gebhart/patrepeval huggingface dataset:
Potential basis of glyphosate resistance in California rigid ryegrass (Lolium rigidum) (2003)

Glyphosate-resistant rigid ryegrass has been identified in California, but research has yet to elucidate the resistance mechanism. The objectives of this study were to examine the differences between sensitive and resistant rigid ryegrass in absorption and distribution of glyphosate, in vivo and in vitro absorption by chloroplasts, and shikimic acid accumulation after glyphosate treatment. Foliar absorption and distribution of 14C-glyphosate did not differ 1 to 3 d after treatment (DAT) between the susceptible (S) and resistant (R) biotypes. Absorption of 14C-glyphosate by isolated chloroplasts also did not differ between the S and R biotypes. After foliar application of 14C-glyphosate, chloroplasts were isolated from treated leaves from both biotypes. Accumulation of 14C-glyphosate in the chloroplasts did not differ between the two biotypes. Shikimic acid level increased significantly in the S biotype after treatment with glyphosate at 2.24 kg ai ha−1 to levels 10-fold greater than in the R biotype 11 DAT. Shikimic acid in the germination media at 2 to 5 mM did not affect seed germination of S and R biotypes but drastically decreased the length of coleoptiles of both at 5 DAT. Thus, biotype differences in sensitivity or metabolism of shikimic acid do not explain differences in sensitivity to glyphosate.
Multistack optimization for data-path chip layout (1991)

A special multistack structure and optimization technique to partition, place, and wire the data-path macros in the form of the multistack structure are described, taking into account the connectivity of all the chip logic (data path, control logic, chip drivers, on-chip memory). The overall objective is: to fit the circuits within the chip boundary; to ensure data-path internal wirability; as well as external stack wirability to the other circuits; and to minimize wire lengths for wirability and timing. A tool for automatic multistack optimization has been implemented and applied successfully to layout high-density data path chips.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
DNA strand transfer reactions catalyzed by vaccinia topoisomerase I. (1992)

Vaccinia virus DNA topoisomerase I forms a 3'-phosphoryl intermediate with duplex DNAs containing the conserved binding/cleavage motif 5'CCCTT decreases. Covalently bound enzyme is capable of transferring the incised DNA strand to a heterologous DNA acceptor containing a 5'OH terminus. Both intramolecular and intermolecular religation reactions are catalyzed. Intramolecular strand transfer occurs to the noncleaved strand of the DNA duplex and results in formation of a hairpin loop. Intermolecular religation to an exogenous DNA strand is favored over hairpin formation and requires the potential for base pairing between the acceptor and the noncleaved strand of the donor complex. As few as 4 potential base pairs are sufficient to support intermolecular transfer. These results in vitro are consistent with the proposal that vaccinia topoisomerase can catalyze sequence-specific strand transfer during genetic recombination in vivo (Shuman, S. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 10104-10108.).
Craving decrease with topiramate in outpatient treatment for cocaine dependence: an open label trial (2008)

More randomized placebo-controlled trials with topiramate for cocaine dependants should be performed to evaluate preliminary evidence.
Gravity-aware handheld Augmented Reality (2011)

This paper investigates how different stages in handheld Augmented Reality (AR) applications can benefit from knowing the direction of the gravity measured with inertial sensors. It presents approaches to improve the description and matching of feature points, detection and tracking of planar templates, and the visual quality of the rendering of virtual 3D objects by incorporating the gravity vector. In handheld AR, both the camera and the display are located in the user's hand and therefore can be freely moved. The pose of the camera is generally determined with respect to piecewise planar objects that have a known static orientation with respect to gravity. In the presence of (close to) vertical surfaces, we show how gravity-aligned feature descriptors (GAFD) improve the initialization of tracking algorithms relying on feature point descriptor-based approaches in terms of quality and performance. For (close to) horizontal surfaces, we propose to use the gravity vector to rectify the camera image and detect and describe features in the rectified image. The resulting gravity-rectified feature descriptors (GREFD) provide an improved precision-recall characteristic and enable faster initialization, in particular under steep viewing angles. Gravity-rectified camera images also allow for real-time 6 DoF pose estimation using an edge-based object detection algorithm handling only 4 DoF similarity transforms. Finally, the rendering of virtual 3D objects can be made more realistic and plausible by taking into account the orientation of the gravitational force in addition to the relative pose between the handheld device and a real object.
Spinal Cord Repair With Acidic Fibroblast Growth Factor as a Treatment for a Patient With Chronic Paraplegia (2004)

This case demonstrated significant motor recovery attained in a patient with chronic paraplegia following a repair surgery with nerve graft and growth factor.
Reward Augmented Maximum Likelihood for Neural Structured Prediction (2016)

A key problem in structured output prediction is direct optimization of the task reward function that matters for test evaluation. This paper presents a simple and computationally efficient approach to incorporate task reward into a maximum likelihood framework. By establishing a link between the log-likelihood and expected reward objectives, we show that an optimal regularized expected reward is achieved when the conditional distribution of the outputs given the inputs is proportional to their exponentiated scaled rewards. Accordingly, we present a framework to smooth the predictive probability of the outputs using their corresponding rewards. We optimize the conditional log-probability of augmented outputs that are sampled proportionally to their exponentiated scaled rewards. Experiments on neural sequence to sequence models for speech recognition and machine translation show notable improvements over a maximum likelihood baseline by using reward augmented maximum likelihood (RAML), where the rewards are defined as the negative edit distance between the outputs and the ground truth labels.
Biological activity of human immunodeficiency virus type 1 Vif requires membrane targeting by C-terminal basic domains (1995)

Human immunodeficiency virus type 1 (HIV-1) encodes a Vif protein which is important for virus replication and infectivity. Vif is a cytoplasmic protein which exists in both membrane-associated and soluble forms. The membrane-associated form is an extrinsic membrane protein which is tightly associated with the cytoplasmic side of membranes. We have analyzed the mechanism of membrane targeting of Vif and its role in HIV-1 replication. Mutagenesis studies demonstrate that C-terminal basic domains are required for membrane association. Vif mutations which disrupt membrane association also inhibit HIV-1 replication, indicating that membrane localization of Vif is likely to be required for its biological activity in vivo. Membrane binding of Vif is almost completely abolished by trypsin treatment of membranes. These results demonstrate that membrane localization of Vif requires C-terminal basic domains and interaction with a membrane-associated protein(s). This interaction may serve to direct Vif to a specific cellular site, since immunofluorescence staining and plasma membrane fractionation studies show that Vif is localized predominantly to an internal cytoplasmic compartment rather than to the plasma membrane. The mechanism of membrane targeting of Vif is different in some respects from that of other extrinsic membrane proteins, such as Ras, Src, and MARCKS, which utilize a basic domain together with a lipid modification for membrane targeting. Membrane targeting of Vif is likely to play an important role in HIV-1 replication and thus may be a therapeutic target.
Ejection Fraction Improvement by ??-Blocker Treatment in Patients with Heart Failure (1998)

Because ejection fraction (EF) is one of the most important predictors of survival in patients with left ventricular (LV) dysfunction and because Packer showed a large reduction in mortality figures with carvedilol, in contrast to former studies with bisoprolol and metoprolol, we investigated if this difference in survival may be related to a difference in improvement of LV function by different β-blockers. We searched the MEDLINE database and all reference lists of articles obtained through the search for the relation between β-blocker treatment and improvement in EF. Forty-one studies met the criteria and we added two of our own studies. Four hundred and fifty-eight patients were treated with metoprolol with a mean follow-up of 9.5 months and a mean increase in EF of 7.4 EF units. One thousand thirty patients were treated with carvedilol with a mean follow up of 7 months and a mean increase in EF of 5.7 EF units. One hundred ninety-nine patients were treated with bucindolol with a mean follow-up of 4 months and a mean increase in EF of 4.6 EF units. Several small studies with nebivolol, atenolol, and propranolol were also studied and, when combined, the mean increase in EF was 8.6 EF units. When patients with idiopathic and ischemic cardiomyopathies were compared, the average increase in EF units was 8.5 vs. 6.0, respectively. The use of β-blocker treatment in heart failure patients, irrespective of the etiology, improved LV function in almost all studies and it appears that the differences amongβ-blockers and among etiologies is small and probably insignificant. However, there is a difference in survival rate when the various β-blockers are compared, suggesting that mechanisms other than improvement of LV function by β-blockers are responsible for the difference in survival.
Predisposition to atypical hemolytic uremic syndrome involves the concurrence of different susceptibility alleles in the regulators of complement activation gene cluster in 1q32 (2005)

The efficiency of the complement system as an innate immune defense mechanism depends on a fine control that restricts its action to pathogens and prevents non-specific damage to host tissues. Genetic and functional analyses have shown that this critical control of complement activation may be impaired in atypical hemolytic uremic syndrome (aHUS) patients. Mutations in HF1, MCP or FI have been found in aHUS patients, but incomplete penetrance of the disease in individuals carrying these mutations is relatively frequent and no genetic defect has yet been found in a majority of aHUS patients. We report here the identification of a specific SNP haplotype block, spanning the MCP gene in the regulators of complement activation gene cluster, which is over-represented in aHUS patients and strongly associates with the severity of the disease. Linkage disequilibrium analyses suggest that this SNP haplotype also includes the CR1, DAF and C4BP genes. Initial studies identified two SNPs in the haplotype that influence the transcription activity of the MCP promoter in transient transfection experiments. Notably, the SNP haplotype block was found to be particularly frequent among patients who carry mutations in HF1, MCP or FI. These findings and the identification of aHUS patients carrying mutations in two complement regulatory genes provide an important insight into the etiology of aHUS. Together, they suggest that complement regulatory molecules act as a protein network and that multiple hits, involving plasma- and membrane-associated complement regulatory proteins, are necessary to impair protection to host tissues and to confer significant predisposition to aHUS.
Locked nucleic acid: modality, diversity, and drug discovery (2017)

Over the past 20 years, the field of RNA-targeted therapeutics has advanced based on discoveries of modified oligonucleotide chemistries, and an ever-increasing understanding of how to apply cellular assays to identify oligonucleotides with improved pharmacological properties in vivo. Locked nucleic acid (LNA), which exhibits high binding affinity and potency, is widely used for this purpose. Our understanding of RNA biology has also expanded tremendously, resulting in new approaches to engage RNA as a therapeutic target. Recent observations indicate that each oligonucleotide is a unique entity, and small structural differences between oligonucleotides can often lead to substantial differences in their pharmacological properties. Here, we outline new principles for drug discovery exploiting oligonucleotide diversity to identify rare molecules with unique pharmacological properties.
Targeted Replacement of the Mouse Apolipoprotein E Gene with the Common Human APOE3 Allele Enhances Diet-induced Hypercholesterolemia and Atherosclerosis (1997)

Apolipoprotein (apo) E, a constituent of several lipoproteins, is a ligand for the low density lipoprotein receptor, and this interaction is important for maintaining cholesterol and triglyceride homeostasis. We have used a gene replacement strategy to generate mice that express the human apoE3 isoform in place of the mouse protein. The levels of apoE mRNA in various tissues are virtually the same in the human apoE3 homozygous (3/3) mice and their littermates having the wild type mouse allele (+/+). Total cholesterol and triglyceride levels in fasted plasma from the 3/3 mice were not different from those in the +/+ mice, when maintained on a normal (low fat) chow diet. We found, however, notable differences in the distribution of plasma lipoproteins and apolipoprotein E between the two groups: beta-migrating lipoproteins and plasma apoB100 levels are decreased in the 3/3 mice, and the apoE distribution is shifted from high density lipoproteins to larger lipoprotein particles. In addition, the fractional catabolic rate of exogenously administered remnant particles without apoE was 6-fold slower in the 3/3 mice compared with the +/+ mice. When the 3/3 and +/+ animals were fed a high fat/high cholesterol diet, the 3/3 animals responded with a dramatic increase (5-fold) in total cholesterol compared with the +/+ mice (1.5-fold), and after 12 weeks on this same diet the 3/3 animals developed significantly (at least 13-fold) larger atherosclerotic plaques in the aortic sinus area than the +/+ animals. Thus the structural differences between human APOE3 and mouse ApoE proteins are sufficient to cause an increased susceptibility to dietary-induced hypercholesterolemia and atherosclerosis in the 3/3 mice.
Long-Term Impact of Neonatal Breast-Feeding on Body Weight and Glucose Tolerance in Children of Diabetic Mothers (2002)

Early neonatal ingestion of breast milk from diabetic mothers may increase risk of becoming overweight and, consequently, developing IGT during childhood. Additional studies are needed to assess long-term consequences that might result from the type of neonatal nutrition in ODM.
Cavity perturbation method for characterization of liquid crystals up to 35 GHz (2004)

Liquid Crystals (LCs) are very promising agile materials for tunable microwave components [Z]. Hence, precise microwave measurements are required. In this paper the measurement results of two LCs are presented using a cavity perturbation method with two cavities at 9GHz between -25°C and 45°C and at 3SGHz between -10/sl degC and 80sl degC. The cavities are rectangular waveguide resonators with two insertion holes for LC-filled FTFE-tubes. The complex permittivity as well as the complex permeability of these samples are extracted. The tunability of the LCs are measured by using an external magnetostatic field in order to orient the LC-molecules. Besides the quasi-standard LC K15, a novel mixture is investigated, having a higher tunability and lower losses compared to K1S at microwaves.
The Association Between Use of Electronic Media in Bed Before Going to Sleep and Insomnia Symptoms, Daytime Sleepiness, Morningness, and Chronotype (2013)

This study investigated whether the use of a television, computer, gaming console, tablet, mobile phone, or audio player in bed before going to sleep was associated with insomnia, daytime sleepiness, morningness, or chronotype. 532 students aged 18-39 were recruited from lectures or via e-mail. Respondents reported the frequency and average duration of their in-bed media use, as well as insomnia symptoms, daytime sleepiness, morningness-eveningness preference and bedtime/rise time on days off. Mean time of media use per night was 46.6 minutes. The results showed that computer usage for playing/surfing/reading was positively associated with insomnia, and negatively associated with morningness. Mobile phone usage for playing/surfing/texting was positively associated with insomnia and chronotype, and negatively associated with morningness. None of the other media devices were related to either of these variables, and no type of media use was related to daytime sleepiness.
The First Dose of a Haemophilus influenzae Type b Conjugate Vaccine Reactivates Memory B Cells: Evidence for Extensive Clonal Selection, Intraclonal Affinity Maturation, and Multiple Isotype Switches to IgA2 (1999)

The Ab response of a healthy adult to the first dose of a Haemophilus influenzae type b capsular polysaccharide (HibCP) conjugate vaccine was studied at the level of Ig gene usage by circulating Ab-secreting cells. Forty-one IgA and 17 IgG mRNA sequences were obtained. The major part of the response was confined to IgA Ab-secreting cells, and 72% of the IgA sequences were derived from the progeny of a single rearranged B cell. These sequences could be arranged in a genealogical tree showing multiple somatic mutations and at least two intraclonal isotype switches to IgA2. Fourteen somatic mutations were shared by this clonal progeny, indicating that extreme clonal selection had occurred early in the clonal development. Taking into account the frequency of somatic mutations and the clone size, it was evident that the responding cell population must have originated from a mutated, highly selected, and expanded population of cells existing before vaccination, i.e., memory B cells. The dominating heavy and light chains of the response were combined in a Fab that bound HibCP. It was shown that the shared heavy and light chain mutations increased the affinity for HibCP considerably, indicating that the clonal selection had been driven by affinity. Pre-existing memory cells in unvaccinated adults may explain several features of Ab responses to polysaccharide vaccines and may play a role in acquiring the ability to respond to pure polysaccharides during infancy.
Molecular Analysis of a Saccharomyces cerevisiae Mutant with Improved Ability To Utilize Xylose Shows Enhanced Expression of Proteins Involved in Transport, Initial Xylose Metabolism, and the Pentose Phosphate Pathway (2003)

Differences between the recombinant xylose-utilizing Saccharomyces cerevisiae strain TMB 3399 and the mutant strain TMB 3400, derived from TMB 3399 and displaying improved ability to utilize xylose, were investigated by using genome-wide expression analysis, physiological characterization, and biochemical assays. Samples for analysis were withdrawn from chemostat cultures. The characteristics of S. cerevisiae TMB 3399 and TMB 3400 grown on glucose and on a mixture of glucose and xylose, as well as of S. cerevisiae TMB 3400 grown on only xylose, were investigated. The strains were cultivated under chemostat conditions at a dilution rate of 0.1 h(-1), with feeds consisting of a defined mineral medium supplemented with 10 g of glucose liter(-1), 10 g of glucose plus 10 g of xylose liter(-1) or, for S. cerevisiae TMB 3400, 20 g of xylose liter(-1). S. cerevisiae TMB 3400 consumed 31% more xylose of a feed containing both glucose and xylose than S. cerevisiae TMB 3399. The biomass yields for S. cerevisiae TMB 3400 were 0.46 g of biomass g of consumed carbohydrate(-1) on glucose and 0.43 g of biomass g of consumed carbohydrate(-1) on xylose. A K(s) value of 33 mM for xylose was obtained for S. cerevisiae TMB 3400. In general, the percentage error was <20% between duplicate microarray experiments originating from independent fermentation experiments. Microarray analysis showed higher expression in S. cerevisiae TMB 3400 than in S. cerevisiae TMB 3399 for (i) HXT5, encoding a hexose transporter; (ii) XKS1, encoding xylulokinase, an enzyme involved in one of the initial steps of xylose utilization; and (iii) SOL3, GND1, TAL1, and TKL1, encoding enzymes in the pentose phosphate pathway. In addition, the transcriptional regulators encoded by YCR020C, YBR083W, and YPR199C were expressed differently in the two strains. Xylose utilization was, however, not affected in strains in which YCR020C was overexpressed or deleted. The higher expression of XKS1 in S. cerevisiae TMB 3400 than in TMB 3399 correlated with higher specific xylulokinase activity in the cell extracts. The specific activity of xylose reductase and xylitol dehydrogenase was also higher for S. cerevisiae TMB 3400 than for TMB 3399, both on glucose and on the mixture of glucose and xylose.
Synthesis of Unsaturated Polyazamacrolides from the Ladybird Beetle Subcoccinella vigintiquatuorpunctata (2001)

The pupal defensive secretion of the ladybird beetle Subcoccinella vigintiquatuorpunctata consists of a mixture of macrocyclic polyamines (polyazamacrolides, PAMLs) dominated by three dimeric, 30-membered bislactones (1, 2, and 3), which represent the three possible head-to-tail combinations of the two building blocks (S)-(Z)-11-(2-hydroxyethylamino)-5-tetradecenoic acid (4) and (S)-(5Z,8Z)-11-(2-hydroxyethylamino)-5,8-tetradecadienoic acid (5). We now report the synthesis of these three alkaloids via a route involving the nucleophilic opening of a chiral aziridine as a common step.
Genomic Amplification with Transcript Sequencing (1988)

A sequencing method called genomic amplification with transcript sequencing (GAWTS) is described that is based on amplification with the polymerase chain reaction (PCR). GAWTS bypasses cloning and increases the rate of sequence acquisition by at least fivefold. The method involves the attachment of a phage promoter onto at least one of the PCR primers. The segments amplified by PCR are transcribed to further increase the signal and to provide an abundance of single-stranded template for reverse transcriptase-mediated dideoxy sequencing. An end-labeled reverse transcriptase primer complementary to the desired sequence generates the additional specificity required to generate unambiguous sequence data. GAWTS can be performed on as little as a nanogram of genomic DNA. The rate of GAWTS can be increased by coamplification and cotranscription of multiple regions as illustrated by two regions of the factor IX gene. Since GAWTS lends itself well to automation, further increases in the rate of sequence acquisition can be expected.