gebhart/patrepeval huggingface dataset:
Transposon Tc1-derived, sequence-tagged sites in <i>Caenorhabditis elegans</i> as markers for gene mapping (1996)

We present an approach to map large numbers of Tc1 transposon insertions in the genome of Caenorhabditis elegans. Strains have been described that contain up to 500 polymorphic Tc1 insertions. From these we have cloned and shotgun sequenced over 2000 Tc1 flanks, resulting in an estimated set of 400 or more distinct Tc1 insertion alleles. Alignment of these sequences revealed a weak Tc1 insertion site consensus sequence that was symmetric around the invariant TA target site and reads CAYATATRTG. The Tc1 flanking sequences were compared with 40 Mbp of a C. elegans genome sequence. We found 151 insertions within the sequenced area, a density of approximately 1 Tc1 insertion in every 265 kb. As the rest of the C. elegans genome sequence is obtained, remaining Tc1 alleles will fall into place. These mapped Tc1 insertions can serve two functions: (i) insertions in or near genes can be used to isolate deletion derivatives that have that gene mutated; and (ii) they represent a dense collection of polymorphic sequence-tagged sites. We demonstrate a strategy to use these Tc1 sequence-tagged sites in fine-mapping mutations.
Identification of B cell adaptor for PI3‐kinase (BCAP) as an Abl interactor 1‐regulated substrate of Abl kinases (2005)

In previous work we showed that Abl interactor 1 (Abi-1), by linking enzyme and substrate, promotes the phosphorylation of Mammalian Enabled (Mena) by c-Abl. To determine whether this mechanism extends to other c-Abl substrates, we used the yeast two-hybrid system to search for proteins that interact with Abi-1. By screening a human leukocyte cDNA library, we identified BCAP (B-cell adaptor for phosphoinositide 3-kinase) as another Abi-1-interacting protein. Binding experiments revealed that the SH3 domain of Abi-1 and the C-terminal polyproline structure of BCAP are involved in interactions between the two. In cultured cells, Abi-1 promoted phosphorylation of BCAP not only by c-Abl but also by v-Abl. The phosphorylation sites of BCAP by c-Abl were mapped to five tyrosine residues in the C-terminal region that are well conserved in mammals. These results show that Abi-1 promotes Abl-mediated BCAP phosphorylation and suggest that Abi-1 in general coordinates kinase-substrate interactions.
Multisite Reproducibility of Results Obtained by the Broth Microdilution Method for Susceptibility Testing of <i>Mycobacterium abscessus</i> , <i>Mycobacterium chelonae</i> , and <i>Mycobacterium fortuitum</i> (1999)

A multicenter study was conducted to assess the interlaboratory reproducibility of broth microdilution testing of the more common rapidly growing pathogenic mycobacteria. Ten isolates (four Mycobacterium fortuitum group, three Mycobacterium abscessus, and three Mycobacterium chelonae isolates) were tested against amikacin, cefoxitin, ciprofloxacin, clarithromycin, doxycycline, imipenem, sulfamethoxazole, and tobramycin (M. chelonae only) in four laboratories. At each site, isolates were tested three times on each of three separate days (nine testing events per isolate) with a common lot of microdilution trays. Agreement among MICs (i.e., mode +/- 1 twofold dilution) varied considerably for the different drug-isolate combinations and overall was best for cefoxitin (91.7 and 97.2% for one isolate each and 100% for all others), followed by doxycycline, amikacin, and ciprofloxacin. Agreement based on the interpretive category, using currently suggested breakpoints, also varied and overall was best for doxycycline (97.2% for one isolate and 100% for the rest), followed by ciprofloxacin and clarithromycin. Reproducibility among MICs and agreement by interpretive category was most variable for imipenem. Based on results reported from the individual sites, it appears that inexperience contributed significantly to the wide range of MICs of several drugs, especially clarithromycin, ciprofloxacin, and sulfamethoxazole. New interpretive guidelines are presented for the testing of M. fortuitum against clarithromycin; M. abscessus and M. chelonae against the aminoglycosides; and all three species against cefoxitin, doxycycline, and imipenem.
Flaxseed Improves Lipid Profile without Altering Biomarkers of Bone Metabolism in Postmenopausal Women (2002)

The risk of cardiovascular disease and osteoporosis drastically increases at the onset of menopause. Phytoestrogens have been suggested to inhibit bone loss and protect the cardiovascular system, in part by improving lipid profiles. The purpose of the present study was to examine the effects of flaxseed, a rich source of the phytoestrogens called lignans, on lipid metabolism and biomarkers of bone turnover in postmenopausal women. Postmenopausal women who were not on hormone replacement therapy were assigned to one of two treatment groups in a double-blind randomized study. Women were asked to consume 40 g of either ground flaxseed or wheat-based comparative control regimen daily for 3 months. In addition, all subjects received 1,000 mg calcium and 400 IU vitamin D daily. Flaxseed supplementation lowered (P < 0.05) both serum total cholesterol and non-high-density lipoprotein cholesterol by 6%, whereas the comparative control regimen had no such effect. Flaxseed regimen reduced serum levels of both low-density- and high-density-lipoprotein cholesterol by 4.7% and triglyceride by 12.8%, albeit not statistically significant. Serum apolipoprotein A-1 and apolipoprotein B concentrations were significantly (P < 0.005) reduced by 6 and 7.5%, respectively, by the flaxseed regimen. Markers of bone formation and resorption were not affected by either of the treatments. The findings of this study indicate that flaxseed supplementation improves lipid profiles but has no effect on biomarkers of bone metabolism in postmenopausal women.
Compatibility of Mating Preferences (2016)

Human mating is a complex phenomenon. Although men and women have different preferences in mate selection, there should be compatibility in these preferences since human mating requires agreement of both parties. We investigate how compatible the mating preferences of men and women are in a given property such as age, height, education and income. We use dataset of a large online dating site (N = 44, 255 users). (i) Our findings are based on the "actual behavior" of users trying to find a date online, rather than questions about a "hypothetical" partner as in surveys. (ii) We confirm that women and men have different mating preferences. Women prefer taller and older men with better education and higher income then themselves. Men prefer just the opposite. (iii) Our findings indicate that these differences complement each other. (iv) Highest compatibility is observed in income with 95 %. This might be an indication that income is in the process of becoming more important than other properties, including age, in our modern society. (v) An evolutionary model is developed which produces similar results.
Properties of matrix‐assisted laser desorption. Measurements with a time‐to‐digital converter (1991)

Some properties of matrix-assisted laser desorption have been studied using single-ion-counting methods and a time-to-digital converter. The methods allow examination of the process for irradiances near the reported threshold for observation with a transient recorder. All measurements were made using bovine insulin as a test compound. We present direct evidence that an irradiance threshold near 10(6) W cm-2 exists for ion production, and that the process is a collective effect, either involving a large number of molecular ions (approximately 10(4) in a successful event or none at all. Above the threshold, the yield is found to scale with a high power (4th to 6th) of the irradiance. Measurements of initial velocity distributions indicate an axial velocity spread corresponding to approximately 50 eV and a radial velocity spread corresponding to approximately 2.4 eV. Thus the ejection or extraction mechanism appears to be strongly asymmetric.
Role of macrophages in experimental malaria: IV--Bioassay of silica in immunity against Plasmodium berghei infection. (1997)

Silica treated mice when challenged with Plasmodium berghei showed increase in duration of prepatent(PP) and survival period (SP) and median survival day(MSD) as compared with controls. Daily parasite density curve during the course of infection was similar to control. Response to the parasite challenge, however, was dependent on the dose of silica. No increase in SP at 0.7 mg and in PP at 35 mg (cumulative doses) dose was observed. A dose upto 5 mg per mouse before challenge resulted in protection of the animal. No mortality was recorded in mice which received silica alone (35 mg; 5 mg/day x 7 days). Death due to lethal P.berghei infection could be delayed or prevented by altering/reducing the functional activities of macrophages during the course of infection.
Rate-Distortion Balanced Data Compression for Wireless Sensor Networks (2016)

This paper presents a data compression algorithm with error bound guarantee for wireless sensor networks (WSNs) using compressing neural networks. The proposed algorithm minimizes data congestion and reduces energy consumption by exploring spatio-temporal correlations among data samples. The adaptive rate-distortion feature balances the compressed data size (data rate) with the required error bound guarantee (distortion level). This compression relieves the strain on energy and bandwidth resources while collecting WSN data within tolerable error margins, thereby increasing the scale of WSNs. The algorithm is evaluated using real-world data sets and compared with conventional methods for temporal and spatial data compression. The experimental validation reveals that the proposed algorithm outperforms several existing WSN data compression methods in terms of compression efficiency and signal reconstruction. Moreover, an energy analysis shows that compressing the data can reduce the energy expenditure and, hence, expand the service lifespan by several folds.
Pathophysiology and treatment of deep-vein thrombosis and pulmonary embolism. (1985)

The pathophysiology of deep-vein thrombosis (DVT) and pulmonary embolism (PE) is briefly discussed, and the efficacy, dosage and administration, laboratory monitoring, and adverse effects of thrombolytic agents, heparin, and warfarin are reviewed. Acute therapy of DVT and PE is usually initiated with intravenous heparin; however, thrombolytic agents such as streptokinase and urokinase may be preferred in patients with massive PE or severe DVT when clot lysis rather than clot stabilization is deemed necessary. For DVT or PE, an intravenous loading dose of streptokinase or urokinase is given, followed by a continuous infusion of the drug. Therapy with streptokinase is continued for 24 hours in patients with PE and for 72 hours in those with DVT; urokinase is continued for 12 hours in patients with PE. Monitoring of blood coagulation tests during thrombolytic therapy is recommended primarily for ensuring that a lytic state is achieved. Intravenous heparin is preferred for acute treatment of DVT or PE; controversy exists regarding whether administration by continuous infusion or intermittent bolus injection is superior. Heparin dosage is usually adjusted to maintain the activated partial-thromboplastin time (APTT) ratio between 1.5 and 2.5; however, the ideal therapeutic range has never been firmly established. After acute treatment with heparin, most patients should continue to receive either warfarin or subcutaneous heparin for several months to prevent recurrent thromboembolism. Bleeding is the major adverse effect of thrombolytic agents and anticoagulants. The risk of bleeding with heparin and warfarin therapy increases with excessive prolongation of the APTT and prothrombin time (PT), respectively. Future clinical trials should further define the role of thrombolytic agents in the treatment of DVT and PE and the efficacy of less-intense warfarin therapy for pulmonary embolism or arterial thromboembolic events.
Analgesic and Antipyretic Activities of an Aqueous Extract and of the Flavone Linarin of<i>Buddleia cordata</i> (1996)

The dried aqueous extract of leaves of Buddleia cordata (loganiaceae) and its main flavonoid glycoside, linarin, have been evaluated for analgesic and antipyretic effects in mice and rats, respectively. Both the extract and linarin exerted significant and dose-dependent analgesic and antipyretic activities, the first being obtained against a chemical stimulus (writhing a test in mice) and the second being obtained by a pyretogenic stimulus (yeast-induced hyperthermia test). Furthermore, the response of the animals in the hot plate test was modified by linarin and an aqueous extract. These activities were similar to that showed by morphine sulfate (MS) and they were inhibited by naxolone pretreatment, a specific morphinic antagonist compound. These findings lead to the conclusion that the aqueous extract and linarin exert central analgesic properties. On the other hand, linarin was shown to be responsible for the antipyretic activity of this species.
Removing celiac disease-related gluten proteins from bread wheat while retaining technological properties: a study with Chinese Spring deletion lines (2009)

The consequences of these data are discussed with regard to reducing the load of T-cell stimulatory epitopes in wheat, and to contributing to the design of CD-safe wheat varieties.
IL‐9 is important for T‐cell activation and differentiation in autoimmune inflammation of the central nervous system (2011)

Experimental autoimmune encephalomyelitis (EAE) is generally believed to be an autoimmune disease of the central nervous system (CNS) caused by myelin-specific Th1 and/or Th17 effector cells. The underlying cellular and molecular mechanisms, however, are not fully understood. Using mice deficient in IL-9 (IL-9(-/-) ), we showed that IL-9 plays a critical role in EAE. Specifically, IL-9(-/-) mice developed significantly less severe EAE than their WT counterparts following both immunization with myelin proteolipid protein (PLP)(180-199) peptide in the presence of Complete Freund's Adjuvant (CFA), and adoptive transfer of PLP(180-199) peptide-specific effector T cells from WT littermates. EAE-resistant IL-9(-/-) mice exhibited considerably fewer infiltrating immune cells in the CNS, with lower levels of IL-17 and IFN-γ expression, than their WT littermates. Further studies revealed that null mutation of the IL-9 gene resulted in significantly lower levels of PLP(180-199) peptide-specific IL-17 and IFN-γ production. Moreover, IL-9(-/-) memory/activated T cells exhibited decreased C-C chemokine receptors (CCR)2, CCR5, and CCR6 expression. Interestingly, IL-10 was significantly increased in IL-9(-/-) mice compared with WT littermates. Importantly, we found that IL-9-mediated Th17-cell differentiation triggers complex STAT signaling pathways.
Investigations of magnetic amplifiers with feedback (1958)

Sine wave carrier excited magnetic amplifiers have been investigated to determine if the figure of merit can be improved through the use of feedback techniques. It is shown that the power gain can be made unlimited but that a finite rise time is preserved. Hence the figure of merit as ordinarily defined becomes meaningless. It is shown, however, that voltage gain divided by rise time remains nearly constant under feedback and is a more suitably defined figure of merit.
Arizona State University (2011)

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A 40,000-dalton protein from Dictyostelium discoideum affects assembly properties of actin in a Ca2+-dependent manner. (1982)

A 40,000-dalton protein that affects the assembly properties of actin in a Ca2+-dependent manner has been purified from Dictyostelium discoideum. Gel filtration chromatography indicates that the native form of this protein is a monomer. A major effect of this protein is to reduce the sedimentability of F-actin in a stoichiometric fashion. Nearly complete loss of sedimentability is observed at ratios of the 40,000-dalton protein to actin of greater than 1:10. At low stoichiometries, this protein can accelerate the rate of actin assembly under certain experimental conditions. These effects of the 40,000-dalton protein on the actin assembly properties described above require calcium ion. The 40,000-dalton protein does not exert its effects by proteolyzing actin. Furthermore, peptide maps demonstrate that this protein is not a proteolytic fragment of actin.
Parsing the Wall Street Journal with the inside-outside algorithm (1993)

We report grammar inference experiments on partially parsed sentences taken from the Wall Street Journal corpus using the inside-outside algorithm for stochastic context-free grammars. The initial grammar for the inference process makes no ,assumption of the kinds of structures and their distributions. The inferred grammar is evaluated by its predicting power and by comparing the bracketing of held out sentences imposed by the inferred grammar with the partial bracketings of these sentences given in the corpus. Using part-of-speech tags as the only source of lexical information, high bracketing accuracy is achieved even with a small subset of the available training material (1045 sentences): 94.4% for test sentences shorter than 10 words and 90.2% for sentences shorter than 15 words.
Labeling of cells with ferumoxides–protamine sulfate complexes does not inhibit function or differentiation capacity of hematopoietic or mesenchymal stem cells (2005)

Two FDA-approved agents, ferumoxides (Feridex), a suspension of superparamagnetic iron oxide (SPIO) nanoparticles and protamine sulfate, a drug used to reverse heparin anticoagulation, can be complexed and used to label cells magnetically ex vivo. Labeling stem cells with ferumoxides-protamine sulfate (FePro) complexes allows for non-invasive monitoring by MRI. However, in order for stem cell trials or therapies to be effective, this labeling technique must not inhibit the ability of cells to differentiate. In this study, we examined the effect of FePro labeling on stem cell differentiation. Viability, phenotypic expression and differential capacity of FePro labeled CD34 + hematopoietic stem cells (HSC) and mesenchymal stem cells (MSC) were compared with unlabeled control cells. Colony-forming unit (CFU) assays showed that the capacity to differentiate was equivalent for labeled and unlabeled HSC. Furthermore, labeling did not alter expression of surface phenotypic markers (CD34, CD31, CXCR4, CD20, CD3 and CD14) on HSC, as measured by flow cytometry. SDF-1-induced HSC migration and HSC differentiation to dendritic cells were also unaffected by FePro labeling. Both FePro-labeled and unlabeled MSC were cultured in chondrogenesis-inducing conditions. Alcian blue staining for proteoglycans revealed similar chondrogenic differentiation for both FePro-labeled and unlabeled cells. Furthermore, collagen X proteins, indicators of cartilage formation, were detected at similar levels in both labeled and unlabeled cell pellets. Prussian blue staining confirmed that cells in labeled pellets contained iron oxide, whereas cells in unlabeled pellets did not. It is concluded that FePro labeling does not alter the function or differentiation capacity of HSC and MSC. These data increase confidence that MRI studies of FePro-labeled HSC or MSC will provide an accurate representation of in vivo trafficking of unlabeled cells.
LED Flicker: A Drawback or an Opportunity? (2013)

In this paper we examine the flicker of commercial LED lamps and with the help of volunteers we explore the parameter space (frequency and duty cycle) in order to find pulsing operating conditions under which the light fluctuations are not visually perceived. The results show that LEDs under mains voltage manifest the most extreme cases of flicker and we also confirm that under pulsing mode the overall impression is of higher brightness which is an opportunity for energy savings. The results also show that the background color and luminance contrast is of high importance. Finally we propose an easy method for consumers to detect flickering of light sources under mains voltage.
Monitoring the combustion quality in internal combustion engines using the spark plug as a plasma probe (1975)

A method of monitoring the quality of combustion in spark ignition gasoline engines using the spark plug's center electrode as a plasma probe is presented. Due to the ionized species remaining in the burned gases after combustion, a current is induced in a network attached to the spark plug's center electrode. The time dependence of this induced current is shown to correlate with the presence or absence and the time of occurance of the pressure component due to combustion in pressure transducer signals recorded simultaneously. Based on these correlations, three types of burns could be recognized from plasma probe signals: good burns, slow burns, and misfires. The specific correlation between the absence of a pressure component due to combustion and a corresponding absence of a plasma probe signal was used to form the basis for the operation of a one-channel engine misfire monitoring circuit.
Reconfigurable Bowtie Antenna Using Metal-Insulator Transition in Vanadium Dioxide (2015)

A new method to reconfigure, tune or program an antenna is presented and validated through a fabricated proof-of-concept prototype. The method relies on the changing electrical properties of a smart material, vanadium dioxide ( VO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ), across its solid-to-solid phase transition. The phase change in the material is induced thermally. The developed device is a monolithically integrated VO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -based antenna that changes resonant frequency on demand. Details and challenges related to the design, fabrication and integration of VO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> thin films with antennas, as well as the measurement setup, are discussed. Measurement results match well with theory and simulations. Results unveil a new technique for reconfiguring antennas and suggest further studies and improvements could lead to more exciting results and make vanadium dioxide thin-films an alternate solution for multi-functional antennas. This work is the first prototype to implement this new reconfiguration mechanism in antennas in the gigahertz range and to present results during the VO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> metal-to-insulator phase transition.
A reduced complexity EPR4 post-processor (1998)

A reduced-complexity Extended Partial Response Class 4 (EPR4) detector implemented as a post-processor following a Partial Response Class 4 (PR4) Viterbi detector is described. Previous work showed that a post-processor architecture eliminates the speed bottleneck associated with an EPR4 Viterbi detector while providing comparable performance. The post-processor uses EPR4 metrics to detect and correct minimum distance EPR4 error-events in the binary sequence at the output of a PR4 Viterbi detector. In the new approach, the complexity is greatly reduced without sacrificing performance by considering only those EPR4 error-events deemed most-likely based on their PR4 metrics.