gebhart/patrepeval huggingface dataset:
The PmrA/PmrB and RcsC/YojN/RcsB systems control expression of the <i>Salmonella</i> O‐antigen chain length determinant (2006)

Summary The lipopolysaccharide (LPS) is the outermost component of the cell envelope in Gram‐negative bacteria. It consists of the hydrophobic lipid A, a short non‐repeating core oligosaccharide and a distal polysaccharide termed O‐antigen. We report here that the PmrA/PmrB and RcsC/YojN/RcsB two‐component systems of Salmonella enterica serovar Typhimurium independently promote transcription of the wzz st gene, which encodes a protein that determines the chain length of the O‐antigen. We show that the regulatory proteins PmrA and RcsB footprint partially overlapping regions of the wzz st promoter stimulating transcription from the same start site. Induction of the PmrA/PmrB or RcsC/YojN/RcsB systems increased the fraction of LPS molecules containing 16–35 O‐antigen subunits, leading to heightened resistance to serum. The LPS of a rcsB null mutant exhibited an altered mobility in the O‐antigen subunits attached to the lipid A‐core region when separated on a SDS/PAGE gel, suggesting that RcsB may regulate additional LPS genes. Inactivation of the wzz st gene eliminated the enhanced swarming behaviour exhibited by the rcsB mutant. That multiple regulatory systems control wzz st expression suggests that the Wzz st protein is required under different environmental conditions.
Anterior Cervical Plating Reverses Load Transfer Through Multilevel Strut-Grafts (2000)

Anterior multilevel cervical plating effectively increases stiffness and decreases local cervical motion after corpectomy. However, anterior cervical plating also reverses graft loads and excessively loads the graft in extension, which may promote pistoning and failure of multilevel constructs.
p53 is essential for DNA methylation homeostasis in naïve embryonic stem cells, and its loss promotes clonal heterogeneity (2017)

DNA methylation is a key regulator of embryonic stem cell (ESC) biology, dynamically changing between naïve, primed, and differentiated states. The p53 tumor suppressor is a pivotal guardian of genomic stability, but its contributions to epigenetic regulation and stem cell biology are less explored. We report that, in naïve mouse ESCs (mESCs), p53 restricts the expression of the de novo DNA methyltransferases Dnmt3a and Dnmt3b while up-regulating Tet1 and Tet2, which promote DNA demethylation. The DNA methylation imbalance in p53-deficient (p53<sup>-/-</sup>) mESCs is the result of augmented overall DNA methylation as well as increased methylation landscape heterogeneity. In differentiating p53<sup>-/-</sup> mESCs, elevated methylation persists, albeit more mildly. Importantly, concomitant with DNA methylation heterogeneity, p53<sup>-/-</sup> mESCs display increased cellular heterogeneity both in the "naïve" state and upon induced differentiation. This impact of p53 loss on 5-methylcytosine (5mC) heterogeneity was also evident in human ESCs and mouse embryos in vivo. Hence, p53 helps maintain DNA methylation homeostasis and clonal homogeneity, a function that may contribute to its tumor suppressor activity.
Aptamer/AuNP Biosensor for Colorimetric Profiling of Exosomal Proteins (2017)

Exosomes constitute an emerging biomarker for cancer diagnosis because they carry multiple proteins that reflect the origins of parent cells. Assessing exosome surface proteins provides a powerful means of identifying a combination of biomarkers for cancer diagnosis. We report a sensor platform that profiles exosome surface proteins in minutes by the naked eye. The sensor consists of a gold nanoparticle (AuNP) complexed with a panel of aptamers. The complexation of aptamers with AuNPs protects the nanoparticles from aggregating in a high-salt solution. In the presence of exosomes, the non-specific and weaker binding between aptamers and the AuNP is broken, and the specific and stronger binding between exosome surface protein and the aptamer displaces aptamers from the AuNP surface and results in AuNP aggregation. This aggregation results in a color change and generates patterns for the identification of multiple proteins on the exosome surface.
Structure and Conformational Behavior of Biopolymers by Density Functional Calculations Employing Periodic Boundary Conditions. I. The Case of Polyglycine, Polyalanine, and Poly-α-aminoisobutyric Acid in Vacuo (2001)

Fully quantum mechanical calculations exploiting periodic boundary conditions (PBC) have been applied to the study of four different regular structures (alpha- and 3(10)-helix, fully extended and repeated gamma-turns) of the infinite polypeptides of glycine, alanine, and alpha-aminoisobutyric acid (Aib) in vacuo. alpha-Helix is predicted to be the most stable conformer for polyalanine and polyglycine, being stabilized over the 3(10)-helix mainly by more favorable dipole-dipole interactions. Contrary to previous suggestions, steric effects and hydrogen-bond strengths are comparable for both helix structures. 3(10)-Helix is preferred for poly-Aib, since in this case alpha-helix is strongly distorted due to unfavorable intrachain repulsions. Extended structures and repeated gamma-turns are much less stable than helix structures for all of the polypeptides examined, mainly due to the absence of favorable long-range interactions. The optimized geometries are in good agreement with the available experimental data and reveal a remarkable dependence on the nature of the residue forming the polypeptides; at the same time the electronic and structural parameters of each residue strongly depend on the secondary structure of the polypeptides.
Protection of the transiently ischemic cat retina by zinc-desferrioxamine. (1994)

Protection of the cat retina against ischemia and reperfusion injury by Zn-DFO was evident, most probably through its inhibitory effect on the generation of hydroxyl radicals during reperfusion.
Chicken Broth AAC1 as a Dietary Supplement Inhibits Pain Transmission and Decreases Serum C‐Reactive Protein Levels In a Model of TMJ Disorder (2016)

Objective The goal of this study was to determine if the dietary inclusion of the commercially available chicken broth AAC1 could repress nocifensive behaviors and PKA expression associated with a clinically relevant model of temporomandibular joint (TMJ) disorder caused by prolonged jaw opening. Background Routine dental visits for molar extractions or root canals, or to the orthodontist can result in an injury to the TMJ or muscles of mastication if the jaw is held open for long periods of time or is opened to near maximal even for a short period of time. However, the pathophysiological and cellular mediators that underlie the development of chronic orofacial pain associated with TMJ disorder are not well understood. Chicken broth has been often thought of as having beneficial immune effects and may represent an innovative and safe alternative treatment for chronic inflammatory diseases. Methods Male Sprague‐Dawley rats were used to investigate the effects AAC1 on behavioral and cellular changes associated with prolonged jaw opening. A surgical retractor was placed around the bottom and top incisors and the jaw held at near maximal opening for 20 minutes. Withdrawal responses to mechanical stimuli were determined following jaw opening for up to 7 days by applying calibrated von Frey filaments to the cutaneous area over the masseter. Some animals received 0.5% solid (w/v) AAC1 dissolved in their drinking water for two weeks prior to jaw opening. After 7 days, animals were euthanized and the upper spinal cord and trigeminal ganglia were removed to study changes in the expression of PKA utilizing immunohistochemistry. Serum samples were collected to determine the levels of C‐reactive protein using an ELISA. Results Near maximal jaw opening was induced a sustained increase in the number of nocifensive responses to mechanical stimuli over the masseter area for 7 days. This increased sensitivity correlated with increased levels of PKA expression in both the upper spinal cord and the trigeminal ganglia, and elevated serum levels of C‐reactive protein. Dietary inclusion of AAC1 was able to suppress nocifensive behaviors, PKA expression, and decreased levels of C‐reactive protein associated with prolonged jaw opening. Conclusion Our findings provide evidence that dietary inclusion of chicken broth AAC1 inhibits transmission of pain signals and represses levels of inflammatory mediators in serum and nerve cells and thus, may by a useful nutraceutical supplement to help manage inflammatory pain associated with TMJ disorder. Support or Funding Information Support provided by International Dehydrated Foods
Influence of conjugation of doxorubicin to transferrin on the iron uptake by K562 cells via receptor‐mediated endocytosis (1993)

The influence of conjugation of doxorubicin to holotransferrin on the receptor-mediated endocytosis of and on the iron uptake from transferrin was studied using K562 cells. 125I-labelled transferrin and doxorubicin-transferrin conjugates were used in the binding, dissociation, and ligand-exchange experiments at 0 degree C, and 59Fe,125I-labelled (double-labelled) ligands were used in the endocytosis, iron uptake, and recycling experiments at 37 degrees C. The binding affinity of conjugates was about half of that of transferrin. Binding of 125I-labelled ligands was blocked by both unlabelled ligands to the same degree, however, it was not blocked at all by an 8000-fold excess of doxorubicin. After saturation bindings, slightly more 125I-labelled conjugates dissociated from the surface of cells than transferrin. Exchange of 125I-labelled ligands for unlabelled ligands resulted in different EC50 values (defined as the concentration of unlabelled ligand at which half as much radioligand is exchanged for unlabelled ligand as would be exchanged at infinitely high concentration of unlabelled ligand under similar assay conditions). While transferrin exchanged transferrin with an EC50 value close to the binding affinity, conjugates exchanged conjugates with much lower efficiency. The heterolog exchange experiments yielded EC50 values inbetween the two extrema. For studying iron uptake, K562 cells were loaded with the double-labelled ligands either at 37 degrees C (endosome-loading only) or at 0 degree C (surface-loading only). Results obtained for the endocytosis of, the iron uptake from, and the recycling of double-labelled ligands indicate that (a) the rate of iron uptake is smaller from conjugates than from transferrin, (b) there are at least two parallel recycling processes for both ligand.receptor complexes, and (c) each time constant characterizing the different steps of iron uptake via receptor-mediated endocytosis is smaller for conjugates than for transferrin (or, the half times characterizing the different steps are higher for conjugates than for transferrin). Endocytosis and iron uptake were unaffected by free doxorubicin (12.5 microM) or colchicine (1 mM). Benzyl alcohol (30 mM) slowed down the rate of both endocytosis and iron uptake, while dithiothreitol (5 mM) decreased the rate of iron uptake and increased the rate of endocytosis. N-Ethylmaleimide (1 mM) completely stopped both endocytosis and iron uptake. The results suggest that the binding of conjugates to the surface of cells is governed by the binding of the transferrin part of conjugates to the transferrin receptor. However, conjugation of doxorubicin to transferrin seems to influence all properties of transferrin.(ABSTRACT TRUNCATED AT 400 WORDS)
Plasma melatonin levels in psoriasis. (1988)

Melatonin is synthesized and secreted by the pineal gland. A daily rhythm of melatonin secretion, with high plasma values during the dark period, has been found in all vertebrates studied so far. In psoriatics, several hormones, including GH and prolactin, have altered chronobiology, and some studies in humans suggest that melatonin affects the levels of GH and prolactin. We investigated circadian melatonin rhythm in 13 male psoriatics and 13 healthy males with an RIA specific for measuring the hormone in plasma. Samples were taken at 6 a.m., 8 a.m., 12.00, 4 p.m., 8 p.m. and 2 a.m. Differences in (mean +/- SD) plasma melatonin levels were analysed by Student's t-test. Our results show that psoriatic patients had lost the nocturnal peak and usual circadian rhythm of melatonin secretion. Levels of melatonin were significantly lower than in controls at 2 a.m., and higher at 6 and 8 a.m. and at 12 noon. Further investigations of this disorder of melatonin secretion in psoriasis are needed to understand its significance.
Recovery of Gold and Silver from Ores by Hydrometallurgical Processing (1983)

Abstract The Bureau of Mines has played an important role in the revival of precious-metal mining in the Western United States. During the past 30 years, many techniques used by industry to recover gold and silver were pioneered and developed by the Bureau of Mines. In 1952, technology was developed to strip gold from granular activated carbon and allow the carbon to be reused. In 1969, the heap leaching concept was applied to low-grade gold and silver ores and mine wastes. Heap leaching in conjunction with carbon adsorption-desorption permits very low value material to be economically processed. In 1970, an oxidation treatment based on hypochlorite was developed to increase the recovery of gold from carbonaceous gold ores by cyanidation. In the early 1950's, attempts were made to employ carbon-in-pulp technology to recover gold from ores, but the fixed price of gold and increasing operational costs made cyanidation unprofitable. The Bureau of Mines and Homestake Mining Co. jointly operated a carbon-in-pulp pilot plant, and the technology was used in full-scale production at the Homestake Mine in 1972. In 1973, a pressure stripping method, which decreased the time needed for the stripping step, was developed to desorb gold and silver from carbon. An alcohol desorption method, developed in 1976, also decreased the carbon stripping time. In 1979, an agglomeration pretreatment was developed that permitted clayey precious metal ores to be heap-leached. Almost all precious-metal-mining companies use at least one of the above techniques in production facilities.
The prodomain of BMP4 is necessary and sufficient to generate stable BMP4/7 heterodimers with enhanced bioactivity in vivo (2015)

Bone morphogenetic proteins 4 and 7 (BMP4 and BMP7) are morphogens that signal as either homodimers or heterodimers to regulate embryonic development and adult homeostasis. BMP4/7 heterodimers exhibit markedly higher signaling activity than either homodimer, but the mechanism underlying the enhanced activity is unknown. BMPs are synthesized as inactive precursors that dimerize and are then cleaved to generate both the bioactive ligand and prodomain fragments, which lack signaling activity. Our study reveals a previously unknown requirement for the BMP4 prodomain in promoting heterodimer activity. We show that BMP4 and BMP7 precursor proteins preferentially or exclusively form heterodimers when coexpressed in vivo. In addition, we show that the BMP4 prodomain is both necessary and sufficient for generation of stable heterodimeric ligands with enhanced activity and can enable homodimers to signal in a context in which they normally lack activity. Our results suggest that intrinsic properties of the BMP4 prodomain contribute to the relative bioactivities of homodimers versus heterodimers in vivo. These findings have clinical implications for the use of BMPs as regenerative agents for the treatment of bone injury and disease.
Objective Functions for Multi-Way Number Partitioning (2010)

The number partitioning problem is to divide a set of integers into a collection of subsets, so that the sum of the numbers in each subset are as nearly equal as possible. There are at least three natural objective functions for number partitioning. One is to minimize the largest subset sum, another is to maximize the smallest subset sum, and the third is to minimize the difference between the largest and smallest subset sums. I show that contrary to my previous claims, no two of these objective functions are equivalent for partitioning numbers three or more ways. Minimizing the largest subset sum or maximizing the smallest subset sum correspond to different practical applications of number partitioning, and both allow a recursive strategy for finding optimal solutions that is very effective in practice. Finally, a completely new version of this recursive strategy appears to reduce the asymptotic complexity of the algorithm, and results in orders of magnitude improvement over the best previous results for multi-way partitioning.
Recent developments in X-ray imaging with micrometer spatial resolution (2006)

X-ray detectors for imaging with a spatial resolution in the micrometer and submicrometer range have been developed at synchrotron radiation sources since 1996. The detectors consist of a scintillator, a light microscopy optic and a charge-coupled device (CCD). The scintillator converts part of the X-ray stopped by a material into a visible-light image which is projected onto the CCD by the light optics. A resolution of 0.5 microm FWHM has been achieved using a 1 microm-thick europium-doped Lu3Al5O12 film. The detective quantum efficiency of the detector is mainly limited by the low absorption of X-rays in the thin layer of the scintillator. To increase the absorption, and therefore reduce the exposure time, new scintillators (Lu2O3:Eu3+, Gd2O3:Eu3+, Lu2SiO5:Ce, Gd3Ga5O12:Eu3+, CdWO4) have been investigated. These were fabricated using sol-gel and liquid-phase epitaxy processes. Finally, the first fast microtomography experiment including radiation hardness of the optic is shown. This detector uses a high-intensity white beam with 60 keV effective energy and a fast CCD camera at up to 60 frames s(-1).
Detection of Strongyloides stercoralis infection among cancer patients in a major hospital in Kelantan, Malaysia (2014)

This study showed that laboratory testing may be considered as a diagnostic investigation for S. stercoralis among immunocompromised cancer patients.
Deletion of Protein Tyrosine Phosphatase 1b Improves Peripheral Insulin Resistance and Vascular Function in Obese, Leptin-Resistant Mice via Reduced Oxidant Tone (2009)

Deletion of PTP1B improved both endothelium dependent and independent NO-mediated dilation and reduced superoxide generation in db/db mice. PTP1B deletion did not affect any vascular function in lean mice. Taken together, these data reveal a role for peripheral insulin resistance as the mediator of vascular dysfunction in obesity.
Dependence of the Electrophoretic Mobility of DNA in Gels on Field Intermittency (1985)

The electrophoretic mobility of double helical DNA in agarose and polyacrylamide gels increases as a function of time after the electric field is applied to the gel and decreases after the field is terminated. The changes are large for long (more than 10 kb) molecules. The effects of other variables are indicated.
Erythropoietin production by a human testicular germ cell line (1983)

An established human testis germ cell line (1411-H) was found to produce significant amounts of erythropoietin (Ep), the primary regulator of erythropoiesis. Media conditioned by the 1411-H cells stimulated erythropoiesis both in vivo and in vitro. This activity was neutralized by anti-Ep. This continuous cell line provides a unique model for the study of the mechanisms of control of Ep biogenesis.
Routing Scalability: An Operator's View (2010)

The Internet and its associated global routing table continues to grow with time. Will the current routing infrastructure be able to scale itself to sustain such growth? Over the past several years, many efforts have been devoted to address this important question. This paper presents a unique view from a network operator's perspective. We first clarify the definition of the routing scaling problem in practical terms by providing the relevant background information. We point out several reality issues that, if overlooked, may impede the adoption and deployment of a solution. Based on our operational experiences, we identify several requirements for potential solutions, and provide brief comments on the existing solutions.
Characterizing Urban Vehicle-to-Vehicle Communications for Reliable Safety Applications (2019)

The IEEE 802.11p-based dedicated short range communication (DSRC) is essential to enhance driving safety and improve road efficiency by enabling rapid cooperative message exchanging. However, there is a lack of good understanding on the DSRC performance in urban environments for vehicle-to-vehicle (V2V) communications, which impedes its reliable and efficient application. In this paper, we first conduct intensive data analytics on V2V performance, based on a large amount of real-world DSRC communications trace collected in Shanghai city, and obtain several key insights as follows. First, among many context factors, the non-line-of-sight (NLoS) link condition is the major factor degrading V2V performance. Second, the durations of line-of-sight (LoS) and NLoS transmission conditions follow power law distributions, which indicate that the probability of experiencing long LoS/NLoS conditions both could be high. Third, the packet inter-reception (PIR) time distribution follows an exponential distribution in the LoS conditions but a power law in the NLoS conditions, which means that the consecutive packet reception failures rarely appear in the LoS conditions but can constantly appear in the NLoS conditions. Based on these findings, we propose a context-aware reliable beaconing scheme, called CoBe, to enhance the broadcast reliability for safety applications. The CoBe is a fully distributed scheme, in which a vehicle first detects the link condition with each of its neighbors by machine learning algorithms, then exchanges such link condition information with its neighbors, and finally selects the minimal number of helper vehicles to rebroadcast its beacons to those neighbors in bad link condition. To analyze and evaluate the CoBe performance, a two-state Markov chain is devised to model beaconing behaviors. The extensive trace-driven simulations are conducted to demonstrate the efficacy of CoBe.
Arginase is overactive in psoriatic skin (2010)

Arginase is overactive in psoriatic skin, leading to a relative increase in the consumption of arginine. We therefore hypothesize a relative decrease in NO synthase-derived NO production. NO donors may be effective topical treatments for psoriasis.
Studies on quinophthalone pigments (1971)

ベンジジン類からDoebner-Millerの方法により6, 6'-ビキナルジン類を合成し, これらと無水フタル酸およびテトラバロゲノ無水フタル酸との脱水縮合反応によって, 新規なビスキノフタロン黄色顔料 (下記一般式) を合成した。得られた顔料の色相, 耐光性, 耐溶剤性などを調べた結果, 次のことが明らかとなった。6, 6'-なピキナルジン類と無水フタル酸との縮合で得られた顔料は, 鮮明な色相をもっていたが耐光性が悪く, 高沸点溶剤にわずかに溶解した。6, 6'-ピキナルジン類とテトラハロゲノ無水フタル酸との縮合で得られた顔料は, 全般に鮮明な色相とすぐた耐光性をもち, 5, 5', 8, 8'-テトラクPル-6, 6'-ビキナルジンとテトラバ官ゲノ無水フタル酸との縮合で得られた顔料を除いてはきわめてすぐれた耐溶剤性をもっていた。Z-Z-Z-Z-OC-OC-HC-N-X-Y-X-Y-N-CH-OC-OC-Z-Z-Z-Z