gebhart/patrepeval huggingface dataset:
Volatile Retention and Morphological Properties of Microencapsulated Tributyrin Varied by Wall Material and Drying Method (2016)

Butyric acid is an important short-chain fatty acid for intestinal health and has been shown to improve certain intestinal disease states. A triglyceride containing 3 butyric acid esters, tributyrin (TB) can serve as a source of butyric acid; however, the need to target intestinal delivery and mitigate unpleasant sensory qualities has limited its use in food. Microencapsulation, the entrapment of one or more cores within a matrix, may provide a solution to the aforementioned challenge. This research primarily focused on the influence of (1) wall material: whey and soy protein isolate (WPI and SPI, respectively) and gamma-cyclodextrin (GCD), (2) wall additives: inulin of varying chain length, and (3) processing method: spray or oven drying (SD or OD, respectively) on the morphological properties and volatile retention of TB within microcapsules. SPI-based microcapsules retained significantly less (P < 0.001) TB compared to WPI-based microcapsules as measured by gas chromatography. The inclusion of inulin in the SD WPI-based microcapsules increased (P < 0.001) TB retention over WPI-based microcapsules without inulin. Inulin inclusion into WPI-based microcapsules resulted in a smoother, minimally-dented, circular morphology as compared to noninulin containing WPI-based microcapsules as shown by scanning electron microscopy. GCD and TB OD microcapsules retained more (P < 0.001) TB (94.5% ± 1.10%) than all other WPI, WPI-inulin, and GCD TB SD microcapsules. When spray dried, the GCD-based microcapsules exhibited (P < 0.001) TB retention than all other microcapsules, indicating the GCD may be unsuitable for spray drying. These findings demonstrate that microencapsulated TB in GCD can lead to minimal TB losses during processing that could be utilized in functional food applications for intestinal health.
Contribution of the Disulfide Bond of the A Subunit to the Action of <i>Escherichia coli</i> Heat-Labile Enterotoxin (1998)

Escherichia coli heat-labile enterotoxin (LT) consists of an A subunit and five B subunits. These subunits oligomerize into an assembled holotoxin within the periplasm. Structural analysis of LT has revealed that the A subunit interacts with the B subunit through its carboxy terminus. This indicates that the carboxy-terminal portion of the protein is required for assembly of holotoxin in the periplasm. However, it is not known whether other regions of the A subunit contribute to the assembly. The A subunit constituting the holotoxin contains a disulfide bond between Cys-187 and Cys-199. It has been observed in many proteins that the intramolecular disulfide bond is deeply involved in the function and tertiary structure of the protein. We speculated that the disulfide bond of the A subunit contributes to the assembly in the periplasm, although the bond is not a structural element of the carboxy-terminal portion of the A subunit. We replaced these cysteine residues of the A subunit by oligonucleotide-directed site-specific mutagenesis and analyzed the LTs produced by cells containing the mutant LT genes. The amount of the mutant holotoxin produced was small compared with that of the wild-type strain, indicating that the disulfide bond of the A subunit contributes to the structure which functions as the site of nucleation in the assembly. A reconstitution experiment in vitro supported the notion. Subsequently, we found that the mutant A subunit constituting holotoxin is easily degraded by trypsin and that in cells incubated with mutant LTs, the lag until the intracellular cyclic AMP begins to accumulate is longer than in cells incubated with native LTs. These results might be useful for the analysis of the interaction of LT with target cells at the molecular level.
The Cellular and Subcellular Localization of Huntingtin-Associated Protein 1 (HAP1): Comparison with Huntingtin in Rat and Human (1998)

The cellular and subcellular distribution of HAP1 was examined in rat brain by light and electron microscopic immunocytochemistry and subcellular fractionation. HAP1 localization was also determined in human postmortem tissue from control and Huntington's disease (HD) cases by light microscopic immunocytochemistry. At the cellular level, the heterogeneity of HAP1 expression was similar to that of huntingtin; however, HAP1 immunoreactivity was more widespread. The subcellular distribution of HAP1 was examined using immunogold electron microscopy. Like huntingtin, HAP1 is a cytoplasmic protein that associates with microtubules and many types of membranous organelles, including mitochondria, endoplasmic reticulum, tubulovesicles, endosomal and lysosomal organelles, and synaptic vesicles. A quantitative comparison of the organelle associations of HAP1 and huntingtin showed them to be almost identical. Within HAP1-immunoreactive neurons in rat and human brain, populations of large and small immunoreactive puncta were visible by light microscopy. The large puncta, which were especially evident in the ventral forebrain, were intensely HAP1 immunoreactive. Electron microscopic analysis revealed them to be a type of nucleolus-like body, which has been named a stigmoid body, that may play a role in protein synthesis. The small puncta, less intensely labeled, were primarily mitochondria. These results indicate that the localization of HAP1 and huntingtin is more similar than previously appreciated and provide further evidence that HAP1 and huntingtin have localizations consistent with roles in intracellular transport. Our data also suggest, however, that HAP1 is not present in the abnormal intranuclear and neuritic aggregates containing the N-terminal fragment of mutant huntingtin that are found in HD brains.
Activating Ly-49 NK Receptors: Central Role in Cytokine and Chemokine Production (2001)

In an attempt to understand potential novel functions of receptors in vivo, we evaluated gene expression after cross-linking the activating Ly-49D mouse NK receptor. Gene expression was evaluated using a mouse GEM 2 microarray chip (Incyte Genomics, St. Louis, MO). Each chip displays a total of 8734 elements. The strongly induced genes fell into two categories: 1) soluble factors and 2) apoptotic genes. The majority of the strongly induced mRNAs as analyzed by microarray hybridization were chemokine genes. RNase protection assays and chemokine protein production analysis validated the microarray results, as cross-linking the Ly-49D mouse NK receptor induced high levels of IFN-gamma, lymphotactin, macrophage-inflammatory protein (MIP)1alpha, and MIP1beta. This gene expression was specific because other chemokines were not induced by anti-Ly-49D receptors. In addition, a series of pharmacological inhibitors were used to identify the key signaling pathways involved in the cellular response. The primary Ly-49D signaling for IFN-gamma production is predominantly mediated through Src kinase pathways involving membrane proximal events, whereas MIP1alpha and MIP1beta gene induction is more complex and may involve multiple biochemical pathways. Thus, we conclude that a primary role for the activating NK receptors in vivo may be to trigger soluble factor production and regulation of the immune response. This would place NK cells and their activating Ly-49 receptors as important initiators of microbial immunity and key elements of the innate immune system.
Quorum Sensing between <i>Pseudomonas aeruginosa</i> Biofilms Accelerates Cell Growth (2011)

This manuscript describes the fabrication of arrays of spatially confined chambers embossed in a layer of poly(ethylene glycol) diacrylate (PEGDA) and their application to studying quorum sensing between communities of Pseudomonas aeruginosa. We hypothesized that biofilms may produce stable chemical signaling gradients in close proximity to surfaces, which influence the growth and development of nearby microcolonies into biofilms. To test this hypothesis, we embossed a layer of PEGDA with 1.5-mm wide chambers in which P. aeruginosa biofilms grew, secreted homoserine lactones (HSLs, small molecule regulators of quorum sensing), and formed spatial and temporal gradients of these compounds. In static growth conditions (i.e., no flow), nascent biofilms secreted N-(3-oxododecanoyl) HSL that formed a gradient in the hydrogel and was detected by P. aeruginosa cells that were ≤8 mm away. Diffusing HSLs increased the growth rate of cells in communities that were <3 mm away from the biofilm, where the concentration of HSL was >1 μM, and had little effect on communities farther away. The HSL gradient had no observable influence on biofilm structure. Surprisingly, 0.1-10 μM of N-(3-oxododecanoyl) HSL had no effect on cell growth in liquid culture. The results suggest that the secretion of HSLs from a biofilm enhances the growth of neighboring cells in contact with surfaces into communities and may influence their composition, organization, and diversity.
Oxygen sensing by electrochemical pumping (1981)

An oxygen pumping structure using ZrO2 electrochemical cells is described for measuring the percentage of O2 in a high-temperature gaseous environment. The device output is linearly proportional to the O2 percentage, has a weak dependence on temperature, and does not require a reference atmosphere.
HEV Control Strategy for Real-Time Optimization of Fuel Economy and Emissions (2000)

<div class="htmlview paragraph">Hybrid electric vehicles (HEV's) offer additional flexibility to enhance the fuel economy and emissions of vehicles. The Real-Time Control Strategy (RTCS) presented here optimizes efficiency and emissions of a parallel configuration HEV. In order to determine the ideal operating point of the vehicle's engine and motor, the control strategy considers all possible engine-motor torque pairs. For a given operating point, the strategy predicts the possible energy consumption and the emissions emitted by the vehicle. The strategy calculates the “replacement energy” that would restore the battery's state of charge (SOC) to its initial level. This replacement energy accounts for inefficiencies in the energy storage system conversion process. User- and standards-based weightings of time-averaged fuel economy and emissions performance determine an overall impact function. The strategy continuously selects the operating point that is the minimum of this cost function. Previous control strategies employed a set of static parameters optimized for a particular drive cycle, and they showed little sensitivity to subtle emissions tradeoffs. This new control strategy adjusts its behavior based on the current driving conditions. Simulation results of the RTCS and of a static control strategy on a PNGV-type baseline parallel HEV (42 kW engine and a 32 kW motor) using ADVISOR are presented. Comparison of the simulations demonstrates the flexibility and advantages of the RTCS. Compared to an optimized static control strategy, the RTCS reduced NOx emissions by 23% and PM emissions by 13% at a sacrifice of only 1.4% in fuel economy.</div>
Housing investment in Finland (1990)

The high volatility of both housing investment and housing prices has raised questions about the determinants of housing investment in Finland. In this paper we estimate investment equations for the period 1972 -1987. The exceptional durability of houses makes housing investment sensitive to interest rates as well as to changes in the liquidity constraints due to money market liberalization during the 1980's. Here, we confirm the applicability of Tobin's q theory of investment as an explanation for housing investment. Therefore housing investment can be successfully and sufficiently explained with the ratio of nominal housing prices to their construction costs. However, we observed structural changes in the model of housing investment and the q theory gives a better description for supply of houses in the latter half of the estimation period 1980-87.
Bactericidal/permeability-increasing protein—Lessons learned from the phase III, randomized, clinical trial of rBPI21 for adjunctive treatment of children with severe meningococcemia (2001)

As the largest therapeutic trial conducted in pediatric critical care, the phase III trial of rBPI21 demonstrates important principles that can influence the design of future trials targeting rare, life-threatening diseases.
MALE STERILITY IN SOYBEAN (GLYCINE MAX). II. PHENOTYPIC EXPRESSION OF THE ms4 MUTANT (1985)

Observations on the reproductive biology of a male‐sterile mutant ( ms4 ) of soybean, Glycine max (L.) Merr., demonstrated that male sterility was the result of a syndrome of abnormalities that influenced the function of the postmeiotic microspore mother cells (MMCs). Cytokinesis following telophase II was absent, incomplete, or disoriented, resulting in cells with different numbers of nuclei. Postmeiotic cells demonstrated various abnormalities in the formation of pollen walls. The nature of the exine ranged from absence through amorphous accumulations of sporopollenin to stratified layers. Infrequently, anther locules functioned properly, and normal pollen was differentiated. The extent and frequency of cytokinesis varied both between and within locules of single anthers. Temperature influenced the frequency of cytokinesis. At temperatures of 35 C day/32 C night, cytokinesis did not occur. Male sterility was concluded to result from the cumulative effects of various abnormalities, all of which involve functions of the postmeiotic MMCs' plasmalemmas.
Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction (2014)

An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation.
Decreased level of PDGF-stimulated receptor autophosphorylation by fibroblasts in mechanically relaxed collagen matrices (1993)

The goal of our studies was to characterize the interrelationship between extracellular matrix organization and fibroblast proliferation in response to growth factors. We compared fibroblasts in monolayer culture with cells in contracted collagen matrices that were mechanically stressed or relaxed. In response to platelet-derived growth factor (PDGF), DNA synthesis by fibroblasts in mechanically relaxed collagen matrices was 80-90% lower than in monolayer culture and 50% lower than in mechanically stressed matrices. Fibroblasts in monolayer and contracted collagen matrix cultures contained similar levels of PDGF receptors, but differed in their autophosphorylation response. Cells in mechanically relaxed matrices showed lowest levels of autophosphorylation, 90% less than cells in monolayer culture. Experiments comparing receptor expression and capacity for PDGF-stimulated autophosphorylation showed that cells in mechanically relaxed collagen matrices never developed normal receptor autophosphorylation. Furthermore, when mechanically stressed collagen matrices were switched to mechanically relaxed conditions, capacity for receptor autophosphorylation decreased within 1-2 h and remained low. Based on immunomicroscopic observations and studies on down-regulation of receptors by PDGF binding, it appeared that most PDGF receptors in monolayer or contracted collagen matrix cultures were localized on the cell surface and accessible to PDGF binding. In related studies, we found that EGF receptors of fibroblasts in mechanically relaxed collagen matrices also showed low levels of autophosphorylation in response to EGF treatment. Based on these results, we suggest that mechanical interactions between cells and their surrounding matrix provide regulatory signals that modulate autophosphorylation of growth factor receptors and cell proliferation.
Plasma Adenosine Levels in Peri-Menopausal Women Having Frequent Hot Flushes (2005)

Increased plasma adenosine in peri-menopausal women may be associated with frequent hot flushes.
CORD: Cost-effective (and nearly overhead-free) Order-Recording and Data race detection (2006)

Chip-multiprocessors are becoming the dominant vehicle for general-purpose processing, and parallel software will be needed to effectively utilize them. This parallel software is notoriously prone to synchronization bugs, which are often difficult to detect and repeat for debugging. While data race detection and order-recording for deterministic replay are useful in debugging such problems, only order-recording schemes are lightweight, whereas data race detection support scales poorly and degrades performance significantly. This paper presents our CORD (cost-effective order-recording and data race detection) mechanism. It is similar in cost to prior order-recording mechanisms, but costs considerably less then prior schemes for data race detection. CORD also has a negligible performance overhead (0.4% on average) and detects most dynamic manifestations of synchronization problems (77% on average). Overall, CORD is fast enough to run always (even in performance-sensitive production runs) and provides the support programmers need to deal with the complexities of writing, debugging, and maintaining parallel software for future multi-threaded and multi-core machines.
Organic CO Prodrugs: Structure–CO‐Release Rate Relationship Studies (2017)

Carbon monoxide (CO) is an endogenously produced gasotransmitter in mammals, and may have signaling roles in bacteria as well. It has many recognized therapeutic effects. A significant challenge in this field is the development of pharmaceutically acceptable forms of CO delivery with controllable and tunable release rates. Herein, the structure-release rate studies of the first class of organic CO prodrugs that release CO in aqueous solution at neutral pH is described.
A Kernel for Time Series Based on Global Alignments (2007)

We propose in this paper a new family of kernels to handle time series, notably speech data, within the framework of kernel methods which includes popular algorithms such as the support vector machine. These kernels elaborate on the well known dynamic time warping (DTW) family of distances by considering the same set of elementary operations, namely substitutions and repetitions of tokens, to map a sequence onto another. Associating to each of these operations a given score, DTW algorithms use dynamic programming techniques to compute an optimal sequence of operations with high overall score, in this paper we consider instead the score spanned by all possible alignments, take a smoothed version of their maximum and derive a kernel out of this formulation. We prove that this kernel is positive definite under favorable conditions and show how it can be tuned effectively for practical applications as we report encouraging results on a speech recognition task.
Enhanced nitrogen incorporation by pulsed laser annealing of GaNxAs1−x formed by N ion implantation (2002)

We demonstrate that pulsed laser annealing followed by rapid thermal annealing greatly enhances incorporation of substitutional N in N+-implanted GaAs. Films implanted to 1.8% N exhibit a fundamental band gap of 1.26 eV (a band gap reduction of 160 meV), corresponding to an N activation efficiency of 50%. The optical and crystalline quality of the synthesized film is comparable to GaNxAs1−x thin films of similar composition grown by epitaxial growth techniques. Compared to films produced by N+ implantation and rapid thermal annealing only, the introduction of pulsed laser annealing improves N incorporation by a factor of 5. Moreover, we find that the synthesized films are thermally stable up to an annealing temperature of 950 °C.
Double-blind, Randomized, 8-week Placebo-controlled followed by a 16-week open label extension study, with the LPA1 receptor antagonist SAR100842 for Patients With Diffuse Cutaneous Systemic Sclerosis (2018)

BACKGROUND Preclinical studies suggest a role for lysophosphatidic acid (LPA) in the pathogenesis of systemic sclerosis (SSc). OBJECTIVES SAR100842, a potent selective oral antagonist of LPA1 receptor, was assessed for safety, biomarkers and clinical efficacy in patients with diffuse cutaneous SSc (dcSSc). METHODS An 8-week double-blind, randomized, placebo-controlled study followed by a 16-week open label extension with SAR100842 was performed in patients with early dcSSc and a baseline Rodnan skin score (mRSS) of at least 15. The primary endpoint was safety during the double-blind phase of the trial. Exploratory endpoints included the identification of a LPA-induced gene signature in patients 'skin. RESULTS 17 of 32 subjects were randomized to placebo and 15 to SAR100842; 30 patients participated in the extension study. The most frequent adverse events reported for SAR100842 during the blinded phase were headache, diarrhea, nausea and fall and the safety profile was acceptable during the extension part. At Week 8, mean reduction in mRSS was numerically greater in the SAR100842 compared to placebo (mean change [SD]: -3.57 [4.18] versus -2.76 [4.85]; difference [95% CI]: -1.2 [-4.37 to 2.02], p=0.46). A greater reduction of LPA related genes was observed in skin of SAR100842 group at Week 8, indicating LPA target engagement. CONCLUSION SAR100842, a selective orally available LPA receptor antagonist, was well tolerated in patients with dcSSc. MRSS improved during the study although not reaching significance, and additional gene signature analysis suggested target engagement. These results need to be confirmed in a larger controlled trial. This article is protected by copyright. All rights reserved.
Flexible architectural support for fine-grain scheduling (2010)

To make efficient use of CMPs with tens to hundreds of cores, it is often necessary to exploit fine-grain parallelism. However, managing tasks of a few thousand instructions is particularly challenging, as the runtime must ensure load balance without compromising locality and introducing small overheads. Software-only schedulers can implement various scheduling algorithms that match the characteristics of different applications and programming models, but suffer significant overheads as they synchronize and communicate task information over the deep cache hierarchy of a large-scale CMP. To reduce these costs, hardware-only schedulers like Carbon, which implement task queuing and scheduling in hardware, have been proposed. However, a hardware-only solution fixes the scheduling algorithm and leaves no room for other uses of the custom hardware. This paper presents a combined hardware-software approach to build fine-grain schedulers that retain the flexibility of software schedulers while being as fast and scalable as hardware ones. We propose asynchronous direct messages (ADM), a simple architectural extension that provides direct exchange of asynchronous, short messages between threads in the CMP without going through the memory hierarchy. ADM is sufficient to implement a family of novel, software-mostly schedulers that rely on low-overhead messaging to efficiently coordinate scheduling and transfer task information. These schedulers match and often exceed the performance and scalability of Carbon when using the same scheduling algorithm. When the ADM runtime tailors its scheduling algorithm to application characteristics, it outperforms Carbon by up to 70%.