even when compared with vaccinated children with pertussis. To characterize the isolated strains, we performed assays for susceptibility to erythromycin and sulfamethoxazole-trimethoprim, and we examined the genomic DNAs by pulsed-field gel electrophoresis. The results showed a high degree of genetic stability among B. parapertussis strains regardless of time of collection and geographical distribution.
Acquisition and loss of a neuronal Ca2+/calmodulin-dependent protein kinase during neuronal differentiation. (1991)

Calcium ions play a critical role in neural development. Insights into the ontogeny of Ca(2+)-signaling pathways were gained by investigating the developmental expression of granule cell-enriched Ca2+/calmodulin-dependent protein kinase (CaM kinase-Gr) in the cerebellum and hippocampus of the rat. Neurons of these brain regions displayed characteristic schedules by which they acquired and lost CaM kinase-Gr during differentiation. In the cerebellum, granule cells did not begin to express CaM kinase-Gr until after birth when they migrated into the granule cell layer, and this expression persisted in the adult. Purkinje cells expressed CaM kinase-Gr prenatally and lost this expression by postnatal day 14. In contrast, the granule and pyramidal cells of the hippocampus expressed the enzyme prenatally and in the adult. Moreover, CaM kinase-Gr was localized to the processes and nuclei of developing neurons. This subcellular localization together with the scheduled expression of CaM kinase-Gr can serve to regulate a developing neuron's sensitivity to Ca2+ at different subcellular levels.
Computer applications in geography (1992)

Computers and Geographical Data. Statistical Methods. Computers in Cartography. Remote Sensing. Simulation. Geographical Information Systems. Appendices. References. Index.
Deoxyribozymes: New players in the ancient game of biocatalysis (1999)

The repetitive and extraordinarily stable polynucleotide chains of DNA serve as an ideal storage system for genetic information. Although it is best known for its helical structure and relatively inert character, in vitro selection can be used to compel DNA to perform a surprising variety of chemical reactions. These artificial DNA enzymes or 'deoxyribozymes' generate large chemical rate enhancements and demonstrate precise substrate recognition, much like their protein and RNA counterparts. Recent studies with these prototypic deoxyribozymes indicate that DNA has a substantial untapped potential for intricate structure formation that could be exploited in novel chemical and biological catalysis.
Subpicosecond optoelectronic study of resistive and superconductive transmission lines (1987)

We have studed the propagation of subpicosecond electrical pulses on coplanar resistive and superconductive Nb transmission lines. Pulses with 0.9 ps full width at half maximum were generated and detected by shorting fast photoconductive switches with 80 fs laser pulses. Dramatic improvements in propagation characteristics were achieved when the Nb was superconductive. We observed the strong dispersion and attenuation predicted to occur for frequency components near the superconducting enery gap frequency.
[Subrenal capsule assay--an experimental study and clinical application to chemosensitivity tests]. (1987)

We have attempted to investigate the usefulness of the subrenal capsule assay (SRCA). Initially, we compared the results of antitumor activities of 27 anticancer drugs obtained using the SRCA in BDF1 mice and the subcutaneous transplantation assay in nude mice, and it became clear that these results correlated well. It was thus apparent that the antitumor activity of drugs could be evaluated faster, more cheaply and more easily using the SRCA. In the SRCA, the overall success rate for growing tumors (with a tumor growth rate of more than 1.0) from patients was 79% (106/134) and the success rates for each tumor type were as follows: malignant lymphoma 90%, ovarian cancer 87%, sarcoma 77%, breast cancer 76%, colorectal cancer 73% and renal cancer 58%. In a retrospective analysis of correlation between the antitumor activities assayed by the SRCA and the respective clinical responses, 11 out of 25 trials were true positive (79%) and 7 trials were true negative (64%). The sensitivity and specificity levels of this test were 73% and 70%, respectively. The tumor growth inhibition rates were correlated well with the clinical responses. The advantages of the SRCA are: it has a high success rate; it allows rapid evaluation; it can be applied for masked compounds; and it has a good clinical correlation. These advantages indicate that the SRCA is of potential value as a predictive test for selection of anticancer drugs on an individual patient basis.
Epigenetic markers of prostate cancer in plasma circulating DNA (2012)

Epigenetic differences are a common feature of many diseases, including cancer, and disease-associated changes have even been detected in bodily fluids. DNA modification studies in circulating DNA (cirDNA) may lead to the development of specific non-invasive biomarkers. To test this hypothesis, we investigated cirDNA modifications in prostate cancer patients with locally confined disease (n = 19), in patients with benign prostate hyperplasias (n = 20) and in men without any known prostate disease (n = 20). This initial discovery screen identified 39 disease-associated changes in cirDNA modification, and seven of these were validated using the sodium bisulfite-based mapping of modified cytosines in both the discovery cohort and an independent 38-patient validation cohort. In particular, we showed that the DNA modification of regions adjacent to the gene encoding ring finger protein 219 distinguished prostate cancer from benign hyperplasias with good sensitivity (61%) and specificity (71%). We also showed that repetitive sequences detected in this study were meaningful, as they indicated a highly statistically significant loss of DNA at the pericentromeric region of chromosome 10 in prostate cancer patients (p = 1.8 × 10(-6)). Based on these strong univariate results, we applied machine-learning techniques to develop a multi-locus biomarker that correctly distinguished prostate cancer samples from unaffected controls with 72% accuracy. Lastly, we used systems biology techniques to integrate our data with publicly available DNA modification and transcriptomic data from primary prostate tumors, thereby prioritizing genes for further studies. These data suggest that cirDNA epigenomics are promising source for non-invasive biomarkers.
Production of components of extracellular matrix by cultured rat Sertoli cells (1986)

Sertoli cells from rats aged 15, 20, and 25 days were cultured in plastic dishes and extracted with Triton X-100 (0.1 percent w/v) or sodium deoxycholate (2 percent w/v). Residues left after extraction were found to contain three proteins characteristic of extracellular matrix (fibronectin, collagen IV, and laminin). These proteins were identified by four methods: indirect immunofluorescence, co-migration with standard proteins on electrophoresis in polyacrylamide gels, immunoblotting (Western blots), and immunoprecipitation after incubating the Sertoli cells with [35S]methionine. In addition, fibronectin was identified by immunoelectron microscopy with a second antibody conjugated to colloidal gold. In the same cell residues, heparan sulfate was tentatively identified by the first of these methods. The cells used in these studies were shown, by electron microscopy, to be essentially pure cultures of Sertoli cells (greater than 95% pure). Since 100 percent of the cells examined showed positive and specific immunofluorescent staining with well-characterized antibodies to the four components of the extracellular matrix, and since studies with colloidal gold revealed the presence of fibronectin closely associated with and inside cells identified by electron microscopy as Sertoli cells, it must be concluded that Sertoli cells synthesize these four proteins and presumably heparan sulfate. Evidently, cultured Sertoli cells can synthesize and secrete some of the components of an extracellular matrix.
Obesity is associated with increased red blood cell folate despite lower intake and serum levels of this vitamin among adults in the United States (LB411) (2014)

Background: Folates are essential cofactors in various metabolic pathways. Limited evidence has investigated how obesity affects folate metabolism. We investigated the association between body mass index (BMI) and obesity‐related metabolic factors with blood folate status. Methods: A representative study population of 3829 US adults was derived from the National Health and Nutrition Examination Survey (2003‐2006). Regression analyses were performed to examine the association between BMI and obesity‐related metabolic factors with serum folate and red blood cell (RBC) folate. Results: Serum folate levels were lowest in both the underweight and obese groups, closely paralleling with the lower dietary folate intakes in these two groups. In contrast, RBC folate incrementally increased with BMI. Regression analyses demonstrated a negative relationship between BMI and serum folate, but a positive relationship for RBC folate. These relationships were significant for 19‐50 year old individuals, but not for elders (蠅 51 yrs). Conclusion: Obesity is associated with decreased serum folate, and concurs with lower total intake among the obese. In contrast, obesity is positively associated with increased RBC folate. These relationships are significant for young and middle‐aged adults, but not for elders. RBC folate appears to be a better biomarker of cellular folate status in obese individuals. Grant Funding Source : Supported in part by the USDA/NIFA grant (2014‐67017‐21762, ZL), the USDA Hatch grant (MAS00454, ZL) and the funding from Rays of Hope Center of Breast Cancer Research, Baystate Medical Center (ZL)
Chondrocyte matrix metalloproteinase-8: up-regulation of neutrophil collagenase by interleukin-1 beta in human cartilage from knee and ankle joints. (1996)

The loss of aggrecan from articular cartilage may lead to the development of osteoarthritis (OA). Degradation products of human aggrecan, generated in vivo by enzymatic cleavages, have been identified in synovial fluid of patients with rheumatoid arthritis and OA. One matrix metalloproteinase (MMP), stromelysin (MMP-3), and an unidentified proteinase called "aggrecanase" are believed to generate these products in pathologic conditions. Thus far, only one proteinase, neutrophil collagenase (MMP-8), has been shown in vitro to be capable of cleavage of the aggrecan molecule at the "aggrecanase" site. In this study, we compare the presence and distribution of MMP-3 and MMP-8 in cartilages from two different joints of normal human donors. We determined whether mRNA for MMP-8 is expressed in normal human articular cartilage from different joints. In addition, we compared differences in MMP-8 and MMP-3 gene expression between human ankle and knee cartilage after in vitro stimulation by interleukin (IL)-1 beta. These two joints were chosen because the incidence of symptomatic and radiographic OA varies between the different joints. The knee is the most frequently involved joint, whereas the ankle (talocrural) joint is relatively rarely affected. Message for MMP-8 was detected in untreated cartilage from normal knee joints, but not in untreated cartilage of normal ankle joints. Message for MMP-3 was detectable in most of the knee and ankle cartilages. Messenger RNA expression for both MMPs could be up-regulated by IL-1 beta. The highest doses of IL-1 beta appeared to be most effective in stimulation of mRNA for MMP-3, whereas MMP-8 expression was more sensitive to lower doses of IL-1 beta. The fact that ankle cartilage with a low incidence of OA does not express MMP-8, whereas knee cartilage with a high incidence of OA does not express MMP-8, whereas knee cartilage with a high incidence of OA does constitutively express MMP-8, suggests that MMP-8 might be one of the key enzymes in the pathogenesis of osteoarthritis. This is further supported by our finding that the earliest signs of cartilage degradation were very similar to those found in IL-1 beta-treated explants.
Mechanism of tissue fusion in argon laser‐welded vein‐artery anastomoses (1988)

The mechanism of laser vascular tissue welding remains unknown. This study compared the acute tissue response and long-term healing of sutured and laser-welded anastomoses of vein segments used to bypass ligated canine femoral arteries. For each procedure, one anastomosis was formed using running 6-0 polypropylene suture (control), and the other anastomosis was formed using argon laser tissue welding (experimental). The vein grafts were harvested at 4 (n = 2), 8 (n = 1), 12 (n = 1), and 16 (n = 2) weeks, and selected samples were evaluated by histologic examination, electron microscopy, tensile strength testing, and by measuring the formation of [3H]hydroxyproline as an index of collagen synthesis. Examination of successful laser fusions immediately after they were formed showed bonding of collagen to collagen and elastin to collagen. Follow-up evaluations showed that the precision of tissue apposition affected the rate of healing and tensile strength. Laser-welded anastomoses demonstrated a progression of healing similar to sutured repairs, with remodeling of fibrous tissue and collagen being the primary component of weld integrity. This study demonstrates that sutured and argon laser-welded vein-artery anastomoses heal comparably up to 16 weeks postoperatively, and that laser welding is a satisfactory alternative to sutured anastomoses.
Two-Tier Precoding for FDD Multi-Cell Massive MIMO Time-Varying Interference Networks (2014)

Massive MIMO is a promising technology in future wireless communication networks. However, it raises a lot of implementation challenges, for example, the huge pilot symbols and feedback overhead, requirement of real-time global CSI, large number of RF chains needed, and high computational complexity. We consider a two-tier precoding strategy for multi-cell massive MIMO interference networks, with an outer precoder for inter-cell/inter-cluster interference cancellation, and an inner precoder for intra-cell multiplexing. In particular, to combat with the computational complexity issue for the outer precoding, we propose a low complexity online iterative algorithm to track the outer precoder under time-varying channels. We follow an optimization technique and formulate the problem on the Grassmann manifold. We develop a low complexity iterative algorithm, which converges to the global optimal solution under static channels. In time-varying channels, we propose a compensation technique to offset the variation of the time-varying optimal solution. We show with our theoretical result that, under some mild conditions, perfect tracking of the target outer precoder using the proposed algorithm is possible. Numerical results demonstrate that the two-tier precoding with the proposed iterative compensation algorithm can achieve a good performance with a significant complexity reduction compared with the conventional two-tier precoding techniques in the literature.
Gisting conversational speech in real time (1993)

The authors describe additions and modifications to a prototype system for analyzing air traffic contol (ATC) communication. The primary goal of the effort was to achieve real-time performance. This involved both system architectural and algorithmic modifications. The task of the system is to extract the gist of activity as it is monitored. In the ATC domain this involves identifying those flights that are present and classifying each flight as a departure, arrival, or other. The system combines a variety of techniques from speaker-identification, speech recognition, natural-language processing, and artificial intelligence. Continuous processing versions of the algorithms have been constructed and it has been demonstrated that real-time performance is possible by distributing the processing over a small number of workstations. To accomplish this task, a flexible software task-construction tool that allows simple specification of complex systems, supporting both dataflow and client/server models, has been developed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Contribution of Sialic Acid to the Voltage Dependence of Sodium Channel Gating (1997)

A potential role for sialic acid in the voltage-dependent gating of rat skeletal muscle sodium channels (rSkM1) was investigated using Chinese hamster ovary (CHO) cells stably transfected with rSkM1. Changes in the voltage dependence of channel gating were observed after enzymatic (neuraminidase) removal of sialic acid from cells expressing rSkM1 and through the expression of rSkM1 in a sialylation-deficient cell line (lec2). The steady-state half-activation voltages (Va) of channels under each condition of reduced sialylation were approximately 10 mV more depolarized than control channels. The voltage dependence of the time constants of channel activation and inactivation were also shifted in the same direction and by a similar magnitude. In addition, recombinant deletion of likely glycosylation sites from the rSkM1 sequence resulted in mutant channels that gated at voltages up to 10mV more positive than wild-type channels. Thus three independent means of reducing channel sialylation show very similar effects on the voltage dependence of channel gating. Finally, steady-state activation voltages for channels subjected to reduced sialylation conditions were much less sensitive to the effects of external calcium than those measured under control conditions, indicating that sialic acid directly contributes to the negative surface potential. These results are consistent with an electrostatic mechanism by which external, negatively charged sialic acid residues on rSkM1 alter the electric field sensed by channel gating elements.
Use of fluo-3 to measure cytosolic Ca2+ in platelets and neutrophils. Loading cells with the dye, calibration of traces, measurements in the presence of plasma, and buffering of cytosolic Ca2+ (1990)

A description is given of the methodology, and problems encountered, for the use of a new fluorescent Ca2(+)-indicator dye, fluo-3, in neutrophils and platelets. The higher Kd and longer excitation wavelength of fluo-3 can have significant advantages over fura-2. Although neutrophils and platelets are used as examples, these observations will be applicable to other cell types. The Kd of fluo-3 for binding Ca2+ at 37 degrees C was measured and found to be 864 nM; the previously published value was 400 nM at 22 degrees C. The Kd of fluo-3, like that of fura-2, is therefore very temperature-dependent. Protocols for loading cells, and preventing leakage of fluo-3, are described; probenecid, known to inhibit fura-2 leakage from cells, was found to be essential to get good fluo-3 signals from platelets. Calibration of fluo-3 fluorescence signals to [Ca2+] and methods for obtaining maximum and minimum fluorescence signals are described; these methods differ from those used with fura-2. Agonist-stimulated responses of fluo-3-loaded neutrophils and platelets are shown, and the calculated cytosolic [Ca2+] is comparable with that previously obtained with fura-2. Responses of cells in the presence of plasma are also shown; such measurements, unobtainable with quin2, fura-2 or indo-1, are possible with fluo-3, owing to its longer excitation wavelengths. Co-loading of cells with bis-(o-aminophenoxy)ethane-NNN'N'-tetra-acetic acid and fluo-3 is included as an example of how cytosolic [Ca2+] can be buffered and manipulated. Many of these observations will be of value when using fluo-3 (or other Ca2(+)-indicator dyes) in most cell types.
Effects of HMG-CoA Reductase Inhibitors on Endothelial Function (2004)

Certain pleiotropic activities reported for 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors (statins) are related to reductions in cellular cholesterol biosynthesis and isoprenoid levels. In endothelial cells, these metabolic changes contribute to favorable effects on nitric oxide (NO) bioavailability. Given the essential role of NO in preserving vascular structure and function, this effect of statins is of considerable therapeutic importance. Statins have been demonstrated to restore endothelial NO production by several mechanisms, including upregulating endothelial NO synthase (eNOS) protein expression and blocking formation of reactive oxygen species. In this article, we will discuss additional ways in which statins restore endothelial NO production and improve endothelial function. (1) Statins modulate membrane microdomain formation, resulting in reduced expression of proteins that specifically inhibit eNOS activation. (2) Statins reduce sterol biosynthesis, thus interfering with the formation of pathologic microdomains, including cholesterol crystalline structures. This observation has important implications for plaque stabilization, as these microdomains contribute to cholesterol crystal formation and endothelial apoptosis. Finally, (3) statins improve endothelial function by interfering with oxidative stress pathways through both enzymatic and nonenzymatic mechanisms. The relationships between membrane microdomains, cholesterol biosynthesis, and endothelial function will be discussed.
An efficient deletion mutant packaging system for defective herpes simplex virus vectors: potential applications to human gene therapy and neuronal physiology. (1990)

We have previously described a defective herpes simplex virus (HSV-1) vector system that permits the introduction of virtually any gene into nonmitotic cells. pHSVlac, the prototype vector, stably expresses Escherichia coli beta-galactosidase from a constitutive promoter in many human cell lines, in cultured rat neurons from throughout the nervous system, and in cells in the adult rat brain. HSV-1 vectors expressing other genes may prove useful for studying neuronal physiology or performing human gene therapy for neurological diseases, such as Parkinson disease or brain tumors. A HSV-1 temperature-sensitive (ts) mutant, ts K, has been used as helper virus; ts mutants revert to wild type. In contrast, HSV-1 deletion mutants essentially cannot revert to wild type; therefore, use of a deletion mutant as helper virus might permit human gene therapy with HSV-1 vectors. We now report an efficient packaging system for HSV-1 vectors using a deletion mutant, D30EBA, as helper virus; virus is grown on the complementing cell line M64A. pHSVlac virus prepared using the deletion mutant packaging system stably expresses beta-galactosidase in cultured rat sympathetic neurons and glia. Both D30EBA and ts K contain a mutation in the IE3 gene of HSV-1 strain 17 and have the same phenotype; therefore, changing the helper virus from ts K to D30EBA does not alter the host range or other properties of the HSV-1 vector system.