gebhart/patrepeval huggingface dataset:
Identification and characterization of embryonic stem cell‐derived pacemaker and atrial cardiomyocytes (2005)

The aim of this study was to identify and functionally characterize cardiac subtypes during early stages of development. For this purpose, transgenic embryonic stem cells were generated using the alpha-myosin heavy chain promoter driving the expression of the enhanced green fluorescent protein (EGFP). EGFP-positive clusters of cells were first observed as early as 7 days of development, thus, even before the initiation of the contractile activity. Flow cytometry and single-cell fluorescence measurements evidenced large diversities of EGFP intensity. Patch-clamp experiments showed EGFP expression exclusively in pacemaker and atrial but not ventricular cells. The highest fluorescence intensities were detected in pacemaker-like cardiomyocytes. In accordance, multielectrode-array recordings of whole embryoid bodies confirmed that the pacemaker center coincided with strongly EGFP-positive areas. The cardiac subtypes displayed already at this early stage differential characteristics of electrical activity and ion channel expression. Thus, quantitation of the alpha-myosin heavy chain driven reporter gene expression allows identification and functional characterization of early cardiac subtypes.
Mucosal Drug Delivery (2001)

This review focuses on epithelial drug transport mechanisms in mucosal drug delivery: the final step of a four-part process. Reference is made to the mucosae lining the oral cavity and the gastrointestinal tract, the two mucosae most often succumbing to the side effects of cytotoxic chemotherapeutic drugs. This review will be devoted to carrier-mediated transport, particularly as it relates to the intestinal dipeptide transporter PepT1. This transporter protein appears to be enriched in tumor epithelial cells, to be rather robust to the cytotoxic effects of chemotherapeutic drugs, and to lend itself to the molecular engineering of drugs that target this transporter in tumor epithelial cells. In contrast to the gastrointestinal tract, much less is known about the type and capacity of drug transport processes in the buccal epithelial cells and about how these processes may be altered in disease state (including cancer) and be manipulated pharmaceutically to optimize drug absorption.
Heavy oil expansions gather momentum worldwide (1995)

Cold production, wormholes, foamy oil mechanism, improvements in thermal methods, and horizontal wells are some of the processes and technologies enabling expansion of the world`s heavy oil/bitumen production. Such processes were the focus of the International Heavy Oil Symposium in Calgary, June 19--21. Unlike conventional oil production, heavy oil/bitumen extraction is more a manufacturing process where technology enables the business and does not just add value. The current low price spreads between heavy oil/light oil indicate that demand for heavy oil is high. The paper first discusses the price difference between heavy and light oils, then describes heavy oil production activities in Canada at Cold Lake, in Venezuela in the Orinoco belt, and at Kern River in California.
Textural Analysis of Cheese (1979)

Six textural characteristics, hardness, cohesiveness, adhesiveness, elasticity, gumminess, and chewiness, were measured by Instron Testing Machine for 11 cheese samples ranging from Parmesan to processed cheese. These objective textural measurements correlated closely with a panel's measurements. The textural measures were also in close correlation with composition and pH of cheese samples. An approach was demonstrated for evaluation of the multi-dimensional system. Chewiness, which only can be calculated in the traditional method, may be measured directly with the technique.
A Diet Enriched with the Omega-3 Fatty Acid Docosahexaenoic Acid Reduces Amyloid Burden in an Aged Alzheimer Mouse Model (2005)

Epidemiological studies suggest that increased intake of the omega-3 (n-3) polyunsaturated fatty acid (PUFA) docosahexaenoic acid (DHA) is associated with reduced risk of Alzheimer's disease (AD). DHA levels are lower in serum and brains of AD patients, which could result from low dietary intake and/or PUFA oxidation. Because effects of DHA on Alzheimer pathogenesis, particularly on amyloidosis, are unknown, we used the APPsw (Tg2576) transgenic mouse model to evaluate the impact of dietary DHA on amyloid precursor protein (APP) processing and amyloid burden. Aged animals (17-19 months old) were placed in one of three groups until 22.5 months of age: control (0.09% DHA), low-DHA (0%), or high-DHA (0.6%) chow. beta-Amyloid (Abeta) ELISA of the detergent-insoluble extract of cortical homogenates showed that DHA-enriched diets significantly reduced total Abeta by >70% when compared with low-DHA or control chow diets. Dietary DHA also decreased Abeta42 levels below those seen with control chow. Image analysis of brain sections with an antibody against Abeta (amino acids 1-13) revealed that overall plaque burden was significantly reduced by 40.3%, with the largest reductions (40-50%) in the hippocampus and parietal cortex. DHA modulated APP processing by decreasing both alpha- and beta-APP C-terminal fragment products and full-length APP. BACE1 (beta-secretase activity of the beta-site APP-cleaving enzyme), ApoE (apolipoprotein E), and transthyretin gene expression were unchanged with the high-DHA diet. Together, these results suggest that dietary DHA could be protective against beta-amyloid production, accumulation, and potential downstream toxicity.
AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome (2010)

AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.
The cytochrome oxidases of Bacillus subtilis: mapping of a gene affecting cytochrome aa3 and its replacement by cytochrome o in a mutant strain (1989)

A mutant of Bacillus subtilis has been isolated that fails to grow on succinate as the source of carbon, yet grows on glucose. Intact cells of the mutant and cytoplasmic membranes derived therefrom lack cytochromes a and a3 but contain a cytochrome o-like pigment, which forms a photodissociable compound with CO and is reactive with oxygen. The mutation in the genome has been located and lies at about 130° on the chromosomal map between the metC and pyrD loci. The designation cox is suggested for this gene.
Investigation into the microbial flora of healing and non-healing decubitus ulcers. (1981)

Seventy-four pressure lesions in fifty-three geriatric patients were observed at weekly intervals to determine the bacterial flora and the healing index of each lesion, expressed as initial area of lesion (cm2) - final area of lesion (cm2) divided by time in days. The micro-organisms which caused infection included Staphylococcus aureus, Proteus mirabilis, Pseudomonas aeruginosa, Bacteroides fragilis and Bacteroides asaccharolyticus. Many lesions contained a mixed flora. P mirabilis and Ps aeruginosa were associated with necrotic (p less than 0.005) and enlarging (p less than 5 x 10(-7)) lesions. Bacteroides spp were associated with necrotic lesions (p less than 0.05). The presence of S aureus in a lesion was not associated with any particular trend in healing index. The implications of the microbiological findings are discussed.
In vivoengineering of organs: The bone bioreactor (2005)

Treatment of large defects requires the harvest of fresh living bone from the iliac crest. Harvest of this limited supply of bone is accompanied by extreme pain and morbidity. This has prompted the exploration of other alternatives to generate new bone using traditional principles of tissue engineering, wherein harvested cells are combined with porous scaffolds and stimulated with exogenous mitogens and morphogens in vitro and/or in vivo. We now show that large volumes of bone can be engineered in a predictable manner, without the need for cell transplantation and growth factor administration. The crux of the approach lies in the deliberate creation and manipulation of an artificial space (bioreactor) between the tibia and the periosteum, a mesenchymal layer rich in pluripotent cells, in such a way that the body's healing mechanism is leveraged in the engineering of neotissue. Using the "in vivo bioreactor" in New Zealand White rabbits, we have engineered bone that is biomechanically identical to native bone. The neobone formation followed predominantly an intramembraneous path, with woven bone matrix subsequently maturing into fully mineralized compact bone exhibiting all of the histological markers and mechanical properties of native bone. We harvested the bone after 6 weeks and transplanted it into contralateral tibial defects, resulting in complete integration after 6 weeks with no apparent morbidity at the donor site. Furthermore, in a proof-of-principle study, we have shown that by inhibiting angiogenesis and promoting a more hypoxic environment within the "in vivo bioreactor space," cartilage formation can be exclusively promoted.
Skeletal muscle fatigue in normal subjects and heart failure patients. Is there a common mechanism? (1998)

Skeletal muscle fatigue develops gradually during all forms of exercise, and develops more rapidly in heart failure patients. The fatigue mechanism is still not known, but is most likely localized to the muscle cells themselves. During high intensity exercise the perturbations of the Na+ and K+ balance in the exercising muscle favour depolarization, smaller action potentials and inexcitability. The Na+, K+ pump becomes strongly activated and limits, but does not prevent the rise in extracellular Na+, K+ pump concentration and intracellular Na+ concentration. However, by virtue of its electrogenic property the pump may contribute in maintaining excitability and contractility by keeping the cells more polarized than the ion gradients predict. With prolonged exercise perturbations of Na+ and K+ are smaller and fatigue may be associated with altered cellular handling of Ca2+ and Mg2+. Release of Ca2+ from the sarcoplasmic reticulum (SR) is reduced in the absence of changes of the cellular content of Ca2+ and Mg2+. In heart failure several clinical reports indicate severe electrolyte perturbations in skeletal muscle. However, in well controlled studies small or insignificant changes are found. We conclude that with high intensity exercise perturbations of Na+ and K+ in muscle cells may contribute to fatigue, whereas with endurance type of exercise and in heart failure patients the skeletal muscle fatigue is more likely to reside in the intracellular control of Ca2+ release and reuptake.
PAM programming environments: practice and experience (2002)

Digital Equipment's Paris Research Laboratory started to investigate the use of FPGA-based reconfigurable hardware accelerators in 1988. We call them PAMs for Programmable Active Memories. Over the past six years, we have designed and implemented four generations of PAM hardware and four generations of PAM programming environments. Several dozen people, ranging from inexperienced students to senior hardware designers, have used our systems. A wide range of applications belonging to several important application domains have demonstrated the interest of these novel computing devices. In this paper we present the software lessons we draw from this collective experience.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Efficient Mechanism Design (1997)

We study Bayesian mechanism design in situations where agents ’ information may be multi-dimensional, concentrating on mechanisms that lead to efficient allocations. Our main result is that a generalization of the well-known Vickrey-Clarke-Groves mechanism maximizes the planner’s “revenue ” among all efficient mechanisms. This result is then used to study multiple object auctions in situations where bidders have privately known “demand curves” and extended to include situations with complementarities across objects or externalities across bidders. We also illustrate how the main result may be used to analyze the possibility of allocating both private and public goods ef-Þciently when budget balance considerations are important. The generalized VCG mechanism, therefore, serves to unify many results in mechansim design theory. 1
Automated Arterial Input Function Extraction for T1-Weighted DCE-MRI (2003)

2 , consisting of 3-D gradient echo acquisitions acquired over a period of approximately 3.5 minutes, with a temporal resolution of 5-8.5 s was used. Baseline T1 was calculated using 3 acquisitions with different flip angles. Concentration of contrast agent was estimated from the change in T1 during the dynamic series. An intravenous contrast agent bolus of less than 10 s duration was manually injected. Acquisitions in the lung and prostate utilised similar protocols, but with 4 s and 2.3 s temporal resolution, respectively, and with the bolus administered using a power injector. AIF estimation: 1. Manually identify a slice that contains a suitable artery, and does not suffer in-flow effects (note that the use of 3- D acquisition allows significantly reduced in-flow effects compared with multi-slice techniques when a slice in the centre of the volume is selected); 2. Extract the time course for every voxel in slice and identify those that show a maximum in concentration within 20 s of the arrival time (early max voxels); 3. Identify the early max voxels within the top 5% of peak concentrations; 4. Average the resultant time courses together to create a mean AIF. Results and Conclusion The AIF identification method proved to extract plausible AIFs from a range of regions of the body, including the lung and prostate (Fig. 1). The positions of the voxels that contribute to the AIF may be determined and mapped onto an anatomical image, showing that the mean AIF is extracted from voxels positioned in arteries. The selection of the top 5 % of early max voxels ensures that partial volume effects are minimised. Figure 2 shows the results of the technique in a glioma patient scanned twice, showing qualitatively good reproducibility. Figure 3 shows measures of the repeatability of the method across all 6 glioma patients. The method provides an AIF estimate with a minimum of user input and is applicable to any area of the body with a suitable artery. The method shows good scan-rescan reproducibility, even in the case shown using manual bolus administration. References
Identification of an animal ω-3 fatty acid desaturase by heterologous expression in  Arabidopsis (1997)

In animals, fatty acid desaturases catalyze key reactions in the synthesis of arachidonic acid and other polyunsaturated fatty acids. A search of the Caenorhabditis elegans DNA databases, using the sequences of Arabidopsis genes, identified several putative desaturases. Here we describe the characterization of the first of these genes, fat-1. The predicted protein encoded by a fat-1 cDNA showed 32-35% identity with both FAD2 and FAD3 of Arabidopsis. When expressed in transgenic plants, fat-1 resulted in a 90% increase in the proportion of alpha-linolenic acid in root lipids. Wild-type Arabidopsis incorporated omega-6 fatty acids (delta8,11,14-20:3 and delta5,8,11,14-20:4) into membrane lipids but did not desaturate them. By contrast, fat-1 transgenic plants efficiently desaturated both of these fatty acids to the corresponding omega-3 products. These findings indicate that the C. elegans fat-1 gene encodes the first animal representative of a class of glycerolipid desaturases that have previously been characterized in plants and cyanobacteria. The FAT-1 protein is an omega-3 fatty acyl desaturase that recognizes a range of 18- and 20-carbon omega-6 substrates.
Pertuzumab in Combination with Trastuzumab and Chemotherapy in the Treatment of HER2-Positive Metastatic Breast Cancer: Safety, Efficacy, and Progression Free Survival (2014)

A computer based literature search was carried out using PubMed data reported at international meetings (ASCO) up to September 2013 were included.
Acute Treatment of Noise Trauma with Local Caroverine Application in the Guinea Pig (2003)

Intense sound stimulation may result in excessive glutamate release from the inner hair cells, resulting in binding to the postsynaptic glutamate receptors and leading to neuronal degeneration and functional impairment. In this study we investigated the therapeutic effect and time window of caroverine, an N-methyl-D-aspartate and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antagonist, on noise-induced hearing loss Guinea pigs were exposed to one-third octave band noise centered at 6.3 kHz (110 dB sound pressure limit) for 1 h. One or 24 h after noise exposure, caroverine was applied to the round window membrane. Auditory brainstem responses were recorded at regular time intervals. It was shown that caroverine could significantly decrease hearing impairment after noise trauma when applied 1 but not 24 h after noise exposure.
Intrinsic directionality of migrating vascular smooth muscle cells is regulated by NAD+ biosynthesis (2012)

Cell migration is central to tissue repair and regeneration but must proceed with precise directionality to be productive. Directional migration requires external cues but also depends on the extent to which cells can inherently maintain their direction of crawling. We report that the NAD(+) biosynthetic enzyme, nicotinamide phosphoribosyltransferase (Nampt/PBEF/visfatin), mediates directionally persistent migration of vascular smooth muscle cells (SMCs). Time-lapse microscopy of human SMCs subjected to Nampt inhibition revealed chaotic motility whereas SMCs transduced with the Nampt gene displayed highly linear migration paths. Ordered motility conferred by Nampt was associated with downsizing of the lamellipodium, reduced lamellipodium wandering around the cell perimeter, and increased lamellipodial protrusion rates. These protrusive and polarity-stabilizing effects also enabled spreading SMCs to undergo bipolar elongation to an extent not typically observed in vitro. Nampt was found to localize to lamellipodia and fluorescence recovery of Nampt-eGFP after photobleaching revealed microtubule-dependent transport of Nampt to the leading edge. In addition, Nampt was found to associate with, and activate, Cdc42, and Nampt-driven directional persistence and lamellipodium anchoring required Cdc42. We conclude that high-fidelity SMC motility is coordinated by a Nampt-Cdc42 axis that yields protrusive but small and anchored lamellipodia. This novel, NAD(+)-synthesis-dependent control over motility may be crucial for efficient repair and regeneration of the vasculature, and possibly other tissues.
24‐h variation of vigilance in the cockroach Blaberus giganteus (1992)

Our objective was to investigate whether sleep-like states occur in the cockroach, Blaberus giganteus by applying the methods formerly used for another cockroach species, Leucophaea maderae and the scorpions, Heterometrus and Pandinus. The behaviour of isolated animals (n = 10) kept under LD 12:12 h was recorded by time-lapse video for three consecutive 24-h periods. Nine behavioural states were scored for 1-min real-time epochs. Rest was subdivided into 4 sub-states on the basis of body posture and the position of the antennae. The cockroaches showed a nocturnal behaviour exhibiting a bout of locomotion at dark onset which lasted several hours, and a preference for rest in the light period. Immobility with both the body and the antennae touching the substrate (state 1) was the predominating state in the light period. In order to establish whether the sub-states of rest represented different levels of vigilance the arousal threshold was measured by determining the latency of a behavioural response to a vibration stimulus. The levels of arousal differed significantly in four behavioural states in the light period but not in the dark period. In state 1 the animals exhibited the lowest arousal whereas in the activity states arousal was the highest. The state with the highest arousal threshold occurred in the beginning of the light period. Thereafter, arousal progressively increased and remained relatively high during the dark period. The effect of 6-h deprivation of rest by the gentle shaking of the cages whenever the animals were immobile, resulted in a reduced latency to state 1, a small increase of state 1 and a more prominent initial increase of activity during recovery. In conclusion, this study provides evidence for the existence of a 24-h variation of vigilance in the cockroach. It further indicates that a 'rest deficit' gives rise to a compensatory response. The data support the notion that sleep-like states are present in these insects.
Antibiotic uptake by alveolar macrophages. (1980)

Optimal therapy of infections caused by bacteria able to survive within phagocytes requires the use of antibiotics which inactivate these intracellular organisms. To define characteristics that determine entry of antimicrobial agents into phagocytes, we studied the uptake of 14 radiolabeled antibiotics by rabbit AM. Cell-antibiotic mixtures were incubated for 2 hr, and at intervals antibiotic uptake was determined by velocity-gradient centrifugation (separation of cells from extracellular antibiotic). Many drugs failed to penetrate AM readily. Cellular concentrations of penicillin G and three cephalosporin antibiotics were much lower than extracellular levels (C/E = less than 0.1 to 0.4). Gentamicin, isoniazid, and tetracycline attained C/E values of 0.5 to 0.8. The more lipid-soluble antibiotics, refampin, lincomycin, and chloramphenicol, were concentrated approximately twofold (C/E = 2) in AM. Ethambutol (C/E = 7) and two erythromycin preparations (C/E = greater than 20) were markedly accumulated by macrophages. In comparison with other antibiotics tested, the uptake of clindamycin was both massive and rapid (C/E = 50 by 30 min). Ethambutol, erythromycin and clindamycin uptakes by AM are dependent upon oxidative metabolic processes. Detailed characterization of clindamycin uptake confirmed that the drug is accumulated by an active transport system. These findings, in association with studies of antibiotic-mediated influence on phagocytes, should provide information useful in establishing guidelines for optimal antibiotic usage.
TSV process optimization for reduced device impact on 28nm CMOS (2011)

A through-silicon-via (TSV) process is demonstrated on 28nm CMOS baseline with good electrical performance and low cost. TSV leakage, yield, C-V flat-band shift, Cu contamination, and reliability are significantly improved via process optimization. The preferred TSV processing could relax TSV stress and minimize keep-out zone (KOZ). In this study, we also address the impact of multiple-TSVs additive stress impact, TSV signal coupling effect, and TSV depletion impact to assess the power-TSV plug cell in design practice.