gebhart/patrepeval huggingface dataset:
DNA methylation signatures in circulating cell-free DNA for the monitoring of at-risk populations progressing to lung cancer (2015)

Alteration of DNA methylation patterns at the 5′ position of cytosines, in the context of CpG dinucleotides, is one of the most promising epigenetic biomarkers for many biomedical applications and has been actively studied in many diseases and developmental questions for the last twenty years (How Kit et al., 2012). In comparison to genetic alterations such as mutations, which are usually distributed throughout the gene, DNA methylation alterations are concentrated in a defined area, often the promoter, facilitating analysis. DNA methylation can be reliably analyzed in freshly frozen and archived clinical specimens, but more importantly, also in biofluids, that were either in direct contact with the disease (e.g. stool for colorectal, urine for genitourinary or sputum, bronchoalveolar lavages or brushes for lung cancer) or in cell-free circulating DNA isolated from serum or plasma of patients (How Kit et al., 2012).
Architectures for Efficient Scribble Matching (1994)

Scribble matching is a form of partial handwriting recognition that allows like scribbles to be identified. In a companion paper [1] we describe a set of three algorithms which achieve high accuracy on this task. In this paper we address the issue of increasing the computational efficiency of these algorithms by over an order of magnitude to the point where interactive use on a modest platform such as Intel 80386 is possible.
Antibacterial Properties of an In Situ Generated and Simultaneously Deposited Nanocrystalline ZnO on Fabrics (2008)

Zinc oxide (ZnO) nanoparticles were synthesized and deposited on the surface of cotton fabrics using ultrasound irradiation. Optimization of the process resulted in a homogeneous distribution of ZnO nanocrystals, 30 nm in size, on the fabric surface. The mechanism of the ultrasound-assisted coating was proposed. The antibacterial activities of the ZnO-fabric composite were tested against Escherichia coli (Gram negative) and Staphylococcus aureus (Gram positive) cultures. A significant bactericidal effect, even in a 0.75% coated fabric (wt %), was demonstrated.
Study on planarization performance of spin on hardmask (2018)

For multilayer process, the importance of spin on carbon (SOC) material that replaces amorphous carbon layer (ACL) is ever increasing. SOC is an organic polymer with high carbon content formulated in organic solvents for spin-coating application that is cured through baking. In comparison to ACL which is applied by CVD process, SOC material can offer several benefits: lower cost of ownership (CoO) and shorter process time as well as better gap-fill and planarization performances. Thus SOC material of high etch resistance, good gap-fill properties, and global planarization performances over various pattern topographies is desired to achieve fine patterning with high aspect ratio (A/R). In particular, good level of global planarization of spin coated layer over the underlying pattern topographies is important for self-aligned double patterning (SADP) process as it dictates the photolithographic margin. Herein, we report a copolymer SOC resin formulation that exhibits favorable film shrinkage profile and ideal etch resistance properties. By combining the favorable characteristics of each resin — one resin with good shrinkage property and the other with excellent etch resistance into the copolymer, it was possible to achieve desirable level of etch resistance and planarization performances across various pattern topographies of underlying substrate.
Nanoscale Electrodes for Flexible Electronics by Swelling Controlled Cracking (2016)

Nanogap electrodes are realized using pre-patterned electrodes and a swelling controlled cracking method. Parallel fabrication of nanogap electrodes on flexible substrates can be achieved using this method. This swelling-controlled cracking method is promising for fabricating high-performance flexible electronics. UV photodetectors with ZnO nanoparticle-bridged nanogap electrodes exhibit high responsivity and external quantum efficiency.
Up‐regulation of sucrose synthase and UDP‐glucose pyrophosphorylase impacts plant growth and metabolism (2005)

The effects of the overexpression of sucrose synthase (SuSy) and UDP-glucose pyrophosphorylase (UGPase) on plant growth and metabolism were evaluated in tobacco (Nicotiana tabacum cv. Xanthi). T(1) transgenic plants expressing either gene under the control of a tandem repeat cauliflower mosaic virus 35S promoter (2x35S) or a xylem-localized 4CL promoter (4-coumarate:CoA ligase; 4CL) were generated, and reciprocally crossed to generate plants expressing both genes. Transcript levels, enzyme activity, growth parameters, fibre properties and carbohydrate content of stem tissue were quantified. The expression profiles of both genes confirmed the expression pattern of the promoters: 2x35S expressed more strongly in leaves, while 4CL expression was highest in stem tissue. In-depth plant characterization revealed that the single-transgene lines showed significant increases in the height growth compared with corresponding control lines. The double-transgene plants demonstrated an additive effect, proving to be even taller than the single-transgene parents. Several of these lines had associated increases in soluble sugar content. Although partitioning of storage carbohydrates into starch or cellulose was not observed, the increased height growth and increases in soluble carbohydrates suggest a role for SuSy as a marker in sink strength and lend credit to the function of UGPase in a similar role. The up-regulation of these two genes, although not increasing the percentage cellulose content, was effective in increasing the total biomass, and thus the overall cellulose yield, from a given plant.
Nonquaternary Reactivators for Organophosphate-Inhibited Cholinesterases (2011)

A new class of amidine-oxime reactivators of organophosphate (OP)-inhibited cholinesterases (ChE) was synthesized and tested in vitro and in vivo. Compared with 2-PAM, the most promising cyclic amidine-oxime (i.e., 12e) showed comparable or greater reactivation of OP-inactivated AChE and OP-inactivated BChE. To the best of our knowledge, this is the first report of a nonquaternary oxime that has, comparable to 2-PAM, in vitro potency for reactivation of Sarin (GB)-inhibited AChE and BChE. Amidine-oximes were tested in vitro, and reactivation rates for OP-inactivated butyrylcholinesterase (BChE) were greater than those for 2-PAM or MINA. Amidine-oxime reactivation rates for OP-inactivated acetylcholinesterase (AChE) were lower compared to 2-PAM but greater compared with MINA. Amidine-oximes were tested in vivo for protection against the toxicity of nerve agent model compounds. (i.e., a model of Sarin). Post-treatment (i.e., 5 min after OP exposure, i.p,) with amidine oximes 7a-c and 12a, 12c, 12e, 12f, and 15b (145 μmol/kg, i.p.) protected 100% of the mice challenged with the sarin model compound. Even at 25% of the initial dose of amidine-oxime (i.e., a dose of 36 μmol/kg, i.p.), 7b and 12e protected 100% of the animals challenged with the sarin nerve agent model compound that caused lethality in 6/11 animals without amidine-oxime.
The ‘Hospice of the German Nobility’: Changes in the Admission Policy of the Teutonic Knights in the Fifteenth Century (2021)

The Teutonic Order has been called an aristocratic corporation in crisis for the period 1410 to 1466. 1 Crisis, decline, and decay are the words that have been used to mark the condition in which the order found itself in the fifteenth century. 2 And indeed this brotherhood whose task it was to protect Christendom against its enemies got into a long series of difficulties in this period, which in the long run threatened to destroy the very foundations of its existence, at least in the Baltic, where the order by then had its main area of operation. Since the Grand Duke of Lithuania had been converted in 1386 there were, formally, no heathen to be fought. From then on, the only object of the order could be to ensure that the crusading state it had founded prevailed against its mighty catholic contending neighbours Poland and Lithuania. The order had to do this on its own, without the help of the west-European nobility, which in the preceding 116century had come to Prussia in great numbers to hunt down heathen Lithuanians. Only the Livonian branch could still serve Christendom after 1400 by continuing its struggle against the schismatic Russians. The smashing defeat at Tannenberg in 1410 and the humiliating second peace-treaty of Thorn in 1466, in which the grand master had to cede more than half of his territory and strongholds to the Polish king and to accept his overlordship for the remainder, had seriously weakened the cohesion of the order – if they did not already mark the end of its universal ambitions. Add to this the fact that the third branch of the order, which was organized in twelve bailiwicks in the German empire at the same time, had to face the consequences of an economic depression and, for some bailiwicks, increasingly had to put up with the control of territorial lords, 3 and the gloomy background of my story is sketched. In this context, the question nearly automatically is to be raised what connections can be established between these developments and the changes that took place in the conditions of access to the order. Before I focus upon these changes, let us first have a look at the figures.
Lymphatic vessels regulate immune microenvironments in human and murine melanoma (2016)

Lymphatic remodeling in tumor microenvironments correlates with progression and metastasis, and local lymphatic vessels play complex and poorly understood roles in tumor immunity. Tumor lymphangiogenesis is associated with increased immune suppression, yet lymphatic vessels are required for fluid drainage and immune cell trafficking to lymph nodes, where adaptive immune responses are mounted. Here, we examined the contribution of lymphatic drainage to tumor inflammation and immunity using a mouse model that lacks dermal lymphatic vessels (K14-VEGFR3-Ig mice). Melanomas implanted in these mice grew robustly, but exhibited drastically reduced cytokine expression and leukocyte infiltration compared with those implanted in control animals. In the absence of local immune suppression, transferred cytotoxic T cells more effectively controlled tumors in K14-VEGFR3-Ig mice than in control mice. Furthermore, gene expression analysis of human melanoma samples revealed that patient immune parameters are markedly stratified by levels of lymphatic markers. This work suggests that the establishment of tumor-associated inflammation and immunity critically depends on lymphatic vessel remodeling and drainage. Moreover, these results have implications for immunotherapies, the efficacies of which are regulated by the tumor immune microenvironment.
Glycaemic index of different coconut (<i>Cocos nucifera</i>)-flour products in normal and diabetic subjects (2003)

The glycaemic index (GI) of commonly consumed bakery products supplemented with increasing levels of coconut ( Cocos nucifera ) flour was determined in ten normal and ten diabetic subjects. Using a randomized crossover design, the control and test foods were fed in random order on separate occasions after an overnight fast. Blood samples were collected through finger prick before and after feeding and were analysed for glucose levels using a clinical chemistry analyser. The significantly low-GI (< 60) foods investigated were: macaroons (GI 45·7 ( sem 3·0)) and carrot cake (GI 51·8 ( sem 3·3)), with 200–250 g coconut flour/kg ( P <0·05). The test foods with 150 g coconut flour/kg had GI ranging from 61·3 to 71·4. Among the test foods, pan de sal (GI 87·2 ( sem 5·5)) and multigrain loaf (GI 85·2 ( sem 6·8)) gave significantly higher GI with 50 and 100 g coconut flour/kg respectively ( P <0·05). On the other hand, granola bar and cinnamon bread with 50 and 100 g coconut flour/kg respectively gave a GI ranging from 62·7 to 71·6 and did not differ significantly from the test foods with 150 g coconut flour/kg ( P < 0·05). A very strong negative correlation ( r – 0·85, n 11, P < 0·005) was observed between the GI and dietary fibre content of the test foods supplemented with coconut flour. In conclusion, the GI of coconut flour-supplemented foods decreased with increasing levels of coconut flour and this may be due to its high dietary fibre content. The results of the present study may form a scientific basis for the development of coconut flour as a functional food. However, the fat content of coconut flour-supplemented food should always be considered to optimize the functionality of coconut fibre in the proper control and management of diabetes mellitus.
Speeding up the memory hierarchy in Flat COMA multiprocessors (2002)

Scalable Flat Cache Only Memory Architectures (Flat COMA) are designed for reduced memory access latencies while minimizing programmer and operating system involvement. Indeed, to keep memory access latencies low, neither the programmer needs to perform clever data placement nor the operating system needs to perform page migration. The hardware automatically replicates the data and migrates it to the attraction memories of the nodes that use it. Unfortunately, part of the latency of memory accesses is superfluous. In particular, reads often perform unnecessary attraction memory accesses, require too many network hops, or perform necessary attraction memory accesses inefficiently. In this paper, we propose relatively inexpensive schemes that address these three problems. To eliminate unnecessary attraction memory accesses, we propose a small direct-mapped cache called Invalidation Cache (IVC). To reduce the number of network hops, the IVC is augmented with hint pointers to processors. These hint pointers are faster and have more applicability than in older hint schemes. Finally, to speed up necessary accesses to set-associative attraction memories, we optimize the locality of windows in page-mode DRAMs. We evaluate these optimizations with 32-processor simulations of 8 Splash and Perfect Suite applications. We show that these optimizations speed up the applications by an average of 20% at a modest cost.
Nucleation of Epitaxial Graphene on SiC(0001) (2009)

A promising route for the synthesis of large-area graphene, suitable for standard device fabrication techniques, is the sublimation of silicon from silicon carbide at elevated temperatures (>1200 degrees C). Previous reports suggest that graphene nucleates along the (110n) plane, known as terrace step edges, on the silicon carbide surface. However, to date, a fundamental understanding of the nucleation of graphene on silicon carbide is lacking. We provide the first direct evidence that nucleation of epitaxial graphene on silicon carbide occurs along the (110n) plane and show that the nucleated graphene quality improves as the synthesis temperature is increased. Additionally, we find that graphene on the (110n) plane can be significantly thicker than its (0001) counterpart and appears not to have a thickness limit. Finally, we find that graphene along the (110n) plane can contain a high density of structural defects, often the result of the underlying substrate, which will undoubtedly degrade the electronic properties of the material. Addressing the presence of non-uniform graphene that may contain structural defects at terrace step edges will be key to the development of a large-scale graphene technology derived from silicon carbide.
Characteristics of signal propagation in magnetic quantum cellular automata circuits (2011)

Magnetic quantum cellular automata (MQCA) is a nano-scale computational paradigm that utilises magnetic dipolar interaction and coupling to propagate and process binary information. Characteristics of signal propagation in MQCA circuits with pipelined clocking signals are evaluated for the purposes of fast and reliable logic operation. These circuits are simulated via the Landau–Lifshitz–Gilbert equations and object-oriented micro-magnetic framework tool. It is found that signal propagations in the thin nanomagnet circuits are blocked significantly as the damping parameter is increased; however, their switching times decrease as the damping parameter increases. Switching speeds of MQCA structures are improved as the thickness and damping parameter are increased. The results also show that the majority logic gate performs a complete reliable operation for nanomagnet thicker than about 20 nm, whereas for interconnect wire, thickness ranging from only about 20 to 25 nm introduces a successful operation.
Security in migratory interactive web applications (2012)

In ubiquitous environments migratory interactive applications allow users to perform their tasks continuously across various devices. Users can push and pull migratory Web applications from one device to another for various reasons. However, the flexibility of such pervasive applications raises various security issues, such as the risk of theft of private information from the migrated user interfaces or the intrusion of malicious versions of the applications replacing the original ones. In this paper, we analyse such risks and present a number of solutions to address them in a client/server-based solution for supporting secure migration of interactive Web applications.
Mechanisms of beta-adrenergic receptor regulation in cultured chick heart cells. Role of cytoskeleton function and protein synthesis. (1985)

To examine mechanisms by which cardiac tissue regulates the beta-adrenergic receptor and physiological response to beta-adrenergic agonists, we studied the effects of cytoskeletal disrupting agents and inhibition of protein synthesis on receptor properties and contractile response to isoproterenol in intact cultured ventricular cells from embryonic chick heart. Thirty minutes of exposure of intact cells to 1 microM isoproterenol produced loss of the high-affinity state (KD = 4.5 +/- 1.5 nM) of the receptor found in cell membranes with no loss of total receptor number, whereas there was concomitant decline in the contractile response to 1 microM isoproterenol to 41 +/- 16% (SD) of control. Contractile response recovered within 60 minutes of agonist removal to 78 +/- 11% of initial response. There was concomitant recovery of the high-affinity state of the receptor, so that 1 hour after agonist removal there was 72% of the initial proportion of high-affinity receptors. This desensitization of the contractile response, as well as recovery after agonist removal, was markedly blunted by preincubation with cytochalasin B so that contractile responsiveness to isoproterenol was maintained at 77 +/- 13% of the initial response. Colchicine (10 microM) was without effect on the first 30 minutes of agonist-induced desensitization. More prolonged agonist exposure (1 microM isoproterenol for 24 hours) produced colchicine-sensitive loss of receptors from intact cells to 40% of control levels. Full recovery of receptor number occurred over 72 hours; this was completely blocked by cycloheximide (P less than 0.01). Thus, rapid desensitization and resensitization of the beta-receptor-mediated contractile response is associated with alterations in high-affinity agonist binding and appears to be modulated by microfilaments. Receptor down-regulation is dependent on functional microtubules, and recovery of these receptors after agonist removal requires protein synthesis.
Management of Critical Limb Ischemia (2016)

Critical limb ischemia (CLI) is a clinical syndrome of ischemic pain at rest or tissue loss, such as nonhealing ulcers or gangrene, related to peripheral artery disease. CLI has a high short-term risk of limb loss and cardiovascular events. Noninvasive or invasive angiography help determine the feasibility and approach to arterial revascularization. An endovascular-first approach is often advocated based on a lower procedural risk; however, specific patterns of disease may be best treated by open surgical revascularization. Balloon angioplasty and stenting form the backbone of endovascular techniques, with drug-eluting stents and drug-coated balloons offering low rates of repeat revascularization. Combined antegrade and retrograde approaches can increase success in long total occlusions. Below the knee, angiosome-directed angioplasty may lead to greater wound healing, but failing this, any straight-line flow into the foot is pursued. Hybrid surgical techniques such as iliac stenting and common femoral endarterectomy are commonly used to reduce operative risk. Lower extremity bypass grafting is most successful with a good quality, long, single-segment autogenous vein of at least 3.5-mm diameter. Minor amputations are often required for tissue loss as a part of the treatment strategy. Major amputations (at or above the ankle) limit functional independence, and their prevention is a key goal of CLI therapy. Medical therapy after revascularization targets risk factors for atherosclerosis and assesses wound healing and new or recurrent flow-limiting disease. The ongoing National Institutes of Health-sponsored Best Endovascular Versus Best Surgical Therapy in Patients With Critical Limb Ischemia (BEST-CLI) study is a randomized trial of the contemporary endovascular versus open surgical techniques in patients with CLI.
The Safety and Application of Database (2013)

With the development of information technology,database use has occupied an important position,it is for the society and people's daily life plays an irreplaceable role.Safety requirement database is how to prevent the illegal use of the information disclosure,alteration or destruction.This article from the three aspects of the importance of safety,database security strategy and threat factorsare discussed.
Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis (2012)

Continued advances in metabolic engineering are increasing the number of small molecules being targeted for microbial production. Pathway yields and productivities, however, are often suboptimal, and strain improvement remains a persistent challenge given that the majority of small molecules are difficult to screen for and their biosynthesis does not improve host fitness. In this work, we have developed a generalized approach to screen or select for improved small-molecule biosynthesis using transcription factor-based biosensors. Using a tetracycline resistance gene 3' of a small-molecule inducible promoter, host antibiotic resistance, and hence growth rate, was coupled to either small-molecule concentration in the growth medium or a small-molecule production phenotype. Biosensors were constructed for two important chemical classes, dicarboxylic acids and alcohols, using transcription factor-promoter pairs derived from Pseudomonas putida, Thauera butanivorans, or E. coli. Transcription factors were selected for specific activation by either succinate, adipate, or 1-butanol, and we demonstrate product-dependent growth in E. coli using all three compounds. The 1-butanol biosensor was applied in a proof-of-principle liquid culture screen to optimize 1-butanol biosynthesis in engineered E. coli, identifying a pathway variant yielding a 35% increase in 1-butanol specific productivity through optimization of enzyme expression levels. Lastly, to demonstrate the capacity to select for enzymatic activity, the 1-butanol biosensor was applied as synthetic selection, coupling in vivo 1-butanol biosynthesis to E. coli fitness, and an 120-fold enrichment for a 1-butanol production phenotype was observed following a single round of positive selection.