gebhart/patrepeval huggingface dataset:
Expression of the Arabidopsis <scp>WRINKLED</scp> 1 transcription factor leads to higher accumulation of palmitate in soybean seed (2018)

Soybean (Glycine max [L.] Merr.) is a commodity crop highly valued for its protein and oil content. The high percentage of polyunsaturated fatty acids in soybean oil results in low oxidative stability, which is a key parameter for usage in baking, high temperature frying applications, and affects shelf life of packaged products containing soybean oil. Introduction of a seed-specific expression cassette carrying the Arabidopsis transcription factor WRINKLED1 (AtWRI1) into soybean, led to seed oil with levels of palmitate up to approximately 20%. Stacking of the AtWRI1 transgenic allele with a transgenic locus harbouring the mangosteen steroyl-ACP thioesterase (GmFatA) resulted in oil with total saturates up to 30%. The creation of a triple stack in soybean, wherein the AtWRI1 and GmFatA alleles were combined with a FAD2-1 silencing allele led to the synthesis of an oil with 28% saturates and approximately 60% oleate. Constructs were then assembled that carry a dual FAD2-1 silencing element/GmFatA expression cassette, alone or combined with an AtWRI1 cassette. These plasmids are designated pPTN1289 and pPTN1301, respectively. Transgenic events carrying the T-DNA of pPTN1289 displayed an oil with stearate levels between 18% and 25%, and oleate in the upper 60%, with reduced palmitate (<5%). While soybean events harboring transgenic alleles of pPTN1301 had similar levels of stearic and oleate levels as that of the pPTRN1289 events, but with levels of palmitate closer to wild type. The modified fatty acid composition results in an oil with higher oxidative stability, and functionality attributes for end use in baking applications.
Hierarchical Residual-pyramidal Model for Large Context Based Media Presence Detection (2019)

We study media presence detection, that is, learning to recognize if a sound segment (typically lasting for a few seconds) of a long recorded stream contains media (TV) sound. This problem is difficult because non-media sound sources can be quite diverse (e.g. human voicing, non-vocal sounds and non-human sounds), and the recorded sound can be a mixture of media and non-media sound.Different from speech recognition, where the recognizer needs to detect local phonetic variation, the key features used to distinguish media and non-media sounds are non-local features. Motivated by this, we propose a hierarchical model to learn representation of each pre-chunked segment within a long recorded stream jointly, and encourage every local representation to be not sensitive to variations within each segment. We also further explore the effects of techniques including stream based normalization and iteratively imputing missing labels of training dataset. Experimental results indicate that our proposed contextual based methods are effective for media presence detection.
Metal−Polyimide Nanocomposite Films:  Single-Stage Synthesis of Silvered Polyimide Films Prepared from Silver(I) Complexes and BPDA/4,4‘-ODA (2004)

Highly reflective and surface conductive flexible polyimide films have been prepared by the incorporation of silver(I) acetate and 1,1,1-trifluoro-2,4-pentanedione or 1,1,1,5,5,5-hexafluoro-2,4-pentanedione into a dimethylacetamide solution of the poly(amic acid) formed from 3,3‘,4,4‘-biphenyltetracarboxylic dianhydride and 4,4‘-oxydianiline. Thermal curing of the silver(I)-containing poly(amic acid) leads to cycloimidization of the polyimide precursor with concomitant silver(I) reduction yielding reflective and conductive silvered surfaces with properties approaching those of the native metal. The metallized films usually exhibit mechanical and thermal properties close to that of the parent polyimide. Films were characterized by X-ray diffraction, transmission and scanning electron microscopy, and X-ray photoelectron spectroscopy.
Abstract 2354: An E2F signature predicts benefit of adjuvant chemotherapy in early-stage non-small cell lung cancer. (2013)

Abstract Early-stage non-small cell lung cancer (NSCLC) is primarily treated by surgical resection. Unfortunately, after resection, one-third to one-half of early-stage patients will die of metastatic recurrence. Adjuvant chemotherapy (ACT) improves the survival of patients with early-stage disease and has become the standard treatment for patients with resected stage II-III NSCLC. However, the five-year survival advantage of ACT is only 4%-15% suggesting that many patients do not benefit. Given the morbidity associated with ACT, it is imperative to develop new prognostic tools to identify those patients with a high probability of relapse. Toward this end, we have used small inhibitory RNAs targeting multiple E2F pathway components to derive an E2F gene expression signature in vitro. This signature was refined by filtering for its components that were altered in non-small cell lung cancers compared to normal tissue. Principle component analysis was then used to represent the signature which was tested for correlation to overall survival in two large cohorts. The first of the two cohorts was the Molecular Classification of Lung Adenocarcinoma (MCLA) from the Director's Challenge Consortium and the second was a novel database on 444 lung adenocarcinomas treated as a part of Moffitt's Total Cancer Care Network. The E2F signature is strongly prognostic in both cohorts with P values &lt;0.0001. Additionally, using data in the JBR.10 trial (GSE14814) for patients who either did or did not receive ACT we were able to determine that patients having a high E2F signature benefit from ACT (have increased overall survival), whereas patients with a low E2F signature do not. Overall, these results suggest that this approach could be optimized in the clinical setting to distinguish patients likely to benefit from ACT from those who will not. Citation Format: Courtney A. Kurtyka, Dung-Tsa Chen, Lu Chen, William Brazelle, Eric A. Welsh, Anders E. Berglund, Steven A. Eschrich, Matthew B. Schabath, Eric B. Haura, W. Douglas Cress. An E2F signature predicts benefit of adjuvant chemotherapy in early-stage non-small cell lung cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2354. doi:10.1158/1538-7445.AM2013-2354
Inhibitors of cyclic nucleotide phosphodiesterase 3 and 5 as therapeutic agents in heart failure (2006)

Cyclic nucleotide phosphodiesterases (PDE) 3 and 5 regulate cAMP and cGMP signalling in cardiac and smooth muscle myocytes. Important advances in the understanding of the roles of these enzymes have recently been made. PDE3 inhibitors have inotropic and vasodilatory properties, and although they acutely improve haemodynamics in patients with heart failure, they do not improve long-term morbidity and mortality. Although combination therapy with beta-adrenergic receptor antagonists or selective inhibition of specific PDE3 isoforms might result in a more favourable long-term outcome, more clinical data are needed to test this proposition. The role of PDE5 inhibitors in the treatment of cardiac disease is evolving. PDE5 inhibitors cause pulmonary and systemic vasodilation. How these drugs will compare with other vasodilators in terms of long-term outcomes in patients with heart failure is unknown. Recent studies also suggest that PDE5 inhibitors may have antihypertropic effects, exerted through increased myocardial cGMP signalling, that could be of additional benefit in patients with heart failure.
Temperature-Sensitive Paralytic Mutants Are Enriched For Those Causing Neurodegeneration in Drosophila (2002)

Age-dependent neurodegeneration is a pathological condition found in many metazoans. Despite the biological and medical significance of this condition, the cellular and molecular mechanisms underlying neurodegeneration are poorly understood. The availability of a large collection of mutants exhibiting neurodegeneration will provide a valuable resource to elucidate these mechanisms. We have developed an effective screen for isolating neurodegeneration mutants in Drosophila. This screen is based on the observation that neuronal dysfunction, which leads to observable behavioral phenotypes, is often associated with neurodegeneration. Thus, we used a secondary histological screen to examine a collection of mutants originally isolated on the basis of conditional paralytic phenotypes. Using this strategy, we have identified 15 mutations affecting at least nine loci that cause gross neurodegenerative pathology. Here, we present a genetic, behavioral, and anatomical analysis of vacuous (vacu), the first of these mutants to be characterized, and an overview of other mutants isolated in the screen. vacu is a recessive mutation located cytologically at 85D-E that causes locomotor defects in both larvae and adults as well as neuronal hyperactivity. In addition, vacu exhibits extensive age-dependent neurodegeneration throughout the central nervous system. We also identified mutations in at least eight other loci that showed significant levels of neurodegeneration with a diverse array of neuropathological phenotypes. These results demonstrate the effectiveness of our screen in identifying mutations causing neurodegeneration. Further studies of vacu and the other neurodegenerative mutants isolated should ultimately help dissect the biochemical pathways leading to neurodegeneration.
Acute Animal and Human Study of a Tensiometric Pacing Lead Sensor Based on Triboelectricity (2011)

Cardiac contractions bend the implanted cardiac lead body, extend and compress the lead conductors, their insulation and the inserted stylet. Magnitude of lead deflection depends on cardiac muscle contraction forces. The purpose of study was to measure the charge generated due to triboelectric effect between one of the lead conductors and the inserted stylet. The charge was measured by differential charge amplifier being connected to isolation amplifier and power supply. Sensor signal, ECG and intracardiac electrograms were acquired. Three models of custom designed leads were implanted in 8 sheep. Measurements were done in 18 patients undergoing pacemaker implantation and replacement procedures. Atrial and ventricular tensiometric signals were recorded in dual chamber and in single-lead VDD patients. Recordings in sinus rhythm at various AV intervals and in supraventricular tachycardia were done. In average, charge variation between 1 and 600 pC was measured. Tensiometric stylet could be feasible hemodynamic sensor for myocardial contraction detection. Its main advantage is that it is easily exchangeable and universal for all leads.
Tunable Molecular Logic Gates Designed for Imaging Released Neurotransmitters (2015)

Tunable dual-analyte fluorescent molecular logic gates (ExoSensors) were designed for the purpose of imaging select vesicular primary-amine neurotransmitters that are released from secretory vesicles upon exocytosis. ExoSensors are based on the coumarin-3-aldehyde scaffold and rely on both neurotransmitter binding and the change in environmental pH associated with exocytosis to afford a unique turn-on fluorescence output. A pH-functionality was directly integrated into the fluorophore π-system of the scaffold, thereby allowing for an enhanced fluorescence output upon the release of labeled neurotransmitters. By altering the pH-sensitive unit with various electron-donating and -withdrawing sulfonamide substituents, we identified a correlation between the pKa of the pH-sensitive group and the fluorescence output from the activated fluorophore. In doing so, we achieved a twelvefold fluorescence enhancement upon evaluating the ExoSensors under conditions that mimic exocytosis. ExoSensors are aptly suited to serve as molecular imaging tools that allow for the direct visualization of only the neurotransmitters that are released from secretory vesicles upon exocytosis.
Rat incisor dentine contains a factor which alters the phenotypic expression and stimulates chondrogenesis in fibroblast-like cells in vitro. (1990)

A low molecular weight protein fraction isolated under dissociative conditions during the demineralization of rat incisor dentine has the ability to modulate, in culture, the expression of fibroblast-like cells explanted from neonatal rat muscle. The protein fraction enhances the incorporation of 35S-sulphate into a proteoglycan larger in weight than that produced by the uninduced cells; furthermore it induces the production of type II collagen. These changes take place in the absence of cell proliferation as measured by 3H-thymidine incorporation. The altered fibroblast-like cells form nodules and secrete an abundant extracellular matrix which stains for proteoglycan after 7-9 days in culture. These data show that the dentine matrix does contain a factor which can initiate a mitogenesis-independent alteration in the expression of the muscle-explant outgrowth cells. Those changes are consistent with a shift to a chondrogenic mode.
New Sources of Resistance to <i>Phytophthora sojae</i> in the Soybean Plant Introductions (2000)

Single dominant Rps genes have been highly effective in managing Phytophthora sojae. However, numerous physiological races of P. sojae have developed in response to deploying single gene resistance. New sources of resistance with potentially novel Rps genes are needed. A selection of accessions (PI273483 to PI427107) from the United States Department of Agriculture Soybean Germplasm collection were evaluated for resistance to P. sojae using the hypocotyl inoculation technique for Rps genes and the layer test for partial resistance. Of the 1,015 accessions tested, 159 accessions were susceptible to races 7 (vir 1a, 2, 3a, 3c, 4, 5, 6, 7), 17 (1b, 1d, 2, 3a, 3b, 3c, 4, 5, 6, 7), and 25 (1a, 1b, 1c, 1k, 7). However, 162 accessions were resistant to these three races and 32 accessions were resistant to an additional five races chosen specifically to elicit a susceptible interaction with two and three Rps gene combinations. In addition, 55.5% of the 887 accessions tested had high levels of partial resistance or tolerance (scores ≤4.0) to P. sojae. The majority of the accessions that were resistant to all of the races tested and those that had very high levels of partial resistance originated in the Republic of Korea. These results indicate that this region is an area with many sources of resistance to P. sojae for both specific Rps genes and partial resistance.
A Constraint Optimization-Based Resolution of Verification Collisions in Self-Organizing Networks (2014)

The verification of Configuration Management (CM) changes is an important step in the operation of a Self-Organizing Network (SON). In order to perform its tasks, a verification mechanism makes use of an observation and a correction time window. In the first window it assesses the impact of deployed CM changes by monitoring the network's Performance Management (PM) data. Furthermore, it partitions the network in one or more verification areas, detects anomalies within them, and generates CM undo requests, each having the purpose to set CM parameters to some previous state. In the second window it deploys those requests to the network. However, two or more verification areas might be overlapping and share anomalous cells. As a consequence, we have verification collisions preventing two or more generated CM undo requests to be deployed at same time. Thereby, the verification mechanism might not be able to deploy all generated CM undo actions for the given correction window. In this paper, we propose a method that makes use of constraint optimization techniques to identify which requests can be merged together in order to meet the time requirement. We achieve our goal by using constraint softening based on so-called performance rating values of the requests. We evaluate our method in two different scenarios. First, we highlight the need for handling verification collisions by observing CM and PM data of a real Long Term Evolution (LTE) network. Second, a simulation study shows the ability of our method to keep the network performance at a high level.
Anaerobic Ammonium-Oxidizing (Anammox) Bacteria and Associated Activity in Fixed-Film Biofilters of a Marine Recirculating Aquaculture System (2006)

Microbial communities in the biological filter and waste sludge compartments of a marine recirculating aquaculture system were examined to determine the presence and activity of anaerobic ammonium-oxidizing (anammox) bacteria. Community DNA was extracted from aerobic and anaerobic fixed-film biofilters and the anaerobic sludge waste collection tank and was analyzed by amplifying 16S rRNA genes by PCR using anammox-selective and universal GC-clamped primers. Separation of amplified PCR products by denaturing gradient gel electrophoresis and sequencing of the different phylotypes revealed a diverse biofilter microbial community. While Planctomycetales were found in all three communities, the anaerobic denitrifying biofilters contained one clone that exhibited high levels of sequence similarity to known anammox bacteria. Fluorescence in situ hybridization studies using an anammox-specific probe confirmed the presence of anammox Planctomycetales in the microbial biofilm from the denitrifying biofilters, and anammox activity was observed in these biofilters, as detected by the ability to simultaneously consume ammonia and nitrite. To our knowledge, this is the first identification of anammox-related sequences in a marine recirculating aquaculture filtration system, and our findings provide a foundation for incorporating this important pathway for complete nitrogen removal in such systems.
Neural Geometric Level of Detail: Real-time Rendering with Implicit 3D Shapes (2021)

Neural signed distance functions (SDFs) are emerging as an effective representation for 3D shapes. State-of-the-art methods typically encode the SDF with a large, fixed-size neural network to approximate complex shapes with implicit surfaces. Rendering with these large networks is, however, computationally expensive since it requires many forward passes through the network for every pixel, making these representations impractical for real-time graphics. We introduce an efficient neural representation that, for the first time, enables real-time rendering of high-fidelity neural SDFs, while achieving state-of-the-art geometry reconstruction quality. We represent implicit surfaces using an octree-based feature volume which adaptively fits shapes with multiple discrete levels of detail (LODs), and enables continuous LOD with SDF interpolation. We further develop an efficient algorithm to directly render our novel neural SDF representation in real-time by querying only the necessary LODs with sparse octree traversal. We show that our representation is 2–3 orders of magnitude more efficient in terms of rendering speed compared to previous works. Furthermore, it produces state-of-the-art reconstruction quality for complex shapes under both 3D geometric and 2D image-space metrics.
Treatment of Infectious Mastitis during Lactation: Antibiotics versus Oral Administration of Lactobacilli Isolated from Breast Milk (2010)

In this study, 352 women with infectious mastitis were randomly assigned to 3 groups. Women in groups A (n = 124) and B (n = 127]) ingested daily 9 log(10) colony-forming units (CFU) of L. fermentum CECT5716 or L. salivarius CECT5713, respectively, for 3 weeks, whereas those in group C (n =101) received the antibiotic therapy prescribed in their respective primary care centers. Results. On day 0, the mean bacterial counts in milk samples of the 3 groups were similar (4.35-4.47 log(10) CFU/mL), and lactobacilli could not be detected. On day 21, the mean bacterial counts in the probiotic groups (2.61 and 2.33 log(10) CFU/mL) were lower than that of the control group (3.28 log(10) CFU/mL). L. fermentum CECT5716 and L. salivarius CECT5713 were isolated from the milk samples of women in the probiotic groups A and B, respectively. Women assigned to the probiotic groups improved more and had lower recurrence of mastitis than those assigned to the antibiotic group. Conclusions. The use of L. fermentum CECT5716 or L. salivarius CECT5713 appears to be an efficient alternative to the use of commonly prescribed antibiotics for the treatment of infectious mastitis during lactation. ClinicalTrials.gov identifier. NCT00716183.
ECG-based feature tracking in atrial tachyarrhythmias (2003)

A new method for extraction of general features in ECGs with atrial tachyarrhythmias is presented. The method is based on our recent method for atrial signal characterization which sequentially decomposes a time-frequency distribution into a set of parameters. In addition to rate and amplitude, the method tracks information on regularity, waveform, and structure of the atrial signal. The proposed method includes a feature tracker which continuously tracks the structure of the harmonic spectral pattern in order to determine which of a set of archetype waveforms that is best matched. The method also includes a trend detector, which detects significant long-term changes in the time series of frequency estimates. The results, illustrated by signals obtained during different interventions and a test signal, show that the algorithms can discriminate between different types of atrial rhythms.
Nanopillars and arrays of nanoholes fabricated by extreme ultraviolet interferometric laser lithography (2007)

Arrays of holes and pillars were fabricated by multiple exposure interferometric lithography using a table top lambda = 46.9 nm wavelength laser. Size and the feature characteristic is controlled changing the applied exposure dose.
Fast incremental maintenance of approximate histograms (2002)

Many commercial database systems maintain histograms to summarize the contents of large relations and permit efficient estimation of query result sizes for use in query optimizers. Delaying the propagation of database updates to the histogram often introduces errors into the estimation. This article presents new sampling-based approaches for incremental maintenance of approximate histograms. By scheduling updates to the histogram based on the updates to the database, our techniques are the first to maintain histograms effectively up to date at all times and avoid computing overheads when unnecessary. Our techniques provide highly accurate approximate histograms belonging to the equidepth and Compressed classes. Experimental results show that our new approaches provide orders of magnitude more accurate estimation than previous approaches.An important aspect employed by these new approaches is a backing sample , an up-to-date random sample of the tuples currently in a relation. We provide efficient solutions for maintaining a uniformly random sample of a relation in the presence of updates to the relation. The backing sample techniques can be used for any other application that relies on random samples of data.
Quinolonecarboxylic acids. 2. Synthesis and antibacterial evaluation of 7-oxo-2,3 dihydro-7H-pyrido[1,2,3-de][1,4]benzothiazine-6-carboxylic acids (1987)

A series of pyridobenzothiazine acid derivatives was synthesized and their in vitro antibacterial activity was evaluated. The 1,4-benzothiazine intermediates, which by Gould-Jacobs quinoline synthesis produced pyridobenzothiazine acids, were prepared by hydrolytic basic cleavage of substituted 2-aminobenzothiazoles and successive cyclocondensation with 1-bromo-2-chloroethane or alternatively with monochloroacetic acid, hence reduction by LiAlH4. The pyridobenzothiazine acids 10c, 30, and 31 show potent antibacterial activities against Gram-positive and Gram-negative pathogens. Structure-activity relationships are discussed. The compound 9-fluoro-10-(4-methyl-1-piperazinyl)-7-oxo-2,3-dihydro-7H-pyrido[1,2,3-d e] [1,4]benzothiazine-6-carboxylic acid (31) (MF-934) has been found to possess, together with the antibacterial activity, a weak acute toxicity and interesting pharmacokinetic characteristics in several animal species (rat, dog, monkey, man).