gebhart/patrepeval huggingface dataset:
Molded polymer‐coated composite bone void filler improves tobramycin controlled release kinetics (2013)

Infection remains a significant problem associated with biomedical implants and orthopedic surgeries, especially in revision total joint replacements. Recent advances in antibiotic-releasing bone void fillers (BVF) provide new opportunities to address these types of device-related orthopedic infections that often lead to substantial economic burdens and reduced quality of life. We report improvements made in fabrication and scalability of an antibiotic-releasing polycaprolactone-calcium carbonate/phosphate ceramic composite BVF using a new solvent-free, molten-cast fabrication process. This strategy provides the ability to tailor drug release kinetics from the BVF composite based on modifications of the inorganic substrate and/or the polymeric component, allowing extended tobramycin release at bactericidal concentrations. The mechanical properties of the new BVF composite are comparable to many reported BVFs and validate the relative homogeneity of fabrication. Most importantly, fabrication quality controls are correlated with favorable drug release kinetics, providing bactericidal activity to 10 weeks in vitro when the polycaprolactone component exceeds 98% w/w of the total polymer fraction. Furthermore, in a time kill study, tobramycin-releasing composite fragments inhibited S. aureus growth over 48 h at inoculums as high as 10(9) CFU/mL. This customizable antibiotic-releasing BVF polymer-inorganic biomaterial should provide osseointegrative and osteoconductive properties while contributing antimicrobial protection to orthopedic sites requiring the use of bone void fillers.
Fish Oil Decreases Hepatic Lipogenic Genes in Rats Fasted and Refed on a High Fructose Diet (2015)

Fasting and then refeeding on a high-carbohydrate diet increases serum and hepatic triacylglycerol (TAG) concentrations compared to standard diets. Fructose is a lipogenic monosaccharide which stimulates de novo fatty acid synthesis. Omega-3 (n-3) fatty acids stimulate hepatic β-oxidation, partitioning fatty acids away from TAG synthesis. This study investigated whether dietary n-3 fatty acids from fish oil (FO) improve the hepatic lipid metabolic response seen in rats fasted and then refed on a high-fructose diet. During the post-prandial (fed) period, rats fed a FO rich diet showed an increase in hepatic peroxisome proliferator-activated receptor α (PPAR-α) gene expression and decreased expression of carbohydrate responsive element binding protein (ChREBP), fatty acid synthase (FAS) and microsomal triglyceride transfer protein (MTTP). Feeding a FO rich diet for 7 days prior to 48 h of fasting resulted in lower hepatic TAG, lower PPAR-α expression and maintenance of hepatic n-3 fatty acid content. Refeeding on a high fructose diet promoted an increase in hepatic and serum TAG and in hepatic PPAR-α, ChREBP and MTTP expression. FO did not prevent the increase in serum and hepatic TAG after fructose refeeding, but did decrease hepatic expression of lipogenic genes and increased the n-3 fatty acid content of the liver. n-3 Fatty acids can modify some components of the hepatic lipid metabolic response to later feeding with a high fructose diet.
Dense Medium Plasma Environments:  A New Approach for the Disinfection of Water (2001)

The levels to which microbial colony forming units are permitted in various waters fit for human contact are carefully regulated. Conventional chemical and physical approaches usually are complex processes with significant limitations due to the generation of toxic side-products. In this contribution a novel plasma reactor--dense medium plasma reactor--is described, and its efficiency for the disinfection of contaminated water is discussed. It has been shown that owing to the intense stirring of the reaction medium (e.g. contaminated water), as a result of the specially designed spinning electrode and gas-flow system, a volume-character discharge is created, which can efficiently kill bacteria. It has been demonstrated that treatment times as low as 20 s are enough for the total inactivation of microorganisms for 200 mL of 10(5) bacteria/mL contaminated water.
Communication and Control for Quantum Circuits (2010)

Quantum computers will potentially be able to solve certain classes of problems more efficiently than possible on a classical computer. Due to the fragility of quantum data, a large scale quantum computer will require a robust system to enable reliable communication within the datapath. We present a scalable architecture for a quantum computer which specifically addresses communication concerns. Our design minimizes communication error by using a specialized interconnection network to perform long-distance movement. &lt;p&gt; We developed a set of tools to construct and study quantum datapath designs based on ion trap quantum technology. Our tools automatically synthesize and insert the interconnection network used for long-distance communication into the target datapath. We present a set of greedy heuristics to optimize the routing and scheduling of communication within this network and show that our approach performs as well as an optimal case determined using integer linear programming. We study a number of different quantum circuits including randomly generated circuits, quantum adder circuits, and ultimately Shor's factorization algorithm and show that designs using our optimizations significantly improve upon prior work in terms of a probabilistic area delay metric.
Planar chromatography of cholic acid-derivedcis-transisomeric bis-steroidal tetraoxanes (2009)

Seven pairs of cis-trans isomers of bis-steroidal tetraoxanes have been examined by both normal-phase (NP) and reversed-phase (RP) planar chromatography. Unmodified silica gel was used with ethyl acetate-toluene and ethyl acetate-petroleum ether as mobile phases in typical normal-phase systems. CN-silica with the mobile phases methanol-water and acetone-water and RP-18 silica with water-organic modifier (methanol, acetone, or dioxane) mobile phases were used as reversed-phase systems. For the RP systems a good linear correlation was established between RM values and amount ([%] ν/ν ) of organic modifier in the mobile phase (usually r > 0.99). It was found that under both NP and RP conditions cis isomers were more weakly retained than the corresponding trans isomers. The only exception to this was the chromatographic behavior of C(24) methyl esters. It was established that increasing the polarity of substituents at C(24) and C(24a) led to stronger retention in NP systems, i.e. weaker retention in RP systems. Highly selective separation was achieved in all the chromatographic systems investigated. Possible separation mechanisms are discussed on the basis of the results obtained.
Review: Immunologic Reactions Involving Sperm Cells and Preimplantation Embryos (1988)

Evidence that sperm cells share or impart antigenic specificities to fertilized ova and cleaving embryos in animals was first demonstrated indirectly in female animals isoimmunized against sperm or testis cells. While early studies often gave conflicting results, postfertilization infertility effects were occasionally reported. 1 The systematic analysis in animals of anti~ertility e~ects after immunization with sperm or testis preparations resulted in a clearer delineation of the affected stages and modes of action.
Learning the scope of hedge cues in biomedical texts (2009)

Identifying hedged information in biomedical literature is an important subtask in information extraction because it would be misleading to extract speculative information as factual information. In this paper we present a machine learning system that finds the scope of hedge cues in biomedical texts. The system is based on a similar system that finds the scope of negation cues. We show that the same scope finding approach can be applied to both negation and hedging. To investigate the robustness of the approach, the system is tested on the three subcorpora of the BioScope corpus that represent different text types.
The roles of the novel kinase PKD1 and the AKAP yotiao in NMDA receptor signaling (2007)

The most striking feature of the brain is its seemingly endless ability to learn, to adapt to new experiences, and to remember. All of this information is encoded in the connections, or synapses, between neurons. These synapses change during learning and new memory formation in a process called synaptic plasticity. While much has been learned about the molecular mechanisms involved in synaptic plasticity, there is a long way to go before these processes are fully understood. In order to better understand these long-term changes, we focus on the roles of the novel kinase PKD1 (PKD1) and the scaffolding protein yotiao, a member of the A-kinase anchoring protein (AKAP) superfamily. In particular, we look at the roles of these proteins in the intracellular signaling pathways that originate with the NMDA-type glutamate receptor (NMDAR), a well-characterized and important glutamate receptor that plays a critical role in many forms of synaptic plasticity. We show that PKD1 is a downstream target of NMDA receptor signaling and participates in synaptic plasticity by regulating the trafficking of AMPA-type glutamate receptors (AMPARs). Since changes in gene expression are critical for the long-term maintenance of synaptic plasticity, we also look at signaling to the nucleus. In response to certain stimuli, we find that PKD1 is capable of controlling the function of HDACs, a family of transcriptional repressors that regulate gene expression. Finally, we find that yotiao, which binds to NMDARs in a splice variant-dependent way, may play a role in facilitating signaling from the NMDAR to CREB, a transcription factor important to synaptic plasticity. By better understanding the functions of PKD1 and yotiao in neurons, we gain new insights into the molecular mechanisms of synaptic change, and thus, learning and memory.
Initial Experiences with Retrieving Similar Objects in Simulation Data (2003)

Comparing the output of a physics simulation with an experiment, referred to as 'code validation,' is often done by visually comparing the two outputs. In order to determine which simulation is a closer match to the experiment, more quantitative measures are needed. In this paper, we describe our early experiences with this problem by considering the slightly simpler problem of finding objects in a image that are similar to a given query object. Focusing on a dataset from a fluid mixing problem, we report on our experiments with different features that are used to represent the objects of interest in the data. These early results indicate that the features must be chosen carefully to correctly represent the query object and the goal of the similarity search.
Comparison of Optical Imaging Techniques to Quantitatively Assess the Perfusion of the Gastric Conduit during Oesophagectomy (2020)

In this study, four optical techniques—Optical Coherence Tomography, Sidestream Darkfield Microscopy, Laser Speckle Contrast Imaging, and Fluorescence Angiography (FA)—were compared on performing an intraoperative quantitative perfusion assessment of the gastric conduit during oesophagectomy. We hypothesised that the quantitative parameters show decreased perfusion towards the fundus in the gastric conduit and in patients with anastomotic leakage. In a prospective study in patients undergoing oesophagectomy with gastric conduit reconstruction, measurements were taken with all four optical techniques at four locations from the base towards the fundus in the gastric conduit (Loc1, Loc2, Loc3, Loc4). The primary outcome included 14 quantitative parameters and the anastomotic leakage rate. Imaging was performed in 22 patients during oesophagectomy. Ten out of 14 quantitative parameters significantly indicated a reduced perfusion towards the fundus of the gastric conduit. Anastomotic leakage occurred in 4/22 patients (18.4%). At Loc4, the FA quantitative values for “T1/2” and “mean slope” differed between patients with and without anastomotic leakage (p = 0.025 and p = 0.041, respectively). A quantitative perfusion assessment during oesophagectomy is feasible using optical imaging techniques, of which FA is the most promising for future research.
Human Metallothionein Gene Expression Is Upregulated by .BETA.-Thujaplicin: Possible Involvement of Protein Kinase C and Reactive Oxygen Species (2006)

Recently, we discovered that beta-thujaplicin (BT) induces metallothionein (MT) expression in mouse keratinocytes, both in vivo and in vitro. However, the molecular mechanisms by which BT exerts its biological effects have not been elucidated. The purpose of this study is to explore the signal transduction pathway involved in the MT mRNA induction by BT. Using a HaCaT keratinocyte cell line, Northern blotting was performed for analyzing the human MT-IIA mRNA expression levels in combination with BT and a number of protein kinase (PK) inhibitors including H7, HA1004 and a PKC-specific inhibitor chelerythrin. CAT assays with the MT-IIA gene promorter-CAT construct were conducted for examining the transcriptional regulation by BT of MT. A free radical scavenger N-acetylcysteine (NAC) was used for analyzing a role of oxidative stress for the MT gene induction by BT. BT increased MT-IIA gene transcript levels and CAT activity in a dose-dependent fashion in HaCaT cells. The increase in MT-IIA mRNA levels and CAT activity were completely suppressed by H7 but not by HA1004. In addition, chelerythrin prevented BT-inducible MT-IIA promoter activation. Furthermore, NAC suppressed BT-inducible MT-IIA promoter activation. These results demonstrate that BT is a potent activator of the MT-IIA gene promoter and that PKC activation and reactive oxygen species are implicated in BT-inducible MT-IIA gene expression. BT may be a useful tool for dissecting the signal transduction pathway mediating MT-IIA promoter activation.
Thermal-Performance Evaluation of Bicycle Helmets for Convective and Evaporative Heat Loss at Low and Moderate Cycling Speeds (2019)

The main objective of the study was to investigate the thermal performance of five (open and closed) bicycle helmets for convective and evaporative heat transfer using a nine-zone thermal manikin. The shape of the thermal manikin was obtained by averaging the 3D-point coordinates of the head over a sample of 85 head scans of human subjects, obtained through magnetic resonance imaging (MRI) and 3D-printed. Experiments were carried out in two stages, (i) a convective test and (ii) an evaporative test, with ambient temperature maintained at 20.5 ± 0.5 °C and manikin skin temperature at 30.5 ± 0.5 °C for both the tests. Results showed that the evaporative heat transfer contributed up to 51%–53% of the total heat loss from the nude head. For the convective tests, the open helmet A1 having the highest number of vents among tested helmets showed the highest cooling efficiency at 3 m/s (100.9%) and at 6 m/s (101.6%) and the closed helmet (A2) with fewer inlets and outlets and limited internal channels showed the lowest cooling efficiency at 3 m/s (75.6%) and at 6 m/s (84.4%). For the evaporative tests, the open helmet A1 showed the highest cooling efficiency at 3 m/s (97.8%), the open helmet A4 showed the highest cooling efficiency at 6 m/s (96.7%) and the closed helmet A2 showed the lowest cooling efficiency at 3 m/s (79.8%) and at 6 m/s (89.9%). Two-way analysis of variance (ANOVA) showed that the zonal heat-flux values for the two tested velocities were significantly different (p &lt; 0.05) for both the modes of heat transfer. For the convective tests, at 3 m/s, the frontal zone (256–283 W/m2) recorded the highest heat flux for open helmets, the facial zone (210–212 W/m2) recorded the highest heat flux for closed helmets and the parietal zone (54–123 W/m2) recorded the lowest heat flux values for all helmets. At 6 m/s, the frontal zone (233–310 W/m2) recorded the highest heat flux for open helmets and the closed helmet H1, the facial zone (266 W/m2) recorded the highest heat flux for the closed helmet A2 and the parietal zone (65–123 W/m2) recorded the lowest heat flux for all the helmets. For evaporative tests, at 3 m/s, the frontal zone (547–615 W/m2) recorded the highest heat flux for all open helmets and the closed helmet H1, the facial zone (469 W/m2) recorded the highest heat flux for the closed helmet A2 and the parietal zone (61–204 W/m2) recorded the lowest heat flux for all helmets. At 6 m/s, the frontal zone (564–621 W/m2) recorded highest heat flux for all the helmets and the parietal zone (97–260 W/m2) recorded the lowest heat flux for all helmets.
Elastocapillary filling of deformable nanochannels (2007)

The capillary filling speed of wetting liquids of varying viscosity and surface tension in hydrophilic nanochannels with an elastic capping layer has been analyzed. The channels, with a height just below 80nm, are suspended by a thin flexible membrane that easily deforms due to the negative pressure which develops behind the moving meniscus. In the elastocapillary filling of the channels, two opposite effects compete: the decreased cross channel sections increase the flow resistance, while the Laplace pressure that acts as the driving force becomes more negative due to the increased meniscus curvature. Although the meniscus position shows a square root of time behavior as described by the Washburn relation, the net result of the induced bending of the membranes is a definite increase of the filling speed. We propose a relatively straightforward model for this elastocapillary process and present experimental results of the filling speed of ethanol, water, cyclohexane, and acetone that are found to be in good agreement with the presented model, for membrane deflections of up to 80% of the original channel height.
Particle Display: A Quantitative Screening Method for Generating High‐Affinity Aptamers (2014)

Abstract We report an aptamer discovery technology that reproducibly yields higher affinity aptamers in fewer rounds compared to conventional selection. Our method (termed particle display) transforms libraries of solution‐phase aptamers into “aptamer particles”, each displaying many copies of a single sequence on its surface. We then use fluorescence‐activated cell sorting (FACS) to individually measure the relative affinities of &gt;10 8 aptamer particles and sort them in a high‐throughput manner. Through mathematical analysis, we identified experimental parameters that enable optimal screening, and demonstrate enrichment performance that exceeds the theoretical maximum achievable with conventional selection by many orders of magnitude. We used particle display to obtain high‐affinity DNA aptamers for four different protein targets in three rounds, including proteins for which previous DNA aptamer selection efforts have been unsuccessful. We believe particle display offers an extraordinarily efficient mechanism for generating high‐quality aptamers in a rapid and economic manner, towards accelerated exploration of the human proteome.
A Catalytic Enantioselective Conjugate Addition of Cyanide to Enones (2008)

The first synthetically useful catalytic enantioselective conjugate addition of cyanide to enones is described. The optimized conditions involved a Gd catalyst (5 or 10 mol %) derived from ligands 3 or 4 and a 1:1 ratio of TBSCN and 2,6-dimethylphenol. The reaction exhibited excellent to high enantioselectivity and a wide substrate scope. Moreover, the 1,4-adduct was exclusively produced over the 1,2-adduct. The complete regioselectivity was due both to stabilization of the 1,4-selective silylated polymetallic catalyst (7) using a TBS group and the ability of the asymmetric catalyst to promote retro-cyanation from the 1,2-adduct.
A Relevant Content Filtering Based Framework For Data Stream Summarization (2016)

Social media platforms are a rich source of information these days, however, of all the available information, only a small fraction is of users' interest. To help users catch up with the latest topics of their interests from the large amount of information available in social media, we present a relevant content filtering based framework for data stream summarization. More specifically, given the topic or event of interest, this framework can dynamically discover and filter out relevant information from irrelevant information in the stream of text provided by social media platforms. It then further captures the most representative and up-to-date information to generate a sequential summary or event story line along with the evolution of the topic or event. Our framework does not depend on any labeled data, it instead uses the weak supervision provided by the user, which matches the real scenarios of users searching for information about an ongoing event. We experimented on two real events traced by a Twitter dataset from TREC 2011. The results verified the effectiveness of relevant content filtering and sequential summary generation of the proposed framework. It also shows its robustness of using the most easy-to-obtain weak supervision, i.e., trending topic or hashtag. Thus, this framework can be easily integrated into social media platforms such as Twitter to generate sequential summaries for the events of interest. We also make the manually generated gold-standard sequential summaries of the two test events publicly available for future use in the community.
Circulating catecholamines and metabolic effects of captopril in NIDDM patients (1996)

The reduction of circulating catecholamines could contribute, at least in part, to the captopril-related amelioration of insulin sensitivity.
Analysis of the contribution of HLA genes to genetic predisposition in inflammatory bowel disease. (1996)

Crohn disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBDs) of unknown etiology. First-degree relatives of IBD patients have a 10-fold increase in risk of developing the same disease, and distinct associations between specific HLA types and both CD and UC have been reported. We have evaluated the contribution of genes at the HLA locus to susceptibility in IBD by linkage analysis of highly informative microsatellite polymorphisms in 43 families with multiple affected cases. No evidence for linkage of HLA to IBD was obtained under any of the four models tested. Analysis of HLA haplotype sharing in affected relatives indicated that the relative risk to a sibling conferred by the HLA locus was 1.11 in UC and 0.75 in CD, with upper (95%) confidence limits of 2.41 and 1.37, respectively. This suggests that other genetic or environmental factors are responsible for most of the familial aggregation in IBD.
Non-retinotopic feature integration has a neural pace of its own, as revealed by electrical brain imaging (2009)

When elements appear in quick succession they can integrate across space and time. Using high-density EEG techniques we show that such non-retinotopic feature integration is not time-locked to stimulus onset, but has a timing of its own. We presented a central line, containing a small vernier offset, quickly followed by pairs of non-offset flanking lines. Although the central line itself stays invisible, observers can discriminate its offset within the two resulting motion streams. Observers attended only one stream while we gave one of the flanking lines an offset opposite to that of the central line. Only when this flank offset was in the attended stream did it integrate with the central offset. This unconscious integration was reflected in voltage topographies time-locked to the behavioural response, between 650 and 250 ms before key press. At these latencies statistical parametric mapping of current densities revealed integration effects in high-level visual, prefrontal and central areas. A separate stimulus-locked analysis revealed no such effects. The results show that endogenously timed processes, rather than stimulus-locked, bottom - up processes, underlie non-retinotopic feature integration. The results furthermore show how high-density EEG can monitor visual information with good spatial and excellent temporal resolution.