gebhart/patrepeval huggingface dataset:
Amorphous silicon thin-film transistor active-matrix for reflective cholesteric liquid crystal displays. (2000)

Reflective cholesteric liquid crystal displays (Ch-LCDs) have advantages, such as, high brightness, low power consumption, and wide viewing angle, since they do not need any polarizer, color filter, and backlight. Furthermore, due to their bistability Ch-LCDs can retain their images virtually forever without additional power consumption. But conventional passive-matrix addressing of Ch-LCDs allows only a slow image updating speed. Active-matrix addressing should allow fast image updating or video-rate operation. However, because the threshold voltage of cholesteric, liquid crystal is high (>20V), the switching devices for active-matrix addressing should satisfy required characteristics even under high bias conditions. In order to investigate the applicability of hydrogenated amorphous silicon thin film transistors (a-Si:H TFTs) for the switching devices of active-matrix (AM) Ch-LCDs, the characteristics of conventional and gate offset high voltage a-Si:H TTFs were examined under high bias conditions. And it was concluded that high OFF-current of conventional a-Si:H TFTs and low ON-current of gate offset high voltage a-Si:H TFTs were main problems for reflective AM Ch-LCD applications. In order to improve the TFT characteristics under high bias conditions, we propose two new a-Si:H TFT structures called gate planarized (GP) and buried field plate (BFP) high voltage a-Si:H TFTs. Firstly, in the GP a-Si:H TFTs, we used a thick spin-coated benzocyclobutene (BCB) layer beneath a thin hydrogenated amorphous silicon nitride (a-SiN<sub>x</sub>:H) layer for gate insulator. The GP a-Si:H TFT showed normal TFT characteristic up to V<sub>GS</sub> = V<sub>DS</sub> = ∼100 V without any device failure. But TFT ON-current of GP a-Si:H TFT was reduced due to the introduction of the thick low dielectric BCB layer. Secondly, in the BFP a-Si:H TFT, an offset region and a buried field plate were introduced between the drain/source and gate electrodes to reduce the electric field in the pinch-off region. For this BFP a-Si:H TFT, a low OFF-current (1.04 pA) and a high ON/OFF-current ratio (5.68 x 10<super>6</super>) up to V<sub>GS</sub> = V<sub>DS</sub> = ∼30 V were obtained. Based on our a-Si:H TFTs studies, we designed an a-Si:H TFT active-matrix panel and fabricated the AM Ch-LCDs either by optimizing a-Si:H TFT processing or adopting the GP a-Si:H TFT technology. The fabricated a-Si:H TFT active-matrix panels can be operated at the voltage of 50 and 60V, applied to the data and gate lines, respectively. With the a-Si:H TFT active-matrix panels, the AM Ch-LCDs were fabricated and operated with the frame rate of 60 Hz and the maximum contrast ratio of ∼30.
Cell-Bound IL-8 Increases in Bronchial Epithelial Cells after Arylsulfatase B Silencing due to Sequestration with Chondroitin-4-Sulfate (2009)

The chemokine IL-8 is critically important in inflammatory processes in human tissues, and IL-8 interactions with sulfated glycosaminoglycans have been implicated in modification of inflammatory responses in bronchial epithelium. To determine the role of chondroitin-4-sulfate (C4S) in mediating effects of IL-8, we silenced the enzyme N-acetylgalactosamine-4-sulfatase (arylsulfatase B [ASB]) that removes the 4-sulfate group from C4S, in the IB3-1 and C38 bronchial epithelial cell lines and in normal primary bronchial epithelial cells. When ASB was silenced and IL-8 production stimulated by exposure to TNF-alpha, ASB activity declined by roughly 75%, cellular C4S content increased by over 7.5 microg/mg protein, cell-bound IL-8 increased by over 530 pg/mg protein, and secreted IL-8 declined by over 520 pg/mg protein in all cell lines (P < 0.001). When cell lysates were immunoprecipitated with C4S antibody after ASB silencing and TNF-alpha, the IL-8 content of the immunoprecipitate was approximately 500 pg/mg protein, indicating that most of the cell-bound IL-8 was associated with C4S. Cell fractionation demonstrated that the IL-8 content associated with the cell membranes was about twice that of the cytosolic fraction. Also, ASB appeared to localize in the cell membrane, as well as in lysosomes. Neutrophil attraction to the cell lysates increased after ASB silencing, consistent with increased attraction to the cell-bound IL-8. These findings provide evidence for the influential role of ASB and C4S in the regulation of IL-8 secretion, and suggest that changes in ASB activity and C4S content may have a significant impact on IL-8-mediated inflammatory responses.
REGIONAL ILEITIS (1932)

We propose to describe, in its pathologic and clinical details, a disease of the terminal ileum, affecting mainly young adults, characterized by a subacute or chronic necrotizing and cicatrizing inflammation. The ulceration of the mucosa is accompanied by a disproportionate connective tissue reaction of the remaining walls of the involved intestine, a process which frequently leads to stenosis of the lumen of the intestine, associated with the formation of multiple fistulas. The disease is clinically featured by symptoms that resemble those of ulcerative colitis, namely, fever, diarrhea and emaciation, leading eventually to an obstruction of the small intestine; the constant occurrence of a mass in the right iliac fossa usually requires surgical intervention (resection). The terminal ileum is alone involved. The process begins abruptly at and involves the ileocecal valve in its maximal intensity, tapering off gradually as it ascends the ileum orally for from 8 to 12 inches (20
Calcineurin-NFATc signaling pathway regulates <i>AQP2</i> expression in response to calcium signals and osmotic stress (2006)

The aquaporin (AQP)2 channel mediates the reabsorption of water in renal collecting ducts in response to arginine vasopressin (AVP) and hypertonicity. Here we show that AQP2 expression is induced not only by the tonicity-responsive enhancer binding protein (TonEBP)/nuclear factor of activated T cells (NFAT)5-mediated hypertonic stress response but also by the calcium-dependent calcineurin-NFATc pathway. The induction of AQP2 expression by the calcineurin-NFATc pathway can occur in the absence of TonEBP/NFAT5. Mutational and chromatin immunoprecipitation analyses revealed the existence of functional NFAT binding sites within the proximal AQP2 promoter responsible for regulation of AQP2 by NFATc proteins and TonEBP/NFAT5. Contrary to the notion that TonEBP/NFAT5 is the only Rel/NFAT family member regulated by tonicity, we found that hypertonicity promotes the nuclear translocation of NFATc proteins for the subsequent induction of AQP2 expression. Calcineurin activity was also found to be involved in the induction of TonEBP/NFAT5 expression by hypertonicity, thus further defining the signaling mechanisms that underlie the TonEBP/NFAT5 osmotic stress response pathway. The coordinate regulation of AQP2 expression by both osmotic stress and calcium signaling appears to provide a means to integrate diverse extracellular signals into optimal cellular responses.
Kinetics and mechanism of the reaction between carbon dioxide and amines in aqueous solution (1989)

Rate constants, ΔH‡ and ΔS‡ have been measured by the conductimetric stopped-flow technique for the reaction of carbon dioxide in aqueous solution with the primary amines 2-methoxyethylamine, 2-aminoethanol, 3-aminopropan-1-ol, 2-aminopropan-2-ol, DL-aminopropan-2-ol and the secondary amines 1,1′-iminodipropan-2-ol, 2-amino-2-(hydroxymethyl) propane-1,3-diol, 2,2′-iminodiethanol, 2,2,6,6-tetramethylpiperidin-4-ol, and morpholine. The observed first-order rate constants fit the equation kobs=kAM[R2NH]2+kW[R2NH][H2O]. The much-quoted Danckwerts mechanism is shown to be unlikely.
Significance of Proximal Tubular Metabolism of Advanced Glycation End Products in Kidney Diseases (2005)

Advanced glycation end products (AGEs) are formed by the nonenzymatic Maillard reaction between sugars and proteins. Low-molecular weight AGEs are filtered by renal glomeruli and then reabsorbed and metabolized by proximal tubule cells (PTCs). High-molecular weight AGEs are also delivered to PTCs in proteinuric states. In patients with diabetes, AGE generation is increased, and the actions of AGEs on PTCs are likely involved in the pathogenesis of diabetic nephropathy. In patients with chronic renal failure (CRF), reduced renal metabolism of AGEs likely accounts for the accumulation of AGEs in serum, leading to uremic complications including dialysis-related amyloidosis. AGE precursors such as reactive carbonyl compounds also accumulate in the sera of patients with CRF. It is likely that PTCs take up AGEs and AGE precursors via specific endocytotic receptors or transporters. Megalin is a multiligand endocytotic receptor that is abundantly expressed on PTCs. There is evidence that megalin is involved in the cellular uptake and degradation of AGEs. We previously reported a cell therapy model involving implantation of megalin-expressing cells into experimental mice with renal failure for elimination of uremic toxin proteins. Further studies are needed to clarify the molecular mechanisms of the metabolism of AGEs and their precursors to develop a strategy for the treatment of diabetic nephropathy and uremic complications of CRF.
Characterization of a nuclear factor that binds juxtaposed with ATF3/Jun on a composite response element specifically mediating induced transcription in response to an epidermal growth factor/Ras/Raf signaling pathway. (1997)

We have previously identified a 20-bp sequence that mediates induced transcription in response to EGF, Ras, and Raf but not after TPA or UV stimulation. This composite response element, present in a long terminal repeat of a member within the VL30 family of retrotransposons, contains an AP-1-like site that cooperates in function with a juxtaposed sequence unrelated to known transcription factor-binding sites. Using in vitro translated proteins, we here demonstrate that the AP-1-like site preferentially binds ATF3/c-Jun and ATF3/JunD heterodimers. Results from a functional analysis indicate that the ATF3/c-Jun heterodimer, together with factors interacting with the 3' element, are most likely the important mediators of the response because overexpression of JunD, alone or in combination with ATF3, abolishes Ras-induced transcription. Partial purification by phosphocellulose and DNA-affinity chromatography in combination with Southwestern analyses reveals a 52-kDa protein that specifically binds to the sequence juxtaposed to the AP-1-like site. Scatchard analyses show that this sequence, TTAGTTAC, forms two different complexes with K(d)s of 1.9 x 10(-10) and 2.3 x 10(-9) M, respectively. Together, these results suggest that EGF/Ras/Raf induces transcription via combined activation of ATF3/c-Jun and a 52-kDa nuclear factor, whereas JunD acts as a repressor of this response.
Replacement of the aliphatic chains of Clostridium acetobutylicum by exogenous fatty acids: regulation of phospholipid and glycolipid composition (1992)

The membrane lipid aliphatic chains of Clostridium acetobutylicum ATCC 4259 have been extensively modified by growth in biotin-free medium containing vitamin-free casein hydrolysate supplemented with either elaidic acid, oleic acid, or mixtures of palmitic and oleic acids. Growth with elaidic acid resulted in polar lipids containing 88.6% 18:1 acyl chains and 94.5% 18:1 ether-linked chains. Growth with oleic acid resulted in comparable levels of enrichment of the lipids with 18:1 chains and C19 chains containing cyclopropane rings. When cells were grown with mixtures of palmitic and oleic acids, the ether-linked chains of the plasmalogens were greater than or equal to 64% 18:1 plus C19 chains containing cyclopropane rings at all ratios of oleic to palmitic acid in the medium. The acyl chains reflected the palmitic acid content of the medium more closely. Marked changes were observed in both phospholipid and glycosyldiglyceride compositions as the lipid acyl and ether-linked chains became more enriched with unsaturated and cyclopropane chains. The ratio of the glycerol acetal of plasmenylethanolamine to phosphatidylethanolamine increased, the ratio of cardiolipin to phosphatidylglycerol decreased, and the ratio of diglycosyldiglyceride to monoglycosyldiglyceride increased. However, the monoglycosyldiglyceride/diglycosyldiglyceride ratio was lower for cells grown on 100% oleic acid than for cells grown on 60 or 80% oleic acid. In the membranes of cells grown on 100% oleic acid, the ratio of glycolipids to phospholipids was lower than that found in cells grown on 60% oleic acid. These results indicate that C. acetobutylicum regulates its polar lipid composition in a complex manner involving phospholipids and glycosyldiglycerides. These changes can affect the equilibria between those lipids that form bilayers and those lipids that tend to form nonlamellar phases when enriched with unsaturated aliphatic chains. Phosphoglycolipids of unknown structure were also observed in cells grown either with biotin or with fatty acids. The content of the most abundant phosphoglycolipid also varied with the degree of unsaturation of the cellular lipids.
A G-Rich Sequence within the <i>c-kit</i> Oncogene Promoter Forms a Parallel G-Quadruplex Having Asymmetric G-Tetrad Dynamics (2009)

Guanine-rich DNA sequences with the ability to form quadruplex structures are enriched in the promoter regions of protein-coding genes, particularly those of proto-oncogenes. G-quadruplexes are structurally polymorphic and their folding topologies can depend on the sample conditions. We report here on a structural study using solution state NMR spectroscopy of a second G-quadruplex-forming motif (c-kit2) that has been recently identified in the promoter region of the c-kit oncogene. In the presence of potassium ions, c-kit2 exists as an ensemble of structures that share the same parallel-stranded propeller-type conformations. Subtle differences in structural dynamics have been identified using hydrogen-deuterium exchange experiments by NMR spectroscopy, suggesting the coexistence of at least two structurally similar but dynamically distinct substates, which undergo slow interconversion on the NMR timescale.
Oxidation of cycloalkan[b]indoles with iodine pentoxide(I2O5). (1987)

Oxidation of cycloalkan [b] indoles (3) with iodine pentoxide (I2O5) in 80% aqueous tetrahydrofuran (THF) at room temperature regioselectively afforded 6-oxocycloalkan [b] indoles (4) in various yields. The yield of this oxidation depends on the size of the ring fused with the indole nucleus. The essential reaction species is I2O5, not HIO3, which might be generated by hydrolysis of I2O5 in the aqueous reaction medium. Oxidation of 1-hydroxytetrahydrocarbazole (5) under the above conditions afforded spiro oxindoles 6 and 7 in 36 and 39% yields, respectively, accompanied with only a trace of 1-oxotetrahydrocarbazole (4a).
Theoretical Aspects of Energy Confinement in Spheromaks (1996)

Despite the poor global energy confinement observed in spheromak experiments to date, the long-term prospects may be favorable as spheromaks are scaled to larger size and higher temperatures. The present performance is traced to excessive magnetic energy loss at the edge compared to tokamaks and heat transport due to magnetic fluctuations, both of which should scale away as the temperature increases.
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2 (2012)

Supplementary data are available at Bioinformatics online.
<title>Complex spectral interferometry OCT</title> (1998)

This contribution presents a new OCT technique. In this technique the complex scattered field is detected and used to compute the complex scattering potential of the object. The basic principle is outlined and first experimental measurements on a glass plate and on human skin in vitro are shown.
The Propionate of Heme Binds N<sub>4</sub>O<sub>2</sub> Schiff Base Antimalarial Drug Complexes (2000)

Schiff base N4O2 complexes offer a flexible template on which to develop novel antimalarial drug complexes that inhibit the aggregation of hemozoin, a detoxification product of the malaria parasite Plasmodium falciparum. The efficacies of these complexes are dependent on the charges of the complexes. Further evidence suggests that these complexes inhibit hemozoin formation via a specific drug/heme propionate salt that prevents the formation of the requisite axial propionato linkage in the repeating dimeric unit of the hemozoin aggregate.
Inhibitors for the Immuno‐ and Constitutive Proteasome: Current and Future Trends in Drug Development (2012)

Proteolytic degradation is an essential cellular process which is primarily carried out by the 20S proteasome core particle (CP), a protease of 720 kDa and 28 individual subunits. As a result of its central functional role, the proteasome represents an attractive drug target that has been extensively investigated during the last decade and validated by the approval of bortezomib by the US Food and Drug Administration (FDA). Currently, several optimized second-generation proteasome inhibitors are being explored as anticancer drugs in clinical trials, and most of them target both constitutive proteasomes (cCPs) and immunoproteasomes (iCPs). However, selective inhibition of the iCPs, a distinct class of proteasomes predominantly expressed in immune cells, appears to be a promising therapeutic rationale for the treatment of autoimmune disorders. Although a few selective agents have already been identified, the recently determined crystal structure of the iCP will further promote the development and optimization of iCP-selective compounds.
Bitconeview: visualization of flows in the bitcoin transaction graph (2015)

Bitcoin is a digital currency whose transactions are stored into a public ledger, called blockchain, that can be viewed as a directed graph with more than 70 million nodes, where each node represents a transaction and each edge represents Bitcoins flowing from one transaction to another one. We describe a system for the visual analysis of how and when a flow of Bitcoins mixes with other flows in the transaction graph. Such a system relies on high-level metaphors for the representation of the graph and the size and characteristics of transactions, allowing for high level analysis of big portions of it.
Orthonormal polynomial vectors and least squares approximation for a discrete inner product. (1995)

We give the solution of a discrete least squares approximation problem in terms of orthonormal polynomial vectors with respect to a discrete inner product. The degrees of the polynomial elements of these vectors can be dierent. An algorithm is constructed computing the coecients of recurrence relations for the orthonormal polynomial vectors. In case the weight vectors are prescribed in points on the real axis or on the unit circle, variants of the original algorithm can be designed which are an order of magnitude more ecient. Although the recurrence relations require all previous vectors to compute the next orthonormal polynomial vector, in the real or the unit-circle case only a xed number of previous vectors are required. As an application, we approximate a vector-valued function by a vector rational function in a linearized least squares sense.
A method for driving control authority transition for cooperative autonomous vehicle (2015)

Many researchers have reported that a decline in driving concentration caused by drowsiness or inattentiveness is one of the primary sources of serious car accidents. One of the most well-known methods to measure a driver's concentration is called driver state monitoring, where the driver is warned when he or she is falling asleep based on visual information of the face. On the other hand, autonomous driving systems have garnered attention in recent years as an alternative plan to reduce human-caused accidents. This system shows the possibility of realizing a vehicle with no steering wheel or pedals. However, lack of technical maturity, human acceptance problems, and individual desire to drive highlight the demand to keep human drivers in the loop. For these reasons, it is necessary to decide who will be responsible for driving the vehicle and adjusting the vehicle control system. This is known as the driving control authority. In this paper, we present a system that can suggest transitions in various driving control authority modes by sensing a decline of the human driver's performance caused by drowsiness or inattentiveness. In more detail, we identify the problems of the legacy driving control authority transition made only with vision-based driver state recognition. To address the shortcomings of this method, we propose a new recommendation method that combines the vision-based driver state recognition results and path suggestion of an autonomous system. Experiment results of simulated drowsy and inattentive drivers on an actual autonomous vehicle prototype show that our method has better transition accuracy with fewer false-positive errors compared with the legacy transition method that only uses vision-based driver state recognition.
Mutation of<i>YCS4</i>, a Budding Yeast Condensin Subunit, Affects Mitotic and Nonmitotic Chromosome Behavior (2002)

The budding yeast YCS4 gene encodes a conserved regulatory subunit of the condensin complex. We isolated an allele of this gene in a screen for mutants defective in sister chromatid separation or segregation. The phenotype of the ycs4-1 mutant is similar to topoisomerase II mutants and distinct from the esp1-1 mutant: the topological resolution of sister chromatids is compromised in ycs4-1 despite normal removal of cohesins from mitotic chromosomes. Consistent with a role in sister separation, YCS4 function is required to localize DNA topoisomerase I and II to chromosomes. Unlike its homologs in Xenopus and fission yeast, Ycs4p is associated with chromatin throughout the cell cycle; the only change in localization occurs during anaphase when the protein is enriched at the nucleolus. This relocalization may reveal the specific challenge that segregation of the transcriptionally hyperactive, repetitive array of rDNA genes can present during mitosis. Indeed, segregation of the nucleolus is abnormal in ycs4-1 at the nonpermissive temperature. Interrepeat recombination in the rDNA array is specifically elevated in ycs4-1 at the permissive temperature, suggesting that the Ycs4p plays a role at the array aside from its segregation. Furthermore, ycs4-1 is defective in silencing at the mating type loci at the permissive temperature. Taken together, our data suggest that there are mitotic as well as nonmitotic chromosomal abnormalities associated with loss of condensin function in budding yeast.
Ambient light cancellation in photoplethysmogram application using alternating sampling and charge redistribution technique (2015)

To overcome a large DC offset, ambient light interference, and optical path variation, a robust PPG readout chip is fabricated using 0.13-μm CMOS process. Against the large DC offset, a saturation detection and current feedback method can compensate a current of up to 30 μA. To be robust against optical path variation, an automatic emitting light compensation method is adopted. To remove the ambient light interference, we propose an alternating sampling and charge redistribution technique, in which no additional power is consumed, and only three differential switches and one capacitor are required. The PPG readout channel consumes 26 μW and has a input referred current noise of 260 pArms.