gebhart/patrepeval huggingface dataset:
Identification of varicella-zoster virus strains by PCR analysis of three repeat elements and a PstI-site-less region (1995)

We established a method of identifying varicella-zoster virus (VZV) strains, especially those of the Oka vaccine, in patients with clinical VZV infections. The DNAs of 30 clinically isolated strains and 4 laboratory strains including the Oka vaccine strain and its parent VZV strain, were analyzed by PCR with four sets of primers for the four variable regions, R2, R4, R5, and a region without a PstI site (PS). R4 was unstable in four laboratory VZV strains and was excluded from the study. The other regions were stable in several passages in cell culture. The number of copies in R2 and R5 were distributed from 2 to 13 and from 1 to 3, respectively, in the strains analyzed. The vaccine strain had seven copies in R2 and two copies in R5, and it was PS negative. Among 30 clinical isolates, 3, 23, and 11 strains had the same characteristics as the vaccine strain in R2, R5, and PS, respectively. Therefore, by this method, 97.2% of the isolates were distinguished from the Oka vaccine strain. This strategy will be useful in diagnosing VZV infections induced by the vaccine strain.
ChemInform Abstract: A Novel Synthesis of Pyrimidobenzodiazepines. (1990)

Abstract The title compounds (VII) are synthesized as shown in the reaction scheme.
The effect of CYP2C9, VKORC1 genotypes and old age on warfarin pharmacologic sensitivity in korean patients with thromboembolic disease. (2011)

The therapeutic dose of warfarin is dependent upon intrinsic patient characteristics that are highly variable. We assessed the effects of CYP2C9, VKORC1 1173 C/T polymorphisms, and old age on warfarin dosing and sensitivity by measuring plasma S-/R-warfarin levels in Korean patients. INR and the plasma S-/R-warfarin concentrations were determined in 58 patients who had the VKORC1 1173C/T CYP2C9 genotypes, were on a long-term anticoagulation regimen with warfarin, and took a daily dose of warfarin. The pharmacokinetic sensitivity of warfarin was significantly higher in the CYP2C9 *1/*3 genotypes than in the CYP2C9 *1/*1 genotypes [ratio of S-warfarin concentration/dose, 0.53 vs. 0.21; p=0.01]. Pharmacodynamic sensitivity in older patients (≥ 75 years) with the CYP2C9 *1/*1 and VKORC1 1173 TT genotypes was significantly higher as compared to younger patients (<75 years) [Ratio of INR/S-warfarin concentration, 4.88 vs. 3.41; p = 0.026]. The CYP2C9*3 allele and old age (≥ 75 years) with the VKORC1 1173 T allele were also associated with increased risk of over-anticoagulation. The increase of over-anticoagulation risk and warfarin sensitivity is related to the CYP2C9*3 allele and old age with the VKORC1 1173 T allele in Korean patients with thromboembolic disease. These findings suggest that a lower initial and maintenance dose should be considered for the patients with CYP2C9 *3 allele and advanced age in this patient population. However, due to the limited number of patients in the study population, our finding needs to be confirmed by a larger, well-controlled study.
ACE2 Receptor Expression and Severe Acute Respiratory Syndrome Coronavirus Infection Depend on Differentiation of Human Airway Epithelia (2005)

Studies of patients with severe acute respiratory syndrome (SARS) demonstrate that the respiratory tract is a major site of SARS-coronavirus (CoV) infection and disease morbidity. We studied host-pathogen interactions using native lung tissue and a model of well-differentiated cultures of primary human airway epithelia. Angiotensin converting enzyme 2 (ACE2), the receptor for both the SARS-CoV and the related human respiratory coronavirus NL63, was expressed in human airway epithelia as well as lung parenchyma. As assessed by immunofluorescence staining and membrane biotinylation, ACE2 protein was more abundantly expressed on the apical than the basolateral surface of polarized airway epithelia. Interestingly, ACE2 expression positively correlated with the differentiation state of epithelia. Undifferentiated cells expressing little ACE2 were poorly infected with SARS-CoV, while well-differentiated cells expressing more ACE2 were readily infected. Expression of ACE2 in poorly differentiated epithelia facilitated SARS spike (S) protein-pseudotyped virus entry. Consistent with the expression pattern of ACE2, the entry of SARS-CoV or a lentivirus pseudotyped with SARS-CoV S protein in differentiated epithelia was more efficient when applied to the apical surface. Furthermore, SARS-CoV replicated in polarized epithelia and preferentially exited via the apical surface. The results indicate that infection of human airway epithelia by SARS coronavirus correlates with the state of cell differentiation and ACE2 expression and localization. These findings have implications for understanding disease pathogenesis associated with SARS-CoV and NL63 infections.
Characterization and Taxonomic Significance of Lipopolysaccharides of Leptospira interrogans Serovar hardjo (1989)

Lipopolysaccharides (LPSs) from Leptospira interrogans serovar hardjo (reference strain hardjoprajitno and strain hardjobovis) were prepared by the hot phenol-water procedure. High yields of LPSs were found in the phenol phase. Gel electrophoresis of the phenol phase LPSs showed similar patterns for all strains in contrast to the different patterns found in the water phase LPSs. Sugar composition was also similar among all strains with rhamnose as the predominant sugar. Mannosamine was detected by high performance thin layer and gas-liquid chromatography. 2-Keto-3-deoxyoctonic acid (KDO) was comparable with authentic KDO by paper chromatography. Periodate oxidation at near neutral pH with or without prior hydrolysis showed that most of the KDO was substituted. The fatty acid composition of strain hardjobovis LPS was slightly different from that of the reference strain hardjoprajitno. Myristic and 3-hydroxymyristic acid were not detected in any of the LPS preparations. In conjunction with genetic and other data, the two strains are sufficiently different to be regarded as members of two separate species sharing common antigens. There is sufficient evidence to rename the hardjoprajitno strain type L. interrogans hardjo-p, and the hardjobovis strain type L. borgpeterseni hardjo-b.
Portrait of Haifa in 1948: The Poet, the Bay and the Mountain (2012)

Yehuda Amichai is one of the twentieth century’s (and Israel’s) leading poets. Historically, Amichai belongs to the group of writers who founded “Israeli literature” in the 1950s and early ’60s, and were dubbed the “Generation of the State” because they were the first authors to publish in the State of Israel after it was established. Amichai and his peers rebelled against their predecessors’ grandiose, ideological verse and proclaimed that “understatement” and individualism would be two of their guiding principles. While doing research for my book, <i>Yehuda Amichai: The Making of Israel’s National Poet</i> (UPNE, 2008), I discovered 100 love letters that Amichai sent from Haifa to New York during 1947–1948. These are both a literary account and a historical testimony of great value. Amichai’s portraits of Haifa during those months have never been discussed. In this article, I describe the way the letters bring to life Haifa’s magnificent landscapes and the struggle of the Jewish city from Amichai’s unique point of view.
ULTRASONIC BRACELET PROBE DEVICE FOR THE INSPECTION OF TUBE BUTT WELDS (1969)

Tube butt welds in boilers were not subject to 100 percent inspection, and leakages at them were confirmed as a significant cause of boiler outage. Consequently, it was concluded that it would be feasible to inspect a complete weld with a circumferential array of angle probes--the bracelet probe device. Three regional laboratories had particular requirements and a full description of the devices developed to meet these is given. Also the extensive advantages offered by the bracelet probe device are listed.
Materials analysis using x-ray linear attenuation coefficient measurements at four photon energies (2005)

The analytical properties of an accurate parameterization scheme for the x-ray linear attenuation coefficient are examined. The parameterization utilizes an additive combination of N compositional- and energy-dependent coefficients. The former were derived from a parameterization of elemental cross-sections using a polynomial in atomic number. The compositional-dependent coefficients are referred to as the mixture parameters, representing the electron density and higher order statistical moments describing elemental distribution. Additivity is an important property of the parameterization, allowing measured x-ray linear attenuation coefficients to be written as linear simultaneous equations, and then solved for the unknown coefficients. The energy-dependent coefficients can be determined by calibration from measurements with materials of known composition. The inverse problem may be utilized for materials analysis, whereby the simultaneous equations represent multi-energy linear attenuation coefficient measurements, and are solved for the mixture parameters. For in vivo studies, the choice of measurement energies is restricted to the diagnostic region (approximately 20 keV to 150 keV), where the parameterization requires N >or= 4 energies. We identify a mathematical pathology that must be overcome in order to solve the inverse problem in this energy regime. An iterative inversion strategy is presented for materials analysis using four or more measurements, and then tested against real data obtained at energies 32 keV to 66 keV. The results demonstrate that it is possible to recover the electron density to within +/-4% and fourth mixture parameter. It is also a key finding that the second and third mixture parameters cannot be recovered, as they are of minor importance in the parameterization at diagnostic x-ray energies.
Literature study of metallic ternary and quanternary hydrides (1975)

Metallic hydrides are being considered as an attractive solution to storage problems involved in using hydrogen as an alternative fuel. In this application, the unclassified literature was surveyed to find metallic ternary hydride systems of the type MM'H/sub x/; M is a transition element, a member of the rare earth element series, or a member of the actinide element series, and M' is a transition element. Reported quaternary hydrides of the same metallic element series were also reviewed. The hydride-forming systems found and some of their most interesting properties are summarized. Recent advances in the understanding of the absorption characteristics and the stability of these hydride materials are reviewed. (auth)
Cold storage for Iowa grown apples. (1914)

In continuing its investigation of cold storage for Iowa grown apples, upon which a partial report was made in September, 1909*, the horticultural section of the Iowa Agricultural Experiment Station has found further evidence that the principal commercial varieties of apples grown in the state may be handled with profit. The four years’ work with many different varieties all gives support to the value of this practice to Iowa apple men.\nSince 1909 the Station has also developed many other new facts of importance to Iowa apple growers, not the least of them pertaining to the freezing of apples and their storage value when frozen. Careful tests indicate that apples which are frozen upon the trees in the fall can be safely placed in cold storage if allowed to thaw out gradually on the tree before picking, unless the fruit is broken down by the freeze. Apples which are frozen in cold or common storage will not be seriously injured if thawed out below freezing temperature.
Immunotoxin-mediated inhibition of chronic lymphocytic leukemia cell proliferation in humans. (1989)

We evaluated the cytotoxicity of the immunotoxin OKT1-SAP on fresh B-chronic lymphocytic leukemia (B-CLL) cells from 31 consecutive patients. OKT1-SAP comprised the OKT1 (CD5) monoclonal antibody disulfide linked to saporin-6 (SAP) ribosome-inactivating protein from the plant Saponaria officinalis. The effect of OKT1-SAP on target CD5-positive B-CLL cells was estimated using an in vitro proliferation inhibition assay in which control or OKT1-SAP-treated B-CLL cells were induced to proliferate by sequential stimulation with insolubilized anti-C3b receptor CB04 (CD35) antibody and low molecular weight B-cell growth factor. In 90% of patients, OKT1-SAP specifically suppressed B-CLL cell proliferation in a dose-related manner (50% inhibitory concentration, 4.0-6.8 nM). Taken together the findings reported in this article provide information relevant to the clinical development of immunotoxins because: (a) the in vitro conditions under which B-CLL cell proliferation is inhibited by OKT1-SAP are achievable in vivo without nonspecific toxicity according to our previous toxicology and pharmacokinetics studies in primates; and (b) the B-CLL cell proliferation inhibition assay described here provides a basis for future comparative studies.
Land-Use Classification Using Taxi GPS Traces (2012)

Detailed land use, which is difficult to obtain, is an integral part of urban planning. Currently, GPS traces of vehicles are becoming readily available. It conveys human mobility and activity information, which can be closely related to the land use of a region. This paper discusses the potential use of taxi traces for urban land-use classification, particularly for recognizing the social function of urban land by using one year's trace data from 4000 taxis. First, we found that pick-up/set-down dynamics, extracted from taxi traces, exhibited clear patterns corresponding to the land-use classes of these regions. Second, with six features designed to characterize the pick-up/set-down pattern, land-use classes of regions could be recognized. Classification results using the best combination of features achieved a recognition accuracy of 95%. Third, the classification results also highlighted regions that changed land-use class from one to another, and such land-use class transition dynamics of regions revealed unusual real-world social events. Moreover, the pick-up/set-down dynamics could further reflect to what extent each region is used as a certain class.
Overexpression of Protein Targeting to Glycogen (PTG) in Rat Hepatocytes Causes Profound Activation of Glycogen Synthesis Independent of Normal Hormone- and Substrate-mediated Regulatory Mechanisms (1998)

Protein targeting to glycogen (PTG), also known as PPP1R5, is a widely expressed member of a growing family of proteins that target protein phosphatase-1 (PP-1) to glycogen particles. Because PTG also binds to glycogen synthase and phosphorylase kinase, it has been suggested that it serves as a "scaffold" for efficient activation of glycogen synthesis. However, very little is known about the metabolic effects of PTG. In this study, we have used recombinant adenovirus to overexpress PTG in primary rat hepatocytes, a cell type with high glycogenic capacity. We find that overexpression of PTG potently activates glycogen synthesis in cultured hepatocytes. Surprisingly, the glycogenic effect of PTG is observed even in the complete absence of carbohydrates or insulin in the culture medium. Furthermore, glycogenolytic agents such as forskolin or glucagon are largely ineffective at activating glycogen degradation in PTG overexpressing hepatocytes, even though large increases in cAMP levels are demonstrated. These metabolic effects of PTG overexpression are accompanied by a 3.6-fold increase in glycogen synthase activation state and a 40% decrease in glycogen phosphorylase activity. Our results are consistent with a model in which PTG overexpression "locks" the hepatocyte in a glycogenic mode, presumably via its ability to promote interaction of enzymes of glycogen metabolism with PP-1.
Annexin-Mediated Matrix Vesicle Calcification in Vascular Smooth Muscle Cells (2008)

In bone, osteoblasts and chondrocytes synthesize matrix vesicles (MVs) that interact with collagen to initiate calcification. MVs have been identified in human calcified arteries but are poorly characterized. The objective of this study is to determine the role of annexins and fetuin-A in MV formation and activity during calcification in bovine vascular smooth muscle cells (BVSMCs). BVSMCs were treated with control or calcification (high phosphorus) media, and cellular MVs were isolated by collagenase digestion and secreted MVs were isolated from cultured media by ultracentrifugation. The results showed that alkaline phosphatase (ALP) activity was significantly increased in MVs from calcified BVSMCs compared with noncalcified BVSMCs, as was annexin II and VI content and (45)Ca uptake. We also determined that MVs from calcifying BVSMCs could mineralize type I collagen but not type II collagen in the absence of cells in a dose- and time-dependent manner. Blockade of annexin calcium channel activity by K201 significantly decreased ALP activity and reduced the ability of the MVs to subsequently calcify on collagen, whether the K201 was added during or after MV formation. Furthermore, cellular MVs had significantly increased ability to calcify on collagen compared with secreted MVs, likely because of their increased ALP activity and annexin II content but low fetuin-A content. In conclusion, our results suggest that mineralization in VSMCs requires both active MVs and an interaction of the MVs with type I collagen, and both steps require annexin activity.
The role of p38 mitogen-activated protein kinase in IL-1 beta transcription. (1999)

Several reports have shown that bicyclic imidazoles, specific inhibitors of the p38 mitogen-activated protein kinase (MAPK), block cytokine synthesis at the translational level. In this study, we examined the role of p38 MAPK in the regulation of the IL-1beta cytokine gene in monocytic cell lines using the bicyclic imidazole SB203580. Addition of SB203580 30 min before stimulation of monocytes with LPS inhibited IL-1beta protein and steady state message in a dose-dependent manner in both RAW264.7 and J774 cell lines. The loss of IL-1beta message was due mainly to inhibition of transcription, since nuclear run-off analysis showed an approximately 80% decrease in specific IL-1 RNA synthesis. In contrast, SB203580 had no effect on the synthesis of TNF-alpha message. LPS-stimulated p38 MAPK activity in the RAW264.7 cells was blocked by SB203580, as measured by the inhibition of MAPKAP2 kinase activity, a downstream target of the p38 MAPK. CCAATT/enhancer binding protein (C/EBP)/NFIL-6-driven chloramphenicol acetyltransferase (CAT) reporter activity was sensitive to SB203580, indicating that C/EBP/NFIL-6 transcription factor(s) are also targets of p38 MAPK. In contrast, transfected CAT constructs containing NF-kappaB elements were only partially inhibited (approximately 35%) at the highest concentration of SB203580 after LPS stimulation. As measured by EMSA, LPS-stimulated NF-kappaB activation was not affected by SB203580. Overall, the results demonstrate, for the first time, a role for p38 MAPK in IL-1beta transcription by acting through C/EBP/NFIL-6 transcription factors.
Rayleigh backscattering in optical fiber recirculating delay lines (1986)

We derive the backscattering impulse response of a recirculating fiber delay line. The response consists of periodic discontinuities that occur at multiples of the loop transit time. The magnitude of each discontinuity is found to depend only on the coupling coefficient and the number of recirculations and is independent of both propagation loss and loop length. A graphical aid for describing the response of the system is also presented.
Epitaxial lift-off of large-area GaAs multi-junction solar cells for high efficiency clean and portable energy power generation (2014)

Epitaxial lift-off (ELO) is a processing technique that enables thin epitaxial layers grown on GaAs substrate to be “peeled off” from the host substrate. The ELO process offers several key advantages for both performance enhancement and cost reduction of III-V electronic and optoelectronic devices. The epitaxial films can be transferred to new support substrates that are thin, flexible, lightweight, and with higher thermal conductivity than the original growth substrate. The GaAs substrate can be reused multiple times without any performance degradation. We have developed an ELO process capable of lifting off large areas of semiconductor material from substrates up to 6 inches in diameter without any degradation of material quality or performance characteristics. Solar cells with a 33% efficiency under 1-sun AM 1.5 and 31% efficiency at 1-sun under AMO were demonstrated using ELO. Production of this technology for fabricating thin, flexible large-area multi-junction solar cell arrays with very high efficiency has been established. Light weight portable solar sheets for remote charging have been produced. Other applications include electric-powered, unmanned aerial vehicles (UAVs), space satellites, and terrestrial solar concentrator systems.
Quantitative Assessment of Islets of Langerhans Encapsulated in Alginate (2010)

Improved methods have recently been developed for assessing islet viability and quantity in human islet preparations for transplantation, and these measurements have proven useful for predicting transplantation outcome. The objectives of this study were to adapt these methods for use with microencapsulated islets, to verify that they provide meaningful quantitative measurements, and to test them with two model systems: (1) barium alginate and (2) barium alginate containing a 70% (w/v) perfluorocarbon (PFC) emulsion, which presents challenges to use of these assays and is of interest in its own right as a means for reducing oxygen supply limitations to encapsulated tissue. Mitochondrial function was assessed by oxygen consumption rate measurements, and the analysis of data was modified to account for the increased solubility of oxygen in the PFC-alginate capsules. Capsules were dissolved and tissue recovered for nuclei counting to measure the number of cells. Capsule volume was determined from alginate or PFC content and used to normalize measurements. After low oxygen culture for 2 days, islets in normal alginate lost substantial viable tissue and displayed necrotic cores, whereas most of the original oxygen consumption rate was recovered with PFC alginate, and little necrosis was observed. All nuclei were recovered with normal alginate, but some nuclei from nonrespiring cells were lost with PFC alginate. Biocompatibility tests revealed toxicity at the islet periphery associated with the lipid emulsion used to provide surfactants during the emulsification process. We conclude that these new assay methods can be applied to islets encapsulated in materials as complex as PFC-alginate. Measurements made with these materials revealed that enhancement of oxygen permeability of the encapsulating material with a concentrated PFC emulsion improves survival of encapsulated islets under hypoxic conditions, but reformulation of the PFC emulsion is needed to reduce toxicity.