gebhart/patrepeval huggingface dataset:
Comparative genomics and evolution of genes encoding bacterial (p)ppGpp synthetases/hydrolases (the Rel, RelA and SpoT proteins). (2001)

In the gram-negative model organism Escherichia coli, the effector molecule of the stringent response, (p)ppGpp, is synthesized by two different enzymes, RelA and SpoT, whereas in the gram-positive model organism Bacillus subtilis only one enzyme named Rel is responsible for this activity. Rel and SpoT also possess (p)ppGpp hydrolase activity. BLAST searches were used to identify orthologous genes in databases. The construction and bootstrapping of phylogenetic trees allowed classification of these orthologs. Four groups could be distinguished: With the exception of Neisseria and Bordetella (beta subdivision), the RelA and SpoT groups are exclusively found in the gamma subdivision of proteobacteria. Two Rel groups representing the actinobacterial and the Bacillus/Clostridium group were also identified. The SpoT proteins are related to the gram positive Rel proteins. RelA proteins carry substitutions in the HD domain (Aravind and Koonin, 1998, TIBS 23: 469-472) responsible for ppGpp degradation. A theory for the evolution of the specialized, paralogous relA and spoT genes is presented: After gene duplication of an ancestral rellike gene, the spoT and relA genes evolved from the duplicated genes. The distribution pattern of the paralogous RelA and SpoT proteins supports a new model of linear bacterial evolution (Gupta, 2000, FEMS Microbiol. Rev. 24: 367-402). This model postulates that the gamma subdivision of proteobacteria represents the most recently evolved bacterial lineage. However, two paralogous, closely related genes of Porphyromonas gingivalis (Cytophaga-Flavobacterium-Bacteroides phylum) encoding proteins with functions probably identical to the RelA and SpoT proteins do not fit in this model. Completely sequenced genomes of several obligately parasitic organisms (Treponema pallidum, Chlamydia species, Rickettsia prowazekii) and the obligate aphid symbiont Buchnera sp. APS as well as archaea do not contain rel-like genes but they are present in the Arabidopsis genome. In crosslinking experiments using different analogs of ppGpp as crosslinking reagents and RNA polymerase preparations of Escherichia coli, binding of ppGpp to distinct regions at the C-terminus of the beta subunit (the RpoB gene product) and/or at the N-terminus of the beta subunit (the RpoC gene product) was observed previously. RpoB and RpoC sequences of the species which do not possess a rel like gene do not exhibit specific insertions or deletions in the ppGpp binding regions.
Evaluating two-handed input techniques (1999)

This paper reports our ongoing design and evaluation of two-handed input techniques for several common tasks found in desktop interfaces: specifying simple geometric shapes, navigating in a large document and navigating between windows on a desktop.
Neutron-scattering studies of concentrated oxide sols (1983)

Small-angle neutron scattering (SANS) and light scattering have been used to study the interactions between particles (diameter < 20 nm) in silica and ceria sols covering a wide range of concentration. Structure factors, S(Q), have been determined which have been compared with those calculated for a model hard-sphere (HS) potential. At low sol concentrations (≲ 10–2 g cm–3) interactions are dominated by double-layer repulsion which is most pronounced at low electrolyte concentrations (ca. 10–4 mol dm–3). At higher sol concentrations (≳ 10–1 g cm–3) the effects of electrolyte concentration become less important and the form of S(Q) is similar to that of a HS system, in which the effective interaction diameter is greater than the diameter of the sol particles. Preliminary SANS studies on mixtures of titania and iron oxide sols using the contrast variation technique are also described from which information on the compatibility and structure of each component has been obtained.
Using bacterial biomarkers to identify early indicators of cystic fibrosis pulmonary exacerbation onset (2011)

Acute periods of pulmonary exacerbation are the single most important cause of morbidity in cystic fibrosis patients, and may be associated with a loss of lung function. Intervening prior to the onset of a substantially increased inflammatory response may limit the associated damage to the airways. While a number of biomarker assays based on inflammatory markers have been developed, providing useful and important measures of disease during these periods, such factors are typically only elevated once the process of exacerbation has been initiated. Identifying biomarkers that can predict the onset of pulmonary exacerbation at an early stage would provide an opportunity to intervene before the establishment of a substantial immune response, with major implications for the advancement of cystic fibrosis care. The precise triggers of pulmonary exacerbation remain to be determined; however, the majority of models relate to the activity of microbes present in the patient's lower airways of cystic fibrosis. Advances in diagnostic microbiology now allow for the examination of these complex systems at a level likely to identify factors on which biomarker assays can be based. In this article, we discuss key considerations in the design and testing of assays that could predict pulmonary exacerbations.
Erythroid Progenitor Proliferation is Stimulated by Phenoxyacetic and Phenylalkyl Acids (1996)

Short-chain fatty acids, such as butyrate and propionate, are under investigation as therapeutic stimulants of fetal hemoglobin production in the beta-hemoglobin disorders. Significant limitations to these fatty acids and derivatives as optimal therapeutics are their rapid metabolism in vivo and their induction of cell growth arrest in the G1 phase of the cell cycle. This antiproliferative activity is related to their inhibition of metabolic transport pumps which are essential for cell proliferation. Other small carbon compounds, the phenylalkyl acids, phenoxyacetic acids, and phenylacetic acids, which are structurally resistant to oxidative metabolism, are shown here to induce fetal globin production in human erythroid cultures at concentrations of 0.2 mM, lower than those required for most other fatty acids. Certain of these compounds were found not to inhibit cellular neutral amino acid transport function in erythroid cells, nor to inhibit erythroid colony (Bfu-e) growth. Certain of these compounds even stimulated human Bfu-e proliferation in vitro beyond that induced by optimal concentrations of hematopoietic growth factors. The combination of increased fetal globin chain production by these compounds and their stimulatory effects on erythropoiesis result in an increase in Hb F-expressing erythroid cells in culture several-fold greater than that achieved by the butyrates. These new compounds thus have the potential to provide superior therapy for the beta-hemoglobinopathies and other anemias.
The pro‐region of the yeast prepro‐α‐factor is essential for membrane translocation of human insulin‐like growth factor 1 <i>in vivo</i> (1992)

Four yeast secretion signals, the 19-amino-acid invertase signal sequence, the 17-amino-acid acid-phosphatase signal sequence, and the pre-sequence and prepro-sequence of prepro-alpha-factor have been used to look for the secretion of recombinant human insulin-like growth factor 1 (IGF1) from Saccharomyces cerevisiae. Only the prepro-sequence, often referred to as the alpha-factor leader and consisting of an N-terminal 19-amino-acid pre-sequence or signal sequence attached to a 66-amino-acid pro-region, permits secretion of IGF1. The signal sequences alone do not allow the translocation of IGF1 into the endoplasmic reticulum. This is evident from the fact that IGF1-like molecules, to which the signal sequences are still attached, accumulate intracellularly in the cytosol. Fusion of the pro-region of the alpha-factor leader to the C-terminus of the acid-phosphatase and invertase signal sequences allows IGF1 to be secreted once again. These results reveal the essential role of the pro-region of the alpha-factor leader in the secretion of IGF1 and indicate that it may have a function in guiding a nascent IGF1 polypeptide to a state in which translocation can occur.
Dendritic Carbene Metal Carbazole Complexes as Photoemitters for Fully Solution-Processed OLEDs (2019)

Light-emitting carbene-metal amide complexes bearing first- and second-generation carbazole dendron ligands are reported, (AdL)M(Gn), (M = Cu and Au; Gn carbazole dendrimer generation, where n = 1 and 2; AdL = adamantyl-substituted cyclic (alkyl)(amino)carbene). The thermal stability of the complexes increases with each dendrimer generation. Cyclic voltammetry indicates that the highest occupied molecular orbital/lowest unoccupied molecular orbital energy levels are largely unaffected by the size of the dendron, while first reduction and oxidation processes show a quasi-reversible character. The gold complexes in toluene at room temperature show photoluminescent quantum yields of up to 51.5% for the first and 78% for the second generation. Varied temperature transient photoluminescence decay is consistent with a thermally activated process, indicating a delayed fluorescence-type emission mechanism. Neat films show excited state lifetimes composed of prompt and dominant sub-microsecond delayed components, with radiative constants of up to 106 s–1. Solution-processed organic light-emitting diodes for first-generation copper and gold dendrimers (AdL)M(G1) have been fabricated with external quantum efficiencies of 5.5% for copper and 10.3% for gold at practical brightness.
5 (1998)

Bauer, C.; Bouma, M. G.; Buurman, W. A.; Sargin, B.; Bulut, K.; Larsen, R.; Marzi, I. Author Information
Ultra-low power wake -up receivers for wireless sensor networks (2008)

The realization of truly ubiquitous wireless sensor networks (WSN) demands ultra-low power wireless communication capability. Because the radio transceiver consumes power whenever it is active, it most efficient to leave the receiver off and wake it up asynchronously only when needed. A dedicated wake-up receiver can continuously monitor the channel, listening for a wake-up signal from other nodes and activating the main receiver upon detection. By maximizing the node sleep time without compromising network latency, the use of a wake-up receiver can improve overall network performance. Wake-up receivers are also applicable in asymmetric links such as "active" RFID, where the tag listens in standby mode until queried by a reader. <p> In order to be practical, the power consumption of the wake-up receiver must be minimized while still preserving adequate sensitivity to detect the wake-up signal. This thesis explores the specific requirements and challenges for the design of a dedicated wake-up receiver, leading to the design of two prototype receivers implemented in 90 nm CMOS technology and incorporating RF-MEMS resonators. The first prototype combines all required blocks in a low power test system, including a simple RF front-end and mixed-signal baseband. The final wake-up receiver design uses a novel "uncertain-IF" architecture to achieve a sensitivity of -72 dBm at 2 GHz while consuming just 52 uW from a 0.5 V supply. The power consumption is nearly an order-of-magnitude below previously published receiver designs for WSN.
(INVITED) 10GBASE-T for 10Gb/s full duplex ethernet LAN transmission over structured copper cabling (2008)

This paper reviews key features of the 10 GBASE-T standard for full duplex 10 Gb/s transmission over structured copper cabling in the LAN environment. Tradeoffs in implementing 10 GBASE-T transceivers are discussed. We then present the first implementation of 10 GBASE-T in digital CMOS technology (0.13 mum). This transceiver also supports lower speeds for backward compatibility with legacy Ethernet ports. In 10 GBASE-T mode, the transceiver operates over four pairs of balanced cabling where each pair is driven by an 800 MS/s DAC and each pair has a receiver that includes an active echo cancellation circuit and an 800 MS/sec ADC. The power consumption when operating over a 100 m channel in 10 GBASE-T mode is 10.5 W. The transceiver also includes precoders, crosstalk cancellers, matrix equalizers and an LDPC encoder and decoder.
Role of Dopamine D2-like Receptors in Cocaine Self-Administration: Studies with D2 Receptor Mutant Mice and Novel D2 Receptor Antagonists (2002)

Dopamine receptor subtypes have been classified generally as D1-like (e.g., D1, D5) or D2-like (D2, D3, D4), and converging evidence suggests that D2-like receptors may be especially important in mediating the abuse-related effects of cocaine. However, it has been difficult to differentiate the roles of the D2-like receptor subtypes in the behavioral effects of cocaine because of the relatively low selectivity of drugs for D2, D3, and D4 receptors in vivo. The goal of the present series of studies was to investigate the contributions of D2-like receptor subtypes in the reinforcing effects of cocaine using new genetic and pharmacological tools. First, we evaluated cocaine self-administration behavior, and related effects of nonselective D2-like drugs, in mutant mice that lack the D2 receptor but express D3 and D4 receptors. When high doses of cocaine on the descending limb of the cocaine dose-effect function were available, D2 mutant mice self-administered at higher rates than their heterozygous or wild-type littermates, but the ascending limb of the cocaine dose-effect function did not differ between genotypes. Elevated rates of drug intake were not attributable to nonspecific increases in response rate, because response rates maintained by presentation of a range of food concentrations were significantly lower in D2 mutant mice than in wild-type mice. In wild-type mice, pretreatment with the D2-like antagonist eticlopride increased rates of self-administration of high doses of cocaine, and the D2-like agonist quinelorane served as a positive reinforcer when substituted for cocaine. However, these effects of eticlopride and quinelorane were not observed in mice that lacked the D2 receptor. Next, we compared the effects of novel antagonists selective for different D2 receptor subtypes on cocaine self-administration behavior in outbred rats. In rats, a D2 selective antagonist increased rates of self-administration of high doses of cocaine and also combinations of cocaine and the D2-like agonist quinelorane, whereas D3/D4 antagonists were ineffective. Collectively, these findings suggest that the D2 receptor is not necessary for cocaine self-administration, but this receptor subtype is involved in mechanisms that limit rates of high-dose cocaine self-administration. Our results also suggest that D3 and D4 receptors do not play major roles in the modulation of cocaine self-administration by D2-like drugs.
Verification of AIRS boresight accuracy using coastline detection (2003)

The longitude and latitude of the centroids of the Atmospheric Infrared Sounder (AIRS) infrared spectrometer footprints are calculated by the Level 1a calibration software based on transformations of scan angles, instrument alignment angles relative to the Earth Observing System Aqua spacecraft, and the spacecraft ephemeris. The detection of coastline crossings is used to determine the accuracy of these coordinates. Tests using simulated AIRS data derived from real Moderate Resolution Imaging Spectroradiometer (MODIS) Terra satellite 10-/spl mu/m window data indicate that an accuracy of 1.7 km is easily achievable with modest amounts of data, such as should be available from AIRS by launch +90 days. This accuracy is a small fraction of the 13.5-km AIRS footprint and is consistent with the accuracy required by the Level 2 software. Preliminary results from actual AIRS data indicate that the algorithm works as predicted. For combined use of the AIRS 13.5-km footprints with MODIS 1-km footprints, accuracy of the order of 0.5 km is desirable. This accuracy may be achievable with several months of data, but depends on the accuracy of the reference map and whether a sufficient number of large clear homogeneous surface scenes can be found.
Firing exotic fuels in a gas turbine (1984)

Recent extensive tests of substitute fuels derived from coal liquefaction and shale oil focused on combustion and thermal efficiencies and emissions. The results indicate that these fuels perform well, and they can be used just as satisfactorily as the diesel oil for which the machine was designed. 4 figures, 1 table.
Symbolic Description of Factorial Models for Analysis of Variance (1973)

G. N. Wilkinson, C. E. Rogers, Symbolic Description of Factorial Models for Analysis of Variance, Journal of the Royal Statistical Society. Series C (Applied Statistics), Vol. 22, No. 3 (1973), pp. 392-399
Test and screening strategies for large memories (2003)

The possibilities and limits of testing and screening large memories are reviewed. Practical results are given. The procedures for the qualification test of different types of memories are discussed. The concept of test strategy is introduced. Future trends in testing large memories are presented. It is shown that AC, functional, and DC test should be performed under several different conditions to help determine the correct testing strategy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
THE POLYSACCHARIDE PRODUCED BY AZOTOBACTER INDICUM (1957)

A procedure was developed for the isolation and purification of the polysaccharide produced by Azotobacter indicum which resulted in a product containing approximately 5% ash, 0.4–0.6% nitrogen, and 40% carbon. Qualitative tests showed the absence of galactose, pentoses, ketoses, and amino and methylated sugars, and the presence of glucose and a uronic acid. A technique for determining combined uronic acids resulted in a value of 30% uronic acid on the untreated (unhydrolyzed) polysaccharide, and the remaining components were determined by analysis of the material after acid hydrolysis. The relatively severe conditions required to hydrolyze the polysaccharide indicate that the components are present in the pyranose form. The results obtained when the hydrolyzates were analyzed by paper chromatography, the spectrophotometric reactions of Dische, and other specific quantitative assays showed that the polysaccharide is a polymer of glucose, glucuronic acid, and an aldoheptose in the ratio of 3: 2: 1. Infrared analysis confirmed the presence and relative proportion of the uronic acid residues and indicated that the sugar units of the polysaccharide are probably in the beta configuration.
Glypican-3 Promotes the Growth of Hepatocellular Carcinoma by Stimulating Canonical Wnt Signaling (2005)

Abstract Glypican-3 (GPC3) is a heparan sulfate proteoglycan that is bound to the cell membrane by a glycosyl-phosphatidylinositol anchor. GPC3 is expressed by most hepatocellular carcinomas but not by normal hepatocytes and benign liver lesions. We report here that GPC3 stimulates the in vitro and in vivo growth of hepatocellular carcinoma cells by increasing autocrine/paracrine canonical Wnt signaling. Coimmunoprecipitation experiments showed that GPC3 is able to form complexes with Wnts, and cell-binding assays indicated that GPC3-expressing cells have an increased capacity to bind Wnt. Collectively, these results suggest that GPC3 stimulates Wnt activity by facilitating the interaction of this polypeptide with its signaling receptors. Surprisingly, in contrast to the current model that proposes that Wnt-glypican binding is mediated by the heparan sulfate chains, we found that the nonglycanated GPC3 core protein can form complexes with Wnts. Furthermore, we showed that the glycosaminoglycan chains are not required for the stimulatory effect on Wnt signaling and hepatocellular carcinoma growth.
Fever's End (2014)

Once I had two husbands. The first I married wearing red in the sunshine after the storms. And we laughed and kissed and told ourselves how lucky we were the storms had passed...
[Hydroxyapatite particulate artificial bone for repairing sunken deformation of frontal bone following removal of dermoid cyst]. (2007)

It is a simple and viable method to repair sunken deformation of frontal bone with hydroxyapatite particulate artificial bone.
Genetic analysis of uidA expression in enterohaemorrhagic Escherichia coli serotype 0157:H7 (1994)

Isolates of enterohaemorrhagic Escherichia coli serotype O157:H7 do not exhibit beta-glucuronidase (GUD) activity; however, they carry nucleotide sequences for the uidA gene that encodes the GUD enzyme. Polymerase chain reaction analysis using uidA-specific primers confirmed that a genetic region homologous in size to the E. coli uidA structural gene, including the regulatory region, was present in E. coli O157:H7 isolates. DNA sequencing analysis of the regulatory region and the 5' terminus of the uidA gene of E. coli O157:H7 showed a base substitution in the putative -10 promotor region and at 93 bases downstream from the initiation codon. Neither base alteration, however, appeared to affect uidA allele gene expression in the O157:H7 isolates. Immunoblotting of cell extracts with an anti-GUD antibody showed that E. coli O157:H7 isolates produced an antibody-reactive protein that was homologous in size to E. coli GUD, but no GUD activity was observed in cell-free extracts of these isolates. These results suggest that the antibody-reactive protein produced by E. coli O157:H7 may be an inactive GUD enzyme. Sequencing of the uidA structural gene in O157:H7 showed the presence of 18 additional nucleotide base substitutions, but only six altered the amino acid sequence. Also, there were two frame shift mutations, 18 bases apart, that altered the sequence of six consecutive amino acids. These genetic alterations in the uidA structural gene of O157:H7 may account for the absence of GUD activity in this serotype.
Localization, Identification, and Excision of Murine Adipose Depots (2014)

Obesity has increased dramatically in the last few decades and affects over one third of the adult US population. The economic effect of obesity in 2005 reached a staggering sum of $190.2 billion in direct medical costs alone. Obesity is a major risk factor for a wide host of diseases. Historically, little was known regarding adipose and its major and essential functions in the body. Brown and white adipose are the two main types of adipose but current literature has identified a new type of fat called brite or beige adipose. Research has shown that adipose depots have specific metabolic profiles and certain depots allow for a propensity for obesity and other related disorders. The goal of this protocol is to provide researchers the capacity to identify and excise adipose depots that will allow for the analysis of different factorial effects on adipose; as well as the beneficial or detrimental role adipose plays in disease and overall health. Isolation and excision of adipose depots allows investigators to look at gross morphological changes as well as histological changes. The adipose isolated can also be used for molecular studies to evaluate transcriptional and translational change or for in vitro experimentation to discover targets of interest and mechanisms of action. This technique is superior to other published techniques due to the design allowing for isolation of multiple depots with simplicity and minimal contamination.
Plasma profiling determinants of matrix homeostasis in paediatric dilated cardiomyopathy (2010)

These unique findings show that a specific plasma matrix metalloproteinase/tissue inhibitor of metalloproteinase profile occurs in paediatric dilated cardiomyopathy when compared to the cases of normal children. These distinct differences in the determinants of myocardial matrix structure and function may contribute to the natural history of dilated cardiomyopathy in children and may provide a novel biomarker platform in paediatric dilated cardiomyopathy.