gebhart/patrepeval huggingface dataset:
Swelling and Gelatinization of Oat Starches (1996)

A comparison was made between the structure and physicochemical properties of starches extracted from five normal and one naked cultivar of oat. There was little difference in the molecular size or polydispersity of the native amylose and amylopectin determined by gel permeation chromatography (GPC), or in the unit chain distribution of isoamylase-debranched amylopectin, where three peaks were resolved at modal degree of polymerization of 15, 23, and 46. Apparent, total, and A-amylose (difference between apparent and total amylose due to lipid complexing) contents ranged from 19.7 to 22.0%, 27.5 to 29.8%, and 7.1 to 8.1, respectively, with lipid content, as fatty acid methyl esters, ranging from 0.66 to 0.75% on a dry basis and comprising the following fatty acids : 46.6% C16 ; 2.1% C18 ; 15.0% C18 :1 ; 35.3% C18 :2, and 0.7% C18 :3. The naked oat starch had the lowest lipid content and Δ-amylose. Lintner type solubilization in 2M HCl (six days of incubation at 35°C) ranged from 56.6 to 60.0% of the original dry α-glucan. The 80°C swelling factor corresponding to postgelatinization swelling (determined by a blue dextran dye exclusion method) ranged from 8.6 to 10, with the naked oat being at the top of the range. At this temperature, the amount of α-glucan leached from the granules ranged from 4.1 to 6.6% (dry basis), where the highest value corresponded to the naked oat. Amylose (determined colorimetrically) accounted for 42.1-47.6% of the α-glucan in the leachate. No intermediate material could be detected by GPC. Damaged starch levels were very low in the starches analyzed (1.9-2.2% on a dry basis). The high proportion of branched α-glucan in the leachate was confirmed by GPC and was attributed to the fragile nature of the gelatinized oat starch granules. Gelatinization parameters by differential scanning calorimetry were 44.7-47.3, 56.2-59.5, and 68.7-73.7°C for T 0 , T p and T c respectively, with ΔH ranging from 8.1 to 9.5 J/g. The mean diameter of native granules, determined by Coulter Counter, ranged from 4.96 to 5.63 μm, with the naked oat starch being at the low end.
Comparison of Electropolymerized Thiazine Dyes as an Electrocatalyst in Enzymatic Biofuel Cells and Self Powered Sensors (2009)

This paper details the comparison of different electropolymerized thiazine electrocatalysts for NADH oxidation. Electropolymerized thiazines have been shown to be electrocatalysts for NADH, but no comprehensive comparison of their properties in the same environment has been performed. The electropolymerization and electrocatalysis is very dependent on chemical and electrochemical environment, so the thiazines (methylene green, methylene blue, toluidine blue, azure a, azure b, and azure c) were all electropolymerized in the same chemical and electrochemical environment and tested for NADH electrocatalysis. All of the thiazines can be electropolymerized to form stable polymer modified electrodes on glassy carbon electrodes and all shown electrocatalytic activity toward NADH. However, each polymer has different properties and therefore would be employed in different applications, depending on whether open circuit potential, current density, or lifetime is the most important condition of the biofuel cell. This paper further compares NAD-dependent glucose dehydrogenase bioelectrocatalysis with poly(methylene green) and poly(methylene blue) electrocatalysts in terms of sensitivity to glucose and biofuel cell performance.
Getting Started in Gene Orthology and Functional Analysis (2010)

construct this category of ortholog groups, we first need to identify pairs of
System for analyzing high-resolution three-dimensional coronary angiograms (1996)

Three-dimensional (3-D) high-resolution coronary angiograms offer a means for visualizing the entire coronary arterial tree from any orientation and for detecting and quantitating coronary arterial stenoses. Previously, a skilled operator had to perform several hours of tedious manual analysis using an interactive graphical user-interface (GUI) system (Tree Trace) to analyze a 3-D angiogram. The authors have devised an improved GUI system, consisting of three tools for analyzing 3-D angiograms. The Artery Extractor first performs automatic image-analysis operations to extract the central axes of the arterial tree. Next, using the Artery Display tool and results from the Artery Extractor, the operator can visualize structures in the angiogram and compute various measurements. Finally, the aforementioned Tree Trace tool can be used to manually correct irregularities in the automatically generated results of the Artery Extractor. The system greatly reduces operator analysis time, gives exactly reproducible results, uses true 3-D image-processing operations, and provides a comprehensive interface for visualizing and quantifying features of the 3-D coronary arteries.
Manual Acupuncture Suppresses the Expression of Proinflammatory Proteins Associated with the NLRP3 Inflammasome in the Hippocampus of SAMP8 Mice (2017)

MA can improve the learning and memory capabilities of SAMP8 mice. The negative regulation of the NLRP3/Caspase-1 pathway in the hippocampus may be a possible mechanism of MA in the treatment of AD.
Specific protein changes during memory acquisition and storage (1989)

Abstract Changes in several distinct types of neuronal proteins are now known to be associated with learning. In this review, we will summarize the properties of these proteins and relate these properties to prominent theories of the biochemical basis of memory.
Expanding and understanding the CRISPR toolbox for <i>Bacillus subtilis</i> with MAD7 and dMAD7 (2020)

The CRISPR-Cas9 system has become increasingly popular for genome engineering across all fields of biological research, including in the Gram-positive model organism Bacillus subtilis. A major drawback for the commercial use of Cas9 is the IP landscape requiring a license for its use, as well as reach-through royalties on the final product. Recently an alternative CRISPR nuclease, free to use for industrial R&D, MAD7 was released by Inscripta (CO). Here we report the first use of MAD7 for gene editing in B. subtilis, in which editing rates of 93% and 100% were established. Additionally, we engineer the first reported catalytically inactive MAD7 (dMAD7) variant (D877A, E962A, and D1213A) and demonstrate its utility for CRISPR interference (CRISPRi) at up to 71.3% reduction of expression at single and multiplexed target sites within B. subtilis. We also confirm the CRISPR-based editing mode of action in B. subtilis providing evidence that the nuclease-mediated DNA double-strand break acts as a counterselection mechanism after homologous recombination of the donor DNA.
Anti-obesity drugs (2008)

An emerging theme is to use combination therapies that are directed towards several targets or leverage existing gastrointestinal satiety hormonal signals. By using combination therapies, it is anticipated that greater weight loss will be achieved compared to monotherapy.
The Recovery of Posterior Cornea and Anterior Lens Radii by a Novel Ray-Tracing Method (2004)

A telecentric image-computing algorithm produces accurate image positions. A two-step cubic regression produces accurate estimates of R2 and R3 (errors approximately 10 mm). This error increases with axial shift (approximately 10 mm) and digitization (approximately 10 mm). The new method does better than a standard method ignoring all the errors and tends to handle digitization error better. The new method works well on a toroidal anterior cornea. Testing on model/real eyes is required. Efforts are continuing to refine methods for videophakometry.
ASCT2/SLC1A5 controls glutamine uptake and tumour growth in triple-negative basal-like breast cancer (2015)

Alanine, serine, cysteine-preferring transporter 2 (ASCT2; SLC1A5) mediates uptake of glutamine, a conditionally essential amino acid in rapidly proliferating tumour cells. Uptake of glutamine and subsequent glutaminolysis is critical for activation of the mTORC1 nutrient-sensing pathway, which regulates cell growth and protein translation in cancer cells. This is of particular interest in breast cancer, as glutamine dependence is increased in high-risk breast cancer subtypes. Pharmacological inhibitors of ASCT2-mediated transport significantly reduced glutamine uptake in human breast cancer cell lines, leading to the suppression of mTORC1 signalling, cell growth and cell cycle progression. Notably, these effects were subtype-dependent, with ASCT2 transport critical only for triple-negative (TN) basal-like breast cancer cell growth compared with minimal effects in luminal breast cancer cells. Both stable and inducible shRNA-mediated ASCT2 knockdown confirmed that inhibiting ASCT2 function was sufficient to prevent cellular proliferation and induce rapid cell death in TN basal-like breast cancer cells, but not in luminal cells. Using a bioluminescent orthotopic xenograft mouse model, ASCT2 expression was then shown to be necessary for both successful engraftment and growth of HCC1806 TN breast cancer cells in vivo. Lower tumoral expression of ASCT2 conferred a significant survival advantage in xenografted mice. These responses remained intact in primary breast cancers, where gene expression analysis showed high expression of ASCT2 and glutamine metabolism-related genes, including GLUL and GLS, in a cohort of 90 TN breast cancer patients, as well as correlations with the transcriptional regulators, MYC and ATF4. This study provides preclinical evidence for the feasibility of novel therapies exploiting ASCT2 transporter activity in breast cancer, particularly in the high-risk basal-like subgroup of TN breast cancer where there is not only high expression of ASCT2, but also a marked reliance on its activity for sustained cellular proliferation.
Reprogramming metastatic melanoma cells to assume a neural crest cell-like phenotype in an embryonic microenvironment (2006)

Human metastatic melanoma cells express a dedifferentiated, plastic phenotype, which may serve as a selective advantage, because melanoma cells invade various microenvironments. Over the last three decades, there has been an increased focus on the role of the tumor microenvironment in cancer progression, with the goal of reversing the metastatic phenotype. Here, using an embryonic chick model, we explore the possibility of reverting the metastatic melanoma phenotype to its cell type of origin, the neural-crest-derived melanocyte. GFP-labeled adult human metastatic melanoma cells were transplanted in ovo adjacent to host chick premigratory neural crest cells and analyzed 48 and 96 h after egg reincubation. Interestingly, the transplanted melanoma cells do not form tumors. Instead, we find that transplanted melanoma cells invade surrounding chick tissues in a programmed manner, distributing along host neural-crest-cell migratory pathways. The invading melanoma cells display neural-crest-cell-like morphologies and populate host peripheral structures, including the branchial arches, dorsal root and sympathetic ganglia. Analysis of a melanocyte-specific phenotype marker (MART-1) and a neuronal marker (Tuj1) revealed a subpopulation of melanoma cells that invade the chick periphery and express MART-1 and Tuj1. Our results demonstrate the ability of adult human metastatic melanoma cells to respond to chick embryonic environmental cues, a subset of which may undergo a reprogramming of their metastatic phenotype. This model has the potential to provide insights into the regulation of tumor cell plasticity by an embryonic milieu, which may hold significant therapeutic promise.
Probing Surfaces With The Atomic Force Microscope (1988)

The Atomic Force Microscope can resolve features on conducting or nonconducting surfaces down to the atomic level. The heights of features are recorded as a sharp tip scans over the surface in parallel scans. The interaction between the tip and the surface is the interaction potential between atoms. Individual carbon atoms separated by 0.146 nm have been resolved on graphite. Ordered structure on the "native" oxide of silicon has been observed. Rows of molecules that are separated by 0.5 nm have been resolved in an organic monolayer. The key to the operation of an AFM is the development of a system for sensing tracking forces that are small enough to avoid damaging the surface. The images in this report were obtained by sensing with electron tunneling the deflection 1 - 10 nm) of springs (k 0.1 - 100 N/m) fabricated from silicon oxide or fine wires.
Mechanisms of mutagenesis by chloroacetaldehyde. (1989)

A number of bifunctional chemical mutagens induce exocyclic DNA lesions. For example, 2-chloroacetaldehyde (CAA), a metabolite of vinyl chloride, readily reacts with single-stranded DNA to predominantly form etheno lesions. Here, we report on in vivo mutagenesis caused by CAA treatment of DNA in vitro. These experiments used partially duplex phage M13AB28 replicative form DNA in which a part of the lacZ gene sequence was held in single-stranded form to direct reaction with CAA. CAA-treated partial duplex DNA was transfected into Escherichia coli, and the induced base changes were defined by DNA sequencing. These experiments suggested that CAA treatment induced mutations at cytosines, much less efficiently at adenines, but not at guanines or thymines. Among mutations targeted to cytosine, 80% were C-to-T transitions and 20% were C-to-A transversions. Application of a post-labeling method detected dose-dependent formation of ethenoadenine and ethenocytosine in CAA treated DNA. These data indicate that ethenocytosine is a highly efficient mutagen with properties suggestive of a non-instructional DNA lesion in vivo. Paradoxically, ethenoadenines are efficiently bypassed by a mechanism which appears to be largely nonmutagenic.
A radiopharmaceutical for imaging areas of lymphocytic infiltration: 123I-interleukin-2. Labelling procedure and animal studies (1992)

The labelling of interleukin-2 (IL-2) with 123I and its in vivo application for imaging chronic pathological lymphocytic infiltrations are described. The lactoperoxidase/glucoseoxidase technique was the labelling method of choice leading to immunoreactive IL-2 with high specific activity. Labelled IL-2 was injected in diabetes-prone non-obese diabetic (NOD) mice with pancreatic lymphocytic infiltration. As control animals, Balb/c mice were used. As specificity control, monoclonal antibodies AMT13 and UCHT1, bovine serum albumin and α-lactalbumin were radioiodinated and injected in mice. Eighteen NOD mice and four control Balb/c mice were used for gamma camera imaging experiments. Fifty-four NOD and 20 Balb/c mice were used for time course single organ counting and autoradiography. Gamma camera images showed that radioactivity accumulated in the pancreatic region from the 10th minute onwards in NOD mice injected with 123I-IL-2 but not in Balb/c mice, or in NOD mice injected with control radiopharmaceuticals. These findings were confirmed by counting the radioactivity present in single organs. Autoradiography of NOD pancreas, after injection of labelled IL-2, showed that radioactivity was specifically associated with infiltrating lymphocytes. In conclusion, this technique is highly specific and easy to perform and we suggest its application in humans for in vivo detection of areas of lymphocytic infiltration.
DEMONSTRATION‐BASED BEHAVIOR PROGRAMMING FOR EMBODIED VIRTUAL AGENTS (2008)

We present a novel technique for behavioral animation through data‐driven behavior synthesis. This technique has two key features: it provides natural character behavior and has a programming‐by‐demonstration interface. Thus we can quickly create compelling autonomous virtual agents that exhibit stylized behavior. First, the human user demonstrates behavior for the character by specifying its high‐level actions (e.g., with a joystick) during an interactive session. Each demonstration is recorded as a sequence of discrete actions. Later, the character synthesizes novel behavior by concatenating segments of action sequences. The choice of segments is guided by simulations that predict fitness. Thus our technique operates such as a cognitive model, providing a character with deliberative decision making. The actions are abstract and can be mapped to any pertinent motions, even procedurally synthesized motions. Thus our technique complements character animation algorithms. We empirically show that our O(log n ) technique is scalable, robust when provided with sufficient data, produces effective behavior for a number of problem domains, and is faster than traditional planning. Also, the interface is intuitive enough that character behavior can be created by nontechnical users.
Peroxidase-Mediated Virucidal Systems (1970)

Peroxidase (myeloperoxidase or lactoperoxidase), hydrogen peroxide, and a halide such as iodide, bromide, or chloride form a potent virucidal system that is effective against polio and vaccinia viruis, particularly at a low pH. The peroxidase-halide-hydrogen peroxide system may contribute to the host defense against certain viral infections.
DATABASE DESIGN FOR HIGH-SPEED CATAMARANS (1995)

This paper describes the database CATSSD (CATamaran Support System Design) developed by the authors for preliminary catamaran design. The catamaran database structure is described and to illustrate its use, an example of a 30 metre catamaran designed for 35 knot service speed is presented.
Cro Repressor Protein and Its Interaction with DNA (1983)

The recently determined three-dimensional structure of Cro repressor protein from bacteriophage λ suggests how this DNA-binding protein recognizes its sequence-specific binding sites on the bacteriophage genome. In this paper we describe the presumed complex between Cro and DNA and discuss its implications for DNA-protein recognition in general. We also describe results suggesting that the structures of a number of other sequence-specific DNA-binding proteins may contain an a-helical region similar to that seen in the presumed DNA-binding region of Cro.
Unsupervised Credit Detection in TV Broadcast Streams (2010)

This paper proposes an unsupervised method for detecting credits in TV streams. Identifying credits in TV streams allows to precisely determining boundaries of TV programs and hence, to extract specific and high valuable TV programs. The proposed detection solution is based on the temporal stability of opening and closing credits. Consequently, from a linear TV stream, we detect sequences that are broadcasted several times on a stable schedule with a clustering-based approach. These repeated sequences include opening and closing credits but also commercials, trailers etc. In order to select, among repeated sequences, those which are effectively credits, their temporal stability and their metadata consistency are analyzed. Since recurring programs are usually broadcasted at the same time(s) of the day, the temporal distribution of occurrences of each repeated sequence is studied. The Electronic Program Guide (EPG) is then used to validate the selected sequences and to distinguish between opening and closing credits. This method is entirely unsupervised and no prior information is required. Extensive experimental results validating our approach are presented.
Detection of Explosives with a Fluorescent Nanofibril Film (2007)

A new type of fluorescence sensory material has been developed from an alkoxycarbonyl-substituted carbazole-cornered tetracycle. Films fabricated from such materials are shown to be efficient in detecting explosive vapor, probably owing to the extended 1D molecular stacking between the component molecules and intrinsic nanoporous morphology thus formed within the film. The former facilitates long-range exciton migration, while the latter favors adsorption and diffusion of gaseous adsorbates within the film. A combination of these two characteristics enables efficient fluorescence quenching of the film by gaseous quenchers.
[Influenza activity in China from 2000 to 2001]. (2003)

Influenza was not prevalent in China from 2000 to 2001. The antigenic drifts of H3N2 and B/Victoria-like viruses occurred. Two antigenically distinct genetic lineages of influenza B viruses were still co-circulating in men in China. Two genetically distinct lineages of influenza A (H1N1) virus were also co-circulating in men in China.
O<sub>2</sub>/pH Multisensor Based on One Phosphorescent Dye (2010)

A new sensor is described based on a phosphorescent metalloporphyrin dye incorporated in a polymeric membrane, which allows measurement of the two important analytes, oxygen and pH. In such a sensor, the bifunctional dye is quenched by O(2) altering its phosphorescence intensity and lifetime (0-21 kPa O(2)), whereas protonation of the dye causes a major change in the absorption spectrum and also reduces the phosphorescence intensity. As a result, quantification and continuous monitoring of the two analytes can be achieved by (i) simultaneous phosphorescence intensity (O(2), pH) and lifetime (O(2)) measurements and (ii) parallel phosphorescence lifetime (O(2)) and ratiometric absorbance (pH) measurements. Although the first method generally requires sensor calibration in intensity mode, the second provides internal referencing and calibration-free capabilities for both analytes. This approach can be extended to sensing of some other analytes.
Groovy package templates (2009)

We show how package templates, a modularization mechanism originally developed for statically typed languages like Java and C#, can be applied to and implemented in a dynamic language like Groovy, by using the language's capabilities for meta-programming. We then consider a set of examples and discuss dynamic PT from the viewpoints of code modularization and reuse, and dynamic adaption of classes at runtime.
Predicting Cotton Seedling Emergence for Cold Tolerance: Gossypium hirsutum L. (2010)

Breeding cotton for stress tolerance is a priory of most cotton breeding programs. One of the stresses for cotton is cold that affects lint and yield quality. A total of 95 cotton genotypes belonging to G. hirsutum L. were screened at 5 different laboratory tests to determine the best screening test to predict field emergence. Field emergence percentages ranged from 38% to 77% for the 28th day after planting. A standard germination test was performed at 30oC. Cool germination percentages were measured at 13oC, 15oC and 18oC. Multiple regressions were used to determine the degree of association between variables. Predicting field emergence with combinations of 30oC and 18oC tests was better than other tests alone.
MC <sup>2</sup> (2004)

Java is becoming an important platform for memory-constrained consumer devices such as PDAs and cellular phones, because it provides safety and portability. Since Java uses garbage collection, efficient garbage collectors that run in constrained memory are essential. Typical collection techniques used on these devices are mark-sweep and mark-compact. Mark-sweep collectors can provide good throughput and pause times but suffer from fragmentation. Mark-compact collectors prevent fragmentation, have low space overheads, and provide good throughput. However, they can suffer from long pause times. Copying collectors can provide higher throughput than either of these techniques, but because of their high space overhead, they previously were unsuitable for memory-constrained devices. This paper presents MC<sup>2</sup> (Memory-Constrained Copying), a copying generational garbage collector that meets the needs of memory-constrained devices with soft real-time requirements. MC<sup>2</sup> has low space over-head and tight space bounds, prevents fragmentation, provides good throughput, and yields short pause times. These qualities make MC<sup>2</sup> attractive for other environments, including desktops and servers.