gebhart/patrepeval huggingface dataset:
A review of cancer cachexia and abnormal glucose metabolism in humans with cancer. (1992)

In 1919, glucose intolerance became the earliest recognized metabolic abnormality in cancer patients. Prior to the development of severe malnutrition, colon, gastric, sarcoma, endometrial, prostate, localized head, neck, and lung cancer patients had many of the metabolic abnormalities of type II (noninsulin dependent) diabetes mellitus. These metabolic abnormalities include glucose intolerance, an increase in both hepatic glucose production (HGP) and glucose recycling, and insulin resistance. In a study of over 600 cancer patients, a diabetic pattern of glucose tolerance test was noted in over one-third of the patients. An increased rate of HGP, commonly seen in diabetics, has been noted in almost all types of cancer patients studied to date. Etiology of the increased glucose production in the cancer patient is not known, but abnormalities in the counter regulatory hormones, especially growth hormone, may contribute to the development of abnormal glucose metabolism. A second possible stimulus for the increase in HGP could be the glucose needs of the tumor. Abnormally high glucose utilization rates in small amounts of tumor tissue have recently been described. This suggests that small tumors may have large needs for glucose calories. An increase in anaerobic glycolysis in the tumor tissue can increase lactate production in the tumor-bearing human, thus supplying substrate to the liver to increase glucose production rates. In this paper, the nature of abnormal glucose metabolism in cancer patients is described.
A 34MB/s-Program-Throughput 16Gb MLC NAND with All-Bitline Architecture in 56nm (2008)

In the diverse world of NAND flash applications, higher storage capacity is not the only imperative. Increasingly, performance is a differentiating factor and is also a way of creating new markets or expanding existing markets. While conventional memory uses, for actual operations, every other cell along a selected word line (WL) [1], this design simultaneously exercises them all. A performance improvement of at least 100% is derived from this all-bitline (ABL) architecture relative to conventional chips. Additional techniques push performance to even higher levels.
Mycobacterium vaccae NCTC 11659, a Soil-Derived Bacterium with Stress Resilience Properties, Modulates the Proinflammatory Effects of LPS in Macrophages (2023)

Inflammatory conditions, including allergic asthma and conditions in which chronic low-grade inflammation is a risk factor, such as stress-related psychiatric disorders, are prevalent and are a significant cause of disability worldwide. Novel approaches for the prevention and treatment of these disorders are needed. One approach is the use of immunoregulatory microorganisms, such as <i>Mycobacterium vaccae</i> NCTC 11659, which have anti-inflammatory, immunoregulatory, and stress-resilience properties. However, little is known about how <i>M. vaccae</i> NCTC 11659 affects specific immune cell targets, including monocytes, which can traffic to peripheral organs and the central nervous system and differentiate into monocyte-derived macrophages that, in turn, can drive inflammation and neuroinflammation. In this study, we investigated the effects of <i>M. vaccae</i> NCTC 11659 and subsequent lipopolysaccharide (LPS) challenge on gene expression in human monocyte-derived macrophages. THP-1 monocytes were differentiated into macrophages, exposed to <i>M. vaccae</i> NCTC 11659 (0, 10, 30, 100, 300 µg/mL), then, 24 h later, challenged with LPS (0, 0.5, 2.5, 250 ng/mL), and assessed for gene expression 24 h following challenge with LPS. Exposure to <i>M. vaccae</i> NCTC 11659 prior to challenge with higher concentrations of LPS (250 ng/mL) polarized human monocyte-derived macrophages with decreased <i>IL12A</i>, <i>IL12B</i>, and <i>IL23A</i> expression relative to <i>IL10</i> and <i>TGFB1</i> mRNA expression. These data identify human monocyte-derived macrophages as a direct target of <i>M. vaccae</i> NCTC 11659 and support the development of <i>M. vaccae</i> NCTC 11659 as a potential intervention to prevent stress-induced inflammation and neuroinflammation implicated in the etiology and pathophysiology of inflammatory conditions and stress-related psychiatric disorders.
Risk Assessment in Geotechnical Engineering: Stability Analysis of Highly Variable Soils (2012)

The paper will review the state-of-the-art in the use of finite element methods for modeling geotechnical engineering problems involving non-typical geometries and highly variable soil properties. Examples will focus on slope stability analyses in which traditional limit equilibrium methods, and even well-established probabilistic methodologies may lead to misleading results.
A new mutation responsible for severe G6PD deficiency in two ethnic Chinese with different clinical presentations: determination by a direct PCR sequencing technique. (1992)

To test the hypothesis that clinical manifestation in G6PD deficiency correlates with a molecular lesion, we investigated the G6PD gene of two Chinese Americans both of whom had G6PD deficiency, but who manifested different clinical presentations. In this study, we have developed a direct PCR sequencing protocol to examine the human G6PD gene. By using optimized PCR conditions with internal primers, we were able to amplify a 4.2 kb DNA fragment (covering exon 3 through 13 of the G6PD gene) of consistently high quality. From this we were then able to generate high quality single-stranded DNA templates by asymmetric PCR for subsequent sequencing. We also overcame the crossband problem by using internal primers, high temperature reaction with Taq I DNA polymerase, and/or sequencing with gene 32 protein. We could consistently amplify exons 1 and 2 despite their high G/C content by substituting 75% of dGTP with deoxy-7-deaza-guanosine triphosphate. By using this novel approach, we have identified a new mutation at cDNA position 1376 from G to T, which causes substitution of Leu for Arg at amino acid position 459. This mutation has not been reported in other ethnic groups. It is the only genetic defect in the coding regions of the G6PD gene of these two G6PD deficient individuals. We speculate that in addition to a defect in the G6PD gene, other factors also play a role in the clinical manifestation of G6PD deficiency.
Layer-2 Path Discovery Using Spanning Tree MIBs (2002)

Layer-2 network topology discovery has become critical for areas of multimedia network management. For example, the topology can be used to help locate areas of congestion or to find the path between a pair of hosts (e.g., a pair experiencing poor VoIP performance). Little work is available for automatically finding the layer-2 topology of such networks. This paper presents an approach to find the topology based on tables for the spanning tree algorithm available through SNMP. The approach is being used as part of Avaya Inc.&amp;apos;s ExamiNet(TM), a tool for assessing IP telephony readiness in customer networks, and has been run on an example enterprise network.
The genome sequence of Samia ricini, a new model species of lepidopteran insect (2020)

Samia ricini, a gigantic saturniid moth, has the potential to be a novel lepidopteran model species. Samia ricini is far more resistant to diseases than the current model species Bombyx mori, and therefore can be more easily reared. In addition, genetic resources available for S. ricini rival those for B. mori: at least 26 ecoraces of S. ricini are reported and S. ricini can hybridize with wild Samia species, which are distributed throughout Asian countries, and produce fertile progenies. Physiological traits such as food preference, integument colour and larval spot pattern differ among S. ricini strains and wild Samia species so that those traits can be targeted in forward genetic analyses. To facilitate genetic research in S. ricini, we determined its whole genome sequence. The assembled genome of S. ricini was 458 Mb with 155 scaffolds, and the scaffold N50 length of the assembly was ~ 21 Mb. In total, 16,702 protein coding genes were predicted. While the S. ricini genome was mostly collinear with that of B. mori with some rearrangements and few S. ricini-specific genes were discovered, chorion genes and fibroin genes seemed to have expanded in the S. ricini lineage. As the first step of genetic analyses, causal genes for "Blue," "Yellow," "Spot," and "Red cocoon" phenotypes were mapped to chromosomes.
Assessment of Phenotype Microarray plates for rapid and high-throughput analysis of collateral sensitivity networks (2019)

The crisis of antimicrobial resistance is driving research into the phenomenon of collateral sensitivity. Sometimes, when a bacterium evolves resistance to one antimicrobial, it becomes sensitive to others. In this study, we have investigated the utility of Phenotype Microarray (PM) plates for identifying collateral sensitivities with unprecedented throughput. We assessed the relative resistance/sensitivity phenotypes of nine strains of Staphylococcus aureus (two laboratory strains and seven clinical isolates) towards the 72 antimicrobials contained in three PM plates. In general, the PM plates reported on resistance and sensitivity with a high degree of reproducibility. However, a rigorous comparison of PM growth phenotypes with minimum inhibitory concentration (MIC) measurements revealed a trade-off between throughput and accuracy. Small differences in PM growth phenotype did not necessarily correlate with changes in MIC. Thus, we conclude that PM plates are useful for the rapid and high-throughput assessment of large changes in collateral sensitivity phenotypes during the evolution of antimicrobial resistance, but more subtle examples of cross-resistance or collateral sensitivity cannot be identified reliably using this approach.
Preoperative Oral-Bowel Preparation Using Sodium Picosulfate and Magnesium Citrate Combination Powder for Left-Sided Colorectal Cancer: A Prospective Study (2022)

Objective This study aimed to determine if induction of sodium picosulfate and magnesium citrate (SPMC) preparation leads to adequate surgery for left-sided colorectal cancer (CRC). Summary of Background Data Adequate bowel cleansing is vital for safe and accurate colorectal surgery. Ingestion of laxatives for bowel cleansing may be associated with a broad spectrum of adverse effects during surgical intervention. Methods A single-center prospective study was conducted with hospitalized patients scheduled operation for left-sided CRC. All enrolled patients were instructed to consume normal diet until before preparation. Twenty-seven patients underwent preoperative SPMC preparation. Results The primary endpoint of this study was the 30-day postoperative morbidity rate, which was 23%, and no postoperative complication was higher than Clavien-Dindo grade 3. The primary anastomosis rate was 100%, and there was no anastomotic leakage. The colonic cleansing grades were 1 or 2 according to the bowel preparation scale for surgical assessment in 89% of the patients. The acceptability of the cleansing procedure by the patients assessed by a questionnaire was 85%, and the acceptability of the SPMC preparation by the medical staff was 93%. The surgical procedures included 18 laparoscopies, 6 robotic surgeries, and 3 laparotomies. The median operation time was 165 minutes, and the median blood loss was &amp;lt;50 cc. The median sodium serum concentration was significantly decreased after surgery. Conclusion Ingestion of an SPMC preparation as a cleansing procedure was judged to be adequate for curative surgery in patients with left-sided colorectal cancer.
Optical properties of a one-dimensional photonic crystal containing a graphene-based hyperbolic metamaterial defect layer (2017)

The transmission properties of a one-dimensional defective photonic crystal have been investigated using the transfer matrix method. A layer of graphene-based hyperbolic metamaterial whose optical axis is tilted with respect to the interface is taken as a defect. It is shown that two kinds of the defect modes can be found in the band gaps of the structure for TM-polarized waves. One kind is created at the frequency range in which the principle elements of the effective permittivity tensor of the defect layer have the same signs. The frequency of this kind of defect mode is independent from the orientation of the optical axis of the defect layer. The other one is created at the hyperbolic dispersion frequency range. Such a defect mode appears due to the anisotropic behavior of the defect layer and its frequency strongly depends on the orientation of the optical axis. Unlike the conventional defect modes, the magnetic field of this defect mode is localized around the defect layer.
Myeloid-specific TAK1 deletion results in reduced brain monocyte infiltration and improved outcomes after stroke (2018)

Our results showed that deletion of myeloid TAK1 resulted in smaller infarcts and improved functional outcomes at the peak of inflammation (day 3) and a reduction in brain-infiltrating immune cells that were primarily monocytes. Myeloid TAK1 deletion was also protective at 7 days post MCAo, reflecting a detrimental role of myeloid TAK1 in the progression of ischemic injury.
Variability of change detection results for 2011 Tohoku, Japan earthquake using very high-resolution satellite images (2014)

The Tohoku earthquake of March 11, 2011, caused very huge tsunamis and widespread devastation. Various very highresolution satellites quickly captured the details of affected areas, and were used for disaster management. In this study, very high-resolution pre- and post-event Geoeye-1 satellite images were used to identify damages. Change detection procedure was used to obtain estimation from the damages. However based on the selected zone and the number of categories selected for the change detection some variability was detected in the results. This paper analyses the effects of these parameters on the change detection results and discuss about the amount of errors and also the correlation between the results for different zones selection. It was observed that the amount of changes vary based on the selections and there is no linear relation between the quantitative results. This issue was investigated through various examples using 2011 Tohoku, Japan earthquake with very high resolution satellite images.
Lipids and infant formulas (1998)

The ultimate goal in the design of infant formula is to achieve the outcome seen in breast fed infants. This review of lipids in infant formulas for term infants begins by referring to the lipid composition of human milk, and relates that to differences in lipid digestion and metabolism which exist between breast fed and formula fed infants and which may significantly influence fatty acid bioavailability. Recommendations are made for the lipid content and fatty acid composition of term infant formulas (especially for lauric, linoleic, alpha-linolenic, long chain 20 and 22C n-3 and n-6 polyunsaturated fatty acids and the trans fatty acids). Further research is required to define more clearly the long term nutritional, growth and developmental effects of structured lipids in formulas for term infants. More information is required on the differential handling of LCPUFA and other fatty acids at the organ and cellular level. There is a need for large (multi-centre) randomized studies to determine the short and long term functional effects of LCPUFA supplementation. Further research and development is required to determine a commercial source of LCPUFA which is safe, effective and economic. Further information is required on the short and long term effects of cholesterol intake during infancy, and in particular its relationship to LCPUFA metabolism. Long term studies should be initiated to determine the relationship of infant diet (especially saturated fatty acid and cholesterol intake) to the development of cardiovascular disease.
Molecular biology of voltage‐gated K+ channels in heart (1994)

The recent cloning of numerous voltage-activated K+ channels provides new information concerning the architecture of K+ channel proteins. The combination of molecular genetic and biophysical methods gives us a new insight into the molecular mechanisms of K+ channel pharmacology.
Recurrent nets that time and count (2000)

The size of the time intervals between events conveys information essential for numerous sequential tasks such as motor control and rhythm detection. While hidden Markov models tend to ignore this information, recurrent neural networks (RNN) can in principle learn to make use of it. We focus on long short-term memory (LSTM) because it usually outperforms other RNN. Surprisingly, LSTM augmented by "peephole connections" from its internal cells to its multiplicative gates can learn the fine distinction between sequences of spikes separated by either 50 or 49 discrete time steps, without the help of any short training exemplars. Without external resets or teacher forcing or loss of performance on tasks reported earlier, our LSTM variant also learns to generate very stable sequences of highly nonlinear, precisely timed spikes. This makes LSTM a promising approach for real-world tasks that require to time and count.
Improved performance CMUT-on-CMOS devices using ALD hafnium oxide insulation layer (2014)

Higher transmit sensitivity and receive sensitivity at lower bias voltages would be achieved by CMUTs when their structure converges to an ideal parallel plate structure without an insulation layer. Using an insulation layer with high relative dielectric constant (high-K) helps achieving this goal with increased capacitance and large electric field in the vacuum gap. The effect of the insulation layer is more pronounced for high frequency, small gap CMUTs, where large pressures can be generated with smaller displacements. In this paper, we present a simple model for optimal insulation layer properties and significant improvement in both transmit and receive sensitivity by replacing the silicon nitride (Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> ) insulation layer with high-K hafnium oxide (HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) for a low temperature CMUT-on-CMOS process. Experiments are performed on parallel fabricated test CMUTs with 50-nm gap and 16.5-MHz center frequency to measure and compare pressure output and receive sensitivity for PECVD Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> and HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> insulation layers. Results for this particular design show 6-dB improvement in receive sensitivity (V/Pa) with the collapse voltage reduced by one half. Successful CMUT-on-CMOS integration with high-k dielectric is also demonstrated.
Network design in cells: Optimization of metabolic networks (2009)

The DNA of living organisms is an emerging substrate for engineering. Owing to rapid improvements in technology, the cost of reading and writing DNA will likely be nominal in the near future, enabling easy fabrication of DNA. But the question is, What DNA sequence do we make? Given the vast capabilities of living organisms, from sensing, to signaling and communication, to motility, to chemical synthesis, the possibilities of engineered organisms are enormous. Unfortunately, the mapping from DNA sequence to function is not well understood, and determining the sequence required for a given function is not straightforward. We are motivated in particular by applications in bioenergy, where engineered microbes can be used to synthesize chemical fuels from carbon dioxide. To inform engineering, we use metabolic models to computationally predict and design the metabolism of the microbes. These models are essentially network flow models, and optimizing metabolic flow amounts to a difficult network design problem. We discuss GDLS (Genetic Design through Local Search), a heuristic we have developed for solving this network design problem. Our heuristic, which is related to the M algorithm for limited search trellis decoding of convolutional codes, results in effective, low-complexity search of the design space. We have applied GDLS to iAF1260, a detailed metabolic model of Escherichia coli, to predict modifications of the E. coli genome for overproduction of fatty acids-an intermediate to hydrocarbon fuels-and we are currently in the process of implementing these modifications and validating the experimental phenotype.
Nanostructured polymer matrix for oligonucleotide separation (2006)

A nanostructured copolymer matrix has successfully separated oligonucleotides with high resolution by CE using a very short separation channel which simulates the real microchip condition for the first time. The triblock copolymer, E(45)B(14)E(45) (B20-5000) with E, B, and subscript denoting oxyethylene, oxybutylene, and segment length, respectively, has a unique temperature-dependent viscosity-adjustable property and a dynamic coating ability in 1xTBE buffer (89 mM Tris, 89 mM boric acid, 2 mM EDTA in Milli-Q water). The B-block is hydrophilic at low temperatures, e.g., 4 degrees C, and the polymer solution has a very low viscosity of about 100 cP in a 32.5% w/v solution. At room temperatures, the B-block becomes hydrophobic due to a breakdown of hydrogen bonds between B-blocks and water, and the polymer matrix forms a body-centered cubic structure at high concentrations. Oligonucleotide sizing markers ranging from 8 to 32 base could be successfully separated with one-base resolution in a 1.5 cm long separation channel by E(45)B(14)E(45) in its gel-like state.
Total Syntheses of Murrayamine E, I, and K (2015)

We describe efficient synthetic routes to murrayamine A (mukoenine C), O-methylmurrayamine A, mahanine, O-methylmahanine, and murrayamine D and the first total syntheses of murrayamine E, I, and K. Key steps are a palladium-catalyzed construction of the carbazole framework and an annulation of the pyran ring, which is either catalyzed by phenylboronic acid or promoted by a Lewis acid.
Stationary distributions for fluid flow models with or without brownian noise (1995)

We consider a process with reflection at the origin and paths which are piecewise linear or Brownian, with the drift and variance constants being determined by the state of an underlying finite Markov process; the purely linear case corresponds to fluid flow models of current interest in telecommunications engineering. It is shown that the stationary distribution is phase-type, and various algorithms for computing the phase representation are given, some iterative with each step involving a matrix inversion and some based upon spectral expansion of the phase generator. Mathematically, the point of view is Markov additive processes, and some key tools are time-reversal and auxiliary Markov processes obtained by observing the underlying Markov process when the additive component is at a maximum
A non-foster monopole array (2012)

Antenna arrays enable beamforming and multiple-input multiple output (MIMO) communication schemes, but performance suffers as the element size and spacing is reduced. A non-Foster matching network for an electrically-small 2-element monopole array is proposed to overcome the performance limitations of passive matching. Full-wave simulation and stability analysis show that the proposed network is stable and the reactance of both the even and odd modes can be cancelled simultaneously over a wide bandwidth using ideal negative capacitors and negative resistors.