gebhart/patrepeval huggingface dataset:
Dimensionality and Size Scaling of Coordinated Ca2+ Dynamics in MIN6 β-cell Clusters (2014)

Pancreatic islets of Langerhans regulate blood glucose homeostasis by the secretion of the hormone insulin. Like many neuroendocrine cells, the coupling between insulin-secreting β-cells in the islet is critical for the dynamics of hormone secretion. We have examined how this coupling architecture regulates the electrical dynamics that underlie insulin secretion by utilizing a microwell-based aggregation method to generate clusters of a β-cell line with defined sizes and dimensions. We measured the dynamics of free-calcium activity ([Ca(2+)]i) and insulin secretion and compared these measurements with a percolating network model. We observed that the coupling dimension was critical for regulating [Ca(2+)]i dynamics and insulin secretion. Three-dimensional coupling led to size-invariant suppression of [Ca(2+)]i at low glucose and robust synchronized [Ca(2+)]i oscillations at elevated glucose, whereas two-dimensional coupling showed poor suppression and less robust synchronization, with significant size-dependence. The dimension- and size-scaling of [Ca(2+)]i at high and low glucose could be accurately described with the percolating network model, using similar network connectivity. As such this could explain the fundamentally different behavior and size-scaling observed under each coupling dimension. This study highlights the dependence of proper β-cell function on the coupling architecture that will be important for developing therapeutic treatments for diabetes such as islet transplantation techniques. Furthermore, this will be vital to gain a better understanding of the general features by which cellular interactions regulate coupled multicellular systems.
Palladium-catalysed asymmetric allylic alkylation in the presence of a chiral ‘light fluorous’ phosphine ligand (2001)

The easily accessible, enantiopure (R)-(+)-2-diarylphosphino-2′-alkoxy-1,1′-binaphthyl 1 bearing three fluorous ponytails is an efficient ligand in the palladium-catalysed asymmetric allylic substitution of 1,3-diphenylprop-2-enyl acetate affording chiral products of up to 87% ee.
Design Rules for Electroforming in the LIGA Process (2004)

Design rules for electroforming that avoid design flaws are presented. The physical background and interlink to the perceptions in the literature that sum up those rules are outlined. The characteristic dimensionless groups that are needed to identify the regime at which each electroforming process is run are summarized so that the relevance of each design rule can be determined. It is also shown how image possessing helps to visualize design flaws quickly, i.e., without the effort of a full simulation. All design rules do not rely on the details of the galvanic bath, but only on the knowledge of the flow regime and plating regime. Thus a first step to a simple design evaluation for the nonexpert is outlined. © 2004 The Electrochemical Society. All rights reserved.
Virtual reality technology for the clinician (2015)

Summary form only given. Virtual reality technology has progressed substantially in recent years, with system costs diminishing. Adoption has been mixed, and sometimes without a strong body of research, which certainly poses safety risks for the patient and professional challenges for the clinician. While building a strong body of data that would lead to “best practices” will take time, this Workshop can assist by giving a broad and unbiased coverage of the technology and predicting trends for the future. Practical issues with adoption will also be discussed, as well as cost considerations.
RLIP76 Protein Knockdown Attenuates Obesity Due to a High-fat Diet (2013)

Feeding a Western high-fat diet (HFD) to C57BL/6 mice induces obesity, associated with a chronic inflammatory state, lipid transport, and metabolic derangements, and organ system effects that particularly prominent in the kidneys. Here, we report that RLIP76 homozygous knock-out (RLIP76(-/-)) mice are highly resistant to obesity as well as these other features of metabolic syndrome caused by HFD. The normal increase in pro-inflammatory and fibrotic markers associated with HFD induced obesity in wild-type C57B mice was broadly and nearly completely abrogated in RLIP76(-/-) mice. This is a particularly striking finding because chemical markers of oxidative stress including lipid hydroperoxides and alkenals were significantly higher in RLIP76(-/-) mice. Whereas HFD caused marked suppression of AMPK in wild-type C57B mice, RLIP76(-/-) mice had baseline activation of AMP-activated protein kinase, which was not further affected by HFD. The baseline renal function was reduced in RLIP76(-/-) mice as compared with wild-type, but was unaffected by HFD, in marked contrast to severe renal impairment and glomerulopathy in the wild-type mice given HFD. Our findings confirm a fundamental role of RLIP76 in regulating the function of obesity-promoting pro-inflammatory cytokines, and provide a novel mechanism for targeted therapy of obesity and metabolic syndrome.
Bug Localization with Combination of Deep Learning and Information Retrieval (2017)

The automated task of locating the potential buggy files in a software project given a bug report is called bug localization. Bug localization helps developers focus on crucial files. However, the existing automated bug localization approaches face a key challenge, called lexical mismatch. Specifically, the terms used in bug reports to describe a bug are different from the terms and code tokens used in source files. To address that, we present a novel approach that uses deep neural network (DNN) in combination with rVSM, an information retrieval (IR) technique. rVSM collects the feature on the textual similarity between bug reports and source files. DNN is used to learn to relate the terms in bug reports to potentially different code tokens and terms in source files. Our empirical evaluation on real-world bug reports in the open-source projects shows that DNN and IR complement well to each other to achieve higher bug localization accuracy than individual models. Importantly, our new model, DNNLOC, with a combination of the features built from DNN, rVSM, and project's bug-fixing history, achieves higher accuracy than the state-of-the-art IR and machine learning techniques. In half of the cases, it iscorrect with just a single suggested file. In 66% of the time, acorrect buggy file is in the list of three suggested files. With 5 suggested files, it is correct in almost 70% of the cases.
Visual analog scale (VAS) and time trade-off (TTO) preferences for side effects (SE) of chemoradiation (chemoXRT): A comparison of patients (pts) and caregivers (CG). (2010)

9056 Background: CG provide clinicians valuable information about treatment-related SE they see pts experience. As part of a larger study, we prospectively assessed the preferences of pts and CG for chemoXRT-related SE. Methods: Pts with GYN or GI cancers scheduled for chemoXRT and their CG were separately interviewed prior to initiation of treatment. The VAS was used to evaluate 21 health states (5 anchor states + 16 SE); TTO used for the 16 SE. For the VAS, SE were rated on a scale of 0=worst to 100=best. The TTO involved choosing between Treatment A for time 6 weeks with SEi (i = SE under consideration) and Treatment B with SE= acute nausea/vomiting for x weeks (where x < 6 weeks). Pts and CG were asked to specify a time x for when they considered Treatment A equivalent to Treatment B. VAS and TTO scores were converted to a scale of 0.0 to 1.0 (0=least preferred;1=most preferred). Mann-Whitney and Kruskal-Wallis tests were used to analyze data. Results: Preferences were assessed for 110 pts and 97 CG. Median ages of pts and CG were 53.8 yrs (range 31.6 to 81.4) and 53.4 years (range 19.5 to 86.2), respectively. The majority of CG were female (n=63). CG included pts' spouse/partner (n=65), adult children (n=10), sibling (n=6), other relative (n=8), and friend (n=8). Overall, CG had more favorable VAS and TTO scores than pts. By VAS, CG gave significantly more favorable ratings for current health (0.85 vs 0.73, p<.001), alopecia (0.54 vs 0.44, p=.02), changes in appetite (0.48 vs 0.40, p=.02), delayed nausea (0.49 vs 0.41, p=.03), acute nausea (0.68 vs 0.60, p=.02), delayed vomiting (0.44 vs 0.36, p=.03), and acute vomiting (0.65 vs 0.50, p=.005). By TTO, CG were significantly more willing than pts to accept intestinal obstruction (0.63 vs 0.53, p=.036), rectovaginal fistula (0.56 vs 0.40, p=.047) and acute nausea (0.92 vs 0.88, p=.014). Conclusions: CG perceptions of chemoXRT-related SE are significantly more favorable than pts' perceptions at baseline. Awareness of differences in perspective is an important concept for pts, CG, and clinicians to acknowledge. Further efforts are needed to determine whether the experience of pts during treatment influence CG preferences over time. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Merck
Nanotechnology in Corneal Neovascularization Therapy—A Review (2013)

Nanotechnology is an up-and-coming branch of science that studies and designs materials with at least one dimension sized from 1-100 nm. These nanomaterials have unique functions at the cellular, atomic, and molecular levels. The term "nanotechnology" was first coined in 1974. Since then, it has evolved dramatically and now consists of distinct and independent scientific fields. Nanotechnology is a highly studied topic of interest, as nanoparticles can be applied to various fields ranging from medicine and pharmacology, to chemistry and agriculture, to environmental science and consumer goods. The rapidly evolving field of nanomedicine incorporates nanotechnology with medical applications, seeking to give rise to new diagnostic means, treatments, and tools. Over the past two decades, numerous studies that underscore the successful fusion of nanotechnology with novel medical applications have emerged. This has given rise to promising new therapies for a variety of diseases, especially cancer. It is becoming abundantly clear that nanotechnology has found a place in the medical field by providing new and more efficient ways to deliver treatment. Ophthalmology can also stand to benefit significantly from the advances in nanotechnology research. As it relates to the eye, research in the nanomedicine field has been particularly focused on developing various treatments to prevent and/or reduce corneal neovascularization among other ophthalmologic disorders. This review article aims to provide an overview of corneal neovascularization, currently available treatments, and where nanotechnology comes into play.
Protection of Arabidopsis thaliana against Leaf-Pathogenic Pseudomonas syringae by Sphingomonas Strains in a Controlled Model System (2011)

Diverse bacterial taxa live in association with plants without causing deleterious effects. Previous analyses of phyllosphere communities revealed the predominance of few bacterial genera on healthy dicotyl plants, provoking the question of whether these commensals play a particular role in plant protection. Here, we tested two of them, Methylobacterium and Sphingomonas, with respect to their ability to diminish disease symptom formation and the proliferation of the foliar plant pathogen Pseudomonas syringae pv. tomato DC3000 on Arabidopsis thaliana. Plants were grown under gnotobiotic conditions in the absence or presence of the potential antagonists and then challenged with the pathogen. No effect of Methylobacterium strains on disease development was observed. However, members of the genus Sphingomonas showed a striking plant-protective effect by suppressing disease symptoms and diminishing pathogen growth. A survey of different Sphingomonas strains revealed that most plant isolates protected A. thaliana plants from developing severe disease symptoms. This was not true for Sphingomonas strains isolated from air, dust, or water, even when they reached cell densities in the phyllosphere comparable to those of the plant isolates. This suggests that plant protection is common among plant-colonizing Sphingomonas spp. but is not a general trait conserved within the genus Sphingomonas. The carbon source profiling of representative isolates revealed differences between protecting and nonprotecting strains, suggesting that substrate competition plays a role in plant protection by Sphingomonas. However, other mechanisms cannot be excluded at this time. In conclusion, the ability to protect plants as shown here in a model system may be an unexplored, common trait of indigenous Sphingomonas spp. and may be of relevance under natural conditions.
Catalytic Steam Gasification of Pine Sawdust. Effect of Catalyst Weight/Biomass Flow Rate and Steam/Biomass Ratios on Gas Production and Composition (1999)

Pine sawdust catalytic steam gasification has been studied in a fluidized bed at a relatively low temperature, 700 °C. The Ni−Al catalyst used was prepared by coprecipitation and calcined at 750 °C for 3 h. The influence of the catalyst weight/biomass flow rate (W/mb) and steam/biomass (S/B) ratios on the product distribution and on the quality of the gas product obtained was analyzed. An increase of the W/mb ratio increases the total gas, H2, CO, and CO2 yields, while CH4 and C2 yields decrease. An increase of the S/B ratio increases H2 and CO2 yields while CO and CH4 yields decrease. This fact can be explained by steam reforming and water-gas shift reactions. The increase of the S/B ratio also has a positive effect on the life of the catalyst. The gas composition and gas yields at initial time have also been studied. For W/mb ratios > 0.5 h, the gas composition at initial time is similar to that for thermodynamic equilibrium for different S/B ratios. The influence of the S/B ratio on gas yield at initial time is more marked, up to a ratio of 1.5.
Long-Term Telemetric Recording of Arterial Pressure and Heart Rate in Mice Fed Basal and High NaCl Diets (2000)

Research examining the control of arterial pressure in mice has primarily relied on tail-cuff plethysmography and, more recently, on tethered arterial catheters. In contrast, the radiotelemetry method has largely become the "gold standard" for long-term monitoring of arterial pressure and heart rate in rats. Whereas smaller telemetry probes have recently been developed, no published studies have used radiotelemetric monitoring of arterial pressure in mice, largely because of a relatively low success rate in small mice (ie, <30 g body weight). We report on the development of a protocol for the use of these probes to continuously monitor arterial pressure and heart rate in mice as small as 19 g body weight. To test the accuracy and reliability of this method, adult C57/BL6 mice were monitored for 3 weeks during exposure to a basal followed by a high NaCl diet. The results demonstrate that carotid and aortic placements of the telemetry probe provide equally accurate monitoring of arterial pressure and heart rate, but the carotid placement has a much greater rate of success. Exposure to a high NaCl diet increases both the amplitude of the arterial pressure rhythm (+ 6.0+/-0.6 mm Hg, approximately 32%) and the average mean arterial pressure (+ 8.6+/-1.1 mm Hg, approximately 8%), as would be predicted from previous studies in NaCl-resistant rats. Thus, the data demonstrate that telemetric recording of long-term arterial pressure and heart rate provides a powerful tool with which to define the mechanisms of cardiovascular control in mice.
The impact of MP3 and the future of digital entertainment products (1999)

MP3, or MPEG Layer 3 Audio, is a format for compressing digital audio developed by the Motion Picture Experts Group, a standards organization that has developed a number of digital standards for video and audio. MP3 has become a very popular format for storing music digitally. Fueled by the explosive growth of the Internet, MP3 has become the most popular format for music files, both legal and illegal (unauthorized digital copies of copyrighted works).
Optimized Programming Scheme Enabling Linear Potentiation in Filamentary HfO<sub>2</sub> RRAM Synapse for Neuromorphic Systems (2016)

In this brief, we demonstrate the multilevel cell (MLC) characteristics of an HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -based resistive memory (RRAM) array as a synaptic element for neuromorphic systems. We utilize various programming schemes to linearly change the resistance state with either set voltage/pulse ramping or gate voltage ramping. Our results reveal that the MLC relates to the size of the conductive filament involved in the movement of oxygen vacancies with respect to applying pulses. Thus, by optimizing the pulse for a set condition, such as an identical pulse, we achieve linearly increased MLC behavior, thereby enabling a high accuracy for pattern recognition in neuromorphic systems.
Power optimization methodology for the IBM POWER7 microprocessor (2011)

Meeting the power budget of the 8 four-way simultaneous multithreading core IBM POWER7® microprocessor without compromising the aggressive performance targets presented a considerable challenge to the design team. Major innovations in the power modeling and power reduction methodologies have been introduced at all levels of the design, including microarchitecture, logic, circuits, postlayout tuning, and technology optimizations. In order to use effectively design resources available for power reduction, the team needed to understand precisely where the power was spent and the sensitivity to design parameters. A new power modeling methodology was deployed that allowed the team to evaluate the impact of design changes and various power reduction actions before sending them to the designers.
Estimation of Spatiotemporal Sensitivity Using Band-limited Signals with No Additional Acquisitions for <i>k−t</i> Parallel Imaging (2018)

In the present study, k - t SENSE was identified as a suitable base method to be improved achieving both short acquisition times and a cost-effective reconstruction. To enhance these characteristics of base method, a novel implementation is proposed, estimating the x - f sensitivity without the need for an explicit scan of the reference signals. Experimental results showed that the acquisition, computational times and image quality for the proposed method were improved compared to the standard k - t SENSE method.
Mechanochemical synthesis of a hydroxycarbonate form of layered magnesium aluminum hydroxides (2008)

Mechanical activation of a mixture of magnesium hydroxide, aluminum hydroxide, and sodium bicarbonate in an AGO-2 planetary mill, followed by water washing leads to the formation of a layered magnesium aluminum hydroxide. The double hydroxide obtained at a magnesium hydroxide to aluminum hydroxide ratio of 3:1 is essentially phase-pure and contains both carbonate and bicarbonate ions in its interlayer spaces. The synthesized double hydroxide was characterized by x-ray diffraction, IR spectroscopy, thermogravimetry, differential thermal analysis, and chemical analysis.
Exploring the distribution of online healthcare information (2003)

Motivated by the importance of retrieving comprehensive healthcare information, we analyzed how information about 12 concepts related to a widely available healthcare topic is distributed across 145 high-quality webpages. The analysis reveals that the distribution of the concepts follows a power law where a few pages contain many concepts, while the majority contains less than half the concepts. The analysis also reveals the existence of general, specialized, and sparse pages, in addition to the large number of pages that users must visit before they have access to all the concepts. These results provide insights into expert search procedures, and motivate the design of future search systems that guide users in the retrieval of comprehensive information.
REVIEWS OF BOOKS (1998)

Journal Article REVIEWS OF BOOKS Get access Schubert and his World: a Biographical Dictionary By Peter Clive pp. xxvi + 310. ( Clarendon Press, Oxford, 1997, £29. 95. ISBN 0-19-816582-X. ) SUZANNAH CLARK SUZANNAH CLARK Search for other works by this author on: Oxford Academic Google Scholar Music and Letters, Volume 79, Issue 1, February 1998, Pages 126–127, https://doi.org/10.1093/ml/79.1.126 Published: 01 February 1998
Crystal Structures of Staphylococcus epidermidis Mevalonate Diphosphate Decarboxylase Bound to Inhibitory Analogs Reveal New Insight into Substrate Binding and Catalysis (2011)

The polyisoprenoid compound undecaprenyl phosphate is required for biosynthesis of cell wall peptidoglycans in gram-positive bacteria, including pathogenic Enterococcus, Streptococcus, and Staphylococcus spp. In these organisms, the mevalonate pathway is used to produce the precursor isoprenoid, isopentenyl 5-diphosphate. Mevalonate diphosphate decarboxylase (MDD) catalyzes formation of isopentenyl 5-diphosphate in an ATP-dependent irreversible reaction and is therefore an attractive target for inhibitor development that could lead to new antimicrobial agents. To facilitate exploration of this possibility, we report the crystal structure of Staphylococcus epidermidis MDD (1.85 Å resolution) and, to the best of our knowledge, the first structures of liganded MDD. These structures include MDD bound to the mevalonate 5-diphosphate analogs diphosphoglycolyl proline (2.05 Å resolution) and 6-fluoromevalonate diphosphate (FMVAPP; 2.2 Å resolution). Comparison of these structures provides a physical basis for the significant differences in K(i) values observed for these inhibitors. Inspection of enzyme/inhibitor structures identified the side chain of invariant Ser(192) as making potential contributions to catalysis. Significantly, Ser → Ala substitution of this side chain decreases k(cat) by ∼10(3)-fold, even though binding interactions between FMVAPP and this mutant are similar to those observed with wild type MDD, as judged by the 2.1 Å cocrystal structure of S192A with FMVAPP. Comparison of microbial MDD structures with those of mammalian counterparts reveals potential targets at the active site periphery that may be exploited to selectively target the microbial enzymes. These studies provide a structural basis for previous observations regarding the MDD mechanism and inform future work toward rational inhibitor design.