gebhart/patrepeval huggingface dataset:
Anchoring 9,371 Maize Expressed Sequence Tagged Unigenes to the Bacterial Artificial Chromosome Contig Map by Two-Dimensional Overgo Hybridization (2004)

Our goal is to construct a robust physical map for maize (Zea mays) comprehensively integrated with the genetic map. We have used a two-dimensional 24 x 24 overgo pooling strategy to anchor maize expressed sequence tagged (EST) unigenes to 165,888 bacterial artificial chromosomes (BACs) on high-density filters. A set of 70,716 public maize ESTs seeded derivation of 10,723 EST unigene assemblies. From these assemblies, 10,642 overgo sequences of 40 bp were applied as hybridization probes. BAC addresses were obtained for 9,371 overgo probes, representing an 88% success rate. More than 96% of the successful overgo probes identified two or more BACs, while 5% identified more than 50 BACs. The majority of BACs identified (79%) were hybridized with one or two overgos. A small number of BACs hybridized with eight or more overgos, suggesting that these BACs must be gene rich. Approximately 5,670 overgos identified BACs assembled within one contig, indicating that these probes are highly locus specific. A total of 1,795 megabases (Mb; 87%) of the total 2,050 Mb in BAC contigs were associated with one or more overgos, which are serving as sequence-tagged sites for single nucleotide polymorphism development. Overgo density ranged from less than one overgo per megabase to greater than 20 overgos per megabase. The majority of contigs (52%) hit by overgos contained three to nine overgos per megabase. Analysis of approximately 1,022 Mb of genetically anchored BAC contigs indicates that 9,003 of the total 13,900 overgo-contig sites are genetically anchored. Our results indicate overgos are a powerful approach for generating gene-specific hybridization probes that are facilitating the assembly of an integrated genetic and physical map for maize.
Studies on the stability of a human adenovirus-rabies recombinant vaccine. (1992)

Human adenovirus type 5 containing the rabies virus glycoprotein gene (rHAd-RG1) has potential for the oral vaccination of animals. The stability of this recombinant was tested indoors and outdoors by measuring the loss in virus infectivity. Under indoor conditions the stability of the recombinant virus was studied in an egg yolk-containing commercial stabilizer and a simple buffered salt solution (EBSS; Earle's balanced salt solution) at 4 degrees C and room temperature (24-25 degrees C). Over 16 days, there was a more rapid loss in virus titer at room temperature than at 4 degrees C in both suspending media; however, these differences were slight and may be significant when the overall stability of the vaccine is considered. When the virus was mixed with either 10% (w/v) fox or skunk feces or EBSS, placed on stainless steel disks and the disks kept under ambient conditions (air temperature 24-25 degrees C; relative humidity 45-50%), there was a more rapid decline in virus titer in the fecal suspensions (3% remained after 72 h) than in EBSS (26% remained after 72 h). When bait-coated blister packs of the vaccine were placed in an outdoor location in the fall (October) season, there was a larger drop in the virus titer for vaccines placed in the sun (54% over 32 days) than for those in the shade (40% over 32 days). Incorporating proteinaceous stabilizers in the vaccine samples for outdoor study showed virus stability was not enhanced in their presence.(ABSTRACT TRUNCATED AT 250 WORDS)
Targeted gene disruption reveals an essential role for ceruloplasmin in cellular iron efflux (1999)

Aceruloplasminemia is an autosomal recessive disorder of iron metabolism. Affected individuals evidence iron accumulation in tissue parenchyma in association with absent serum ceruloplasmin. Genetic studies of such patients reveal inherited mutations in the ceruloplasmin gene. To elucidate the role of ceruloplasmin in iron homeostasis, we created an animal model of aceruloplasminemia by disrupting the murine ceruloplasmin (Cp) gene. Although normal at birth, Cp(-/-) mice demonstrate progressive accumulation of iron such that by one year of age all animals have a prominent elevation in serum ferritin and a 3- to 6-fold increase in the iron content of the liver and spleen. Histological analysis of affected tissues in these mice shows abundant iron stores within reticuloendothelial cells and hepatocytes. Ferrokinetic studies in Cp(+/+) and Cp(-/-) mice reveal equivalent rates of iron absorption and plasma iron turnover, suggesting that iron accumulation results from altered compartmentalization within the iron cycle. Consistent with this concept, Cp(-/-) mice showed no abnormalities in cellular iron uptake but a striking impairment in the movement of iron out of reticuloendothelial cells and hepatocytes. Our findings reveal an essential physiologic role for ceruloplasmin in determining the rate of iron efflux from cells with mobilizable iron stores.
Antidote for Factor Xa Anticoagulants (2015)

Oral anticoagulant options have exploded. Dabigatran, a direct thrombin inhibitor, was approved for use in the United States in 2010 for the prevention of stroke in patients with atrial fibrillation; this was rapidly followed by approval of the direct factor Xa inhibitors rivaroxaban, apixaban, and edoxaban within 5 years. The drive for the development of these drugs stemmed from the burdens associated with the use of the anticoagulants that had previously been available for outpatient treatment — subcutaneous heparins and oral vitamin K antagonists. Although these new drugs represent an important advance in anticoagulation therapy, concern over the lack of . . .
PACAP-38 infusion causes sustained vasodilation of the middle meningeal artery in the rat: Possible involvement of mast cells (2014)

The delayed MMA dilatory responses to PACAP-38 infusion were attenuated in MCD and AH-pretreated rats, indicating a role of the MC mediator-histamine in PACAP-38-induced delayed dilation of MA.
Diversity of Epitope and Cytokine Profiles for Primary and Secondary Influenza A Virus-Specific CD8+ T Cell Responses (2001)

Screening with the flow cytometric IFN-gamma assay has led to the identification of a new immunogenic peptide (SSYRRPVGI) [corrected] from the influenza PB1 polymerase (PB1(703--711)) and a mimotope (ISPLMVAYM) from the PB2 polymerase (PB2(198--206)). CD8(+) T cells specific for K(b)PB1(703) make both IFN-gamma and TNF-alpha following stimulation with both peptides. The CD8(+) K(b)PB1(703)(+) population kills PB2(198)-pulsed targets, but cell lines stimulated with PB2(198) neither bind the K(b)PB1(703) tetramer nor become CTL. This CD8(+)K(b)PB1(703)(+) population is prominent in the primary response to an H3N2 virus, although it is much less obvious following secondary challenge of H1N1-primed mice. Even so, we can now account for >40% of the CD8(+) T cells in a primary influenza pneumonia and >85% of those present after H3N2 --> H1N1 challenge. Profiles of IFN-gamma and TNF-alpha staining following in vitro stimulation have been traced for the four most prominent influenza peptides through primary and secondary responses into long-term memory. The D(b)NP(366) epitope that is immunodominant after the H3N2 --> H1N1 challenge shows the lowest frequencies of CD8(+) IFN-gamma(+)TNF-alpha(+) cells for >6 wk, and the intensity of IFN-gamma staining is also low for the first 3 wk. By 11 wk, however, the IFN-gamma/TNF-alpha profiles look to be similar for all four epitopes. At least by the criterion of cytokine production, there is considerable epitope-related functional diversity in the influenza virus-specific CD8(+) T cell response. The results for the K(b)PB1(703) epitope and the PB2(198) mimotope also provide a cautionary tale for those using the cytokine staining approach to identity antigenic peptides.
Development and Validation of the HScore, a Score for the Diagnosis of Reactive Hemophagocytic Syndrome (2014)

The HScore can be used to estimate an individual's risk of having reactive hemophagocytic syndrome. This scoring system is freely available online (http://saintantoine.aphp.fr/score/).
Myocardial protection during transient coronary artery occlusion in man: beneficial effects of regional beta-adrenergic blockade. (1986)

The goal of this study was to verify whether myocardial protection could be achieved via the intracoronary administration of propranolol in patients undergoing percutaneous transluminal coronary angioplasty (PTCA). Accordingly, 21 patients undergoing PTCA were randomly assigned to receive either intracoronary placebo (group A, n = 10) or intracoronary propranolol (group B, n = 11). Three balloon inflations (i.e., coronary artery occlusions) were performed in each patient. Inflations I and II (maximum duration 60 sec) served as control occlusions. Inflation III (maximum duration 120 sec) was performed either after intracoronary administration of saline (2 ml) or propranolol (1.1 +/- 0.2 mg). The following electrocardiographic index of myocardial ischemic injury were measured: (1) time to development of ST segment elevation equal to 0.1 mV and (2) magnitude of ST segment elevation after 60 sec of coronary artery occlusion. Both indexes did not differ significantly between the groups during inflations I and II. In group A the time to development of ST segment elevation of 0.1 mV remained unchanged between the second and third occlusions (25 +/- 5 and 26 +/- 4 sec during inflations II and III, respectively). In group B subselective injection of propranolol into the affected coronary artery significantly prolonged the time to ST segment elevation of 0.1 mV from 19 +/- 4 sec (inflation II) to 53 +/- 9 sec (inflation III; p less than .001). Administration of placebo did not change the magnitude of ST segment elevation 60 sec after coronary artery occlusion between the second and third occlusion in group A (0.16 +/- 0.02 and 0.18 +/- 0.03 mV, respectively).(ABSTRACT TRUNCATED AT 250 WORDS)
A quick method for finding shortest pairs of disjoint paths (1984)

Abstract Let G be a directed graph containing n vertices, one of which is a distinguished source s , and m edges, each with a non‐negative cost. We consider the problem of finding, for each possible sink vertex v , a pair of edge‐disjoint paths from s to v of minimum total edge cost. Suurballe has given an O ( n 2 log n )‐time algorithm for this problem. We give an implementation of Suurballe's algorithm that runs in O ( m log( 1+ m/n ) n ) time and O ( m ) space. Our algorithm builds an implicit representation of the n pairs of paths; given this representation, the time necessary to explicitly construct the pair of paths for any given sink is O (1) per edge on the paths.
A Novel Approach for Micro-electro-mechanical System (MEMS) Vacuum Packaging (2008)

MEMS vacuum packaging is now the impediment of the MEMS appliance in some specified fields. The major problem of current packaging approach is that the packaging process cannot meet the requirement of the ultra low leak. But the process cannot be improved with the existing technology. We propose a novel approach for MEMS vacuum packaging which can remarkably lower the leak rate. This paper analyzed the vacuum maintaining time of the vacuum packaging and compared the current design and new packaging method.
Asymptotically optimal mappings for BICM with M -PAM and M 2 -QAM (2009)

The asymptotic optimality of particular binary labelling rules is proved for M-PAM and M2-QAM constellations in the wideband regime in terms of the so-called parallel-decoding capacity, also known as bit-interleaved coded modulation capacity. Shannon&apos;s ultimate limit of −1.59 dB can be achieved with bit-interleaved coded modulation.
Blind identification and equalization of FIR MIMO channels by BIDS (2002)

This paper presents an algorithm of blind identification and equalization of finite-impulse-response and multiple-input and multiple-output (FIR MIMO) channels driven by colored signals. This algorithm is an improved realization of a concept referred to as blind identification via decorrelating subchannels (BIDS). This BIDS algorithm first constructs a set of decorrelators which decorrelate the output signals of subchannels, and then estimates the channel matrix using the transfer functions of the decorrelators, and finally recovers the input signals using the estimated channel matrix. This BIDS algorithm in general assumes that the channel matrix is irreducible and the input signals are mutually uncorrelated and of sufficiently diverse power spectra. However, for channel matrix identification, this BIDS algorithm only requires the channel matrix to be nonsingular (ie, full rank almost everywhere as opposed to everywhere) and column-wise coprime. Such a channel matrix may have zeros and be of non-minimum phase.
A wideband internal antenna with dual monopole radiation elements (2005)

This letter suggests a novel miniature wideband internal antenna with dual monopole radiation elements for operating at multiband handset applications. It consists of two radiation monopole elements with parallel connection in the limited handset interior space. The proposed antenna can be easily placed in practical handsets because of the small size of 20/spl times/17/spl times/3.5 mm/sup 3/. The measured bandwidth of the proposed antenna shows about 1 GHz from 1.71 (DCS band) to 2.71 GHz (Bluetooth band) with VSWR below 2. It also resonates at global position system (GPS) band of 1.57542 GHz. The electrical and structural characteristics of the proposed antenna make it attractive for use in mobile handset applications.
Block based statistical timing analysis with extended canonical timing model (2005)

Block based statistical timing analysis (STA) tools often yield less accurate results when timing variables become correlated due to global source of variations and path reconvergence. To the best of our knowledge, no good solution is available handling both types of correlations simultaneously.In this paper, we present a novel statistical timing algorithm, AMECT (Asymptotic MAX/MIN approximation & Extended Canonical Timing model), that produces accurate timing estimation by handling both types of correlations simultaneously. An extended canonical timing model is developed to evaluate and decompose correlations between arbitrary timing variables. And an intelligent pruning method is designed enabling trade-off runtime with accuracy.Tested with ISCAS benchmark suites, AMECT shows both high accuracy and high performance compared with Monte Carlo simulation results: with distribution estimation error < 1.5% while with around 350X speed up on a circuit with 5355 gates.
Simultaneous Optimization of Capsule and Tablet Formulation Using Response Surface Methodology (1993)

The study described herein was undertaken to simultaneously optimize the composition of tablet and capsule formulation of an insoluble experimental drug, and to learn more about the effect of the interaction between the ingredients on the basic properties of the final dosage form. Four independent variables were varied in a set of statistically designed experiments, and a number of properties evaluated. A substantial saving in development time and quantity of drug was thereby achieved.
Modeling CTLA4 -linked autoimmunity with RNA interference in mice (2006)

The CTLA4 gene is important for T lymphocyte-mediated immunoregulation and has been associated with several autoimmune diseases, in particular, type 1 diabetes. To model the impact of natural genetic variants of CTLA4, we constructed RNA interference (RNAi) "knockdown" mice through lentiviral transgenesis. Variegation of expression was observed in founders but proved surmountable because it reflected parental imprinting, with derepression by transmission from male lentigenics. Unlike the indiscriminate multiorgan autoimmune phenotype of the corresponding knockout mice, Ctla4 knockdown animals had a disease primarily focused on the pancreas, with rapid progression to diabetes. As with the human disease, the knockdown phenotype was tempered by genetic-modifier loci. RNAi should be more pertinent than gene ablation in modeling disease pathogenesis linked to a gene-dosage variation.
Comparison of Right and Left Ventricular Responses to Left Ventricular Assist Device Support in Patients With Severe Heart Failure (2001)

Reduction of hemodynamic load is a primary factor underlying several important features of reverse remodeling. These findings do not preclude a possible primary role of neurohormonal factors underlying other facets of reverse remodeling during LVAD support.
Definition of the upstream efficiency element of the simian virus 40 late polyadenylation signal by using in vitro analyses. (1992)

The polyadenylation signal for the late mRNAs of simian virus 40 is known to have sequence elements located both upstream and downstream of the AAUAAA which affect efficiency of utilization of the signal. The upstream efficiency element has been previously characterized by using deletion mutations and transfection analyses. Those studies suggested that the upstream element lies between 13 and 48 nucleotides upstream of the AAUAAA. We have utilized in vitro cleavage and polyadenylation reactions to further define the upstream element. 32P-labeled substrate RNAs were prepared by in vitro transcription from wild-type templates as well as from mutant templates having deletions and linker substitutions in the upstream region. Analysis of these substrates defined the upstream region as sequences between 13 and 51 nucleotides upstream of the AAUAAA, in good agreement with the in vivo results. Within this region, three core elements with the consensus sequence AUUUGURA were identified and were specifically mutated by linker substitution. These core elements were found to contain the active components of the upstream efficiency element. Using substrates with both single and double linker substitution mutations of core elements, we observed that the core elements function in a distance-dependent manner. In mutants containing only one core element, the effect on efficiency increases as the distance between the element and the AAUAAA decreases. In addition, when core elements are present in multiple copies, the effect is additive. The core element consensus sequence, which bears homology to the Sm protein complex-binding site in human U1 RNA, is also found within the upstream elements of the ground squirrel hepatitis B and cauliflower mosaic virus polyadenylation signals (R. Russnak, Nucleic Acids Res. 19:6449-6456, 1991; H. Sanfacon, P. Brodmann, and T. Hohn, Genes Dev. 5:141-149, 1991), suggesting functional conservation of this element between mammals and plants.
Extensive gene conversion at thePMS2DNA mismatch repair locus (2007)

Mutations of the PMS2 DNA repair gene predispose to a characteristic range of malignancies, with either childhood onset (when both alleles are mutated) or a partially penetrant adult onset (if heterozygous). These mutations have been difficult to detect, due to interference from a family of pseudogenes located on chromosome 7. One of these, the PMS2CL pseudogene, lies within a 100-kb inverted duplication (inv dup), 700 kb centromeric to PMS2 itself on 7p22. Here, we show that the reference genomic sequences cannot be relied upon to distinguish PMS2 from PMS2CL, because of sequence transfer between the two loci. The 7p22 inv dup occurred prior to the divergence of modern ape species (15 million years ago [Mya]), but has undergone extensive sequence homogenization. This process appears to be ongoing, since there is considerable allelic diversity within the duplicated region, much of it derived from sequence exchange between PMS2 and PMS2CL. This sequence diversity can result in both false-positive and false-negative mutation analysis at this locus. Great caution is still needed in the design and interpretation of PMS2 mutation screens.
Pneumatic Channel Wing Powered-Lift Advanced SuperSTOL Aircraft (2002)

The powered-lift Channel Wing concept has been combined with pneumatic Circulation Control aerodynamic and propulsive technology to generate a Pneumatic Channel Wing configuration intended to have Super-STOL or VSTOL capability while eliminating many of the operational problem areas of the original Channel Wing vehicle. A preliminary design study of this pneumatic vehicle based on previous windtunnel and flight-test data for the two technologies integrated into a simple Pneumatic Channel Wing (PCW) configuration showed very strong Super-STOL potential. Wind-tunnel development and evaluations of a PCW powered model conducted at Georgia Tech Research Institute (GTRI) have shown substantial lift capabilities for the blown configuration (CL values of 8.5 to 9.0). Variation in blowing of the channel was shown to be more efficient than variation in propeller thrust. Also revealed was the ability to operate unstalled at very high angles of attack of 40°-45°, or to achieve very high lift at much lower angle of attack to increase visibility and controllability. In order to provide greater flexibility in SuperSTOL takeoffs and landings, the blown model also displayed the ability to interchange thrust and drag by varying blowing without any moving parts. This paper presents these experimental results, discusses variations in the configuration geometry under development, and extends this integrated technology to advanced design studies of PCW-type vehicles.
Biodesign of a renal-protective peptide based on alternative splicing of B-type natriuretic peptide (2009)

Alternative RNA splicing may provide unique opportunities to identify drug targets and therapeutics. We identified an alternative spliced transcript for B-type natriuretic peptide (BNP) resulting from intronic retention. This transcript is present in failing human hearts and is reduced following mechanical unloading. The intron-retained transcript would generate a unique 34 amino acid (aa) carboxyl terminus while maintaining the remaining structure of native BNP. We generated antisera to this carboxyl terminus and identified immunoreactivity in failing human heart tissue. The alternatively spliced peptide (ASBNP) was synthesized and unlike BNP, failed to stimulate cGMP in vascular cells or vasorelax preconstricted arterial rings. This suggests that ASBNP may lack the dose-limiting effects of recombinant BNP. Given structural considerations, a carboxyl-terminal truncated form of ASBNP was generated (ASBNP.1) and was determined to retain the ability of BNP to stimulate cGMP in canine glomerular isolates and cultured human mesangial cells but lacked similar effects in vascular cells. In a canine-pacing model of heart failure, systemic infusion of ASBNP.1 did not alter mean arterial pressure but increased the glomerular filtration rate (GFR), suppressed plasma renin and angiotensin, while inducing natriuresis and diuresis. Consistent with its distinct in vivo effects, the activity of ASBNP.1 may not be explained through binding and activation of NPR-A or NPR-B. Thus, the biodesigner peptide ASBNP.1 enhances GFR associated with heart failure while lacking the vasoactive properties of BNP. These findings demonstrate that peptides with unique properties may be designed based on products of alternatively splicing.