gebhart/patrepeval huggingface dataset:
Energy consumption analysis of flow-specific medium access and the role of probabilistic preamble sampling in energy and delay performance (2010)

In this paper, we present a novel energy consumption analysis of the flow-specific Cooperative Wireless Sensor Network Medium Access Control (CWS-MAC) protocol utilizing a nine-state radio energy model that includes both steady state and transient state energy consumption behavior. CWS-MAC is a traffic-adaptive, energy-efficient medium access scheme that has been shown in the literature to outperform both traditional contention and non-contention-based approaches by providing medium access service on a per flow basis. We also formally define and quantitatively investigate the technique of probabilistic preamble sampling which provides the ability to trade-off delay performance and energy consumption in the operation of low-power medium access schemes.
Analytical Modeling of Energy Consumption and Thermal Performance of Data Center Cooling Systems: From the Chip to the Environment (2007)

The increasingly ubiquitous nature of computer and internet usage in our society, has driven advances in semiconductor technology, server packaging, and cluster level optimizations, in the IT industry. Not surprisingly this has an impact on our societal infrastructure with respect to providing the requisite energy to fuel these power hungry machines. Cooling has been found to contribute to about a third of the total data center energy consumption, and is the focus of this study. In this paper we develop and present physics based models to allow the prediction of the energy consumption and heat transfer phenomenon in a data center. These models allow the estimation of the microprocessor junction and server inlet air temperatures for different flow and temperature conditions at various parts of the data center cooling infrastructure. For a case study example considered, the chiller energy use was the biggest fraction of about 41% and also the most inefficient. The room air conditioning was the second largest energy component and also the second most inefficient. A sensitivity analysis of plant and chiller energy efficiency with chiller set point temperature and outdoor air conditions is also presented.
Compact substrate heater for use in an oxidizing atmosphere. Professional paper (1994)

A compact heater, designed for the deposition of thin films at high temperatures in an oxidizing atmosphere or vacuum, is described. The heater, including an oxygen-resistant case and the attached substrate, can be loaded into a vacuum deposition chamber through a small-diameter load-lock system, and will operate in 0 to 1 atmosphere of oxygen at temperatures up to at least 800 deg C. Heat is generated resistively, and the substrates are heated directly by thermal conduction. The heater was built specifically to heat substrates during the growth of high-temperature superconducting thin films.
Estimation of uncertainty in respiratory-gated PET images (2011)

Positron Emission Tomography (PET) is a powerful tool for patient diagnosis and assessment of therapy response, which is carried out through comparison of PET measurements from longitudinal scans. However, as with any measurement tool, an estimate of error or uncertainty is required for meaningful comparison of such measurements. We have developed a bootstrap-based method for estimating uncertainty in respiratory-gated PET images. First, we independently reconstruct a set of gated images, each corresponding to a different stage in the respiratory cycle. We then apply a Bayesian framework to estimate parameters of the underlying posterior probability distribution of radioactivity concentration at each voxel, using a Gaussian model with non-negative mean, and considering the variance of the Gaussian model as a nuisance parameter with an asymptotically locally invariant prior. Once the posterior distribution of the radioactivity concentration at each voxel is determined, relevant image statistics are obtained at each voxel, either in closed-form (for the mean and standard deviation), or through numerical methods (for confidence intervals). The mean of the estimated distribution is shown to be a quantitatively better image than that obtained by averaging the set of gated reconstructions, yielding tighter confidence intervals for the values measured at each voxel. The procedure was successfully tested on real PET data.
Tsetse thrombin inhibitor: Bloodmeal-induced expression of an anticoagulant in salivary glands and gut tissue of <i>Glossina morsitans morsitans</i> (1998)

The tsetse thrombin inhibitor, a potent and specific low molecular mass (3,530 Da) anticoagulant peptide, was purified previously from salivary gland extracts of Glossina morsitans morsitans (Diptera: Glossinidae). A 303-bp coding sequence corresponding to the inhibitor has now been isolated from a tsetse salivary gland cDNA library by using degenerate oligonucleotide probes. The full-length cDNA contains a 26-bp untranslated segment at its 5' end, followed by a 63-bp sequence corresponding to a putative secretory signal peptide. A 96-bp segment codes for the mature tsetse thrombin inhibitor, whose predicted molecular weight matches that of the purified native protein. Based on its lack of homology to any previously described family of molecules, the tsetse thrombin inhibitor appears to represent a unique class of naturally occurring protease inhibitors. Recombinant tsetse thrombin inhibitor expressed in Escherichia coli and the chemically synthesized peptide are both substantially less active than the purified native protein, suggesting that posttranslational modification(s) may be necessary for optimal inhibitory activity. The tsetse thrombin inhibitor gene, which is present as a single copy in the tsetse genome, is expressed at high levels in salivary glands and midguts of adult tsetse flies, suggesting a possible role for the anticoagulant in both feeding and processing of the bloodmeal.
Mitochondrial markers predict recurrence, metastasis and tamoxifen-resistance in breast cancer patients: Early detection of treatment failure with companion diagnostics (2017)

Here, we used a data-mining and informatics approach to discover new biomarkers of resistance to hormonal therapy in breast cancer. More specifically, we investigated whether nuclear-encoded genes associated with mitochondrial biogenesis can be used to predict tumor recurrence, distant metastasis and treatment failure in high-risk breast cancer patients. Overall, this strategy allowed us to directly provide <i>in silico</i> validation of the prognostic value of these mitochondrial components in large and clinically relevant patient populations, with >15 years of follow-up data. For this purpose, we employed a group of 145 ER(+) luminal A breast cancer patients, with lymph-node (LN) metastasis at diagnosis, that were treated with tamoxifen, but not any chemotherapy agents. Using this approach, we identified >60 new individual mitochondrial biomarkers that predicted treatment failure and tumor recurrence, with hazard-ratios (HR) of up to 4.17 (<i>p</i>=2.2e-07). These include mitochondrial chaperones (HSPD1, HSPA9), membrane proteins (VDAC2, TOMM70A) and anti-oxidants (SOD2), as well as 18 different mitochondrial ribosomal proteins (MRPs) and >20 distinct components of the OXPHOS complexes. In addition, we combined 4 mitochondrial proteins (HSPD1, UQCRB, MRPL15, COX17), to generate a compact mitochondrial gene signature, associated with a HR of 5.34 (<i>p</i>=1e-09). This signature also successfully predicted distant metastasis and was effective in larger groups of ER(+) (<i>N</i>=2,447), basal (<i>N</i>=540) and HER2(+) (<i>N</i>=193) breast cancers. It was also effective in all breast cancers (<i>N</i>=3,180), if considered together as a single group. Based on this analysis, we conclude that mitochondrial biogenesis should be considered as a new therapeutic target for overcoming tumor recurrence, distant metastasis and treatment failure in patients with breast cancer. In summary, we identified individual mitochondrial biomarkers and 2 compact mitochondrial gene signatures that can be used to predict tamoxifen-resistance and tumor recurrence, at their initial diagnosis, in patients with advanced breast cancer. In the long-term, these mitochondrial biomarkers could provide a new companion diagnostics platform to help clinicians to accurately predict the response to hormonal therapy in ER(+) breast cancer patients, facilitating more personalized and effective treatment. Similarly, these mitochondrial markers could be used as companion diagnostics, to determine which breast cancer patients would benefit most from clinical treatments with mitochondrially-targeted anti-cancer therapeutics. Finally, we also showed that these mitochondrial markers are superior when directly compared with conventional biomarkers, such as Ki67 and PCNA.
Towards the development of selective amine oxidase inhibitors (2002)

Four substrate analogs, 4-(2-naphthyloxy)-2-butyn-1-amine (1), 1,4-diamino-2-chloro-2-butene (2), 1,6-diamino-2,4-hexadiyne (3), and 2-chloro-5-phthalimidopentylamine (4) have been tested as inhibitors against mammalian, plant, bacterial, and fungal copper-containing amine oxidases: bovine plasma amine oxidase (BPAO), equine plasma amine oxidase (EPAO), pea seedling amine oxidase (PSAO), Arthrobacter globiformis amine oxidase (AGAO), Escherichia coli amine oxidase (ECAO), and Pichia pastoris lysyl oxidase (PPLO). Reactions of 1,4-diamino-2-butyne with selected amine oxidases were also examined. Each substrate analog contains a functional group that chemical precedent suggests could produce mechanism-based inactivation. Striking differences in selectivity and rates of inactivation were observed. For example, between two closely related plasma enzymes, BPAO is more sensitive than EPAO to 1 and 3, while the reverse is true for 2 and 4. In general, inactivation appears to arise in some cases from TPQ cofactor modification and in other cases from alkylation of protein residues in a manner that blocks access of substrate to the active site. Notably, 1 completely inhibits AGAO at stoichiometric concentrations and is not a substrate, but is an excellent substrate of PSAO and inhibition is observed only at very high concentrations. Structural models of 1 in Schiff base linkage to the TPQ cofactor in AGAO and PSAO (for which crystal structures are available) reveal substantial differences in the degree of interaction of bound 1 with side-chain residues, consistent with the widely divergent activities. Collectively, these results suggest that the development of highly selective amine oxidase inhibitors is feasible.
Hardware Platforms Benchmark For Real-Time Polyp Detection (2017)

In this article, our concern is the early diagnosis of colorectal cancer from a computeraided detection point of view in order to help physicians in their diagnosis during the gold standard examination: optical video colonoscopy. Since many years, some methods and materials have been developed to reduce the polyp miss rate and to improve detection capabilities. Nevertheless, the real challenge lies in the real-time use of these methods. In this context, more precisely, we focus our attention on the hardware implementation of a previous method we recently introduced in the literature for real-time detection of colorectal polyps, lesions that may degenerate into cancer. This implementation is subject to three performance criteria: real-time processing capabilities, detection rate and necessary computational resources. Six different platforms were tested and compared. If we noticed that only workstation computers are able to perform the detection with a good tradeoff between the three aforementioned criteria, possibilities of architecture optimizations are also identified and discussed in order to achieve real-time performance on platforms with low available computational resources like Raspberry Pi for instance. This latter issue is of major importance for possible integration of the detection algorithm inside smallconnected object like videocapsule, a promising alternative to standard colonoscopy.
Open cycle traveling wave thermoacoustics: Mean temperature difference at the regenerator interface (2003)

In an open cycle traveling wave thermoacoustic engine, the hot heat exchanger is replaced by a steady flow of hot gas into the regenerator to provide the thermal energy input to the engine. The steady-state operation of such a device requires that a potentially large mean temperature difference exist between the incoming gas and the solid material at the regenerator's hot side, due in part to isentropic gas oscillations in the open space adjacent to the regenerator. The magnitude of this temperature difference will have a significant effect on the efficiencies of these open cycle devices. To help assess the feasibility of such thermoacoustic engines, a numerical model is developed that predicts the dependence of the mean temperature difference upon the important design and operating parameters of the open cycle thermoacoustic engine, including the acoustic pressure, mean mass flow rate, acoustic phase angles, and conductive heat loss. Using this model, it is also shown that the temperature difference at the regenerator interface is approximately proportional to the sum of the acoustic power output and the conductive heat loss at this location.
Low Temperature Growth of Photoactive Titania by Atmospheric Pressure Plasma (2009)

Abstract Atmospheric pressure glow discharge plasma CVD was used to deposit thin films of titania at 200 °C using two different precursors. The resulting films were characterised using techniques including XPS, RBS and XRD. It was established that annealing at temperatures as low as 275 °C produced crystalline films that were photocatalytically active. When annealed at 300 °C the photoactivity was greater than that of commercially available “self‐cleaning” titania films. The effects of the different precursors, annealing times and temperatures on the crystallinity and photoactivity are discussed. magnified image
A PCM-Filled Heat Sink for an LED-Based Dental Device (2007)

A new heat sink has been designed that increases the run time of a cavity-filling resin-curing or teeth-bleaching dental device with light emitting diode. The heat sink is a hollowed copper object that is filled with a phase change material. Computational simulations and experimental measurements are presented that show the heat sink with phase change material increases the run time of the device beyond the minimum requirement of six minutes.
Rotatable seal assembly. [Patent application; rotating targets] (1980)

An assembly is provided for rotatably supporting a rotor on a stator so that vacuum chambers in the rotor and stator remain in communication while the chambers are sealed from ambient air, which enables the use of a ball bearing or the like to support most of the weight of the rotor. The apparatus includes a seal device mounted on the rotor to rotate therewith, but shiftable in position on the rotor while being sealed to the rotor as by an O-ring. The seal device has a flat face that is biased towards a flat face on the stator, and pressurized air is pumped between the faces to prevent contact between them while spacing them a small distance apart to avoid the inflow of large amounts of air between the faces and into the vacuum chambers.
Microsomal Triglyceride Transfer Protein (1995)

Microsomal triglyceride transfer protein (MTP) is a lipid transfer protein that is required for the assembly and secretion of very low density lipoproteins by the liver and chylomicrons by the intestine. To further elucidate the nature of the lipid molecule binding and transport site on MTP, we have studied the relative rates at which MTP transports different lipid species. Assay conditions were chosen in which there were minimal changes in the physical properties of the substrate membranes so that transfer rates would reflect MTP-lipid interactions at a membrane surface. Lipid transport rates decreased in order of triglyceride > cholesteryl ester > diglyceride > cholesterol > phosphatidylcholine. Changes in the hydrophobic nature of a lipid molecule by the addition of a fatty acid, modulated the ability of MTP to transport it. Addition of one acyl chain from diglyceride to triglyceride, lysophosphatidylcholine to phosphatidylcholine, or cholesterol to cholesteryl ester increased the rate of MTP-mediated transport 10-fold. In contrast, the lipid transport rate was insensitive to the changes in the structure or charge of the polar head group on phospholipid substrates. Zwitterionic, net negative, or net positive charged phospholipid molecules were all transported at a comparable rate. The ability of MTP to transport lipids is strongly correlated to the binding of these lipids to MTP. Thus, MTP has a specific preference for binding and transporting nonpolar lipid compared with phospholipids, and within a class of lipid molecules, a decrease in polarity increases its tendency to be transported.
Integrated DC-DC converter with an auxiliary output stage for transient suppression (2009)

In this paper, the transistor sizing of an auxiliary output stage in a digitally controlled transient suppression system for fully integrated point-of-load (POL) DC-DC converters is investigated. The auxiliary output stage is added in parallel to the main output switching stage to help reduce output voltage deviation during load transient. The sizing of the auxiliary output stage in relation to the main output stage is studied through analysis and simulation of a 3 W, 12 V to 1 V buck converter. The auxiliary output stage performs well with transistors occupying as little as 5% the area of the main output stage.
One meter square high rate neutron imaging panel based on boron straws (2009)

In order to fully realize the enhanced potential of the powerful neutron scattering technique provided by high intensity facilities like SNS, large area high rate detectors must be developed that do not depend upon the dwindling stock of 3He. We have developed a neutron detector that offers a large sensitive area (1 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), 3D spatial resolution, high sensitivity and high count rate capability, and it is economical and practical to produce. The detector technology is based on <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sup> B thin film conversion of neutrons in long straw-like gas detectors, as a novel and superior replacement of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> He detectors. Twenty-two detector modules, each consisting of 50 straws (1 m long, 4 mm in diameter, natural boron carbide coated), have been constructed and mounted into a robust housing to form a square meter panel detector. Readout electronics including preamplifiers, signal conditioning modules and digitization modules have been designed and tested to meet the required count rate in a 1 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> detector. We have successfully tested the panel detector, by imaging objects of different materials and different shapes. Additionally, one enriched detector module has been fabricated. The enriched module was integrated into the panel and produced a factor of four enhanced sensitivity in agreement with modeling predictions based on five fold higher <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sup> B content. The neutron imaging detector has achieved the required performance for SNS applications and substantially increases performance compared with <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> He while utilizing a cheap and inexhaustible conversion medium.
Discovery of 6-(Aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-<i>a</i>]pyrimidine-2-carboxamides as Potent, Selective Dipeptidyl Peptidase-4 (DPP4) Inhibitors (2010)

Continued structure-activity relationship (SAR) exploration within our previously disclosed azolopyrimidine containing dipeptidyl peptidase-4 (DPP4) inhibitors led us to focus on an imidazolopyrimidine series in particular. Further study revealed that by replacing the aryl substitution on the imidazole ring with a more polar carboxylic ester or amide, these compounds displayed not only increased DPP4 binding activity but also significantly reduced human ether-a-go-go related gene (hERG) and sodium channel inhibitory activities. Additional incremental adjustment of polarity led to permeable molecules which exhibited favorable pharmacokinetic (PK) profiles in preclinical animal species. The active site binding mode of these compounds was determined by X-ray crystallography as exemplified by amide 24c. A subsequent lead molecule from this series, (+)-6-(aminomethyl)-5-(2,4-dichlorophenyl)-N-(1-ethyl-1H-pyrazol-5-yl)-7-methylimidazo[1,2-a]pyrimidine-2-carboxamide (24s), emerged as a potent, selective DPP4 inhibitor that displayed excellent PK profiles and in vivo efficacy in ob/ob mice.
Long‐term durability of the response to desmopressin in female and male nocturia patients (2012)

The decrease in nocturnal voids and improvement in sleep with short-term desmopressin treatment were maintained throughout long-term treatment. A durable gender difference in efficacy in favor of females was observed with desmopressin ODT 25 µg. Further, large-scale long-term trials are needed to confirm the durability of efficacy with gender-specific doses of desmopressin.
Pt-Mal-LHRH, a Newly Synthesized Compound Attenuating Breast Cancer Tumor Growth and Metastasis by Targeting Overexpression of the LHRH Receptor (2016)

A new targeting chemotherapeutic agent, Pt-Mal-LHRH, was synthesized by linking activated cisplatin to luteinizing hormone releasing hormone (LHRH). The compound's efficacy and selectivity toward 4T1 breast cancer cells were evaluated. Carboplatin was selected as the comparative platinum complex, since the Pt-Mal-LHRH malonate linker chelates platinum in a similar manner to carboplatin. Breast cancer and normal cell viability were analyzed by an MTT assay comparing Pt-Mal-LHRH with carboplatin. Cells were also treated with either Pt-Mal-LHRH or carboplatin to evaluate platinum uptake by ICP-MS and cell migration using an in vitro scratch-migration assay. Tumor volume and metastasis were evaluated using an in vivo 4T1 mouse tumor model. Mice were administered Pt-Mal-LHRH (carboplatin molar equivalent dosage) through ip injection and compared to those treated with carboplatin (5 (mg/kg)/week), no treatment, and LHRH plus carboplatin (unbound) controls. An MTT assay showed a reduction in cell viability (p < 0.01) in 4T1 and MDA-MB-231 breast cancer cells treated with Pt-Mal-LHRH compared to carboplatin. Pt-Mal-LHRH was confirmed to be cytotoxic by flow cytometry using a propidium iodide stain. Pt-Mal-LHRH displayed a 20-fold increase in 4T1 cellular uptake compared to carboplatin. There was a decrease (p < 0.0001) in 4T1 cell viability compared to 3T3 normal fibroblast cells. Treatment with Pt-Mal-LHRH also resulted in a significant decrease in cell-migration compared to carboplatin. In vivo testing found a significant reduction in tumor volume (p < 0.05) and metastatic tumor colonization in the lungs with Pt-Mal-LHRH compared to carboplatin. There was a slight decrease in lung weight and no difference in liver weight between treatment groups. Together, our data indicate that Pt-Mal-LHRH is a more potent and selective chemotherapeutic agent than untargeted carboplatin.