gebhart/patrepeval huggingface dataset:
The phenotype of soluble starch synthase IV defective mutants of Arabidopsis thaliana suggests a novel function of elongation enzymes in the control of starch granule formation (2007)

All plants and green algae synthesize starch through the action of the same five classes of elongation enzymes: the starch synthases. Arabidopsis mutants defective for the synthesis of the soluble starch synthase IV (SSIV) type of elongation enzyme have now been characterized. The mutant plants displayed a severe growth defect but nonetheless accumulated near to normal levels of polysaccharide storage. Detailed structural analysis has failed to yield any change in starch granule structure. However, the number of granules per plastid has dramatically decreased leading to a large increase in their size. These results, which distinguish the SSIV mutants from all other mutants reported to date, suggest a specific function of this enzyme class in the control of granule numbers. We speculate therefore that SSIV could be selectively involved in the priming of starch granule formation.
DIFFERENTIAL IMPRINTING AND EXPRESSION OF MATERNAL AND PATERNAL GENOMES (1988)

Article de synthese sur le role et l'expression differentielle des genes d'origine maternelle ou paternelle chez les mammiferes; implications lors du developpement normal et pathologique
Falling asleep at the wheel: Motor vehicle mishaps in persons taking pramipexole and ropinirole (1999)

The authors report a new side effect of the dopamine agonists pramipexole and ropinirole: sudden irresistible attacks of sleep. Eight PD patients taking pramipexole and one taking ropinirole fell asleep while driving, causing accidents. Five experienced no warning before falling asleep. The attacks ceased when the drugs were stopped. Neurologists who prescribe these drugs and patients who take them should be aware of this possible side effect.
The Puzzle of IVF (2006)

This essay seeks to address a puzzling element of the current political and legal struggles over abortion in the United States: if, as pro-life activists insist, embryos are morally equivalent to born, living persons, then why do these activists not oppose in vitro fertilization (IVF) as aggressively as they oppose abortion? IVF accounts for a significant number of destroyed embryos. Constitutionally, IVF appears to be a much more vulnerable target than abortion. And yet, legislative and political attempts to attack and restrict IVF are few, while attempts to erode women's capability to terminate pregnancies are a constant feature of our political and legal landscape.
In vivo therapy of the BCL1 tumor: effect of immunotoxin valency and deglycosylation of the ricin A chain. (1988)

The in vivo therapeutic effects of Fab' and IgG anti-delta (anti-IgD)-ricin A chain immunotoxins were compared in mice bearing the surface IgD-positive BCL1 leukemia. The immunotoxins were prepared with either native or deglycosylated ricin A chain. Immunotoxin therapy was assessed both by the number of cells bearing the BCL1 immunoglobulin idiotype which remained in the spleen 24-48 h after injection with immunotoxin and by adoptive transfer of these spleen cells into normal mice. Immunotoxins prepared with either Fab'-anti-delta or IgG-anti-delta and native A chain induced a dose-dependent reduction in the number of idiotype-positive BCL1 cells present in the spleens of the tumor-bearing mice. The maximal therapeutic response was achieved with 250 micrograms of immunotoxin (containing 80-100 micrograms A chain) per mouse for both immunotoxins, resulting in tumor reduction of approximately 90%. This represents an elimination of 3-4 X 10(8) tumor cells. Reduction in the number of tumor cells was not observed with control reagents including antibody alone, antibody mixed with A chain, or an immunotoxin of irrelevant specificity. A Fab' immunotoxin prepared with deglycosylated ricin A chain was approximately 5-fold more effective as an antitumor reagent than the same immunotoxin prepared with native A chain; thus, optimal therapy was achieved after injection of 50 micrograms of immunotoxin (containing 15-20 micrograms A chain). Since the immunotoxins prepared with deglycosylated A chain were only 2-3-fold more toxic to the mice than those prepared with native A chain, the former resulted in a 2-3-fold increase in the therapeutic index.
Inhibition of fluorouracil-induced stomatitis by oral cryotherapy. (1991)

Mucositis is a significant dose-limiting toxicity associated with fluorouracil (5FU), particularly when it is combined with leucovorin. We hypothesized that oral cryotherapy would cause local vasoconstriction and would temporarily decrease blood flow to the oral mucous membranes. If cryotherapy were used during the time of peak serum 5FU levels, then the oral mucous membranes would have less exposure to 5FU and thus develop less mucositis. To test this hypothesis, 95 patients scheduled to receive their first cycle of 5FU plus leucovorin were randomized to have oral cryotherapy at the time of chemotherapy administration or to serve as a control group. Subsequent mucositis was significantly reduced in the group assigned to receive cryotherapy as judged by the attending physicians (P = .0002) and by the patients themselves (P = .0001). We now routinely recommend this cryotherapy procedure for our patients receiving daily bolus 5FU plus leucovorin.
Serotonin 2A Receptor Signaling Underlies LSD-induced Alteration of the Neural Response to Dynamic Changes in Music (2017)

Abstract Classic psychedelic drugs (serotonin 2A, or 5HT2A, receptor agonists) have notable effects on music listening. In the current report, blood oxygen level-dependent (BOLD) signal was collected during music listening in 25 healthy adults after administration of placebo, lysergic acid diethylamide (LSD), and LSD pretreated with the 5HT2A antagonist ketanserin, to investigate the role of 5HT2A receptor signaling in the neural response to the time-varying tonal structure of music. Tonality-tracking analysis of BOLD data revealed that 5HT2A receptor signaling alters the neural response to music in brain regions supporting basic and higher-level musical and auditory processing, and areas involved in memory, emotion, and self-referential processing. This suggests a critical role of 5HT2A receptor signaling in supporting the neural tracking of dynamic tonal structure in music, as well as in supporting the associated increases in emotionality, connectedness, and meaningfulness in response to music that are commonly observed after the administration of LSD and other psychedelics. Together, these findings inform the neuropsychopharmacology of music perception and cognition, meaningful music listening experiences, and altered perception of music during psychedelic experiences.
Effect of Orientation on Plasmonic Coupling between Gold Nanorods (2009)

Radiative coupling of induced plasmonic fields in metal nanoparticles has drawn increasing attention in the recent literature due to a combination of improved experimental methods to study such phenomena and numerous potential applications, such as plasmonic nanoparticle rulers and plasmonic circuitry. Many groups, including ours, have used a near-exponential fit to express the size scaling of plasmonic coupling. First, we show experimental agreement between previously simulated nanorod coupling and plasmonic coupling in electron beam lithography (EBL) fabricated nanorods using the near-exponential expression. Next, we study the effect of nanoparticle orientation on plasmonic coupling using EBL and DDA simulations. We develop a mathematical relationship that is consistent with our findings and quantitatively describes plasmonic coupling between nanorods as a function of orientation, separation, induced dipole strength, and the dielectric constant of the medium. For applications utilizing plasmonic coupling to become viable with particle shapes that do not have spherical symmetry, such as nanoprisms and nanorods, comparison of the experimental and theoretical results of how particle orientation affects plasmonic coupling is essential.
Robust time-of-arrival self calibration and indoor localization using Wi-Fi round-trip time measurements (2016)

The problem of estimating receiver-sender node positions from measured receiver-sender distances is a key issue in different applications such as microphone array calibration, radio antenna array calibration, mapping and positioning using UWB and mapping and positioning using round-trip-time measurements between mobile phones and Wi-Fi-units. Thanks to recent research in this area we have an increased understanding of the geometry of this problem. In this paper, we study the problem of missing information and the presence of outliers in the given data. We propose a novel hypothesis and test framework that efficiently finds initial estimates of the unknown parameters and combine such methods with optimization techniques to obtain accurate and robust systems. The proposed systems are evaluated using Wi-Fi round-trip time measurements to give a realistic example of indoor localization. The resulting map of the anchor points is validated against ground truth measurements with promising results.
Dose-titration, multicenter study of oral transmucosal fentanyl citrate for the treatment of breakthrough pain in cancer patients using transdermal fentanyl for persistent pain. (1998)

Most patients find a single OTFC dosage that adequately treats breakthrough pain. The optimal dose is found by titration and is not predicted by around-the-clock dose of opioids.
Effect of liposomal confinement on photochemical properties of photosensitizers with varying hydrophilicity (2008)

Preferential tumor localization and the aggregation state of photosensitizers (PSs) can depend on the hydrophilic/hydrophobic nature of the molecule and affect their phototoxicity. In this study, three PSs of different hydrophilicity are introduced in liposomes to understand the structure-photochemistry relationship of PSs in this cellular model system. Absorbance and fluorescence spectra of amphiphilic aluminum (III) phthalocyanine disulfonate chloride adjacent isomer (Al-2), hydrophilic aluminum (III) phthalocyanine chloride tetrasulfonic acid (Al-4), and lipophilic 2-(1-hexyloxyethyl)-2-devinyl pyropheophorbide (HPPH) are compared in a liposomal confined state with free PS in bulk solution. For fluorescence measurements, a broad range of concentrations of both bulk and liposomal confined PSs are examined to track the transition from monomers to dimers or higher order aggregates. Epifluorescence microscopy, absorbance, and fluorescence measurements all confirm different localization of the PSs in liposomes, depending on their hydrophilicity. In turn, the localization affects the aggregation of molecules inside the liposome cell model. Data obtained with such cellular models could be useful in optimizing the photochemical properties of photosensitizing drugs based on their structure-dependent interactions with cellular media and subcellular organelles.
Cancer Immunotherapy: More Is (Much) Better (2015)

Although antibodies against EGFR and HER2 are used to treat cancer, only some patients respond and resistance often emerges. Jacobsen and colleagues present in this issue experimental evidence favoring replacement of the currently applied monoclonal antibodies with oligoclonal mixtures of six synergistic antibodies, simultaneously engaging EGFR, HER2, and also HER3.
On the relationship between the strength of the Brewer‐Dobson circulation and the age of stratospheric air (2006)

The strength of the Brewer‐Dobson circulation is computed for multi‐decadal simulations of a coupled chemistry‐climate model covering the period 1960 to 2100. The circulation strength, as computed from the tropical mass upwelling, generally increases throughout the simulations. The model also includes an age of air tracer which generally decreases during the simulations. The two different transport concepts of mass upwelling and reciprocal of the age of air are investigated empirically from the model simulations. The results indicate that the variables are linearly related in the model but with a change of gradient some time near 2005. Possible reasons for the change of gradient are discussed.
Expression and Characterization of Bioactive Human Thrombopoietin in the Milk of Transgenic Mice (1999)

Human thrombopoietin (hTPO) is the primary physiological regulator of platelet production and plays a pivotal role in promoting the proliferation and maturation of megakaryocytic progenitor cells and megakaryocytes. In this study, transgenic mice were produced harboring either full-length or the erythropoietin (EPO)-like amino-terminal domain of hTPO cDNA sequences fused to the regulatory elements of the bovine beta-casein gene. The transgene RNA was expressed exclusively in the mammary glands of eight transgenic mice, and a trace amount of the transgene was also found in the lungs of one mouse. The full-length form induced efficient expression of the protein with the highest expression level of 1500 microg/ml; however, the EPO-like domain alone expressed the protein at <0.1 microg/ml. The proteins from the two recombinant cDNAs have apparent molecular weights of about 74 and 17 kDa, due to glycosylation in the case of the full-length cDNA. Cell proliferation assay in vitro indicated that both of the recombinant forms stimulated proliferation of the TPO-dependent BaF3-Mpl cells. A positive correlation appeared between the amount of TPO in the milk of lactating animals and their blood platelet levels. About a twofold increase in platelet numbers in the blood was observed after direct subcutaneous injection of the recombinant hTPO at the level of 30 microg/kg of body weight. On the basis of these results, we anticipate that the recombinant hTPO produced efficiently in milk of transgenic mice will have the same activities as the native hTPO in a few in vivo as well as in vitro biochemical aspects.
Synthesis and .beta.-adrenergic antagonism of 2-(aryloxy)-1-(2-piperidyl)ethanols (1988)

A series of erythro- and threo-2-(aryloxy)-1-(2-piperidyl)ethanol derivatives (3) was synthesized from 2-(2-oxiranyl)pyridine for evaluation as beta-antagonists. Most compounds displayed high competitive beta-blocking potency, but they lacked significant beta 1/beta 2 selectivity. The 1-naphthoxy derivative erythro-3b was 17 (beta 1) and 33 (beta 2) times more potent than its open-chain analogue, propranolol. Within the whole series, erythro-3 diastereomers were more potent beta-blockers than the threo-3 isomers, and the potency of the latter seems to be rather insensitive to structural modification. The effect of N-methylation and of interposition of an alkyl chain between the aromatic ring and the side chain, while being detrimental to beta-blocking activity, was less marked than in the classic (aryloxy)propanolamine blockers.
The recrystallization of ion-implantedsilicon layers (1978)

Abstract Rutherford backscattering and channeling (RBS) has been employed to investigate the annealing characteristics of ion-bombarded <111> silicon for a wide range of implant species. The general recrystallization behaviour is that high levels of remnant disorder are observed for high-dose (typically > 1015 ions cm-2) implants of all species investigated, and transmission electron microscopy indicates the presence of a polycrystalline reordered layer in such cases. The magnitude of the remnant disorder (misorientation of grains with respect to the underlying bulk substrate) is observed to increase with both implant dose and original amorphous-layer thickness and to exhibit a slight implant-mass dependence. Although the recrystallization behaviour is qualitatively similar for all species studied, certain species (mainly those soluble in silicon) are found to influence the regrowth process at low implant concentrations. It is suggested that stress/strain effects, attributed to high implanted concentrations, play a major role in the inhibition of epitaxial silicon recrystallization but that species effects can become dominant at lower implant concentrations.
Paraoxonase prevents accumulation of lipoperoxides in low‐density lipoprotein (1991)

Oxidative modification of low-density lipoprotein (LDL) enhances its uptake by macrophages in tissue culture and in vivo may underly the formation of arterial fatty streaks, the progenitors of atheroma. We investigated the possible protection which high-density lipoprotein (HDL) affords against LDL oxidation. The formation of lipoperoxides and thiobarbituric acid reactive substances when LDL was incubated with copper ions was significantly decreased by HDL. The enzyme, paraoxonase (E.C. 3.1.8.1), purified from human HDL, had a similar effect and thus may be the component of HDL responsible for decreasing the accumulation of lipid peroxidation products.
Inactivation of Vegetative Cells, but Not Spores, of Bacillus anthracis , B. cereus , and B. subtilis on Stainless Steel Surfaces Coated with an Antimicrobial Silver- and Zinc-Containing Zeolite Formulation (2003)

Stainless steel surfaces coated with paints containing a silver- and zinc-containing zeolite (AgION antimicrobial) were assayed in comparison to uncoated stainless steel for antimicrobial activity against vegetative cells and spores of three Bacillus species, namely, B. anthracis Sterne, B. cereus T, and B. subtilis 168. Under the test conditions (25 degrees C and 80% relative humidity), the zeolite coating produced approximately 3 log(10) inactivation of vegetative cells within a 5- to 24-h period, but viability of spores of the three species was not significantly affected.
A Hybrid Discriminative/Generative Approach for Modeling Human Activities (2005)

Accurate recognition and tracking of human activities is an important goal of ubiquitous computing. Recent advances in the development of multi-modal wearable sensors enable us to gather rich datasets of human activities. However, the problem of automatically identifying the most useful features for modeling such activities remains largely unsolved. In this paper we present a hybrid approach to recognizing activities, which combines boosting to discriminatively select useful features and learn an ensemble of static classifiers to recognize different activities, with hidden Markov models (HMMs) to capture the temporal regularities and smoothness of activities. We tested the activity recognition system using over 12 hours of wearable-sensor data collected by volunteers in natural unconstrained environments. The models succeeded in identifying a small set of maximally informative features, and were able identify ten different human activities with an accuracy of 95%. 1
Amplitude-preserving nonlinear adaptive multiple attenuation using the high-order sparse Radon transform (2016)

The Radon transform is widely used for multiple elimination. Since the Radon transform is not an orthogonal transform, it cannot preserve the amplitude of primary reflections well. The prediction and adaptive subtraction method is another widely used approach for multiple attenuation, which demands that the primaries are orthogonal with the multiples. However, the orthogonality assumption is not true for non-stationary field seismic data. In this paper, the high-order sparse Radon transform (HOSRT) method is introduced to protect the amplitude variation with offset information during the multiple subtraction procedures. The HOSRT incorporates the high-resolution Radon transform with the orthogonal polynomial transform. Because the Radon transform contains the trajectory information of seismic events and the orthogonal polynomial transform contains the amplitude variation information of seismic events, their combination constructs an overcomplete transform and obtains the benefits of both the high-resolution property of the Radon transform and the amplitude preservation of the orthogonal polynomial transform. A fast nonlinear filter is adopted in the adaptive subtraction step in order to avoid the orthogonality assumption that is used in traditional adaptive subtraction methods. The application of the proposed approach to synthetic and field data examples shows that the proposed method can improve the separation performance by preserving more useful energy.
Differential expression analysis for sequence count data (2010)

Abstract Motivation: High throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq), cell counting. Statistical inference of differential signal in these data needs to take into account their natural variability throughout the dynamic range. When the number of replicates is small, error modeling is needed to achieve statistical power. Results: We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power.Availability: A free open-source R/Biondonductor software package, called "DESeq", is available from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq
Enhanced Degradation of Azoxystrobin in Grapes and Model Systems by Ozone Fumigation during Storage (2015)

This study was conducted to investigate the natural decline in the residues of the world’s most widely used fungicide, azoxystrobin, in model systems and grapes stored in cold rooms and to determine if ozone fumigation during storage has a contribution to the degradation process. The level of the fungicide gradually decreased both in model systems and grapes with the reduction rates of 53 ± 2 and 29 ± 1%, respectively, at the end of storage. Addition of ozone (1.0 ppm) to the storage atmosphere was found to have a significant influence on fungicide degradation both in model systems and grapes and about 90% reduction rates were recorded. This is the first report demonstrating the accelerated degradation of azoxystrobin by the use of ozone gas treatment.
CHARACTERIZATION OF HOST LYMPHOID CELLS IN ANTIBODY-FACILITATED BONE MARROW CHIMERAS (1985)

We have produced stable murine antibody-facilitated (AF) chimeras by the simultaneous injection of P1 bone marrow cells and anti-P2 monoclonal antibody into normal (unirradiated) adult (P1 X P2)F1 recipients. These AF chimeras are healthy, long-lived, and exhibit no overt signs of graft-versus-host disease. They are immunocompetent and tolerant of host, P2-encoded alloantigens. Donor cell engraftment and takeover, monitored by glucosephosphate isomerase isozyme patterns, is usually complete (greater than 95%) in the peripheral blood, bone marrow, and hemopoietic stem cell compartments of long-term (greater than 3 months posttransplantation) AF chimeras. We report here, however, that splenic, lymph node, and thymic leukocytes of AF chimeras represent donor/host chimeric populations. Spleen cell populations of AF chimeras exhibit substantial chimera-to-chimera variation in the preponderant residual host cell type(s) present. Our interpretations of the implications of these findings are discussed.